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Topics in Infrastructure web:
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ACSLS Management
Log in as or su to ACSSA for cmd_proc:
ssh
acssa@acsls-1.loni.ucla.edu
or
su - acssa
Bring CAP or other device offline and back online (in this case CAP 1,1,0) =
vary cap 1,1,0 offline force
vary cap 1,1,0 online
Querying Volumes, Cap, etc
q vol
volid
query volume
volid
q cap
cap id
or simply use q or query and
ACSLS will as for input
Eject Tapes (example: eject volumes 500831, 500837 and 500855 through 500865 to CAP 1,1,0)
eject
cap ID volIDs
eject 1,1,0 500831 500837 500855-500865
Use volrpt to find wrongly placed tapes to be ejected (i.e. 500 tapes in StorageTek? 8500):
Log in as ACSSS for shell commands (don't use su to ensure proper environment variables):
volrpt -d -l -1,{0,1,2,3,4,5,6,7,9} |grep 500
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hasdhshahjasd h asdh jkhkjasdhjh
Install Apache 2.0.58:
cd /tmp
wget
http://apache.mirrormax.net/httpd/httpd-2.0.58.tar.gz
sudo tar -xvzf httpd-2.0.58.tar.gz
cd httpd-2.0.58
sudo ./configure --prefix=/usr/local/apache2 --enable-static-support
sudo make
sudo make install
If you want to move apache to a system different from the compiling system, /usr/local/apache2 should be transportable.
Startup scripts:
sudo ln -s /usr/local/apache2/bin/apachectl /etc/init.d/httpd
For each applicable rc*.d (i.e. init 3, 5, etc) add a symlink to have apache start on boot:
sudo ln -s ../init.d/httpd S50httpd
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Cranium: Compilers
This page contains instructions on how to use the different compilers we have installed in the Cranium cluster like the GCC, Intel and PGI.
GCC
Here is a guide on how to use the GCC compiler. Here is a general description on how to compile with C++:
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How do I use gcc, g++, and gdb?
If you want to use the GNU C (gcc) compiler to compile your code from the command line just type:
% gcc file.c
or
% g++ file.c
This compiles file.c into an executable binary named a.out. If you use Makefiles to compile your programs, then put the following line at the top of your Makefile:
CC=gcc
or
CC=g++
By default our GCC compiler build executables for 64 bits, but if you need to build an executable for 32 bits, set the following variables in the command line or in your Makefile:
setenv CFLAGS "-O2 -m32"
setenv CXXFLAGS "-O2 -m32"
Here are a few options to gcc and g++:
- -o outputfile
- To specify the name of the output file. The executable will be named
a.out unless you use this option.
- -g
- To compile with debugging flags, for use with gdb.
- -L dir
- To specify directories for the linker to search for the library files.
- -l library
- This specifies a library to link with.
- -I dir
- This specifies a directories for the compile to search for when looking
for include files.
For a complete set of options that control compile optimization, use this link.
Now, to check errors on a "correctly" compiled binary you can use the debugger 'gdb'. Here is a typical example of a gcc/gdb session:
% cat hello.c
#include<stdio.h>
main() {
int count;
for (count=0;count<10;count++)
printf("Hello from LONI!\n");
}
% gcc -g hello.c
% gdb ./a.out
GDB is free software and you are welcome to distribute copies of it
under certain conditions; type "show copying" to see the conditions.
There is absolutely no warranty for GDB; type "show warranty" for details.
GDB 4.13 (sparc-sun-solaris2.3),
Copyright 1994 Free Software Foundation, Inc...
(gdb) b main
Breakpoint 1 at 0x10784: file hello.c, line 6.
(gdb) r
Starting program: /home1/b/bozo/./a.out
Breakpoint 1, main () at hello.c:6
6 for (count=0;count<10;count++)
(gdb) s
7 printf("Hello from LONI!\n");
(gdb) p count
$1 = 0
(gdb) disp count
1: count = 0
(gdb) set count=8
(gdb) s
Hello from LONI!
6 for (count=0;count<10;count++)
1: count = 8
(gdb)
7 printf("Hello from LONI!\n");
1: count = 9
(gdb) c
Continuing.
Hello from LONI!
Program exited with code 01.
(gdb) q
%
Here are a few gdb commands:
- help
- Will give you help on most gdb functions. If you wish for help on
a specific command, type help command.
- b function-name
- To set a breakpoint at a function.
- r args
- To run the program. It will run until it reaches a breakpoint.
- s
- To single-step through lines of code.
- c
- To continue until the next breakpoint.
- p variable
- To print a variable's value.
- q
- To quit gdb.
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Intel
The Intel C++ Compiler lets you build and optimize C/C++ applications for Intel IA-32, Intel Extended Memory 64 Technology (Intel EM64T), and Intel Itanium-based systems running Linux operating systems. You can check a detailed user guide by following this link.
For the 64 bit compiler (please check the appropriate paths),
setenv ICCPATH /usr/local/intel_cc-10.1.008_64bit
setenv PATH bin:${PATH}
This should enable you to compile and link programs using the Intel compiler. In case you are using Makefiles, it's
also helpful to set up the path as
Use the Intel compiler,
CC = /usr/local/intel_cc-10.1.008_64bit/bin/icc
Use the Intel Linker,
LD = /usr/local/intel_cc-10.1.008_64bit/bin/icpc
Optimizing with the Intel compiler, most gcc options such as -g, -O2, -O1 should work. Additionally, exclusive
optimizing options are provided as follows:
For parallelizing loops,
-parallel
Enables the auto-parallelizer to generate multithreaded code for loops that can be safely executed in parallel.
General faster optimization,
-fast
Provides a single, simple optimization that enables a collection of optimizations that favor run-time performance.
For targetting specific processors,
-mtune=itanium2
or
-mtune=itanium
For generating vectorized code,
-xS
Can generate SSE4 Vectorizing Compiler and Media Accelerators instructions for future Intel processors that support the
instructions. Can generate SSSE3, SSE3, SSE2, and SSSE4 instructions and it can optimize for future Intel processors.
-xT
Can generate SSSE3, SSE3, SSE2, and SSE instructions for Intel processors, and it can optimize for the Intel
Core Duo processor family.
-xP
Can generate SSE3, SSE2, and SSE instructions for Intel processors, and it can optimize for processors based on Intel
Core microarchitecture and Intel NetBurst microarchitecture, like Intel Core Duo processors, Pentium
4 processors with SSE3, and Intel Xeon processors with SSE3.
Linking with the intel compiler,
icpc -L$(LIBDIR) <.o files> -o
Additionally, if one is using C++ and requires -lstdc++, it's better to specify -lguide -lpthread before -lstdc++ to
avoid linker errors.
PGI
To compile PGI applications for 32 bits, please set the following variables (if you are using a tcsh shell):
Set the PGI variable,
setenv PGI /usr/local/pgi-7.1.3_64bit
Set the variable for the license file,
setenv LM_LICENSE_FILE ${PGI}/license.dat
Include PGI in your current path,
setenv PATH ${PGI}/linux86/7.1-3/bin:${PATH}
Set the compiler variables,
setenv CC ${PGI}/linux86/7.1-3/bin/pgCC
setenv CFLAGS "-O3 -Bstatic_pgi"
If you have to set additional include directories,
INCLUDES = -I/needed_include_path
And, for additional libraries needed when compiling your code,
INCLUDES = -L/needed_library_path
For 64 bits, follow a similar procedure like with 32 bits:
setenv PGI /usr/local/pgi-7.1.3_64bit
setenv PGI /usr/local/pgi-7.1.3_64bit
setenv LM_LICENSE_FILE ${PGI}/license.dat
setenv PATH ${PGI}/linux86-64/7.1-3/bin:${PATH}
setenv CC ${PGI}/linux86-64/7.1-3/bin/pgCC
setenv CFLAGS "-O3 -tp x64 -Bstatic_pgi"
A complete guide for PGI can be found by clicking here. Check also:
PGI User's guide,
PGI Tools guide,
PGI Compiler suite.
Cerebro Rocks: Cluster's Applications
We have a variety of applications to be used by the LONI users who access the Cranium cluster. We use cerebro-rcc.loni.ucla.edu to build/install/upgrade a needed application. Once the application is ready to be used on production, we proceed to copy it into cerebro-rocks.loni.ucla.edu and then, propagate it into all the compute nodes on the cluster. We use rsync as method of propagation having cerebro-rocks as the rsync server. The applications installed on the Cranium (Cerebro Rocks) cluster are shown as follow:
Analyis of Functional Neuro Images
AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes.
Building the application
1. Go to build dir
# cd /tmp/hugo
2. Download binaries from
http://afni.nimh.nih.gov/afni/download/afni/releases/latest
o Download AFNI/SUMA Software latest for Linux (Linux gcc33_64)
o filename: linux_gcc33_64.tar.gz
3. Uncompress the tar file,
# tar -zxvf linux_gcc33_64.tar.gz
# cd linux_gcc33_64
# cp -f * /usr/local/afni-2007529-1644_64bit/bin/.
# mv /usr/local/afni-2007529-1644_64bit/bin/README* /usr/local/afni-2007529-1644_64bit/.
4. Add AFNI Matlab library
o Download AFNI Matlab Library latest for all platforms
o filename: afni_matlab.tgz
o
http://afni.nimh.nih.gov/afni/download/afnimatlab/releases/latest
5. Uncompress the tar file,
# tar -zxvf afni_matlab.tgz
# cd afni_matlab
# mv matlab /usr/local/afni-2007529-1644_64bit/.
6. Add AFNI Sample Data
o Download AFNI/SUMA Sample Data latest for all platforms
o filenames: AFNI_data1.tgz, AFNI_data2.tgz
o
http://afni.nimh.nih.gov/afni/download/data/releases/latest
7. Uncompress the tar file,
# tar -zxvf AFNI_data1.tgz
# cp -rf AFNI_data1 /usr/local/afni-2007529-1644_64bit/dataSample/.
# tar -zxvf AFNI_data2.tgz
# cp -rf AFNI_data2 /usr/local/afni-2007529-1644_64bit/dataSample/.
8. Add SUMA Sample Data
o Download AFNI/SUMA Sample Data latest for all platforms
o filenames: SUMA_demo.tgz, SUMA_StandardMeshes.tgz
9. Uncompress the tar file,
# tar -zxvf SUMA_demo.tgz
# cp -rf suma_demo /usr/local/afni-2007529-1644_64bit/sumaSample/.
# tar -zxvf SUMA_StandardMeshes.tgz
# cp -rf std_mashes /usr/local/afni-2007529-1644_64bit/sumaSample/.
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Automated Image Registration
AIR allows automated registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities. AIR source code written in C is available to the research community free of charge. The code can be compiled for UNIX, PC or Macintosh platforms. Only source code is available (no executables).
Building the application
1) Adquired code from /cxfs/tmp/sysadm/air5.2.5
- Copied to /tmp/air5.2.5
2) ./configure --prefix=/tmp/air5.2.5/bin
o To compile the extended binaries, edit
- /tmp/hugo/air5.2.5/Makefile
- /tmp/hugo/air5.2.5/src/Makefile
as in Makefile.txt and Makefile-src.txt respectively.
Be careful with the TAB spaces on the Makefiles.
3) make all
4) make install
5) Copy binaries
# cp /tmp/air5.2.5/bin/* /usr/local/air5.2.5_64_16/bin/.
6) For 8 and 16 bits binaries, edit src/config.h
#define AIR_CONFIG_OUTBITS 16
to
#define AIR_CONFIG_OUTBITS 8
7) For binaries compiled at 32 bits, set the CFLAGS and CXXFLGS to "-02 -m32" before step (2)
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Brainsuite
BrainSuite is a magnetic resonance (MR) image analysis tool designed for identifying tissue types and surfaces in MR images of the human head.
Building the application
1. Copied exec files from David Shattuck's directory:
# cd /usr/local/brainsuite_32bit/bin
# cp /nethome/users/shattuck/experimental/i386-redhat-linux-gnu/bfc07a_i386-redhat-linux-gnu .
# cp /nethome/users/shattuck/experimental/i386-redhat-linux-gnu/bse07a_i386-redhat-linux-gnu .
# cp /nethome/users/shattuck/experimental/i386-redhat-linux-gnu/pvc07a_i386-redhat-linux-gnu .
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Fast Lexical Analyzer Generator
Flex is a tool for generating programs that recognize lexical patterns in text. There are many applications for Flex, including writing compilers in conjunction with GNU Bison. Flex is a free implementation of the well known Lex program. It features a Lex compatibility mode, and also provides several new features such as exclusive start conditions.
Building the application
# used GNU Make 3.80
1. Uncompress the tar file,
# cd /data/hugo
# tar -zxvf flex-2.5.31.tar.gz
2. Build the package,
# ./configure --prefix=/usr/local/flex-2.5.31_64bit
# make
# make install
3. Copy executable into /usr/local/bin
# cp -rf /usr/local/flex-2.5.31_64bit/bin/flex /usr/local/bin/.
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Fast Light Toolkit
FLTK (pronounced "fulltick") is a cross-platform C++ GUI toolkit for UNIX®/Linux® (X11), Microsoft® Windows®, and MacOS?® X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL?® and its built-in GLUT emulation.
Building the application
1. uncompress tar file,
# cd /data/hugo
# tar -zxvf fltk-1.1.7.tar.gz
# cd fltk-1.1.7
2. configure the package
# mkdir /usr/local/fltk-1.1.7
# ./configure --prefix=/usr/local/fltk-1.1.7 --libdir=/usr/local/lib
3. build the package,
# make ; make install
4. copy libraries to the $prefix
# cp /usr/local/lib/libfltk* /usr/local/fltk-1.1.7_64bit/lib
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Free OpenGL Utility Toolkit
freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. GLUT was originally written by Mark Kilgard to support the sample programs in the second edition OpenGL 'RedBook'. Since then, GLUT has been used in a wide variety of practical applications because it is simple, widely available and highly portable. GLUT (and hence freeglut) allows the user to create and manage windows containing OpenGL contexts on a wide range of platforms and also read the mouse, keyboard and joystick functions.
Building the application
1. Download the code from
http://freeglut.sourceforge.net/index.php#download,
2. uncompress the source code,
# cd /tmp/hugo
# tar -jxvf freeglut-2.4.0.tar.bz2
3. configure the package,
# ./configure --prefix=/usr/local/freeglut-2.4.0_64bit
4. build the package,
# make
# make install
5. copy libraries into /usr/local/lib
# cp -f /usr/local/freeglut-2.4.0_64bit/lib/* /usr/local/lib/.
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FreeSurfer
FreeSurfer is a set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.
Building the application
1. Uncompress the application,
# cd /tmp/hugo
# tar -C /usr/local -zxvf freesurfer-3.0.5.tar.gz
2. A license file is required to enable the tools. One can be obtained for free by registering at:
https://surfer.nmr.mgh.harvard.edu/registration.html
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FMRIB Software Library
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data, written mainly by members of the Analysis Group, FMRIB, Oxford, UK. FSL runs on Apple, PCs (Linux and Windows) and Sun, and is very easy to install.
Building the application
1. download code from
http://www.fmrib.ox.ac.uk/fsl,
2. uncompress the tar file
# tar -C /usr/local -zxvf /cxfs/tmp/sysadm/fsl-4.0.1-sources.tar.gz
3. to build the application
# mv /usr/local/fsl /usr/local/fsl-4.0.1_64bit
# cd /usr/local/fsl-4.0.1_64bit
4. set the main FSL environment variable
# export FSLDIR=/usr/local/fsl-4.0.1_64bit
5. source the FSL environment setup script
# . ${FSLDIR}/etc/fslconf/fsl.sh
6. check if your machine/compiler is supported by default
# ls $FSLDIR/config/$FSLMACHTYPE
---> if not, select the closest match from the directories in $FSLDIR/config and do the following
# cp -r $FSLDIR/config/linux_64-gcc4.1 $FSLDIR/config/$FSLMACHTYPE
7. build the application
# ./build
8. if you want to re-make a particular package in $FSLDIR/src (e.g. flirt) then first set the FSLDEVDIR environment variable to the same as FSLDIR and then just type
# make install
inside the relevant directory.
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GNU Compiler Collection
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
Building the application
1. download code from
http://gcc.gnu.org/mirrors.html,
2. uncompress the tar file
# tar -C /tmp/hugo -jxvf /cxfs/tmp/sysadm/gcc-4.2.0.tar.bz2
3. build the application
# cd /tmp/hugo/gcc-4.2.0
# ./configure --prefix=/usr/local/gcc-4.2.0_64bit
---> be sure you have installed glibc-devel for both 32 and 64bits
currently: glibc-devel-2.3.4-2.36
# make
---> create backups for the executables of the current gcc version in /usr/bin
# make install
4. create symlinks or copy new execs into /usr/bin
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Insight Applications
The following applications illustrate the use of ITK in real-world medical imaging applications. Note these application are found in the InsightApplications module. They differ from the Insight/Examples examples in that they use other systems such as VTK, FLTK and Qt to create turn-key applications. Please make sure that you can compile and link the examples found in Insight/Examples prior to building these applications. The applications are often difficult to compile and run.
Building the application
1. Uncompress the tar file,
# cd /tmp/hugo
# tar -zxvf _InsightApplications_-3.2.0.tar.gz
2. Create build directory,
# mkdir /usr/local/_InsightApplications_-3.2.0_64bit
3. Configure the package,
# ccmake .
Use flags:
BUILD_SHARED_LIBRARIES
ON
ITK_DIR
/tmp/hugo/InsightToolKit-3.2.0 (source code)
CMAKE_INSTALL_PREFIX
/usr/local/InsightApplications-3.2.0_64bit
Hit [c] to configure,
Hit [g] to generate and exit,
4. Build the package,
# make
# make install
5. Copied libraries into /usr/local/lib
# cp -vf /usr/local/InsightApplications/lib/* /usr/local/lib/.
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Insight Toolkit
ITK is an open-source software system to support the Visible Human Project. Currently under active development, ITK employs leading-edge segmentation and registration algorithms in two, three, and more dimensions.
Building the application
# used ccmake version 2.4-patch 6 (2.4-patch 5 used on cerebellum)
# used GNU Make 3.80
1. Uncompress the tar file,
# cd /data/hugo
# tar -zxvf _InsightToolkit_-3.2.0.tar.gz
2. Create build directory,
# mkdir /usr/local/InsightToolkit-3.2.0
3. Configure the package,
# ccmake /data/hugo/InsightToolkit-3.2.0
Use flags:
BUILD_SHARED_LIBRARIES
ON
BUILD_EXAMPLES
0N
BUILD_TESTING
ON
CMAKE_INSTALL_PREFIX
/usr/local/InsightToolkit-3.2.0
Hit [c] to configure,
Hit [g] to generate and exit,
4. Build the package,
# make
# make install
5. Copied execs from build dir to $prefix dir
# cp /data/hugo/InsightToolkit-3.2.0/bin/* /usr/local/InsightToolkit-3.2.0/bin/.
6. Copied library dir into /usr/local/lib
# cp -rvf /usr/local/InsightToolkit/lib/InsightToolkit /usr/local/lib/.
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Java SE Development Kit
The Java SE Development Kit (JDK) includes the Java Runtime Environment (JRE) and command-line development tools that are useful for developing applets and applications.
Building the application
1. download the application from
http://java.sun.com/javase/downloads/index.jsp,
2. install the application,
# cd /tmp/hugo
# chmod +x jdk-6u2-linux-amd64-rpm.bin
# ./jdk-6u2-linux-i586-rpm.bin
---> follow the instructions
3. copy /usr/java into /usr/local
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LONI Applications
- URL: Unknown
- Current Version: Unknown
- Installed Version: Unknown
- Installed at: Unknown
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LONI Data
- URL: Unknown
- Current Version: Unknown
- Installed Version: Unknown
- Installed at: Unknown
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LONI Jar Files
- URL: Unknown
- Current Version: Unknown
- Installed Version: Unknown
- Installed at: Unknown
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LONI Scripts
- URL: Unknown
- Current Version: Unknown
- Installed Version: Unknown
- Installed at: Unknown
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Matlab
MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.
Building the application
1. download code from
http://www.mathworks.com,
2. uncompress the tar file
# cd /hugo/tmp/build-matlab
# tar -xvf boot.ftp
3. build the application
# ./install
---> follow all the instructions from the GUI
4. use SPM5
---> copy all the content of the SPM5 directory into the Matlab directory
# cp -rf /usr/local/spm5 /usr/local/matlab7.4_64bit/.
---> recompile the mex files with the current gcc compiler
# cd /usr/local/matlab7.4_64bit/spm5/src
# make & make install
5. Include SPM5 into the Matlab path
setenv MATLABPATH /usr/local/matlab7.4_64bit/spm5
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Montreal Neurological Institute
The MNI is a teaching and research institute of McGill University in which multidisciplinary teams of basic and clinician scientists work to generate fundamental information about the nervous system and to apply that knowledge to understanding and treating neurological diseases.
Building the application
System:
Linux x86_64
Compiler:
3.4.5
Procedure:
1 netcdf-3.5.0
o setenv CPPFLAGS "-Df2cFortran"
o setenv FC /usr/bin/g77
o setenv FFLAGS "-Wno-globals"
o setenv CXX /usr/bin/g++
o ./configure --prefix=/usr/local/mni
o make ; make install
2. minc-1.4.0
o ./configure --prefix=/usr/local/mni --with-build-path=/usr/local/mni
o make ; make install
3. mni_autogen-0.98v
o ./configure --prefix=/usr/local/mni --with-build-path=/usr/local/mni
o make ; make install
4. ebtks-1.5.0
o ./configure --prefix=/usr/local/mni --with-build-path=/usr/local/mni
o make ; make install
5. N3-1.10
o ./configure --prefix=/usr/local/mni --with-build-path=/usr/local/mni
o make ; make install
6. bicpl-1.4.2
o ./configure --prefix=/usr/local/mni --with-build-path=/usr/local/mni
o make ; make install
7. conglomerate-1.5
o ./configure --prefix=/usr/local/mni --with-build-path=/usr/local/mni
o make ; make install
8. mni_perllib-0.07
o setenv PERLLIB /usr/local/mni/lib
o perl Makefile.PL PREFIX=/usr/local/mni INSTALLDIRS=perl
o make ; make install
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netpbm
Netpbm is a toolkit for manipulation of graphic images, including conversion of images between a variety of different formats. There are over 300 separate tools in the package including converters for about 100 graphics formats. Examples of the sort of image manipulation we're talking about are: Shrinking an image by 10%; Cutting the top half off of an image; Making a mirror image; Creating a sequence of images that fade from one image to another.
Building the application
# used GNU Make 3.80
# requires:
o flex/lex (generate programs for lexical tasks)
o tiff libraries
1. Uncompress the tar file,
# cd /data/hugo
# tar -zxvf netpbm-10.26.42.tgz
2. Build the package. See doc/INSTALL.
# ./configure
o use static library
o define tiff libraries and paths when required
# make
# make package pkgdir=/usr/local/netpbm-10.26.42_64bit
3. To gather all the installable parts into a specified directory, and finally
# installnetpbm
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nifticlib
niftilib is a collection of i/o routines for the nifti1 neuroimage data format. C (nifticlib), Java (niftijlib), Matlab (niftimatlib), and Python (pynifti) code is available. Information about the nifti format is available at http://nifti.nimh.nih.gov/df
Building the application
# used GNU Make 3.80
1. Uncompress the tar file,
# cd /data/hugo
# tar -C /usr/local -zxvf nifticlib-0.3.tar.gz
# cd /usr/local ; mv nifticlib-0.3 nifticlib-0.3_64bit
2. Build the package,
# make all
3. Copy libraries into /usr/local/lib
# cp -rf /usr/local/nifticlib-0.3_64bit/lib /usr/local/lib/.
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R Project for Statistical Computing
R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.
Building the application
# based on R. Magsipoc's compilation on cerebellum (3/6/07)
#
# Build latest version of readline, 64-bit, first with default flags
1. Set flags,
o setenv CFLAGS "-O2 -m64"
o setenv CXXFLAGS "-O2 -m64"
o setenv CPPFLAGS "-I/usr/local/include -I/usr/include"
o setenv LDFLAGS "-L/usr/local/lib -L/usr/lib64"
2. Uncompress package,
# cd /tmp/hugo ; tar -zxvf R-2.4.1.tar.gz
# cd /tmp/hugo/R-2.4.1
3. Configure and build package,
# ./configure --prefix=/usr/local/R-2.4.1_64bit
# make
# make check
# make install
go Up
readline
The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
Building the application
1. Set flags,
o setenv CFLAGS "-O2 -m64"
o setenv CXXFLAGS "-O2 -m64"
o setenv CPPFLAGS "-I/usr/local/include -I/usr/include"
o setenv LDFLAGS "-L/usr/local/lib -L/usr/lib64"
2. Uncompress package,
# cd /tmp/hugo ; tar -zxvf readline-5.2.tar.gz
# cd /tmp/hugo/readline-5.2
3. Configure and build package,
# ./configure --prefix=/usr/local/readline-5.2_64bit
# make
# make install
go Up
Shape Tools
Building the application
Copied directory from Craig Schwartz.
go Up
Statistical Parametric Mapping
Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data. These ideas have been instantiated in software that is called SPM. The SPM is a MATLAB software package and has been designed for the analysis of brain imaging data sequences. The sequences can be a series of images from different cohorts, or time-series from the same subject. The current release is designed for the analysis of fMRI, PET, SPECT, EEG and MEG.
Building the application
1. download code from
http://www.fil.ion.ucl.ac.uk/spm/software/download.html,
2. uncompress the tar file
# tar -C /usr/local -zxvf /cxfs/tmp/sysadm/MatLab/spm5.tar.gz
3. recompile the mex files to work with the current GCC version
# cd /usr/local/spm5/src
# make && make install
4. To enable this package for Matlab, copy the complete directory into the Matlab directory and include it into the Matlab Path
# cp -rf /usr/local/spm5 /usr/local/matlab/.
go Up
Tagged Image File Format
This software provides support for the Tag Image File Format (TIFF), a widely used format for storing image data. Included in this software distribution is a library, libtiff, for reading and writing TIFF, a small collection of tools for doing simple manipulations of TIFF images, and documentation on the library and tools. Libtiff is a portable software, it was built and tested on various systems: UNIX flavors (Linux, BSD, Solaris, MacOS X), Windows, OpenVMS. It should be possible to port libtiff and additional tools on other OSes.
Building the application
# used GNU Make 3.80
1. Uncompress the tar file,
# cd /data/hugo
# tar -zxvf tiff-3.8.2.tar.gz
2. Build the package,
# ./configure --prefix=/usr/local/tiff-3.8.2_64bit
# make
# make install
3. Copy libraries into /usr/local/lib
# cp -rf /usr/local/tiff-3.8.2_64bit/lib/* /usr/local/lib/.
go Up
Visualization Toolkit
The Visualization Toolkit (VTK) is an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. VTK consists of a C++ class library, and several interpreted interface layers including Tcl/Tk, Java, and Python.
Building the application
1. uncompress the tar file,
# cd /tmp/hugo
# tar -zxvf vtk-5.0.2.tar.gz
# cd VTK
2. configure package,
# ccmake .
Use the flags:
BUILD_SHARED_LIBS
ON
CMAKE_INSTALL_PREFIX
/usr/local/vtk-5.0.2
VTK_DATA_ROOT
/tmp/hugo/VTK
VTK_USE_RENDERING
ON
VTK_USE_RPATH
OFF
VTK_WRAP_TCL
ON
3. build package,
# mkdir /usr/local/vtk-5.0.2
# make ; make install
go Up
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Disabled Cranium Production Nodes (Hardware and Testing)
This page is meant to serve as formal notification of disabled nodes, which we do on a near-daily basis. The page will allow us to keep track of reasons for node disablings, while also allowing us to catch nodes that should be returned into production much more easily.
Please file the node under the proper rack category, give a brief justification, the date of the disable, and the responsible
SysAdmin? (to be contacted if the node is believed to remain disabled by oversight).
Nodes with hardware issues are
denoted in RED.
| R1 nodes | Reason | Next Action | Date | Sysadmin |
| cerebro-1-[101-125] | Moved to pipeline-ext.q | HOLD | | |
| cerebro-1-109 | Machine reboots before Boot Agent when instructed to PXE boot | HOLD | 04.22.09 | jpierce |
| R4 nodes | Reason | Next Action | Date | Sysadmin |
| cerebro-4-114 | Issue: No life over serial console, SP, or VGA on boot. | Good parts taken: 2x RAM | 05.05.09 | jpierce |
| cerebro-4-138 | DHCP requests not seen by frontend | HOLD | 04.23.09 | jpierce |
| R8 nodes | Reason | Next Action | Date | Sysadmin |
| cerebro-8-114 | Bad DIMM reported in slot 1, stops boot-up | replace with memory from another machine | 04.23.09 | jpierce |
| cerebro-8-137 | Being used as pipeline-lsh1 | HOLD | 12.15.08 | hdezmora |
| R23 nodes | Reason | Next Action | Date | Sysadmin |
| cerebro-23-101 | Being used as cerebro-lmh3 | Pending 6.2 going live | 12.04.08 | hdezmora |
| cerebro-23-102 | Being used as cerebro-lmh4 | Pending 6.2 going live | 12.04.08 | hdezmora |
| cerebro-23-103 | Being used as cerebro-lsh5 | Pending 6.2 going live | 12.04.08 | hdezmora |
| cerebro-23-104 | Being used as development exec node | HOLD | 02.05.09 | jpierce |
| cerebro-23-105 | Being used as pipeline-lmh1 | HOLD | 12.15.08 | hdezmora |
| cerebro-23-115 | Testing Panasas storage performance | HOLD | 04.07.09 | jpierce |
| cerebro-23-116 | Testing Panasas storage performance | HOLD | 04.07.09 | jpierce |
| cerebro-23-129 | Test install /usr/sge -> /ifs/sge-dev | HOLD | 02.18.09 | jpierce |
| R24 nodes | Reason | Next Action | Date | Sysadmin |
| cerebro-24-111 | Temporarily repurposed to upgrade mgmt servers to CentOS? 5.2 | Configure OS | 04.28.09 | jpierce |
| cerebro-24-112 | Temporarily repurposed to upgrade mgmt servers to CentOS? 5.2 | Install OS | 04.28.09 | jpierce |
| cerebro-24-136 | Repurposed as hsqldb | HOLD | 02.18.09 | jpierce |
| cerebro-24-137 | Repurposed as Rocks 5 frontend | HOLD | 02.19.09 | jpierce |
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Cerebro Rocks: Pre-Node Frontend Configuration
Use these links (in order) to complete the basic frontend configuration:
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loni-sw-2: changelog
Overview - loni-sw-2 is a Cisco 2890, located in Reed Datacenter, Rack 36. It provides network access to the Reed Datacenter, and is connected to loni-core-1 via GigE Fiber LX <-> Reed DC Fiber Panel <-> NRB 225S Rack 26 Fiber Panel <-> NRB Datacenter, Rack 13 Fiber Panel <-> loni-core-1.
Dates are in the format YY_MMDD
08_0313 - dhasson
--
DavidHasson - 12 Mar 2008
loni-sw-3: changelog
Overview - loni-sw-3 is a Cisco 2970-24TS located in the "Production 3" rack, or rack 19. It's connected via dual
GigE? Copper <-> loni-core-1. It's a production switch, which means it's trunked and is intended to support all vlans except management 280.
Dates are in the format YY_MMDD, entries go latest to oldest
08_0710 - dhasson
- Zoned gi0/17 -> dessi-local, vlan 210
- renamed to "nrb-r19-tor1"
08_0313 - dhasson
--
DavidHasson - 13 Mar 2008
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loni-sw-5: changelog
Overview - loni-sw-5 is a SMC 10/100/1000 located in the "Production 3" rack, or rack 19. It's connected via single
GigE? SX Fiber <-> loni-core-1. It's a production switch, which means it's trunked and is intended to support all vlans except management 280.
Dates are in the format YY_MMDD, entries go latest to oldest
08_0313 - dhasson
--
DavidHasson - 13 Mar 2008
loni-sw-6: changelog
Overview - loni-sw-6 is a Linksys SRW2024 located in Reed C Floor IDF. It's connected via
GigE? Fiber SX <-> loni-sw-7 (Reed DC). It's a distribution switch, which means it's trunked and is intended to support the 210 and 104 vlans for windows and linux clients.
Dates are in the format YY_MMDD, entries go latest to oldest
08_0313 - dhasson
--
DavidHasson - 13 Mar 2008
loni-sw-7: changelog
Overview - loni-sw-7 is a Linksys SRW2016 located in Reed DC, Rack 36. It's connected via GigE to loni-sw-2 in the same rack. It is currently only used as a fiber transciever to interconnect loni-sw-6 downstairs with the LONI network.
Dates are in the format YY_MMDD, entries go latest to oldest
08_0313 - dhasson
--
DavidHasson - 13 Mar 2008
RicoMagsipoc? - 23 Jul 2008
Overview - loni-edge is comprised of 2 Cisco Cat3750 in failover mode. These are located in the NRB1 DC, Rack 13.
Dates are in the format YY_MMDD, entries go latest to oldest
08_0723 - rico
- shutdown port 1/0/2. Originally configured for BIRN VPN.
- interface GigabitEthernet1?/0/2
- description loni-edge <-> birn-vpn UPLINK
- switchport access vlan 200
--
RicoMagsipoc? - 23 Jul 2008
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Everyday Systems Administration Tasks
Modifying DNS - Adding & Changing DNS Records for loni.ucla.edu using
nsupdate
Networker Client Setup - How to setup a new client (e.g., server or workstation) to be backed up by networker
--
DavidHasson - 14 Oct 2007
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Configuring your Email client for IMAP
To access your access your email via IMAP you must configure your email client to use SSL.
When configuring your server settings set your Server Name to be:
webmail.loni.ucla.edu
Set your User Name to be your LONI logon name, mine would be:
jtrout
Finally make sure that the secure connection has SSL checked and the default port is set to 993.
If you need a step by step walk through check the links below.
Outlook
http://www.bol.ucla.edu/help/howto/apps/outlook/outlookconfig.html
note: this walk through is for UCLA make sure to change their server names to LONI server names.
Thunderbird
http://www.bol.ucla.edu/software/mac/thunderbird/configure.html
note: this walk through is for UCLA make sure to change their server names to LONI server names.
Mail (Mac)
http://www.bol.ucla.edu/help/howto/apps/mailapp/mailconfig.html
note: this walk through is for UCLA make sure to change their server names to LONI server names.
Entourage
http://www.bol.ucla.edu/help/howto/apps/entourage/entxconfig.html
http://www.bol.ucla.edu/help/howto/apps/entourage/ent2004config.html
note: this walk through is for UCLA make sure to change their server names to LONI server names.
Mozilla
http://www.bol.ucla.edu/software/mac/mozilla/config.html
note: this walk through is for UCLA make sure to change their server names to LONI server names.
Eudora
http://www.bol.ucla.edu/software/mac/eudoraosx/config.html
note: this walk through is for UCLA make sure to change their server names to LONI server names.
Configuring your Email client for POP
To access your access your email via IMAP you must configure your email client to use SSL.
When configuring your server settings set your Server Name to be:
webmail.loni.ucla.edu
Set your User Name to be your LONI logon name, mine would be:
jtrout
Finally make sure that the secure connection has SSL checked and the default port is set to 995.
If you need a step-by-step walkthrough check the links above. The setup is the same for POP as it is for IMAP. Remember to check the UCLA Server Name
mail.ucla.edu to LONI’s Server Name
webmail.loni.ucla.edu
Configuring your Email client for SMTP
SMTP also requires secure authentication; however, the method differs depending on the email client. If you are using outlook, outlook express or Mac's mail SSL will work.
*note if you are using Mac’s Mail program set the SSL authentication to password, do not leave it on the default which is Kerberos 5.
At this point the only other email client that has been tested is Thunderbird. Thunderbird's SSL does not work with Exchange so under Authentication use TLS not SSL. Make sure that the Server Name is
webmail.loni.ucla.edu and your User Name is your LONI account name and everything should work fine.
*note Even though we have not tested other email clients they should work. However, you might have to play around with the configuration to make it work. Try SSL first and if that fails use TLS. Remember SMTP requires your username and password, so make sure not to leave those fields blank or you will not be able to send out emails. For help check out the step-by-step walkthroughs above.
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Accessing the LONI Network Remotely
SSH
SSH is short for Secure Shell. It provides a secure, encrypted method of transmitting information over TCP/IP to ensure the confidentiality, integrity and authenticity of transferred data. This is the preferred method of connectivity to LONI's Unix and Linux computational resources.
To access the LONI network via SSH:
- Obtain an SSH client for Windows, Linux, or MacOSX
- To find out if you already have ssh on a Unix/Linux based machine, type
which ssh
- SSH to
ssh.loni.ucla.edu over port 22 using the your LONI username and password.
- If accessing LONI for the first time, please change your password by following the instructions here.
About the SSH Servers
How to access LONI's SSL VPN
A virtual private network (VPN) is an encrypted connection established between an external user and LONI's network. Once a user successfully establishes a VPN tunnel, they are given full access to internal resources, including network shares, printers and secure compute servers. We have a new, robust SSL VPN to address firewalls that prohibit IPSEC/PPTP traffic. There is minimal setup required (client webapp installation only). This service is accessible
here. See
AccessingtheVPN.pdf below for a comprehensive walk-through.
How to set up a PPTP VPN in Windows
Deprecated. This is meant to be a secondary means of establishing a VPN connection, only if you cannot use the SSL VPN.
32-bit, 64-bit Windows XP
You must have a working internet connection for this procedure to work. Under Network Connections in the Control Panel:
- Select "Create a New Connection."
- Select "Connect to the network at my workplace."
- Select "Virtual Private Network connection."
- Choose an appropriate Company Name. (i.e. LONI VPN)>
- Select "Do not dial an initial connection."
- Use hostname vpn2.loni.ucla.edu
- Select appropriate level of usability.
- Select "Finish."
Use your LONI Windows username and password.
32-bit, 64-bit Windows Vista, Windows 7 or Windows 2008
You must have a working internet connection for this procedure to work. Under the Start Menu:
- Select "Connect To"
- Select "Set up a Connection or Network"
- Select "Connect to a workplace"
- Select "Use my Internet connection (VPN)"
- Use Internet address vpn2.loni.ucla.edu
- Choose an appropriate Destination Name. (i.e. LONI PPTP VPN)
- Select appropriate level of usability.
- Use your LONI username and password and the domain LONI
- Select "Connect"
How to set up a PPTP VPN in Mac OSX
Deprecated. This is meant to be a secondary means of establishing a VPN connection, only if you cannot use the SSL VPN.
- Open Internet Connect in the /Applications folder.
- In Internet Connect, select New VPN (PPTP) Connection Window from the File menu.
- Enter the PPTP server address vpn2.loni.ucla.edu and the appropriate credentials.
- Once you have everything filled out, click the Connect button. Watch the Status field to be sure you are establishing a connection.
- After the connection is up, you can check in the Network pane of System Preferences for a PPTP device.
Use your LONI Windows username and password.
Wireless and VPN on the UCLA campus
To access the network wirelessly while on the UCLA campus:
- Connect to UCLAWLAN.
- Login to LONI VPN using your login credentials.
You do not need to authenticate via the BOL Access Page or the BOL VPN to access the LONI Network
--
RicoMagsipoc - 29 Jan 2009
LONI Grid Computing Notes
To facilitate the submission and execution of compute jobs in this heterogeneous compute environment, SUN's Grid Engine (SGE) is used to virtualize the resources above into a compute service. A grid layer sits atop the compute resources and submits jobs to available resources according to user-defined criteria such as CPU type, processor count, etc.
Cranium Cluster
LONI's Cranium cluster is comprised of two types of compute nodes: Sun Microsystems V20z servers and Sun Microsystems X2200 M1 servers. [ More ]
Basic Grid Engine Commands and Info
In this section, you can find additional information regarding basic commands used on the grid as well as useful tips about jobs status and reasons for job failures. [ More ]
How to monitor the Cranium cluster?
To monitor the health status of the Cranium cluster, you have to be VPN-ed into the LONI private network. Once logged in, please visit this site.
|
Cranium Grid Technical Details
The Cranium cluster has a total of 1152 available processors, with a total of 1152 defined slots to run compute jobs. The cluster is comprised of two types of compute nodes, 296 Sun Microsystems V20z servers with dual 64-bit 2.4GHz AMD Opteron processors and 8Gb of memory, and 80 Sun Microsystems X2200 M1 servers with a dual 64-bit Quad-Core 2.2GHz AMD Opteron processor and 16GB of memory.
The cluster is configured using Rocks Cluster 4.5 and Sun Grid Engine 6.1u4 to schedule, distribute and administer the submitted jobs. All compute nodes and servers are running CentOS release 4.5 as the operating system. The cluster is structured as follows:
- 2 SGE Master nodes in fault-tolerant shadowed configuration (not accessible to the general public)
- 1 SGE Submit node
- qsub.loni.ucla.edu (gui.loni.ucla.edu)
- 1 Pipeline Server node
- 1 Compiler node
- cerebro-rcc.loni.ucla.edu
- SGE Execution nodes
- cerebro-1/8-101 through cerebro-1/8-137 (V20z servers)
- cerebro-23/24-101 through cerebro-23/24-137 (X2200 M1 servers)
- Mounted NFS filesystems
- All /ifs directories (e.g. /ifs/tmp, /ifs/four_d, etc.)
- /ifshome for user home directories
Submitting to Cranium Grid Engine
Summary: Compile code for GNU/Linux, kernel 2.6.9-55.ELsmp. Put executable and data files in /ifs directory. Run qsub on script containing job arguments.
The Sun Grid Engine (SGE) is a job management service intended to accept, schedule, dispatch, and manage remote execution of a large number of standalone, parallel or interactive user jobs. The current version for the Cerebro cluster is 6.1u4. Documentation can be found at http://gridengine.sunsource.net.
- Place all code and data files you wish to use into the appropriate /ifs NFS directory. By default, you can use /ifs/tmp. (NOTE: files older than 28 days are deleted off /ifs/tmp nightly)
- Compile code on cerebro-rcc.loni.ucla.edu using GCC, PGI or Intel compiler
- GCC can be found in /usr/local/bin/gcc or /usr/bin/gcc4,
- Compiler tools for GCC v4.2 can be found in /usr/local/gcc-4.2.0_64bit
- PGI compilers can be found in /usr/local/pgi
- Intel compilers can be found in /usr/local/intel*
- Login to qsub.loni.ucla.edu via SSH. Note that an external user must
a) Log into an SSH proxy such as ssh.loni.ucla.edu first, prior to establishing an SSH connection to a submit node or
b) VPN into LONI network. Instructions on how to establish a VPN connection can be found in http://www.loni.ucla.edu/twiki/bin/view/Infrastructure/GettingOnline
- Source the configuration script
- 'source /usr/sge/loni/common/settings.sh' if your shell is sh/bash
- 'source /usr/sge/loni/common/settings.csh' if your shell is tcsh/csh
- Wrap the executable (line 4) into a shell script containing Grid interpreter primitives (lines 2, 3, and 4)
- Example shell script:
- ) #!/bin/sh
- ) #$ -S /bin/sh
- ) #$ -j y -o /tmp
- ) #$ -l h_vmem=3G
- ) /ifs/tmp/myexecutable /ifs/tmp/inputfile /ifs/tmp/outputfile
- If your job requires more than 2G of memory (up to 8G), specify the amount using "-l h_vmem=[memory]" -- units of K(ilobytes), M(egabytes) or G(igabytes) as in line 3 of the above script. If your job uses 2G or less, you need not specify the h_vmem resource. Jobs exceeding their expected (or default, if unspecified) memory usage, will be terminated immediately. This ensures that we track memory usage of every job carefully, mitigating the likelihood that one process takes down a compute node running multiple jobs from multiple users.
-
Queues: containers for different categories of jobs. Queues provide the corresponding resources for concurrent execution of multiple jobs that belong to the same category. A single queue can group a large set of hosts and a particular host can belong to different queues. The following queues are defined for the Cranium cluster:
1) short.q: There is a 2-CPU-hour hard limit set for this queue. If the job exceeds this time limit, it will be automatically terminated. Any one user can only user 75% of all the slots (CPUs) in this queue. There are approximately 160 slots alloted to short.q.
Submitting jobs:
prompt> qsub -q short.q {name of the script}
2) medium.q: There is a 12-CPU-hour hard limit set for the medium.q. As with the short.q above, if the job exceeds the time limit, it will be automatically terminated. Any one user can only user 75% of its slots (CPUs). There are approximately 104 slots alloted to the queue.
Submitting jobs:
prompt> qsub -q medium.q {name of the script}
3) long.q: There is NO CPU time limit set for the long.q. Subsequently, it has the least number of slots, with 64 CPUs available. Any one user can only user 75% of all the CPUs in this queue.
Submitting jobs:
prompt> qsub -q long.q {name of the script}
4) pipeline.q: This queue is used by the Pipeline server ONLY. There is NO CPU time limit set for this queue.
Submitting jobs:
Using the Pipeline Execution Environment application found here.
The Cranium cluster does not oversubscribe its CPUs; there is a 1-to-1 relationship between a compute job and a CPU. Experience showed that CPU oversubscription, where a single CPU is shared by multiple jobs, caused unpredictability and instability. By default, each CPU (thus, each process) gets 2GB of memory.
Useful Grid Engine commands:
- 'qsub' - Allows grid users to submit job to the cluster.
Options:
- -cwd: Run from current working directory,
- -o {output file}: where to send the standard output,
- -e {error file}: where to send the standard error,
- -N (job name}: Job name for reporting,
- -j y: To merge the output and error messages into a specific file
- -p {value}: Priority level of the submitted job(s).
- -l h_vmem={value}: Memory limit of the job (if unspecified, {value}=2G by default); units of K(ilobytes), M(egabytes) or G(igabytes)
- 'qstat' - Allows grid users to see the status of their submitted job.
Options:
- -f: Display full information of the job,
- -u {username}: Show only username's jobs.
- -j {job-ID} -explain E: Why is my job in Eqw state?
- 'qdel' - Allows grid users to delete jobs from the queue.
Options:
- -u {username}: Allows grid users to delete all their jobs from the queue.
- -f {job-ID}: Allows grid users to delete a job from the queue by specifying the SGE job-ID.
- 'qacct -o {username}' - Allows grid users to extract more specific, runtime status of jobs including error messages
- 'qalter' - Allows grid users to modify a pending batch job,
- 'qhold' - Allows grid users to hold back a pending submitted job,
- 'qhost' - Allows grid users to get information about execution hosts,
- 'qconf' - Allows grid users to get information about the cluster and the queues.
Jobs Status:
- 'qw' - Queued and waiting,
- 'w' - Job waiting,
- 's' - Job suspended,
- 't' - Job transferring and about to start,
- 'r' - Job running,
- 'h' - Job hold,
- 'R' - Job restarted,
- 'd' - Job has been marked for deletion,
- 'Eqw' - An error occurred with the job.
The state E(rror) appears for pending jobs that couldn't be started due to job properties. Why is my job in a 'Eqw' state? Use the commands:
qstat -j job_ID -explain E
or
qacct -j job_ID
Check My Job Status:
- qstat -s prs -u $USER --- check jobs that are pending, running, or suspended
- qstat -t -u $USER --- display the nodes where the job is running
- qstat -ext -s p -u $USER --- display extended information for my pending jobs
- qstat -s h --- jobs in hold status
- qstat -s r --- jobs in running status
- qstat -s r -u $USER --- jobs that are mine and running
- qstat -s s -u $USER --- jobs that are mine and suspended
Host State:
-
'au' - Host is in alarm and unreachable,
-
'u' - Host is unreachable. Usually SGE is down or the machine is down. Check this out.
-
'a' - Host is in alarm. It is normal on if the state of the node is full, it means, if on the node is using most of its resources.
-
'aS' - Host is in alarm and Suspended. If the node is using most of its resources, SGE suspends this node to take any other job unless resources are available.
-
'd' - Host is disabled,
-
'E' - ERROR. This requires the command `qmod -c` to clear the error state.
Common reasons for a job to fail
-
Submission script not formatted properly,
-
SGE cannot find the binary file specified in the job script,
-
Required input files are missing from the startup directory,
-
Environment variables are not set or are set incorrectly,
-
The program is not running out of time,
-
The program's ever starting - it's easy to make typing errors when naming your program,
-
Hardware failure.
To be considered when using the Cranium cluster
-
It is not permitted to run jobs locally on the submit nodes, cerebro-lsn1 and cerebro-lsn2, as well as the master nodes. Doing so will negatively impact the entire cluster. Jobs that inadvertently run on these machines will be subject to immediate termination to ensure proper functioning of the Cranium cluster.
-
Use the appropriate queue when submitting jobs. Remember, the short.q is only for jobs of 2 CPU hours (or less) in duration. If you submit a job longer than 2 CPU hours into this queue, the system automatically kills your job.
-
If your job hasn't started for days because someone has dozens of jobs ahead of yours, it's worth mailing the SysAdmin team,
-
Do not run jobs on the cluster except through SGE,
-
Do not hog large memory machines.
Feel free to contact the
SysAdmin team to the email:
clusteradmins@loni.ucla.edu if you have any question or concern.
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How to Configure a DHCP + JumpStart Server
DHCP Server Configuration
Configure the DHCP server by using the service configuration utility
# dhcpconfig -D -r SUNWbinfiles -p /var/dhcp -a 192.168.4.1 -d data -l 84600 -h dns -y data
Created DHCP configuration file.
Created dhcptab.
Added "Locale" macro to dhcptab.
Added server macro to dhcptab - cerebro-sm.
DHCP server started.
where
-D: configuring DHCP service
-r: data storage module type
-p: DHCP directory path
-a: DNS server IP
-d: DNS domain name
-l: lease length used for address
-hresource in which to place host data, i.e., NIS or DNS
-y: DNS or NIS domain server
Configure the network for DHCP service and create the corresponding macro for that network
# dhcpconfig -N 192.168.0.0 -t 192.168.7.254
Added network macro to dhcptab - 192.168.0.0.
Created network table.
where
-N: network IP
-t: router
Add the PXE client macros to the DHCP configuration, by including vendor options
# dhtadm -A -m PXEClient:Arch:00000:UNDI:002001 -d ':BootSrvA=192.168.4.4:'
# dhtadm -A -s SinstNM -d 'Vendor=SUNW.i86pc,11,ASCII,1,0'
# dhtadm -A -s SinstPTH -d 'Vendor=SUNW.i86pc,12,ASCII,1,0'
# dhtadm -A -s SinstIP4 -d 'Vendor=SUNW.i86pc,10,IP,1,1'
# dhtadm -A -s SrootNM -d 'Vendor=SUNW.i86pc,3,ASCII,1,0'
# dhtadm -A -s SrootPTH -d 'Vendor=SUNW.i86pc,4,ASCII,1,0'
# dhtadm -A -s SrootIP4 -d 'Vendor=SUNW.i86pc,2,IP,1,1'
# dhtadm -A -s SjumpsCF -d 'Vendor=SUNW.i86pc,14,ASCII,1,0'
# dhtadm -A -s SsysidCF -d 'Vendor=SUNW.i86pc,13,ASCII,1,0'
# dhtadm -A -s SbootURI -d 'Vendor=SUNW.i86pc,16,ASCII,1,0'
# dhtadm -M -m 192.168.0.0 -e 'SinstNM="cerebro-sm"'
# dhtadm -M -m 192.168.0.0 -e 'SinstPTH="/export/install/x86_10"'
# dhtadm -M -m 192.168.0.0 -e 'SinstIP4=192.168.4.4'
# dhtadm -M -m 192.168.0.0 -e 'SrootNM="cerebro-sm"'
# dhtadm -M -m 192.168.0.0 -e 'SrootPTH="/export/install/x86_10/Tools/Boot"'
# dhtadm -M -m 192.168.0.0 -e 'SrootIP4=192.168.4.4'
# dhtadm -M -m 192.168.0.0 -e 'BootFile=nbp.SUNW.i86pc'
# dhtadm -M -m 192.168.0.0 -e ':Subnet=255.255.252.0:'
# dhtadm -M -m 192.168.0.0 -d ':Subnet=255.255.252.0:
Router=192.168.7.254:Broadcst=192.168.0.255:NISdmain="loni":
NISservs=192.168.4.2:SinstNM="cerebro-sm":SinstPTH="/export/install/x86_10":
SinstIP4=192.168.4.4:SrootNM="cerebro-sm":SrootPTH="/export/install/x86_10/Tools/Boot":
SrootIP4=192.168.4.4:BootFile="nbp.SUNW.i86pc":DNSdmain="data":DNSserv=192.168.4.1:' (all in a single line)
# dhtadm -M -m cerebro-sm -d ':Include=Locale:Timeserv=192.168.4.4:
LeaseTim=84600:LeaseNeg:DNSdmain="data":DNSserv=192.168.4.1:
SinstNM="cerebro-sm":SinstPTH="/export/install/x86_10":SinstIP4=192.168.4.4:
SrootNM="cerebro-sm":SrootPTH="/export/install/x86_10/Tools/Boot":
SrootIP4=192.168.4.4:BootFile="nbp.SUNW.i86pc":NISdmain="loni":
NISservs=192.168.4.2:' (all in a single line)
BootSrvA: the IP address of the boot (TFTP) server
"Vendor" refers to vendor related options
"Sinst" refers to the JumpStart installing directory
"Sroot" refers to the JumpStart booting directory
BootFile: the filename of the NBP executable located into the boot server, executed by the PXE
To print the macro
# dhtadm -P
Now, verify if the DHCP daemon is running and the service is enabled
# ps -efl | grep -i dhcp
0 S root 1855 1 0 40 20 ? 1612 ? 17:42:56 ? 0:01 /usr/lib/inet/in.dhcpd
# svcs -a | grep dhcp
Create the named table
# pntadm -C 192.168.4.0
List the coonfigured DHCP networks
# pntadm -L
192.168.0.0
192.168.4.0
Add the clients into the DHCP server
# pntadm -A 192.168.5.56 -c cerebro-B-056 -f PERMANENT -i 0100093D118F85 -m 192.168.0.0 192.168.4.0
Here, we are adding node 'cerebro-B-056' as a DHCP client.
-A: IP of the node
-c: name of the node
-f: dynamic or static IP (PERMANENT is for static)
-i: Mac Address (there is a 01 before to the mac address; exclude the ":")
-m: macro (192.168.0.0) + subnet (192.168.4.0)
To check if the machine is already a DHCP client.
# pntadm -P 192.168.4.0 | grep -i b-056
0100093D118F85 01 192.168.5.56 192.168.4.4 Forever 192.168.0.0 cerebro-B-056
If you would like to use dynamic IPs
# pntadm -A 192.168.5.56 -c cerebro-B-056 -f DYNAMIC -i 0100093D118F85 -m 192.168.0.0 192.168.4.0
Add the corresponding entries in the /etc/ethers file. Declare the following variables into the /etc/inet/dhcpsvc.conf file
# echo "INTERFACES=bge0" >> /etc/inet/dhcpsvc.conf
# echo "HOSTS_RESOURCE=dns" >> /etc/inet/dhcpsvc.conf
# echo "HOSTS_DOMAIN=data" >> /etc/inet/dhcpsvc.conf
# echo "ICMP_VERIFY=TRUE" >> /etc/inet/dhcpsvc.conf
# echo "RESCAN_INTERVAL=15" >> /etc/inet/dhcpsvc.conf
# echo "UPDATE_TIMEOUT" >> /etc/inet/dhcpsvc.conf
# echo "BOOTP_COMPAT=automatic" >> /etc/inet/dhcpsvc.conf
Restart the DHCP daemon
# pkill -HUP in.dhcpd
To list the configured DHCP networks
# pntadm -L
JumpStart Server Configuration
First, let's load the Solaris OS distribution into the server. Create the parent install directory
# mkdir /export/install
Create a subdirectory for the Solaris OS distribution
# mkdir /export/install/x86_10
Mount the Solaris OS distribution. In this procedure, we assume an image of the OS is stored on disk. Copy the Solaris OS distribution into the created installation directory
# mount -F hsfs -o ro `lofiadm -a /path_to_isoImage` /mount_point_path
# cd /mount_point_path/Solaris_10/Tools
# ./setup_install_server -b /export/install/x86_10
Verifying target directory...
Calculating the required disk space for the Solaris_10 product
Calculating space required for the installation boot image
Copying the DVD image to disk...
Copying Install Boot Image hierarchy...
Install Server setup complete
the -b option specifies that the server is both, installing and boot servers. Now, create the configuration server directory
# mkdir /export/install/jumpstart
# cd /mount_point_path/Solaris_10/Misc/jumpstart_sample
# cp check /export/install/jumpstart
# cd /export/install/jumpstart
# cat > rules
| # rule_keyword |
rule_value |
begin |
profile |
finish |
| any |
- |
preInstall |
cerebroData |
postInstall |
Configure preInstall and postInstall scripts, the corresponding profile (cerebroData) as well as the jumpstart configuration script, sysidcfg. Then, verify the configuration file syntax
# ./check
Validating rules...
Validating profile cerebroData...
The custom
JumpStart configuration is ok.
Now, share the installation directory and check if the NFS service is running
# cat >> /etc/dfs/dfstab
share -F nfs -o ro,anon=0 -d "Install Server" /export/install
# /etc/init.d/nfs.server start (or)
# svcadm enable -s svc:/network/nfs/server:default
# showmount -e localhost
export list for localhost:
/export/install (everyone)
# shareall
# share
- /export/install ro,anon=0 "Install Server"
Next step is to configure client access
# cd /export/install/x86_10/Solaris_10/Tools
# ./add_install_client -d -s cerebro-sm:/export/install/x86_10 -c cerebro-sm:/export/install/jumpstart -p cerebro-sm:/export/install/jumpstart -b "output-device=ttya" -b "input-device=ttya" SUNW.i86pc i86pc
LONI SSH Gateways
SSH is short for Secure Shell. It provides a secure, encrypted method of transmitting information over TCP/IP to ensure the confidentiality, integrity and authenticity of transferred data. This is the preferred method of connectivity to LONI's Unix and Linux computational resources.
To access the LONI network via SSH:
- Obtain an SSH client for Windows, Linux, or MacOSX
- To find out if you already have ssh on a Unix/Linux based machine, type
which ssh
- SSH to
ssh.loni.ucla.edu over port 22 using the your LONI username and password.
- If accessing LONI for the first time, please change your password by following the instructions here.
--
DavidHasson - 19 Mar 2009
Configuring a Linux box during OS Installation:
- Add Linux box to NIS domain:
- domain: loni
- servers: 128.97.134.82,128.97.134.43,128.97.134.45,128.97.134.46
- Configure NTP
- time server: 128.97.134.82
- Allow only SSH connections in Firewall Config
Configuring a Linux box post OS Installation:
- visudo
- uncommment line '%wheel ALL=(ALL) ALL' to allow sudo
- add line 'Defaults logfile=/var/log/sudo.log' to log sudo use
- add usernames w/ sudo privileges in /etc/group:wheel
- copy doig:/etc/fstab LONI entries into machine's /etc/fstab
- create NFS mountpoint directories
- edit /etc/ssh/sshd_config to EXPLICITLY disable PermitRootLogin?
- edit /etc/hosts.deny by adding line 'ALL: ALL'
- edit /etc/hosts.allow by adding line 'sshd: ALL'
Darwin Streaming Server
Wirecast
--
DavidHasson - 22 May 2008
LONI Services account
To get a LONI Services account, go to the
LONI Services login page.
Calendars
LONI calendars are available
here
Pipeline accounts
Pipeline accounts depend upon a LONI Services account. You must have your account enabled for Pipeline access. Please contact Cornelius Hojatkashani (
chojatk@loni.ucla.edu) for more details
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- Install the "tetex" package binary (current version 3.0-1) by clicking on the blue "+" at the top left corner. See screenshot above. This will take about 30-60 minutes
- Download from Smart CVS site
- Mount disk image
- Copy to Applications folder
Once you have it installed, the LONI CVS information can be found at
here
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LONI Support Request
| Name | Type | Size | Values | Tooltip message |
| TopicClassification? | select | 1 | NoDisclosure?, PublicSupported?, PublicFAQ? | blah blah... |
| OperatingSystem? | checkbox | 3 | OsHPUX?, OsLinux?, OsSolaris?, OsWin? | blah blah... |
| OsVersion? | text | 16 | | blah blah... |
Data Center Power Distribution
MarcSycip - 11 Sep 2008
Matlab Installation Instructions
INSTALLING MATLAB 2008a
- Navigate to \\achilleos\software\Windows\Mathematics\MatLAB
- Run "setup.exe" in the "Matlab2008a-win32" folder for 32-bit Windows, or the "Matlab2008a-win64" folder for 64-bit.
- Note: You don't need to mount it, or copy the files like you might for some other installs
- Matlab 2008a now uses a FLK "File License Key" - which is basically just a renamed PLP. In both cases, it just uses it to figure out what you're licensed to install, as there are tons of toolkits, etc.
- This key is located here: \\achilleos\software\Windows\Mathematics\MatLAB\Licenses\matlab2008a-flk.txt
- The current key is
"00418-05741-12681-23448-02257-40048" for all platforms. If it gets updated, it will be current in the file above.
- The license file to use for all versions of Matlab using the network license is here: \\achilleos\software\Windows\Mathematics\MatLAB\Licenses\matlab-client-license.dat
- You can paste the above URL directly into the box when setup asks for the location. You might need to copy it or use an fqdn in the path if your computer isn't local or doesn't resolve LONI names correctly when on the VPN.
- Install everything to get the desired toolboxes.
MarcSycip - 26 Aug 2008
Infrastructure Meeting Archives
Current Meetings - Meeting notes for the current year (2007).
2006
August 7, 2006
August 14, 2006
August 21, 2006
August 29, 2006
September 5, 2006
September 13, 2006
September 18, 2006
September 25, 2006
October 27, 2006
November 3, 2006
--
DavidHasson - 20 Aug 2007
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Exchange 2007
Exchange 2007 no longer has the frontend/backend topology. It is divided up into server roles: Edge Transport, Hub Transport, Mailbox, Client Access, and Unified Messaging. A good website describing these roles can be found here (
http://www.msexchange.org/tutorials/Introduction-Exchange-2007-Server-Roles.html) Also Exchange 2007 requires a 64-bit version of windows to run.
Mailbox Servers (bellow are some bullet points about the exchange mailbox servers only)
Prerequisite:
Before installing exchange a few programs need to be installed:
IIS, .NET 2.0 Framework, Microsoft Management Console 3.0, and Microsoft Windows
PowerShell?.
- Clustering:
- Only the mailbox servers can be clustered. This means that the servers in the cluster can only have the mailbox exchange serve role and none of the others.
For instructions on how to setup a windows cluster for exchange see Chapter 31 in “SAMS Exchange Server 2007 UNLEASHED.”
- Storage:
- The two mailbox servers are connected to the Sun3510 storage array (See the 3510 write-up for more info) via fibre channel. The servers have a duel port fibre card which allows for load balancing across the two Brocade switches.
- MPIO:
- In order for the mailbox server to address the disks properly MPIO software needs to be installed. Without the MPIO software each server would see double the amount of disks that it should. The reason is that disk info is being mapped to both ports on the fibre card. What the MPIO software does is it recognizes that the same disks sets are being sent through on both ports and it classifies one port as a failover port. This way the server can see the appropriate amount of disks and the server can function as it should. The MPIO software that is being used can be found on Sun’s website. Also keep in mind that these are 64-bit machines and require MPIO software that is compatible with the 64-bit architecture.
When you run the MPIO software you can type “?” for a list of all the commands. The two commands that matter are devinfo and pathinfo. These two commands allow you to manipulate the way in which MPIO functions. For example, to set all the disk to run in failsafe mode you would type: devinfo all FailOver?.
If you type devinfo or pathinfo you can receive an output of the state of the disks. Online documentation is rather sparce. I found something helpful here:
http://209.85.165.104/search?q=cache:iD_QajataMsJ:www.dothill.com/assets/pdfs/SN_MPIO_83-00004226_RevC.pdf+dsmcli&hl=en&ct=clnk&cd=1&gl=us#6
However, I am not sure how long this website will be up. Another option would be to google “dsmcli”.
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JonathanPierce? - 07 Aug 2008
first rev, no permissions
second rev, adding correct permissions
third rev, now i messed things up horribly
- Set ALLOWTOPICVIEW = TwinGeneticsGroup?
- Set ALLOWTOPICCHANGE = SysadmGroup
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NetWorker Troubleshooting
Connection refused / Connection timed out
This indicates that the Networker server wasn't able to connect to the Networker client on the target machine.
- Verify that the client machine is online and reachable over the network.
- Check whether Networker client is installed and running on the client machine.
- Check Networker's 'nsrports' setting: type 'nsrports' on the client, it should return '7937-7967'
- Check iptables configuration on the client, it should allow incoming traffic on ports 7937-7967.
- Telnet from Networker server to the client on port 7937 to verify that connection to the client can be made from server.
Probe job had unrecoverable failure(s), please refer to daemon.raw
- Check for connectivity issues between the Networker server and the client.
- Move the client to the "test" savegroup (or create a new subgroup and move the client to it). Then, try to probe the savegroup with command "savegrp -vvvp test" (substitute the new savegroup name if necessary). If probe succeeds, try to run the savegroup with command "savegrp -vv test". All commands must be run from the Networker server.
Mount point X already exists
This error only occurs when backing up a Virtual Machine through a VCB proxy (for LONI, the proxy is fiske.loni.ucla.edu). The error indicates that previous backup job did not dismount the Virtual Machine completely (it could have been interrupted, etc).
- Login to the VCB proxy and delete the folder X that is referenced in the error message. Also, there is an option in VCB settings file that can take care of that issue by deleting previously mounted folders before attempting a backup job.
For more information about VCB, see this page.
The virtual machine identified by X is unknown
This error only occurs when backing up a Virtual Machine through a VCB proxy (for LONI, the proxy is fiske.loni.ucla.edu). The error indicates that the VCB proxy could not find and contact the virtual machine on the ESX server. More detailed description of the error suggests that the virtual machine may be powered off, or VMware Tools might not be installed on it. If the virtual machine is specified via its name (instead of its FQDN or IP address) then that name must be unique.
Troubleshooting the error:
- Login to the VCB proxy, open command prompt, and navigate to the VCB folder
- Run the 'vcbVmName' command to test whether the VCB proxy can reach the virtual machine:
- vcbVmName -h SERVER -u USER -p PASS -s ipaddr:VM
- SERVER is the ESX server (available in the VCB config file)
- USER is the username for the ESX server (available in the VCB config file)
- PASS is the password for the above (available in the VCB config file)
- VM is the FQDN or IP of the virtual machine (the X)
The above command should find the virtual machine on the ESX server if everything is configured correctly.
For more information about VCB, see this page.
Client X is not properly configured on the NetWorker Server
This error indicates that there is no configuration exists for the given client on the Networker server. This error may also come up when the client's IP address does not correctly resolve to its fully qualified domain name.
- Check whether the Networker client is listed in the Networker Management Console, under Configuration->Clients.
- Check whether the client's IP address correctly resolves to its fully qualified domain name, and vice versa.
1 retry attempted, (interrupted) exiting, aborted due to inactivity
~
Stuck on "starting session: state active"
~
Saveset "NMCASA:/gst_on_vodalus/lgto_gst" is stuck on "starting session: state active"
The workaround reported by the EMC tech. support is as follows:
- Stop the group
- Kill savepsm process
- Stop gst service
- Kill dbsrv9 as warrants
- /etc/init.d/gst start
- /etc/init.d/gst stop
At this stage, if kill is returned during the stop, then start gst and stop until kill is not returned.
There is already a machine using the name: "X"
The error indicates that there is a cached security certificate on Networker server that conflicts with the corresponding client certificate on the client. This can happen when the client's OS has been reinstalled or Networker software on the client has been reinstalled. The newly generated security certificate on the client does not match the one on the server.
The workaround reported by the EMC tech. support is as follows:
- Login to the Networker server as root
- Type "nsradmin -s SERVER -p nsrexec" (where SERVER is the FQDN or IP of the Networker server)
- Type "print type: nsr peer information" to see cached security certificates
- Type "delete name: X" to delete cached security certificate for host X
This deletes the old cached security certificate which causes these messages.
Networker Commands
- Add tape volumes to a newly configured jukebox:
for (( i = 500000 ; i <= 500049 ; i++ )) ; do nsrjb -a -s vodalus.loni.ucla.edu -v -T $i 2>&1 | tee -a nsrjb-a-T_500000-500049.log ; done
- Change location for multiple tapes:
for (( i = 500000 ; i <= 500049 ; i++ )) ; do mmlocate -u -n $i 'STK9310' 2>&1 | tee -a mmlocate_500000-500049.log ; done
- Run tape inventory on multiple slots:
for (( i = 1 ; i <= 50 ; i++ )) ; do nsrjb -I -S $i -v 2>&1 | tee -a nsrjb-I-S_1-50.log ; done
LinhNamVu? - 20 Jul 2007
install red hat 5
- applications/games and entertainemnt
- applications/graphics
- applications/sound and video
- applications/text-based internet
+ development/dev libaries
+ development/dev tools
+ development/legacy software dev
+ servers/dns
+ servers/mail
+ servers/mail/postifx
+ servers/mail/mailman
- servers/mail/sendmail
- servers/print support
- servers/server config tools
on next boot:
set ntp servers
set dns information
turn SELINUX to permissive (will still report errors that selinux would normally not allow, but would still allow it)
copy over /etc/yum.conf
copy over /var/named/* (make sure there is a chroot directory)
copy over /var/mail/spamassasin/*
copy over /var/named.conf
copy over /var/spool/postfix/*
Installing Red Hat-based distributions over HTTP
This guide applies to Red Hat, CentOS?, Fedora and possibly other distributions as well. This example is for Red Hat AS4 i386. Other distributions should be the same, except you will need to point to the appropriate HTTP repository.
- Begin by booting off Installation Disc 1 or a boot-only disc for the distribution you would like to install.
- At the introductory 'boot:' prompt enter 'linux askmethod'
- The installation kernel loads as normal, except it enters text mode.
- For language select the default 'English'.
- Keyboard is typically the default 'us'.
- For Installation Method select 'HTTP'
- Configure an IP Address using either DHCP or static IP. This is the only the IP for the installation itself, so you will have another opportunity to change the system's permanent IP address later on.
- For 'HTTP Setup', point to the correct server and directory. In this case 'Web site name:' can be either 'yum' or 'yum.loni.ucla.edu' and 'Red Hat Enterprise Linux directory:' is 'rhel4as-i386/disc1'
- To confirm that you have a proper installation directory, in a web browser check that topdir contains a RedHat?/base directory.
- When asked if you would like to test the CD, you can select 'skip'. This is typically unnecessary especially since all packages will be fetched over HTTP instead of CD.
- If all goes well you should see an indication that the local installation media was detected successfully.
- Anaconda (the installation GUI) now loads.
- Proceed with the Linux installation as usual.
Tips for New Systems
Current systems:
Workstations
- Dell Precision 390
- Core 2 2.0Ghz or better
- 4Gb Memory or better
- Graphics card:
- nVidia FX550 or better for standard users
- nVidia FX3450 or better for graphics
- 1394 Card
- No floppy
- 5-Button Optical Mouse
- 160Gb SATA or better
- DVD/RW Drive
Desktops
- Dell Optiplex 755 Mini Tower
- XP Home Edition (we have a XP Pro VLK)
- Core 2 2.0Ghz or better
- 2Gb Memory or better
- Graphics card:
- ATI Radeon 2400 XT or better
- nVidia 8800 or better
- 1394 Card
- No floppy
- 5-Button Optical Mouse
- 160Gb SATA or better
- DVD/RW Drive
Monitors
General Ideas
- Purchase with the price break. Usually prices go up linearly with performance, but with a jump right where the premium products start
- Don't price out a machine that is no better than spare machines we have in the lab.
- Always get the cheapest warranty, and the cheapest OS.
- Purchase nVidia if possible, our current software is developed on nVidia
--
DavidHasson - 05 Oct 2007
Special List for the Cranium's Compute Nodes
This page described the different lists used by agentSmith to monitor the entire Cranium cluster. agentSmith uses three host lists to work. All these lists are located in cerebro-admin:/usr/local/loni/admin/nodes and are described as follow:
-
reportingList - This file contains information of all the compute nodes listed to serve in the Cranium cluster. Each line describes a compute node with its hostname, data IP and mgmt IP. This file is not needed to be edited unless we have new computers coming into the Cranium cluster or we decide to change any of the identifiers of the compute nodes (hostname or IPs).
-
blackList - The file describing this list contains the hostname of the compute nodes reported with special issues like the ones powered off because of maintenance or disabled from SGE due to special purposes. These nodes are prevented to be monitored by agentSmith. As a consequence, agentSmith can't change the SGE status of the node or a down node can't be powered off or receive reinstall instructions. When editing this file, just add the hostname of the compute node you would like to include. The file group is owned by admin and its permissions are 664.
To edit any of the two lists, blackList and hwIssuesList, use this link. Note, this page is only accessible by the SysAdmin group members and within the LONI network. Each time the list is updated via web, an email report will be sent to the cluster mailing list. Also, remember there is the option to edit these files from the command line by accessing cerebro-admin.
Created by Hugo Hernandez-Mora on Mon Jun 15th, 2009 @ 13:53:26
DmitriyVinogradov? - 15 Jun 2009
OSTicket Changes
Ticket Lock / Unlock Patch
The ticket unlocking functionality was added to OSTicket using the instructions found in
http://www.osticket.com/forums/showthread.php?t=1066 (credit to
webPragmatist).
The following files have been modified:
/scp/tickets.php
case 'process':
$isdeptmanager=($deptId==$thisuser->getDeptId())?true:false;
switch(strtolower($_POST['do'])):
// *** Added by webPragmatist
case 'unlock_exit':
if($ticket->isLocked() && ($lock=$ticket->getLock()) && !$lock->isExpired()) {
$lock->expire();
header('Location: tickets.php');
}
break;
// *** End addition by webPragmatist
/include/class.lock.php
function renew() {
global $cfg;
$sql='UPDATE '.TICKET_LOCK_TABLE.' SET expire=DATE_ADD(NOW(),INTERVAL '.$cfg->getLockTime().' MINUTE) '.
' WHERE lock_id='.db_input($this->getId());
//echo $sql;
if(db_query($sql) && db_affected_rows()) {
$this->reload();
return true;
}
return false;
}
// *** Added by webPragmatist
// Expire / remove existing lock.
function expire() {
$sql='DELETE FROM '.TICKET_LOCK_TABLE.
' WHERE lock_id='.db_input($this->getId());
//echo $sql;
if(db_query($sql) && db_affected_rows()) {
$this->reload();
return true;
}
return false;
}
// *** End addition by webPragmatist
/include/staff/viewticket.inc.php
<select id="do" name="do"
onChange="this.form.ticket_priority.disabled=strcmp(this.options[this.selectedIndex].value,'change_priority','reopen','overdue')?false:true;">
<option value="">Select Action</option>
<!-- Added by webPragmatist -->
<option value="unlock_exit">Unlock & Exit</option>
<!-- End addition by webPragmatist -->
Additional Columns in Ticket Summary Table
A new column labeled "Assigned To" was added to the ticket summary table that is seen from staff and admin control panel. For this to happen, the following changes were made:
/include/staff/tickets.inc.php
--- tickets.inc.php.old 2009-06-16 11:49:18.000000000 -0700
+++ tickets.inc.php 2009-06-16 12:53:19.000000000 -0700
@@ -158,10 +158,11 @@ $pagelimit=$pagelimit?$pagelimit:PAGE_LI
$page=($_GET['p'] && is_numeric($_GET['p']))?$_GET['p']:1;
-$qselect = 'SELECT ticket.ticket_id,lock_id,ticketID,ticket.dept_id,ticket.staff_id,subject,name,email,dept_name '.
+$qselect = 'SELECT ticket.ticket_id,lock_id,ticketID,ticket.dept_id,ticket.staff_id,st.username,subject,name,ticket.email,dept_name '.
',status,source,isoverdue,ticket.created,pri.* ';
$qfrom=' FROM '.TICKET_TABLE.' ticket LEFT JOIN '.DEPT_TABLE.' dept ON ticket.dept_id=dept.dept_id '.
' LEFT JOIN '.TICKET_PRIORITY_TABLE.' pri ON ticket.priority_id=pri.priority_id '.
+ ' LEFT JOIN '.STAFF_TABLE.' st ON ticket.staff_id=st.staff_id '.
' LEFT JOIN '.TICKET_LOCK_TABLE.' tlock ON ticket.ticket_id=tlock.ticket_id AND tlock.expire>NOW() ';
//get ticket count based on the query so far..
@@ -328,7 +329,8 @@ $basic_display=!isset($_REQUEST['advance
<a href="tickets.php?sort=dept&order=<?=$negorder?><?=$qstr?>" title="Sort By Category <?=$negorder?>">Department</a></th>
<th width="70">
<a href="tickets.php?sort=pri&order=<?=$negorder?><?=$qstr?>" title="Sort By Priority <?=$negorder?>">Priority</a></th>
- <th width="150" >From</th>
+ <th width="150">From</th>
+ <th width="150">Assigned To</th>
</tr>
<?
$class = "row1";
@@ -361,6 +362,7 @@ $basic_display=!isset($_REQUEST['advance
<td nowrap><?=Format::truncate($row['dept_name'],30)?></td>
<td class="nohover" align="center" style="background-color:<?=$row['priority_color']?>;"><?=$row['priority_desc']?></td>
<td nowrap><?=Format::truncate($row['name'],22,strpos($row['name'],'@'))?> </td>
+ <td nowrap><?=$row['username']; ?> </td>
</tr>
<?
$class = ($class =='row2') ?'row1':'row2';
Brief explanation of changes:
- First change modifies the SQL query that is used to retrieve tickets for display in the table. An additional LEFT JOIN statement is added that links ticket's staff ID to the staff table.
- Second change modifies the table header, adding a new column labeled as "Assigned To".
- Third change modifies the loop which outputs one table row at a time, adding a new cell that holds the username of the staff person to which the ticket is assigned (if any).
Fixing "From Address" Bug
OSTicket sent emails with a wrong "From" address, deviating from the settings. The fix is below.
/includes/class.misc.php
--- class.misc.php.old 2008-06-05 12:47:36.000000000 -0700
+++ class.misc.php 2009-02-13 17:35:36.000000000 -0800
@@ -64,9 +64,9 @@
$subject=preg_replace("/(\r\n|\r|\n)/s",'', trim($subject));
$message = preg_replace("/(\r\n|\r)/s", "\n", trim($message));
#Headers
- $headers .= "From: ".$fromname."<".$fromaddress.">".$eol;
- $headers .= "Reply-To: ".$fromname."<".$fromaddress.">".$eol;
- $headers .= "Return-Path: ".$fromname."<".$fromaddress.">".$eol;
+ $headers .= "From: <".$fromaddress.">".$eol;
+ $headers .= "Reply-To: <".$fromaddress.">".$eol;
+ $headers .= "Return-Path: <".$fromaddress.">".$eol;
$headers .= "Message-ID: <".time()."-".$fromaddress.">".$eol;
$headers .= "X-Mailer: osTicket v 1.6".$eol;
if($xheaders) { //possibly attachments...does mess with content type
Brief explanation of changes:
The $headers string building code was simplified, after which the problem disappeared.
CURS Authentication for Staff
The capability to authenticate users through LONI's CURS system to allow access to staff/admin panel was implemented with a few changes to the Staff PHP class.
/includes/class.staff.php
--- class.staff.php.old 2008-03-13 23:53:32.000000000 -0700
+++ class.staff.php 2009-04-17 13:15:46.000000000 -0700
@@ -14,6 +14,19 @@
vim: expandtab sw=4 ts=4 sts=4:
$Id: OSTicketChanges.txt,v 1.4 2009/07/03 00:53:30 dvinogra Exp wwwprod $
**********************************************************************/
+
+/*
+$fname = "/var/www/osticket/debug.txt";
+if (!$fp)
+ $fp = fopen($fname, "a");
+*/
+function dw($line)
+{
+ global $fp;
+ if ($fp)
+ fwrite($fp, date("D M j G:i:s") . ">\t" . $line . "\n");
+}
+
class Staff {
var $udata;
@@ -36,13 +49,45 @@
return ($this->lookup($var));
}
+
+// Start modifications by LONI
function lookup($var){
+ dw("called lookup($var)");
+
+ if (empty($var))
+ return FALSE;
+
$sql=sprintf("SELECT * FROM ".STAFF_TABLE." LEFT JOIN ".GROUP_TABLE." USING(group_id) WHERE %s ",is_numeric($var)?"staff_id=$var":"username='$var'");
$res=db_query($sql);
- if(!$res || !db_num_rows($res))
- return NULL;
+
+ if(!$res || !db_num_rows($res)) // if user is not found, we can try something else
+ {
+ dw("\tuser not found in database");
+ $em = $this->lookup_access_file($var);
+ if ($em != NULL) // check if the user is in a local access file
+ {
+ dw("\tlookup_access_file($var): user found in local access file");
+ if ($this->add_curs_user($var, $em) != NULL) // if successful, try to add user to database or return NULL
+ {
+ dw("\tadd_curs_user($var, $em): user added to database");
+ $res = db_query($sql); // query the database again, now that CURS user has been added to it
+ if(!$res || !db_num_rows($res)) // sanity check - at this point database should have CURS user added to it
+ return NULL; // for some reason, database still can't find the newly added user...
+ }
+ else
+ {
+ dw("\tadd_curs_user($var, $em): user couldn't be added to database");
+ return NULL; // user was found in local access file, but couldn't be added to database
+ }
+ }
+ else
+ {
+ dw("\tlookup_access_file($var): user not found in local access file");
+ return NULL; // user was not found in database and in local access file
+ }
+ }
$row=db_fetch_array($res);
$this->udata=$row;
@@ -59,6 +104,126 @@
return($this->id);
}
+
+ function lookup_curs($un, $pw){
+
+ dw("called lookup_curs($un, ***)");
+
+ if (empty($un) || empty($pw))
+ return FALSE;
+
+ $auth_url = 'https://utilities.loni.ucla.edu/services/user?service=authenticateUser';
+ $info_url = 'https://utilities.loni.ucla.edu/services/user?service=getUserIds';
+ $var_username = 'userEmail';
+ $var_password = 'userPassword';
+
+ $auth_data = array($var_password=>$pw, 'password'=>'usER4Mee');
+ $info_data = array('password'=>'usER4Mee');
+
+ $auth_url .= "&" . $var_username . "=" . $un;
+ $info_url .= "&" . $var_username . "=" . $un;
+
+ $info_response = $this->http_dopost($info_url, $info_data);
+ $info_array = split(":", $info_response);
+
+ if ((count($info_array) >= 4) && ($info_array[0] == "SUCCESS") && !empty($info_array[3]))
+ return TRUE;
+ else
+ return FALSE;
+ }
+
+ function http_dopost($url, $data) {
+
+ $params = array('http' => array(
+ 'method' => 'POST',
+ 'content' => http_build_query($data)
+ ));
+
+ $ctx = stream_context_create($params);
+ $fp = @fopen($url, 'rb', false, $ctx);
+
+ if (!$fp)
+ return false;
+
+ $response = @stream_get_contents($fp);
+ fclose($fp);
+
+ return $response;
+ }
+
+ function lookup_access_file($un){
+
+ dw("called lookup_access_file($un)");
+
+ if (empty($un))
+ return NULL;
+
+ $access_file = "/etc/osticket-staff";
+
+ if (!file_exists($access_file))
+ return NULL;
+
+ $arr_entries = explode("\n", file_get_contents($access_file));
+
+ if (count($arr_entries) < 1)
+ return NULL;
+
+ for ($i = 0; $i < count($arr_entries); $i++)
+ {
+ if (empty($arr_entries[$i]))
+ continue;
+
+ $arr_entry = explode(":", $arr_entries[$i]);
+
+ if (count($arr_entry) < 3)
+ continue;
+
+ dw("\t\tcompare: " . $arr_entry[1] . " == " . $un);
+
+ if (($arr_entry[1] == $un) && ($arr_entry[2] == "1"))
+ return $arr_entry[0];
+ }
+
+ return NULL;
+ }
+
+ function add_curs_user($un, $em){
+
+ dw("called add_curs_user($un, $em)");
+
+ if (empty($un) || empty($em))
+ return FALSE;
+
+ $sql=' SET updated=NOW() '.
+ ',isadmin=1'.
+ ',isactive=1'.
+ ',isvisible=1'.
+ ',onvacation=0'.
+ ',dept_id=1'.
+ ',group_id=1'.
+ ',username='.db_input(Format::striptags($un)).
+ ',firstname='.db_input(Format::striptags($un)).
+ ',email='.db_input($em).
+ ',passwd='.rand(100,999).
+ ',change_passwd=0';
+
+ $sql='INSERT INTO '.STAFF_TABLE.' '.$sql.',created=NOW()';
+
+ if(!db_query($sql) or !($uID=db_insert_id()))
+ {
+ dw("\tcould not add user to database");
+ return FALSE;
+ }
+ else
+ {
+ dw("\tadded user to database");
+ return TRUE;
+ }
+
+ return FALSE;
+ }
+// End modifications by LONI
+
function reload(){
$this->lookup($this->id);
@@ -69,9 +234,44 @@
}
/*compares user password*/
+
+// Start modifications by LONI
function check_passwd($password){
- return (strlen($this->passwd) && strcmp($this->passwd, MD5($password))==0)?(TRUE):(FALSE);
+
+ dw("called check_passwd(<length=" . strlen($password) . ">)");
+
+ if (empty($password))
+ return FALSE;
+
+ $passwd_ok = (strlen($this->passwd) && strcmp($this->passwd, MD5($password))==0)?(TRUE):(FALSE);
+
+ if (!$passwd_ok && ($em = $this->lookup_access_file($this->username)) && $em != FALSE) // if first check failed, it could be a CURS user
+ {
+ dw("\tfirst passwd check failed, trying CURS");
+
+ $passwd_ok = $this->lookup_curs($em, $password);
+ if ($passwd_ok)
+ {
+ dw("\tCURS auth successful");
+
+ $sql = "UPDATE ".STAFF_TABLE." SET updated=NOW()".
+ ",passwd='".md5($password)."'".
+ " WHERE staff_id=".$this->id;
+ if (!db_query($sql))
+ {
+ dw("\tfailed to update database with passwd");
+ }
+ }
+ else
+ {
+ dw("\tCURS auth failed");
+ }
+ }
+
+ return $passwd_ok;
}
+// End modifications by LONI
+
function getTZoffset(){
global $cfg;
Brief explanation of changes:
- First change adds a helper function named dw($line) which writes a string to a debug file. By default, the function's file open statement is commented out, which disables this behavior.
- Second change inserts additional logic into the lookup($var) function. If upon a call to the function the user is not found in the database, a local text file is checked, and if match is found, the user is added to the database (however, user's password is not yet set).
- Third change adds four more functions to the file, named lookup_curs($un, $pw), http_dopost($url, $data), lookup_access_file($un), and add_curs_user($un, $em).
- lookup_curs authenticates given username and password with CURS, using http_dopost function.
- http_dopost sends an HTTP POST request to a given URL with provided data.
- lookup_access_file checks a text access file for a given username (email address).
- add_curs_user adds a user with given username and email address to the database.
- Last change modifies the check_passwd($password) function by adding necessary logic to enable CURS logins into the system.
Adding a new user to OSticket with CURS authentication
- Simply edit /etc/osticket-users to add a new CURS user to OSticket. The file asks for user's short login name, user's email (which is the login name for CURS), and 1/0 enabled/disabled setting. It is advised that you also create this user through OSticket's admin panel, giving it appropriate full name, group and department membership, etc, and specifying any random password. If the new user logs in for the first time and CURS authenticates him successfully, the password will be updated.
ShanrenZhou? - 18 Dec 2006
1. Go to
http://www.crucial.com/company/contacts.asp
2. Click on the 'Live Chat with an expert' picture
3. Prove them with the following information
- Batch number (should start with a "B")
- CT part number
- Quantity
- Name
- Address
- Phone number
- E-mail address
- Exchange Method
4. For Exchange Method, choose 'Wait-to-Receive Exchange'
5. Return the items to the address that Crucial provides and be sure to write down
the RMA number
HowardChou? - 17 Jun 2006
Dell # to call: 1-800-456-3355 extension 7260301
They will ask for your name: " "
company name: it's either UCLA or KST
email address:
sysadm@loni.ucla.edu
phone number: 310-267-5706
address; 635 Charles E. Young drive Suite 225 Los Angeles, CA 90095
The technical support will ask you to perform all sort of tests trying to get the machine working.
Explaining to them you did all sort of testings or else you will sit there with him/her on the phone
for several hours!
enjoy =)
Shanren Zhou - 12 Dec 2006
Dell Live Chat:
http://support.dell.com/support/topics/global.aspx/support/gen/chat
1. Enter service tag: ##XXX## (can be found in the back of the machine) and click submit
2. You will need to fill out your personal contact information in the next page
3. As with the call support, try to convince them that you have done all the testing so you can have
the problem solved in prompt manner
Hardware and Software Order Tracker
| Date-Ordered | Date Received | Requestor | Description | Vendor | Price | Quantity | Version | Comments | PO# |
| 10/27/06 | 10/30/06 | Brian | SPSS 14 for Windows | Software Central | $62 each | 3 | 14 | | |
| 10/18/06 | 11/03/06 | Brian | Adobe Creative Suite 2 for Mac | TRC | $384.50 | 1 | | In Sysadm office | |
| 10/31/06 | 11/14/06 | Rico | Dell Precision 390 for Office group hardware refresh | Dell | $2,511.39 | 4 | | For Office group hardware refresh | |
| 10/31/06 | | JD | Server: Dual Core Xeon Processor 5150 4MB Cache, 2.66GHz, 1333MHz FSB, PE 1950 (222-3382) | Dell | $9,243.30 | 1 | | QUOTE #: 3264014861580NHE90500 & 1580NHE90600 |
| 10/31/06 | | JD | Server: QLogic 2462 Dual Port 4Gbps PCI-E FC HBA (222-0423) | Dell | $3,753.76 | 1 | | QUOTE #: 326403667 | 1580NHE90300 |
| 11/01/06 | 11/06/06 | Ivo | 100 GB 2.5" Hard Drives | CDWG | $149.62 | 2 | | | 1580NHE86100 |
| 11/01/06 | 11/06/06 | Ivo | 2.5" Hard Drive Enclosures | CDWG | $25.67 | 3 | | | 1580NHE86100 |
| 11/01/06 | | Rico | DVD Drive/floppy drive for Sun Fire V20z. | Sun | $936.00 | 6 | | Product Number: X9260A | 1580NHE86300 |
| 11/01/06 | | Rico | 4000WATT AC POWER SUPPLY FOR US (CABLE ATTACHED) | Network Hardware Resale | $2,250.00 | 1 | | | 1580NHE86400 |
| 11/01/06 | | Amanda | Keynote Pavilion Software | KeynotePro? | $19.95 | 1 | | | 1580QHE803 |
| 11/03/06 | | Rico | 1.25" Flexible Nylon Wire Loom 50' | Cable Organizer | $144.95 | 2 | | | 1580QHE899 |
| 11/03/06 | | Rico | 1.25" Flexible Nylon Wire Loom 50' | Cable Organizer | $144.95 | 2 | | | 1580QHE899 |
| 11/06/06 | | Rico | Solaris Only support | Dynamic Systems Inc | $2160.00 | | | | |
| 11/08/06 | | Rico | Sliding Rapid/Versa Rails Universal, PE 2950, Customer Install (310-8194) | Dell | $112.48 EACH | 2 | | |
| 11/09/06 | Received | Rico | Adobe After Effects | TRC | $198.90 EACH | 2 x Windows, 2 x Mac | 7 Professional | In Sysadm office | |
| 11/13/06 | | Rico | PNY NVIDIA Quadro FX 4500 X2 1GB PCIe Graphics Card | Dell | $3099.99 | 1 | For the backup DIVE box for the P41 visit | Order Number: 200611138006 | |
| 11/14/06 | | Rico | Router Board For An Origin 300 System | Great Eastern Technology | $1200.00 EACH | 2 | To upgrade our SGI fileservers from 4 processors to 8 processors each. | | 1580NHF23000 |
| 11/15/06 | | Rico | CT530854: 1GB, 184-pin DIMM Upgrade for a Dell PowerEdge? 2650 (533MHz FSB) System | Crucial | $747.71 Total | 4 | | | |
| 11/15/06 | | Rico | 4 PAIR CAT6 PATCH CABLE | GoCables?.com | $17.91 EACH, Total: $124.12 | 6 | | | |
| 11/22/06 | | Rico | Reference Manager for Windows | digitalriver.com | $247.94 | | | | |
| 11/22/06 | | C. Schwartz | Intel iMac 2.0GHz 20” Display (7013381) | UCLA Computer Store | $999 | | | To be delivered to Craig's office. | |
| 11/23/06 | | Queenie | VMware Workstation 5 (for Windows) | VMware | $189.00 | | Electronic Download Version | | |
| 11/28/06 | | Rico | Mathematica Network License Mgr & Mathematica Network License for Windows | Software Central | $80, $185 | 1 of Each | | | |
| 12/06/06 | | Rico | NUMALINK-1M-SU: Numalink Cable 1 M | Great Eastern Technology | $95.00 EACH | 3 | | For Origin 300 server upgrade. | |
| 12/07/06 | | JD | 146 GB 10,000 RPM Cheetah 10K.7 Ultra320 SCSI Internal Hard Drive (A0451508) | Dell | $345.00 Each, Total: $690.00 | 2 | | For the new patchlink server. | |
| 12/11/06 | 12/11/06 | JD | RHN Management Module | Red Hat | $96.00 EACH | 2 | | Order Number: W2811171 | |
| 12/14/06 | Received | Jonathan | BFG GeForce? 6200 OC 256MB DDR PCI Graphics Card | Best Buy | $156.99 | 1 | | For the frontend machine on our Visualization Cluster | |
| 12/15/06 | | Linda | CMS400..net Ephox MAC editor (10 users only) | Ektron | $359.00 | 1 | | License Key Case #00045516 | 1580NHG06500 |
| 01/02/07 | 01/12/07 | Linh-Nam | John Van Horn's New Computer | Dell | $4,375.74 | 1 | | E-Quote Number: E008539813 | |
| 01/03/07 | | Cornelius | MacBook? Pro 15.4" | Apple | $1,999 | 1 | | | |
| 01/04/07 | | HongWei? | Hitachi 7200 RPM 250GB IDE ATA130 HD | NewEgg? | $69.99 | 1 | | | |
| 01/04/07 | Received | HongWei? | PNY VCG76512SAPB GeForce? 7600GS 512MB 128-bit GDDR2 AGP 4X/8X Video Card | NewEgg? | $142.99 | 1 | | | |
| 01/12/07 | | Rico | KTK-15 Fuse | www.drillspot.com | $8.64 EACH | 3 | | For Multimeter. | |
| 01/22/07 | | Rico | PowerEdge? 1950 | Dell | $2,621.25 | 1 | | For the mail transport and spam filter for our 2007 Exchange setup. | |
| 01/22/07 | | Jonathan | 13W3 to VGA adapter | www.monoprice.com | $8.46 | 1 | | | |
| 02/09/07 | 02/16/07 | Rico | IDE Cables | http://store.cwc-group.com/18ulata33661.html | $0.75 EACH | 5 | | | |
| 02/09/07 | 02/16/07 | Rico | SATA Cables | http://store.cwc-group.com/seatas90180d.html | $1.65 EACH | 5 | | | |
| 02/09/07 | 02/22/07 | Rico | SCSI Cables | http://www.computercablestore.com/detail.aspx?ID=574 | $1.65 EACH | 5 | | | |
| 02/13/07 | | Allan | 500 GB external hard drive | CDWG | $249.37 | 1 | | CDW Part: 993387 | 1580 N HH713 00 |
| 02/13/07 | 02/23/07 | JD | Switch: WS-C2970G-24TS-E | Network Hardware | $2350 | 1 | | For servers in new production rack. | |
| 02/15/07 | | SVG Group | 500 GB external hard drive | CDWG | $249.37 | 1 | | CDW Part: 993387 | |
| 02/20/07 | | Rico | UPS | Dell | $2057.00 + $90 SH | 3 Separate Items | | For production rack. | |
| 02/27/07 | | J. Morra | Keyboard | CDWG | $39.89 | 1 | | CDW Part: 947770 | |
| 03/01/07 | | Linh-Nam | Rack Enclosure | CDWG | $1,173.99 | 1 | | CDW Part: 920138 | |
| 03/01/07 | | Linh-Nam | PDU | CDWG | $273.99 | 1 | | CDW Part: 730516 | |
| 03/01/07 | | Shanren | 146 GB SCSI Hard Drive | Dell | $319.00 | 1 | | For Poweredge 2850. Upgrade to Dell cluster's primary root drive. | |
JonathanPierce? - 10 Jul 2007
The following outlines the steps taken to install Windows XP post-Linux install on PC2. We recovered a LVM partition sized roughly 40GB for the Windows install. The issue in this setup is that A) Windows obviously can't install to the logical volume and B) Windows setup hangs indefinitely after "Setup is inspecting your hardware configuration..." because it doesn't recognize the LVM partition type.
For reference, this is the original output of fdisk -l:
Device Boot Start End Blocks Id System
/dev/hdc1 * 1 13 104391 83 Linux
/dev/hdc2 14 24321 195254010 8e Linux LVM
- Removed var from LVM:
- [root@tono Desktop]# /usr/sbin/lvremove /dev/VolGroup00/LogVol_var
- Do you really want to remove active logical volume "LogVol_var"? [y/n]: y
- Logical volume "LogVol_var" successfully removed
- Removed swap from LVM (only volume with higher PE range than var):
- [root@tono Desktop]# /sbin/swapoff /dev/VolGroup00/LogVol_swap
- [root@tono Desktop]# /usr/sbin/lvremove /dev/VolGroup00/LogVol_swap
- Do you really want to remove active logical volume "LogVol_swap"? [y/n]: y
- Logical volume "LogVol_swap" successfully removed
- Recreated swap (with new lowest available PE number):
- [root@tono Desktop]# /usr/sbin/lvcreate VolGroup00? -n LogVol?_swap -L 1.94G
- Rounding up size to full physical extent 1.97 GB
- Logical volume "LogVol_swap" created
- [root@tono Desktop]# /sbin/mkswap /dev/VolGroup00/LogVol_swap
- Setting up swapspace version 1, size = 2113925 kB
- [root@tono Desktop]# /sbin/swapon -va
- swapon on /dev/VolGroup00/LogVol_swap
- [root@tono Desktop]# cat /proc/swaps
- Filename Type Size Used Priority
- /dev/mapper/VolGroup00-LogVol_swap partition 2064376 0 -2
- Resized LVM less 40G:
- [root@tono Desktop]# /usr/sbin/pvresize --setphysicalvolumesize 146.19G /dev/hdc2
- Physical volume "/dev/hdc2" changed
- 1 physical volume(s) resized / 0 physical volume(s) not resized
- fdisk reports 8225280 bytes per cylinder > resized less roughly [(38*1024*1024*1024)/8225280] cylinders:
- [root@tono Desktop]# /sbin/fdisk /dev/hda2
- Command (m for help): d 2
- Command (m for help): n
- 'primary' > First cylinder: '14' > Last cylinder: '19348'
- Added NTFS partition:
- [root@tono Desktop]# /sbin/fdisk /dev/hda2
- _New primary > Defaults are fine because it's the only remaining space on the disk > 't' to change type > '3' for new partition > '7' to change to NTFS
- Rebooted to verify everything was fine, then (IMPORTANT) saved the output of 'fdisk -l'
- Added NTFS partition using remaining space:
- Device Boot Start End Blocks Id System
- /dev/hdc1 * 1 13 104391 83 Linux
- /dev/hdc2 14 19348 155308387+ 8e Linux LVM
- /dev/hdc3 19349 24321 39945622+ 7 HPFS/NTFS
- Using the same procedure to delete as above in the 'fdisk reports 8225280...' step (but without recreating this time!), deleted partitions 1 and 2. This hides the partitions from Windows.
- Rebooted and installed Windows on the third partition. It's important at this stage that what is now reported as free space is NOT touched. Declaring the third partition type NTFS in Linux makes this simple to visually double check in the Windows installer.
- After install is working, started from our Ubuntu Live CD, then restored the partitions in fdisk.
- Command (m for help): n
- primary > First cylinder: 14 > Last: 19348
- Command (m for help): n
- primary > First cylinder: 19349 > Lsat: 24321
- The partition table is out of order at this point. This is unavoidable because Windows was installed on what it saw as the first partition:
- [root@tono ~]: /sbin/fdisk -l
- Device Boot Start End Blocks Id System
- /dev/hdc1 19349 24321 39945622+ 7 HPFS/NTFS
- /dev/hdc2 * 1 13 104391 83 Linux
- /dev/hdc3 14 19348 155308387+ 8e Linux LVM
then restored GRUB after adding an entry for windows(overwritten by the Windows MBR):
-
- Edited [mount for /dev/hdc2]/grub/menu.lst, updating all references to the new partition scheme and adding:
- title Microsoft Windows XP
- rootnoverify (hd0,0)
- makeactive
- chainloader +1
- root@ubuntu $: grub
- grub > root (hd0,1)
- grub > setup (hd0)
After this procedure, I was able to reboot and select either Windows or Linux.
1) Export from windows:
- From IIS Admin:
- From Certificates Snap-in (run->mmc.exe, add->certificates, computer store, local machine)
2)
openssl pkcs12 -in c:\certs\yourcert.pfx -out c:\certs\cag.pem -nodes
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Resetting your password
You can change your password using the VPN gateway or the LONI Webmail site
Using the change password page on LONI Webmail
- Go to http://password.loni.ucla.edu
- On the page you will see several fields, fill them out as follows:
- Account – username (eg. Joe Bruin has the username jbruin )
- Old password – your current windows password
- New password – what you want your new password to be
- Confirm new password – same as above.
- Click “OK”
- The password will be effective immediately for logging into Windows, accessing mail and using the VPN. It may take 5-10 minutes to propagate the changes to the unix services (e.g. inire, cerebellum, cerebro) or for linux and mac workstations.
--
JonathanTrout - 04 Oct 2007
--
DavidHasson - 04 Oct 2007
--
LinhNamVu - 25 Oct 2007
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PatchLink - perhaps you need to log in?
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Polk Print Cluster
Network Information
- Polk printer Service 10.1.1.113
- DNS entry for polk.loni.ucla.edu is 10.1.1.113
- Cluster service will negotiate which server will be hosting the print service
- On failover, cluster service will switch to the other server.
- Shared Storage vmhba1:1:4:0 (through vmware)
Polk-rs1
- 10.1.1.114
- 192.168.10.5 (internal network interface used by the cluster service)
- [vmfs-local] prod.polk/prod.polk-rs1.vmdk
Polk-rs2
- 10.1.1.115
- 192.168.10.6 (internal network interface used by the cluster service)
- [vmfs-local] prod.polk-rs2/prod.polk-rs2_1.vmdk
Operation
- You can access(add new printers/change settings) the polk printers from any computer
- Administrative access is needed to add printers to it.
Access to Printers hosted the the Cluster Printing Service
-
\\polk\Printers and Faxes
Add a Printer to the Cluster Printing Service
- goto
\\polk\Printers and Faxes in explorer
- add printer there
--
LinhNamVu - 12 Mar 2008
LinhNamVu? - 30 Jan 2007
Setting up RAID on a Solaris 10 6/06 Machine
Install OS
Insert disks (make sure you have the right architecture (sparc,x86))
Install OS (to boot into selected media use STOP+A, then use
More detailed
instructions from sun. Also keep in mind how you want to setup your partitions/disks.
Partitioning
If you want to just mirror the same partitions as installed the OS:
Copy partition layout to other disks with
-
prtvtoc /dev/rdsk/c#t#d#s# | fmthard -s - /dev/rdsk/c#t#d#s#
If you want to create you're own partition setup then create it on one of the empty disks
To format a disk use:
Then make sure the other disks you want in the RAID to have the same partition layout as the one you have
-
prtvtoc /dev/rdsk/c#t#d#s# | fmthard -s - /dev/rdsk/c#t#d#s#
Setup RAID
Choose a naming convention of metadevices for RAID
- dXY (X = disk number in raid) (Y = raid number)
Create devices
-
metainit -f d10 1 1 /dev/dsk/c#t#d#s#
-
metainit -f d20 1 1 /dev/dsk/c#t#d#s#
-
metainit -f d30 1 1 /dev/dsk/c#t#d#s#
-
etc...
Create RAID device.This command will create the initial metadevice for our raid
Attach the first device
-
metattach -f d0 d10 (note: there is one less 'a' in metattach)
The created metadevices will be located in /dev/md/dsk/DEVICE_NAME_HERE
If you are creating a metadevice for the partition that the systems boots off of then you'll need to edit /etc/vfstab and reboot the system and boot into the new metadevice settings. If not you can ignore this step.
-
vi /etc/vfstab
-
lockfs -fa
-
init 6
Attach remaining devices
-
metattach -f d0 d20
-
metattach -f d0 d30
-
etc...
If you want to be able to boot off the other disk if the first one fails then
-
installboot /usr/platform/`uname -i`/lib/fs/ufs/bootblk /dev/rdsk/c0t1d0s0
-
setenv boot-device disk disk1
-
nvstore
-
boot disk1
Maintanence
You can see the status of the disks using
metastat . If you want to see the progress of the syncing then use
metastat -c . In the event one of the drives goes missing, that command will show you. Once you re-insert the new drive you can create it with the above steps and attach it. Running
metastat will show that the drive needs maintanence and running
metasync will tell it that it can start syncing again.
metastat -c will now show the sync progress.
1) Install Rails
FreeBSD Installation
- Install Ports:
- www/apache22
- lang/php5
- lang/ruby19
- devel/ruby19-gems
- Install Gems:
- Install Passenger (this needed CVS last time I checked, though)
- gem install passenger-x.x.x.gem
- passenger-install-apache2-module
Setup VirtualHosts and Apache
Make a rails project
- cd /www/hosts/loni.funtaff.com/docs
- rails loni
- config/database.yml
- mv public/index.html public/index.html.old
- script/plugin source http://svn.techno-weenie.net/projects/plugins/ (only needs to be done once per machine)
- script/plugin install restful_authentication
- script/plugin install http://elitists.textdriven.com/svn/plugins/acts_as_state_machine/trunk/
- script/generate authenticated user session --include-activation --stateful
- rake db:migrate
- script/generate controller home
- config/routes.rb
- map.home '', :controller => 'home', :action => 'index'
- map.resources :users, :member => { :suspend => :put, :unsuspend => :put, :purge => :delete }
- map.activate '/activate/:activation_code', :controller => 'users', :action => 'activate', :activation_code => nil
- map.signup '/signup', :controller => 'users', :action => 'new'
- map.login '/login', :controller => 'session', :action => 'new'
- map.logout '/logout', :controller => 'session', :action => 'destroy'
- controllers/application.rb:class ApplicationController
- include AuthenticatedSystem
- views/home/index.html.erb
Test and create demo user
--
DavidHasson - 14 May 2008
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RebuildRAID - perhaps you need to log in?
Red Hat Systems
2.1AS-i386
- aragon-lvs1
- aragon-lvs2
- aragon-rs1
- aragon-rs2
- dessi-dev
- dessi-lvs1
- dessi-lvs2
- dessi-test
- viola-dev
- viola-rs1
- viola-rs2
- viola-test
3AS-i386
3AS-x86_64
3WS-i386
3WS-x86_64
4AS-i386
4AS-x86_64
4ES-i386
- dessi-lvs3
- dessi-lvs4
- viola-local
4ES-x86_64
4WS-i386
- 10.1.2.44
- accardi
- doig
- heckle
- koba
- renior
- helm
- johnson
- kobayashi
4WS-x86_64
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LinhNamVu? - 07 Dec 2006
Securing an Installationg of SQL Server 2005
To determine the SQL version on SQL Server 2005 open SQL Server Management Studio, connect to the database, then run the following query
SELECT SERVERPROPERTY('productversion'), SERVERPROPERTY ('productlevel'), SERVERPROPERTY ('edition')
Column 1. The product version (for example, "9.00.1399.06").
Column 2. The product level (for example, "RTM").
Column 3. The edition (for example, "Enterprise Edition").
Current versions can be found
here
Taken from
http://www.databasejournal.com/features/mssql/article.php/3461471
It is worth pointing out that the new version of SQL Server has been designed with the "secure by default" principle in mind, resulting in a system with optimum, from the security standpoint, settings. The typical setup avoids installing or activating non-essential components and features which can expose the server and its data to potential attacks. This applies, for example, to SQL Server Agent, Full-Text Search, and Data Transformation Services (all set to manual startup), Analysis, Reporting, and Notification Services, SQL Browser, Service Broker Network Connectivity, Database Mirroring, SQLMail, or SQL Debugging.
Taken from
http://www.sqlsecurity.com/FAQs/SQLSecurityChecklist/tabid/57/Default.aspx
How to secure SQL Server
- Keep up to date on SQL Server service packs and patches
- Audit SQL Server accounts for weak passwords
- Restict access to the SQL Server to only trusted clients
- Use Windows Only authentication where possible
- Store SQL Server backup files in a secure location and encrypted
- Disable all netlibs if the SQL Server is local-only
- Regularly scan the installation with Microsoft's Baseline Security Analyzer
Use Windows Only authentication mode for security if possible
By using integrated security, you can greatly simplify administration by relying on the OS security and saving yourself from maintaining two separate security models. This also keeps passwords out of connection strings.
Take the time to audit SQL logins for null or weak passwords
Use the following code to check for null passwords:
Use master
Select name,
Password
from syslogins
where password is null
order by name
There are a multitude of free and commercial tools to check for weak passwords. SQLPing2 is free and can be used to check for weak and null passwords.
Frequently check group and role memberships
While the SQL Server security model has many enhancements, it also adds the extra layer of permissions that we must monitor to make sure no one has been given more access than they need or that they’ve already circumvented security to elevate themselves. There's also the spectre of user's who have changed roles within the company but the SQL Server permissions structure has not been adjusted. This goes back to assigning object access to groups and not individuals.
Physically secure the SQL Server
Lock it behind a door and lock away the key while you’re at it. Someone sitting in front of the server will always find a way.
Rewrite applications to use more user-defined stored procedures and views
This minimizes the need to give direct access to tables. It gives the developer more control over how data can be accessed.
Enable logging of all user login events
You can also do this via script but using the following code:
xp_instance_regwrite N'HKEY_LOCAL_MACHINE', N'SOFTWARE\Microsoft\MSSQLServer\MSSQLServer',N'AuditLevel', REG_DWORD,3
Check master..Sp_password for trojan code
Compare your production scripts to the default script on a fresh installation and keep that code handy.
Check master..Sp_helpstartup for trojan procedures
Make sure no one has placed a backdoor here. Use Sp_unmakestartup to remove any rogue procedures.
Disable SQL Mail capability unless absolutely necessary
Leaving it open gives a potential attacker another means of delivering potential trojans, viruses, or simply launching a particularly nasty denial of service attack. By itself it is fairly harmless but it can be used to help an attacker.
Remove the Guest user from databases to keep unauthorized users out
This is the default but vigilant in case some dbo gets loose with the access controls. The exception to this is the master and tempdb databases as the guest account is required
Restrict to sysadmins-only access to dangerous stored procedures and extended stored procedures
There are quite a few of them, and this could take some time. Be careful not to do this on a production server first. Test on a development machine so you don’t break any functionality. Below is a list of the ones we recommend you assess:
sp_sdidebug
xp_availablemedia
xp_cmdshell
xp_deletemail
xp_dirtree
xp_dropwebtask
xp_dsninfo
xp_enumdsn
xp_enumerrorlogs
xp_enumgroups
xp_enumqueuedtasks
xp_eventlog
xp_findnextmsg
xp_fixeddrives
xp_getfiledetails
xp_getnetname
xp_grantlogin
xp_logevent
xp_loginconfig
xp_logininfo
xp_makewebtask
xp_msver
xp_regread
xp_perfend
xp_perfmonitor
xp_perfsample
xp_perfstart
xp_readerrorlog
xp_readmail
xp_revokelogin
xp_runweb
Make sure all SQL Server data and system files are installed on NTFS partitions
If someone should gain access to the OS, make sure that the necessary permissions are in place to prevent a catastrophe.
Use a low-privilege user account for SQL Server service rather than LocalSystem? or Administrator
This account should only have minimal privileges (a local user is best) and should help contain an attack to the server in case of compromise. Notice that when using Enterprise Manager or SQL Server Configuration Manager (SQL 2005) to make this change, the ACLs on files, the registry, and user rights are done for you automatically.
Secure the “sa” account with a strong password
This assumes you are using the SQL Server and Windows security mode. If possible, use the Windows Only mode and don't worry about people brute-forcing your 'sa' accounts. Of course, even so you'll want to set a strong password in case someone changes modes on you.
Choose only the network libraries you absolutely require
Better yet, if the SQL Server is local-only then why not disable all network libraries and use shared memory to access the SQL Server? Just use the name '(local)' as the server name. If your SQL Server requires connectivity from other hosts, use the TCP/IP netlib and then determine if SSL is needed.
Make sure the latest OS and SQL Server Service Packs/Hot-Fixes are applied
What different network protocol libraries should I use?
If the database is local-only then disable ALL netlibs and use shared memory to access the SQL Server. If you must connect from remote clients, use TCP/IP and enable encryption (non-trusted subnets) . Only use the alternative netlibs (
NwLink?, Names Pipes, Banyan, etc) if need be in those integration scenarios.
SQL Server 2000 includes the new Super Sockets net-lib which can do SSL over any of the protocols. It is highly recommended you make use of this in lieu of the multi-protocol encryption. Remember that a server certificate must be installed before the encryption can occur. The certificate must match the DNS name of the server and be issues by a certificate authority that the client trusts.
Yet another option if you are using Windows 2000 is IPsec. IPsec will allow you to encrypt ALL traffic between the client and server. This is a good solution when you have complete control over the server and the clients can take the time to learn IPsec policy deployment.
Additional Links
http://msdn2.microsoft.com/en-us/library/ms161948.aspx
Serial Numbers
VMWare Server - VMWare Server is free, but you need to register and keep track of serial numbers regardless. The list is maintained on the Wiki.
VMWare Trials? - We're currently using trials to run our test VM network. Status of trial registrations is maintained on the Wiki.
--
DavidHasson - 14 Oct 2007
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SetUpNIS - perhaps you need to log in?
How to set up a Printer in Windows XP
Under Printers and Faxes in the Control Panel:
- ) select "Add a printer"
- ) Click on "Next."
- ) Select "A network printer...."
- ) Select "Connect to this printer..." and type
\\polk\{printer name}
where {printer name} can be toad, grenoulle, mantella, etc.
- ) Select whether this printer is to be the default printer with {Yes | No}.
- ) Click on "Next."
- ) Select "Finish."
If the username and password prompt comes up, use the following format to enter your credentials:
LONI\{username}
{password}
where {username} is your LONI username and {password} is your LONI password.
How to set up a Printer in OS X
Under Print & Fax panel in the System Preferences:
- ) Click on the '+' sign to add a LONI printer
- ) Select the protocol 'Line Printer Daemon - LPD'
- ) The address is 'polk.loni.ucla.edu'
- ) The queue is the printer name. e.g. toad, grenoulle, mantella, etc.
- ) Select "Add"
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These are the steps to tunnel an SSH connection
Apple Mac OS X
- Install X11
- Launch X11
- type "ssh ${user}@${host} -Y", where ${user} is your username, and ${host} is the hostname of the server you are trying to log into
Windows
- First method- redirect output by setting the DISPLAY variable of your console to your local IP address and having an X-server accept it
- Start X-server (X-Win32)
- Find your IP address
- Open the command prompt
- Type "ipconfig"
- Set the DISPLAY environment variable
- for bash, "set DISPLAY ${IP}:0"
- for csh
- Second method- tunnel X session over SSH Secure Shell
- Start X-server (X-Win32)
- In SSH Secure Shell, click on "Edit" menu item
- Click on "Settings"
- Select "Tunneling" option in the left side of the window
- Verify that the "Tunnel X11 connections" option is selected
- Click "OK"
- restart all SSH connections
This probably won't come up too often, but it's good reference. Arash requested gcc4 on cerebro-cc. Unfortunately, the Sun Freeware edition does not have support for the "-m64" flag compiled in. There are quite a few caveats in compiling from source (note that this applies to Solaris 10 -- I don't know if they're going to replace gcc3 or include it alongside in future distributions):
- This step might be possible using Sun Studio's 'dmake', but just to be safe: download, compile, and install GNU make.
- Download the source for binutils. As of 2.17, it has issues with the amd64 library and ld will spew errors during the gcc build. This patch (loosely based on a fix from OpenSolaris?) fixed for me:
Index: bfd/elf.c
===================================================================
RCS file: /cvs/src/src/bfd/elf.c,v
retrieving revision 1.347
diff -u -2 -r1.347 elf.c
--- bfd/elf.c 23 Jun 2006 02:58:00 -0000 1.347
+++ bfd/elf.c 28 Jun 2006 00:32:08 -0000
@@ -2104,4 +2104,9 @@
break;
+ case SHT_GNU_dof:
+ case SHT_GNU_signature:
+ case SHT_GNU_syminfo:
+ return TRUE;
+
case SHT_GNU_verdef:
elf_dynverdef (abfd) = shindex;
Index: include/elf/common.h
===================================================================
RCS file: /cvs/src/src/include/elf/common.h,v
retrieving revision 1.77
diff -u -2 -r1.77 common.h
--- include/elf/common.h 17 Feb 2006 14:36:26 -0000 1.77
+++ include/elf/common.h 28 Jun 2006 00:41:58 -0000
@@ -341,14 +341,20 @@
#define SHT_GNU_LIBLIST 0x6ffffff7 /* List of prelink dependencies */
-/* The next three section types are defined by Solaris, and are named
+/* The next six section types are defined by Solaris, and are named
SHT_SUNW*. We use them in GNU code, so we also define SHT_GNU*
versions. */
-#define SHT_SUNW_verdef 0x6ffffffd /* Versions defined by file */
-#define SHT_SUNW_verneed 0x6ffffffe /* Versions needed by file */
-#define SHT_SUNW_versym 0x6fffffff /* Symbol versions */
-
-#define SHT_GNU_verdef SHT_SUNW_verdef
-#define SHT_GNU_verneed SHT_SUNW_verneed
-#define SHT_GNU_versym SHT_SUNW_versym
+#define SHT_SUNW_dof 0x6ffffff4 /* Solaris DTrace Object Format */
+#define SHT_SUNW_signature 0x6ffffff6 /* Solaris Cryptographic Framework: Digital Signature */
+#define SHT_SUNW_syminfo 0x6ffffffc /* Symbol information */
+#define SHT_SUNW_verdef 0x6ffffffd /* Versions defined by file */
+#define SHT_SUNW_verneed 0x6ffffffe /* Versions needed by file */
+#define SHT_SUNW_versym 0x6fffffff /* Symbol versions */
+
+#define SHT_GNU_dof SHT_SUNW_dof
+#define SHT_GNU_signature SHT_SUNW_signature
+#define SHT_GNU_syminfo SHT_SUNW_syminfo
+#define SHT_GNU_verdef SHT_SUNW_verdef
+#define SHT_GNU_verneed SHT_SUNW_verneed
+#define SHT_GNU_versym SHT_SUNW_versym
#define SHT_LOPROC 0x70000000 /* Processor-specific semantics, lo */
Index: ld/configure.tgt
===================================================================
RCS file: /cvs/src/src/ld/configure.tgt,v
retrieving revision 1.189
diff -u -2 -r1.189 configure.tgt
--- ld/configure.tgt 23 Jun 2006 18:11:47 -0000 1.189
+++ ld/configure.tgt 28 Jun 2006 00:42:40 -0000
@@ -164,10 +164,10 @@
i[3-7]86-*-solaris2*) targ_emul=elf_i386_ldso
targ_extra_emuls="elf_i386 elf_x86_64"
+ targ_extra_libpath=$targ_extra_emuls
;;
i[3-7]86-*-unixware) targ_emul=elf_i386 ;;
i[3-7]86-*-solaris*) targ_emul=elf_i386_ldso
targ_extra_emuls="elf_i386"
+ targ_extra_libpath=$targ_extra_emuls
;;
i[3-7]86-*-netbsdelf* | Index: ld/emulparams/elf_x86_64.sh
===================================================================
RCS file: /cvs/src/src/ld/emulparams/elf_x86_64.sh,v
retrieving revision 1.17
diff -u -2 -r1.17 elf_x86_64.sh
--- ld/emulparams/elf_x86_64.sh 30 May 2006 16:45:32 -0000 1.17
+++ ld/emulparams/elf_x86_64.sh 28 Jun 2006 00:42:47 -0000
@@ -23,5 +23,5 @@
fi
-# Linux modify the default library search path to first include
+# Linux/solaris modify the default library search path to first include
# a 64-bit specific directory.
case "$target" in
@@ -31,3 +31,7 @@
esac
;;
+ *-*-solaris2*)
+ LIBPATH_SUFFIX=/amd64
+ ELF_INTERPRETER_NAME=\"/lib/amd64/ld.so.1\"
+ ;;
esac
There is a good chance you'll need to inspect and patch by hand beyond 2.17 (if necessary at all).
- (Still binutils:) ./configure --disable-nls, make, and make install.
- The gcc documentation claims bison isn't necessary, but it will error out constantly without it. Download, compile, and install.
- Download gcc4. Solaris doesn't use GNU tar, so you'll get an error during the untar process. I just untarred on my own machine and scp'd the directory.
- I used the following line to configure (this is more for posterity and less of a note):
../src/configure --prefix=/usr/local/gcc4 --with-local-prefix=/usr/local --with-gnu-as --with-as=/usr/local/i386-pc-solaris2.10/bin/as --with-gnu-ld --with-ld=/usr/local/i386-pc-solaris2.10/bin/ld --enable-threads=posix --enable-shared --enable-multilib --disable-nls --with-included-gettext --with-system-zlib --enable-languages=c,c++
- Build, go to lunch, and install.
- Path /usr/local/gcc4/bin and test.
SOPHOS ENTERPRISE CONSOLE WIKI PAGE
Note: There are two parts to Sophos Enterprise Console: The Management Components (Management Server, Management Console, EM Library) & The Database. The easiest way to proceed is to install both parts on the same computer. The parts may be installed on separate machines, but, if the hosts are on different subnets, the two components will not be able to communicate with one another. This guide assumes both the Management Components and the Database are on the same machine.
1. Install the Database and Management Components
- Run the appropriate Enterprise Console Installer
- When asked to populate the database, if host machine is running a 64-bit OS, you must select to populate the database later. Scripts for populating the database will be created in the installation directory (usually C:\Program Files\Sophos\Enterprise Console\DB)
- Specify the SQL Server host and the instance onto which the database will be installed (HOST\INSTANCE)
- Note: The default instance name is MSSQLSERVER
- Note: For simplicity, you should create a new instance called SOPHOS
- A database called SOPHOS3 should be created on the SQL Server.
2. Populate the database manually
- After the Database and Management Server have been installed, open the command prompt and navigate to C:\Program Files\Sophos\Enterprise Console\DB
- For 64-bit operating systems, download the file “install.bat” from the Sophos website and place it in this folder.
- Run install.bat
- If the instance you chose is named SOPHOS, no parameters need to be entered. Otherwise use install.bat [INSTANCE] where [INSTANCE] is the name of the instance the database is installed on. If it’s the host is a domain controller, you must also specify the domain: install.bat [INSTANCE] [DOMAIN].
- This creates the stored procedures and tables for the SOPHOS3 database.
3. Open Enterprise Console (it should automatically connect to the database) for Configuration
- Download the “How to Use Enterprise Console” PDF and follow the instructions to:
- Create and configure a Library for packages
- Create groups and synch them with active directory
- Start Managing Computers
- The primary update source should be: \\HOSTNAME\InterChk\ESXP
- The account used to get updates: LONI\antivirus (Ask a sysadmin for the PW)
- The secondary update source should be directly from Sophos
- Contact BOL or Sophos for UCLA’s Username and Passwords to obtain updates
4. Modify Domain Group Policy so Enterprise Console can properly communicate with clients
- The following exceptions need to be added to the LONI Default Domain Policy’s Firewall Rules (Computer Configuration > Administrative Templates > Network > Network Connections > Windows Firewall ) to allow Sophos Enterprise Console to push out new installations:
Note: In the example below, 128.97.134.20 must be replaced by the specific IP address of the machine on which Enterprise Console is installed.
DOMAIN PROFILE
Program Exceptions:
Allow Local Program Exceptions:
Enabled
Define inbound program exceptions:
C:\Program Files\Sophos\Enterprise Console\Remote Management System:enabled:Sophos
Allow Inbound File and Printer Sharing Exception (from):
128.97.134.20
Allow Inbound Remote Administration Exception (from):
128.97.134.20
Port Exceptions:
Allow Local Port Exceptions:
Enabled
Define inbound port exceptions:
8192:TCP:128.97.134.20:enabled:sophos
8192:UDP:128.97.134.20:enabled:sophos
8193:TCP:128.97.134.20:enabled:sophos
8193:UDP:128.97.134.20:enabled:sophos
8194:TCP:128.97.134.20:enabled:sophos
8194:UDP:128.97.134.20:enabled:sophos
STANDARD PROFILE
Allow Inbound Remote Administration Exception (from):
128.97.134.20
Allow Inbound File and Printer Sharing Exception (from):
128.97.134.20
Port Exceptions:
8192:TCP:128.97.134.20:enabled:sophos
8192:UDP:128.97.134.20:enabled:sophos
8193:TCP:128.97.134.20:enabled:sophos
8193:UDP:128.97.134.20:enabled:sophos
8194:TCP:128.97.134.20:enabled:sophos
8194:UDP:128.97.134.20:enabled:sophos
- The following must be added to the LONI Computer GPO’s Firewall Rules to allow Sophos Enterprise Console to push out new installations:
DOMAIN PROFILE
Allow Inbound Remote Administration Exception (from):
128.97.134.20
Allow Inbound File and Printer Sharing Exception (from):
128.97.134.20
STANDARD PROFILE
Allow Inbound Remote Administration Exception (from):
128.97.134.20
Allow Inbound File and Printer Sharing Exception (from):
128.97.134.20
- Clients may need to be restarted for this change in GPO to take effect. Once these exceptions in the windows firewall have been made, the client should be able to contact the Enterprise Console Server and vice versa.
5. Start Managing Computers
- Open Enterprise Console
- Select the computer(s) you wish to manage, click PROTECT in the top toolbar
- A Protect Wizard will come up. Enter domain admin credentials to allow the installation to go through. If successful, the computer’s icon should no longer be “grayed out”.
- Note: If the installation fails, you can double click the computer’s icon and get more details about why it failed. A “0000002e” error code is a generic error which is most likely caused by a blockage due to a network and/or windows firewall.
- FOR SERVERS: If you can access \\GEER\interchk\ESXP but cannot run setup.exe (e.g. “Path not valid…”)
- Copy the ESXP folder to local C: * Run the setup.exe from there to install Sophos
- Edit the C:\Program Files\Sophos\Autoupdate\iconn.cfg so that primary server points to \\GEER\interchk\ESXP
Installing Sophos on Read Only Domain Controllers
1. Create IPSec Tunnel from RODC to Sophos Server
2. Allow IPSec Tunnel through the Firewall
Note: Steps 3 and 4 only necessary if you get Sophos Error 3051 during installation.
3. Create LONI
SophosSAU?0 account for each RODC
4. For 64bit OS, add to [HKEY_LOCAL_MACHINE\SOFTWARE\WOW6432Node\Sophos\AutoUpdate\Service], otherwise add the following registry keys:
- [HKEY_LOCAL_MACHINE\SOFTWARE\Sophos\AutoUpdate\Service]
- "Download User"="SophosUpdate”
- [HKEY_LOCAL_MACHINE\SOFTWARE\Sophos\AutoUpdate\Service]
- "Download Password"="[enter the password]"
- [HKEY_LOCAL_MACHINE\SOFTWARE\Sophos\AutoUpdate\Service]
- "UserPreset"=dword:00000001
MarcSycip - 17 Sep 2009
Configuring Spamassassin to Pick Up More Spam
- Subscribe SpamAssassin to various rule channels using the saupdate command
- Specifically MIT's OpenProtect? compilation of rules along with the official ones
- Grabs updates from updates.spamassassin.org and saupdates.openprotect.com
-
sa-update --gpgkey D1C035168C1EBC08464946DA258CDB3ABDE9DC10 --channel saupdates.openprotect.com --channel updates.spamassassin.org
- Necessary PGP Keys needed to be downloaded and imported to get updates from openprotect
-
sa-update --import key_file
- Created a bash script in /usr/local/bin/saupdate to run
-
sa-update --gpgkey D1C035168C1EBC08464946DA258CDB3ABDE9DC10 --channel saupdates.openprotect.com --channel updates.spamassassin.org
- Cron job to execute that script every day
-
0 0 * * * /usr/local/bin/saupdate
References
http://saupdates.openprotect.com/
LinhNamVu? - 09 Oct 2007
Special Lists for the Cranium's Compute Nodes
This page describes the special lists used by the Cranium's cluster monitoring script, agentSmith.
Hugo Hernandez - 15 Jun 2009
How to use the Star-P Software to Parallel Process on the Cranium Cluster
Star-P software allows users performing scientific, engineering or analytical computation on array or matrix-based data to use parallel architectures such as multi-core workstations, multi-processor systems, distributed memory clusters and/or utility/cloud-based environments.
The software delivers users of
MatLab and
NumPy (Numeric Python) the ability to:
- Transform serial applications for parallel deployment
- Develop and deploy new parallel applications and algorithms
Visit the official
Star-P website for more information.
To use the Star-P software: Follow the next steps. As a note, users are required to set public/private SSH authentication keys on the Cranium cluster to use the Star-P client. This allows you to SSH into any LONI machine without the need for passwords. Use this link to configure your authentication keys or send an email to support@loni.ucla.edu for assistance.
-
As the software is currently in evaluation, you need to login into one of the Cranium Cluster's compute nodes we configured to run Star-P. This machine is not accessible from all computers in the LONI network, so you need to login into a SSH proxy machine before accessing this compute node.
-
SSH into ssh.loni.ucla.edu,
-
Now, ssh into cerebro-24-114.data.cluster.loni.ucla.edu,
-
Run the command: starpClient (if you don't have /usr/local/bin in your path, then run /usr/local/bin/starpClient). You will have the following output:
-
By typing the qstat command, you can see the number of slots reserved by Star-P to run your parallel MatLab jobs in the Cranium cluster, in this case, 10 slots as shown in your Star-P client configuration file in your home directory.
--Hugo Hernandez - 16 Sep 2009
Compressing and Posting Videos for QT Streaming
Quick and Dirty
- Common Parameters:
- Quicktime container
- Hinted for streaming
- H264 Video, 15fps, Two-pass, De-interlace
- AAC Audio, Mono, 44.1khz
- Three Profiles:
- Large: 640x480 (VGA), 1500kbps video, 64kbps mono ("1500")
- Medium: 352x288 (QIF), 900kbps video, 56kbps mono ("900")
- Small: 320x240 (CIF), 350kbps video, 56kbps mono ("400")
- Naming convention:
- Date format: yy_mmdd
- Files: <date>-<event>-<part>-<bitrate>.mov
-
08_0612-ctsi_sym-intro-900k.mov
- Posting:
- sftp/scp access
-
qtss.loni.ucla.edu:/usr/local/share/DarwinStreamingServer/movies/
- Archiving:
- Access:
-
rtsp://qtss.loni.ucla.edu/
- rtsp (streaming root) is the posting location located above.
Requirements
- Quicktime 7 Pro
- Mac OS (recommended)
Compression
(Work in progress)
--
DavidHasson - 23 Jun 2008
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References on Subversion
This article contains three parts. The first part is for LONI clients who simply want to connect to the LONI subversion repository. The second part is for both admin’s and users as a write-up for various features and tools of subversion. The third part is for LONI admins that want to administrator the websvn site.
Part 1:
To connect to the subversion repository you will need a subversion client. The recommended client is smartsvn. They have a Linux, OS X and Windows version. The software can be found here:
http://www.syntevo.com/smartsvn/download.jsp
Once you have downloaded the software it is time to checkout the code.
When you start the program there should be an option that allows you to check out code. Choose this option. At this point you should be presented with a box asking for “Access Method" Choose:
SVN+SSH
Server Name:
svn.loni.ucla.edu
Repository Path: (This is the path to the location of your repository everyone’s will be different for ccb it would be
/cvs/ccb or pipeline it would be
/cvs/pipeline
Next you will be asked about “Login Name” at this point every project has it own login name. (Ask your project leader for this info.) By early summer of 07 you will be able to use your own login name and password to authenticate rather than the global account.
In the end the path should look like
svn+ssh://@svn.loni.ucla.edu//
IE
svn+ssh://ccb@svn.loni.ucla.edu/cvs/ccb
Note From Ivo
In eclipse menu: window > preferences > team > svn change the default SVN interface from JAVAHL(JNI) to
JavaSVN?(Pure JAVA)“
“Eclipse/Subclipse Use: svn+ssh://svn.loni.ucla.edu/cvs/ccb -- you will be asked for authentication (name/password) later. For more on Subclipse see:
http://subclipse.tigris.org/
Part 2:
1) Basic Subversion Info
a) The Subversion Redbook:
This is the official manual which though published by O'Reilly, is still available for free in PDF & HTML. The nightly build is up-to-date for the latest release of Subversion - v1.3
http://svnbook.red-bean.com/
b) Best Practices for programmer/users read the following:
Chapter 1, section: What is Subversion?
Chapter 1, section: A Quick Start
Chapter 2, section: Subversion in Action
Chapter 3, section: Import
Chapter 3, section: Basic Work Cycle
As the "Basic Work Cycle" write up in the SVN book makes clear, as a user, there are really only a few commands you'll need to know:
- Import - to add an exist project to the SVN system and put it under version control
- Checkout - to get a local "working" copy of this project, now under version control
- Add or Delete - to add or delete files to the project so that SVN is aware of these changes
- Commit - to add changes you make to your local working copy to the SVN server copy of the project
- Update - to receive changes from the server that have been added by someone else
- Info - to get back info on your working copy (can remind you of it's server address and other info)
- Status - lets you know the current status of files in your working copy (helpful when you are about to 'Commit' - it shows what has been added, deleted, modified, etc. since the last commit. svn help status is very informative and makes it clear what all the info in an svn status report means)
- Merge - IF you are jointly working on the same project, merging becomes inevidible. The key to making this as painless as possible, is to put human business rules in place that make it clear who's working on what. In a totally Open Source project with 100s of coders contributing from around the world, that's pretty tough to do - though many projects do it effectively. For us, its much easier to insure we almost never need to merge.
This site (and some of the others below) provide some clear sense of why moving to SVN from CVS is a good idea:
http://www.oreillynet.com/onlamp/blog/2004/09/byebye_cvs_ive_been_subverted.html
As for general info on usage, there's the main Subversion site (
http://subversion.tigris.org/). One can also consult the SVN User Mailing List (which is a very busy list):
http://svn.haxx.se/users/ (archive)
This page also includes lists for TortoiseSVN and Subclipse (see below)
2) Using Subversion to create an automated build system:
This Ars Technica reference really points to all the features specific (and native) to Subversion that make this possible.
http://arstechnica.com/articles/columns/linux/linux-20050406.ars
Your admins may find the following useful, if they plan to install the SVN server on Windows. Doing on a Unix-based OS is really quite easy, and it's well explained in the SVN Redbook.
http://excastle.com/blog/archive/2005/05/31/1048.aspx
3) Subversion binary server (svnserver) + SSL/SSH
a) Fine grained authentication with SVN+SSH:
This is the way we all access our repository. I'm little less concerned with the details of security, but as of v1.3 of Subversion, it is possible to set up very fine grained access rights by group & user. See the following write up by the developer of the PuTTY SSH suite for more info:
http://www.chiark.greenend.org.uk/~sgtatham/svn.html
I would say this is one of the most thorough and insightful detailed descriptions of how to use SVN+SSH
b) basic use of SVN+SSH (using PuTTY)
The following link provides an excellent step-by-step description of how to set up SSH on the server accounts being used, so that on the client you login from, all authentication will be completely automatic. Basically, all SSH suites come with an SSH-agent. You can provide this agent with links to your various keys - public & private.
If you create a public/private key pair on the server account you'll use to login to svn+ssh, then copy that PRIVATE key over to the client where you'll be doing your development, the ssh-agent clients can use this key to auto-magically log you in every time you perform a any transaction with the server. If YOU DON'T set this up, life with Subversion - or any VCS using an SSH encrypted tunnel to protect your data - you will soon loose your mind from all the user/password/passphrase entry you need to do every time you run any command against the server. I CANNOT stress this enough: Set up the ssh-agent, and something like TortoiseSVN (described below) will be no more complicated than using the File Explorer.
Here's the link. The whole document is useful, but the section labeled "Setup SSH" spells out how to rig automatic authentication.
It works like a charm:
http://ozmm.org/docs/subversion_windows_xp.html
You can also check out the following, but the former URL is much more useful and detailed:
http://www.logemann.org/day/archives/000099.html
I would also add this basic scenario works regardless of the client platform you use. I use a nice Cocoa SSH-Agent GUI client for Mac OS X (SSHKeychain -
http://www.sshkeychain.org) which provides a long-lasting (you can set the time out) encrypted tunnels to servers, which all the SVN+SSH software I use on Mac OS X - svnX, command line, and the Netbeans SVN plugin - are all able to take advantage of. Once SSHKeychain opens a tunnel, I can use any one of these SVN tools and never have to login.
Same is true for Linux
(NOTE: The other trick is to follow his recommendation for the SSHD config file - to wit, "# Make sure your SSH configuration file has these lines uncommented: PubkeyAuthentication yes; AuthorizedKeysFile %h/.ssh/authorized_keys"
Just remember, if you run into login/authentication hassles, it probably the SSH setup, not subversion.
c) The PuTTY Windows SSH Suite
Finally, on Linux & Mac OS X, you will have all the SSH/SSL libraries & apps you need as a part of the core OS install. Not so on the every security conscious MS Windows environment. By far, the best way to solve this deficit is to download the complete PuTTY suite of
programs:
PuTTY Download Page:
http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html
Just download the whole shabang. Go down to "A .ZIP file containing all the binaries (except PuTTYtel), and also the help files" and download "putty.zip"
Excellent, thorough PuTTY documentation is available here:
http://www.chiark.greenend.org.uk/~sgtatham/putty/docs.html
For use with SVN, really the ozmm.org link above should suffice
d) Win64:
You're probably wondering why I kept saying win32. It turns out the Win64 version (for those of you using
WindowsXP?/64 on AMD chips, for instance - we have two such setups) of TortoiseSVN is still in alpha. There is a work around, and it is easy to set up and definitely works. It turns out Internet Explorer/32-bit is still installed on WinXP/64 systems (and if MS should change this, you can still get it and install it yourself). You can start up IE32 and use it to peruse files and directories on the local disk. If you install TortoiseSVN just as on Win32, it will work just fine via this route.
The detailed procedure for doing this is:
- i) The path to your 32-bit IE is: C:\Program Files (x86)\Internet Explorer\IEXPLORE.EXE
- ii) You can make a shortcut to this program on your desktop - giving it an appropriate name like "32-bit Internet Explorer"
- iii) Just double-click this shortcut to start up 32-bit IE.
- iv) Use the "Open File" command, selecting the root directory of one of your algorithm projects.
- v) Save a bookmark to this directory.
- vi) You'll now be exploring the contents of that folder in 32-bit IE and TortoiseSVN (if installed) should be available by simply right-clicking on any of the file or directory icons.
You can also modify the 32-bit IE shortcut you create so the "Start In" directory points to the root of all of the projects you want to put under source control (right-click the shortcut and select "Properties"). This way, when you double-click the short-cut, it will automatically come up with a "File Explorer" view of this directory, and you'll be ready to go from there.
The following URLs explain how to set this up:
http://www.jonathanmalek.com/blog/TortoiseSVNOnWindowsXPX64andOtherShellExtensions.aspx
(brief explanation of the problem and some detailed suggested
work-arounds)
http://tortoisesvn.tigris.org/servlets/ProjectDocumentList?folderID=616&expandFolder=616&folderID=616
(link to the TortoiseSVN 64 alpha build)
4) GUIs for Subversion - some available from the Subversion Downloads site at:
http://subversion.tigris.org/project_packages.html
a) Windows (32-bit)
*
SmartSVN? (
http://www.syntevo.com/smartsvn/download.jsp)
*
TortoiseSVN? (
http://tortoisesvn.tigris.org/):
b) Mac OS X
c) Linux
d) JavaSVN
- A Java-only SVN client library - with a client app built around it.
I've not used it before, but have heard good things about it.http://tmate.org/svn/
5) Subversion IDE plugins
a) NetBeans:
I've been using NetBeans since just after it went beta, at a time when you could never get Eclipse to run very long on Mac OS X without crashing and when only NetBeans had full support for Tomcat Servlet & Axis Web Service development - so this is my IDE of choice.
There has been a Subversion plugin for NetBeans for about 3 years.
Used to be you had to go to the NetBeans VCS site to get it, but now the regular
NetBeans? Updater will provide this. You can still get it from the VCS site and install it manually if you like:
http://vcsgeneric.netbeans.org/profiles/index.html
NetBeans plugins for other Version Control Systems are there as well.
As I mentioned above, once I have my ssh-agent (SSHKeychain) running, the NetBeans SVN integration runs like a charm - totally transparent and tightly integrated into the
NetBeans? project view. It turned out
- however - since I had the SVN command line tools + libraries installed via Fink (for historical reasons). There's now a Mac OS X binary installer available that's really easy to use (
http://metissian.com/projects/macosx/subversion/), and the SVN version he puts out generally stays ahead of the Fink release.
Anyway, if you get the following error when using the SVN plugin in
NetBeans:
"Command "LIST_CMD" has failed. Execution string: /bin/sh -c "cd\"/home/me/development/project/src/.svn\"; svn status -v -N --noignore"
The error output follows, check Runtime for the full output of the command.
svn: '.' is not a working copy
there is a simple workaround. You need to just edit the "SVN_CMD"
property in the svn.xml netbeans module config file. Set it to the absolute path of your svn command-line binary (/sw/bin/svn for Fink - /usr/local/bin/svn for the other binary installer pkg). You'll find that config file located at "~/.netbeans/dev/config/vcs/config/svn.xml," though the name of the actual XML file may vary, if you created your own saved profile for the svn plugin
b) Linux:
KDE KDeveloper
c) Eclipse:
Subclipse is it!!! Very popular and functional much longer than the NetBeans SVN plugin I now use:
http://subclipse.tigris.org/
http://www.ugrad.cs.ubc.ca/~cs319/02T2/projects/Subversion-Integration-for-Eclipse/project-description.html
d) IntelliJ:
IntelliJ works well, but it will cost money.
http://plugins.intellij.net/plugins/
d) XCode:
- i) The old-way:
http://maczealots.com/tutorials/xcode-svn/
- ii) it's now integrated via the XCode Plugin Interface - though some have had trouble with it. I think Apple's got most of the kinks worked out now. The following link gives a pretty good description of how to set the XCode Subversion client up to use SSH, though I'm pretty certain the SSHKeychain technique I use would work just fine:
http://bensyverson.com/geek/svnssh/
e) MS Visual Studio:
There are several options, but I laid off VS back in the late 90's, so I can't vouch for them. Given the size of the customer base, I'm certain one or more of these must be very robust, though I expect many folks just use TortoiseSVN. See:
http://ankhsvn.tigris.org/
http://nidaros.homedns.org/subway/
http://www.pushok.com/soft_svn.php
http://blog.dreamprojections.com/archive/2004/12/16/417.aspx
http://forums.microsoft.com/MSDN/ShowPost.aspx?PostID=159736&SiteID=1
http://svn.haxx.se/users/archive-2005-04/1470.shtml
http://www.gungfu.de/facts/wiki/Main/VisualStudio
Part 3:
Web SVN
See who has control of the web repo then you must go to the httpd.conf file. At the bottom of the file you will see a list of repos and what group has access to them. If a user needs access to a repo make sure they are in the group that is associated with the web repo.
If a part of the repo does not want to be password protected then a rewrite rule must be created.
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cerebro-a-020
- 02.16.07 - Opened case 65360293 to replace processors.
cerebro-a-040
- 02.16.07 - Opened case 65360304 to replace processors.
cerebro-a-105
- 02.16.07 - Opened case 65360315 to replace processors.
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How-to Guides
This is an area to post How-to guides on implementations we've done. This is seperate from Standard Operating Procedure (SOP) guides, which state authoritatively how something must be setup. You can write up either how one
would set up something or how you actually
did do it. Guides in this section should not be expected to be 100% reproducible, but rather the steps needed to take to get from scratch to a finished product.
Openfire? - How to setup
OpenFire? as a jabber server using LDAP
LONI Live - The LONI Live web broadcasting solution
Rails - Rails (in progress)
Matlab - How to install Matlab
Sophos Enterprise Console - How to install/configure Sophos Enterprise Console
Windows HPC Cluster Deployment - How to set up and deploy compute nodes for the WHPC Cluster
Submit Jobs to WHPC cluster? - How to submit jobs to the WIndows HPC Cluster
Special Lists for Cranium's Compute Nodes - How to use the special lists for the Cranium's compute nodes
--
DavidHasson - 12 Mar 2008
Everyday Links
Dell KVM - How to access the Datacenter KVM
IsilonAccess? - Isilon access
SANAccess? - SAN Access
Polyvision? - Polyvision Access
Dell Premier Pages - The UCLA/KST Portal for purchasing with Dell.
CDWG - CDW Government, for all fully licensed software, and purchasing any hardware or software outside the realm of Dell or Microsoft.
MSDNAA - Microsoft Developer Network, Academic Alliance - for downloads and licensing for all Microsoft products for development or testing purposes. (Fully commercial licensing and downloads are on CDWG)
Weatherboy - Our APC Environmental monitor. This monitors temperature/humitidy sensors in the NRB Datacenter and the DIVE Racks.
--
DavidHasson - 14 Oct 2007
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Ubuntu Linux
- After install (basic options, most can be set as default) completes, use the local account created (automatically given sudo) to set the root password using the LONI Password Scheme for the host
- Add Linux box to NIS domain
- As root:
-
apt-get install nis
- Specify 'loni' as default domain (or post-install at /etc/defaultdomain)
- Add
ypserver 128.97.134.100 and ypserver 128.97.134.101 to /etc/yp.conf
-
/etc/init.d/nis restart
- Append
nis to the following lines in /etc/nsswitch.conf: passwd, group, shadow, protocols, services, hosts
- Configure NTP time server to 128.97.134.82 (severian)
- As root:
-
apt-get install ntp
- add
server 128.97.134.82 above the rest of the ntp servers in /etc/ntp.conf
- Configure NFS
- As root:
- apt-get install nfs-common nfs-kernel-server quota
- Edit
STATDOPTS="--port 4000 --outgoing-port 4004" in /etc/default/nfs-common
- Edit
RPCMOUNTDOPTS="-p 4002" in /etc/default/nfs-kernel-server
- Edit
RPCRQUOTADOPTS="-p 4003" in /etc/default/quota
-
echo "options lockd nlm_tcpport=4001" > /etc/modprobe.d/options.local
- Configure iptables:
-
iptables -A INPUT -m state --state ESTABLISHED,RELATED -j ACCEPT
-
iptables -A INPUT -p tcp --dport ssh -j ACCEPT
-
iptables -A INPUT -m state --state NEW -m tcp -p tcp --dport 111 -j ACCEPT
-
iptables -A INPUT -m state --state NEW -m tcp -p tcp --dport 2049 -j ACCEPT
-
iptables -A INPUT -m state --state NEW -m tcp -p tcp --dport 4000:4003 -j ACCEPT
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iptables -A INPUT -j REJECT
-
iptables-save > /etc/iptables.rules
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Ubuntu Write-up
The purpose of this write-up is to explain how to get Ubuntu working in case the Boxx needs to be reinstalled.
1. Go to this website and add the new repositories
http://ubuntuguide.org/wiki/Dapper#How_to_add_extra_repositories
Also on that website is a section for installing the Nvidia driver
http://ubuntuguide.org/wiki/Dapper#How_to_install_Graphics_Driver_.28NVIDIA.29
The last thing that needs to be installed for the display drivers is the stuff found on the section eye candy.
http://ubuntuguide.org/wiki/Dapper#Eye_Candy
1.1. The next thing that needs to be installed is the
xorg.conf files so the display can span across all three screens. On abdiesus there should be a file called
Fakespace.tgz. Download that file and uncompress it. In the Fakespace folder there should be a folder called
xorg. In there you will see a number of files. The ones that matter most are
xorg.conf.1024_96.2blend (stereo) and
xorg.conf.60.2blend. (mono). Copy those two files to the
/etc/X11 folder. Once they are in the folder back up the original xorg.conf file and copy over it with the appropriate
xorg.conf.xxxxx.2blend file of your choosing. After that has been compleated restart the gdm by pressing
ctrl +
alt +
Backspace. That is it!
2. To get the video codecs installed go to this website:
http://ubuntuguide.org/wiki/Dapper#How_to_install_Multimedia_Codecs and follow the instructions. Once all the codecs have been installed it is time to install the player. In the command line type
apt-get install mplayer. After that you should be able to play wmv files.
2.1. Make sure that the file is being played in myplayer. If not right click on the file and tell it to open with mplayer.
2.1.1. Once the file is playing a few adjustments need to be made. Right click on the playing video and set it to play
full screen. Then right click on it again and change the Aspect Ratio to
4:3
3. RAID. As of this write-up the Boxx is still using the internal software RIAD. There are plans to change it to hardware, but who knows when that will occur. So until that event here are the instructions to initialize the RAID.
3.1. In the command prompt type:
apt-get install dmraid
mkdir /home/RAID
3.2. Add this line to the
/etc/fstab file:
/dev/mapper/nvidia_eccafiaa1 /home/RAID ntfs nls=utf8,umask=0222 0 0
3.3. In the command prompt type:
mount –a
Ubuntu on Tono
This is documentation of the steps taken to get Tono to where it currently is. Once we're certain we have a working solution, this will be merged with the above information.
- Boot from Ubuntu 6.06.1 (LTS) CD. It incorrectly identifies the primary graphics card as ATI instead of NVIDIA, so X won't start. Edit the line in /etc/X11/xorg.conf:
- Driver "ati"
- to read: Driver "vesa".
- Back at the terminal startx to start up Xorg and begin the install. Please note that it will hang for a very long time at a standard X screen, and it will then hang for a very long time at the splash. Give it some time -- if nothing happens, you'll have to sudo startx, let it boot, CTRL-ALT-BACKSPACE, sudo chown ubuntu:ubuntu ~/.Xauthority, and then "startx" again. I've only had to do this when I got impatient, though.
- Go to this website and add the new repositories http://ubuntuguide.org/wiki/Dapper#How_to_add_extra_repositories. Also on that website is a section for installing the Nvidia driver: http://ubuntuguide.org/wiki/Dapper#How_to_install_Graphics_Driver_.28NVIDIA.29
- The next thing that needs to be installed is the xorg.conf files so the display can span across all three screens. Copy /loni/system/DIVE/Fakespace.tgz to tono and uncompress it. In the Fakespace folder there should be a folder called xorg. In there you will see a number of files. The ones that matter most are xorg.conf.1024_96.2blend (stereo) and xorg.conf.60.2blend. (mono). Copy those two files to the /etc/X11 folder. Once they are in the folder back up the original xorg.conf file and copy over it with the appropriate xorg.conf.xxxxx.2blend file of your choosing. After that has been compleated restart the gdm by pressing ctrl + alt + Backspace. That is it!
- In a terminal: sudo apt-get install xubuntu-desktop. Then, copy xfwm4_4.3.90.2-1_i386.deb from /loni/system/DIVE/xfwm4.deb (renamed on the server for accessibility) to tono, and sudo dpkg -i xfwm4.deb. This is our custom compile of the window manager for true fullscreen. sudo synaptic, search for "xfwm4", highlight it, and then Package > Lock Version. If a security upgrade or native Xinerama fullscreen support becomes available, we'll upgrade and recompile the window manager; otherwise this will prevent the WM from breaking.
- Reboot, change the login session to XFCE, and after entering your username and password, make it the default login session.
- xfce-setting-show and change screensaver options (default will show a random tacky sn and prompt for a password on wake).
- To get the video codecs installed go to this website: http://ubuntuguide.org/wiki/Dapper#How_to_install_Multimedia_Codecs and follow the instructions. Once all the codecs have been installed it is time to install the player. In the command line type apt-get install xine-ui. After that you should be able to play wmv files.
- For each movie type to be played, make sure it's set to open in xine by right-clicking on the file in the explorer (thunar) and setting it through either Properties or Open With.
- Note: to full screen movies in xine, just hit Alt-F11. The same key combination will full-screen 99% of all applications (the only exception noted so far is the terminal).
Notes on how to setup GNOME/Metacity
I don't think we've decided one way or the other which one we're going to choose. The advantage of this method is you don't have to hit ALT-F11 to run Noodle in true full screen. The disadvantage of this method is that you need a script to run mplayer and/or xine, and that there's no method to create a package of our custom compiled metacity without breaking a ridiculous number of dependencies for other packages -- it needs to be recompiled on a complete system reinstall).
- Untar the metacity source (/loni/system/DIVE/metacity-2.14.3.tar.bz), run ./configure --disable-xinerama. It'll spit out a bunch of pkg_config errors -- you'll have to use Synaptic to make sure you have the libraries and dev libraries for whatever packages it wants (if we have to run through this again, we'll make a list of those packages). For certain, though you'll need to:
- sudo apt-get install libgconf2-dev libgtk2.0-dev libstartup-notification0-dev libxrender-dev libxcursor-dev
- Keep running the configure until it finishes, then make, and sudo make install.
- Upon restarting the X server, you'll find that it hangs for a good deal of time upon the splash screen -- this is normal. You can sometimes remedy this by removing your ~/.gnome, ~/.gnome2, and ~/.metacity directories, but this isn't always guaranteed to work.
*If you wind up without any frames on the windows, recompile experimenting with --enable-compositor and --disable-compositor.
I believe the upgrade for a few components will be broken until you reinstall the original metacity package (sudo apt-get --reinstall install metacity), after which you'll have to recompile and reinstall the custom compiled metacity.
In order to run xine in true full screen, you'll need to launch it from a script:
#!/bin/bash
gnome-session-remove gnome-panel; xine -F; gnome-panel&
Movies will either need to be opened from xine's built-in brower, or some Nautilus magic to run the script (modified to accept a movie path argument) upon a double-click of the movie.
How to Create Directories/Files on the FTP Server
The LONI FTP Server is frost. It uses anonymous ftp connections and the access control method is by knowing the complete path of the incoming/outgoing directories.
To create new directories to be shared by using FTP you have to log into ftp.loni.ucla.edu (frost.loni.ucla.edu).
-
As root, go to /public/ftp/incoming (if you would like to use outgoing, just change it in the previous path),
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Create the directory you want to share,
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Change directory permissions to ftp:nobody,
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The system delete the content of the incoming/outgoing directories each 14 days. To prevent a directory will removed, just create a hidden file in the desired directory, i.e., .file_name or whatever (do not forget the 'dot': means hidden file on UNIX/Linux).
The previous procedure is a SysAdmin procedure only. You have to contact one of the system administrators to create the corresponding directory you would like to share and let him know if this directory will be or not a permanent shared directory.
To check the content of your shared directory, connect to the server anonymously via browser, ftp://ftp.loni.ucla.edu/outgoing/shared_dir, or terminal, ftp ftp.loni.ucla.edu/outgoing/shared_dir. Remember, the FTP configuration requires only root access. Users incoming/outgoing have only read access. If any users would like to upload/download files from the LONI FTP Server, they have to know the incoming/outgoing path.
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Setting up a VMware Server
Make sure the proper programs are installed:
yum - y install gcc
yum -y install kernel
yum -y install kernel-devel
yum -y install xinetd
VNCBanksy
Banksy uses OSXVNC to provide VNC connections for clients. While it is a fully functional client, it requires that every user desiring remote access be physically logged into the machine using fast-user switching. At the time of writing, no better solution has been found; OSX 10.5 is slated to offer full Unix support (unlike the obfuscating layers they're adding on top of it now), so we will hopefully be able to implement a better solution then. The procedure is straightforward:
- Fast-switch to Administrator (click on the name of whoever's logged in in the upper right hand corner) -- standard root pw.
- Create a local account (here: "joe") for the user that doesn't conflict with the NIS logon (we've had a hard enough time with NIS in the past)
- Make a copy of the OSXVNC application residing on root's desktop onto the new user's desktop (/Users/joe/Desktop).
- Run OSXVNC under joe's account, click and hold on the icon in the Dock, and set OSXVNC to open at login.
- Explicitly set joe's port. As of the last account creation (10.26.06 - 17:14), the next available port is 5904.
- Configure the other tabs for desktop sharing, etc. on a case by case basis.
- Restart the server.
When you contact the new user, make sure to inform him or her of two things:
1) If the machine crashes or is rebooted, a member of the sysadm team needs to be notified so they can log everybody in.
2) When they wish to terminate their session, they need to close their VNC viewer rather than clicking Apple > Logout. The latter action requires that a member of the sysadm team logs them physically before they can VNC again. This also means that they should close whatever resources they aren't using before logging out, because this is equivalent to a VNC session suspension.
Last update (see bottom).
How do I perform a complete re-install of the cluster?
- You'll need the base, hpc, kernel, os1&2, and viz rolls as a minimum.
- Follow documentation starting here until 2.4: http://www.rocksclusters.org/roll-documentation/viz/4.2.1/adding-the-roll.html
- Hostname: kurosawa(.loni.ucla.edu), IP: 128.97.134.150
- Add a normal user on the frontend, then sync to the nodes with 'rocks-user-sync' (as root). Always use the regular user account for running clustering apps.
- Edit /mothership/config/dmx.conf and set TILE_ROWS, TILE_COLS, and HOSTS (at least) to match the cluster settings.
How do I execute a program under DMX + Chromium?
- On the frontend: launch DMX and change DISPLAY env. variable to match the virtual display along the wall (usually :1).
- Navigate down to /opt/chromium/mothership/config and start the mothership -- python dmx.conf `[app to be tiled]`
- On the back-ends (each one): set DISPLAY env to native X display, if not already done
- Set the CRMOTHERSHIP env variable to kurosawa
- Set the LD_LIBRARY_PATH env variable to /opt/chromium/lib/Linux
- Execute 'crserver'
- Back on the front-end: Set DISPLAY to the DMX server's display (typically :1)
- Set CRMOTHERSHIP and LD_LIBRARY_PATH env variables as above
- Execute 'crappfaker'
How can I automate the Chromium execution process?
- Enable rsh on the compute nodes (http://www.rocksclusters.org/rocks-documentation/4.2.1/customization-rsh.html)
- Make sure ~/.crconfigs has the line "/opt/chromium/mothership/configs/autodmx.conf %m %p"
- Make sure libGl.so and libGL.so.1 are symlinked to libcrfaker.so
- On the back-ends: LD_LIBRARY_PATH must always be set as above, and crserver must be in the path.
- Front-end: set your DISPLAY properly, and execute just with `[app to be tiled]`
How can I compensate for the LCD bezels?
- Instructions are in ~/.Xclients, follow them, remove ~/.dmxrc, logout, login.
How do I execute a program under SAGE?
- Initial setup:
- Navigate to ~/.sage
- Edit fsManager.conf and set fsManager (kurosawa, 128.97.134.150)
- Edit sage.conf and modify appList if necessary to add additional applications (nodeNum - number of nodes app runs on; Init [posX] [posY] [sizeX] [sizeY] - initial position and size of app window, optional; exec [ip] [command])
- Edit stdtile-1.conf (Dimensions - number of cols and rows of tiled display, respectively; Resolution - resolution of each tile; Machines - number of tiled display nodes (does NOT include master); for each DisplayNode? - Name, IP, Monitors (number of tiles it drives)
- Edit tileNodes.list - ip addresses of all cluster nodes, including frontend
- Each time:
- Set environment variables: SAGE_DIRECTORY=~/.sage; PATH=$PATH:$SAGE_DIRECTORY/bin; LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$SAGE_DIRECTORY/lib
- Start SAGE through a right click on the front-end desktop
- Start SAGE GUI through a right click on the front-end desktop (self explanatory from there)
What has been tried to increase cluster performance?
Front-end's video card. It's imperative that the front-end card match the capabilities of the back-ends. If a program can't render well on the front-end itself, it'll be 10x worse trying to pass it over the network. We haven't tested with a vid. card on the front-end that exceeds the back-ends; I honestly can't say one way or the other if it will affect things significantly (but my guess would be no).
Setting jumbo frames. While there's an obvious increase in throughput, both DMX and Chromium are latency sensitive. The expected performance gain was actually quite crippling to the cluster (programs would run in the single-digit FPS range that normally run fine). There is an MTU option in each of the Chromium mothership config files, but setting this appropriate to the changed MTU (and even fiddling around with other numbers) did not make any appreciable difference in the decreased performance.
Reducing cluster size. Unintentional, but interesting results nonetheless. The difference between running a program fullscreen on three nodes and two nodes is negligible (don't have FPS numbers here, though). Based on this and the propaganda provided by the Viz group, one would assume that the cluster will scale nicely, should we decide to upsize it.
Hacking the source. Ridiculous if you don't have a decent graph on coding both graphical and network heavy apps. Highly questionable, considering the time investment necessary to hack around (assuming knowledge of how to do it).
Is a larger Viz cluster feasible/worthwhile?
Short answer: yes, with an if. Long answer: no, with a but.
- DMX
- High-res applications choke easily under DMX, but lower-res ones work fine.
- Chromium
- Only programs written using Chromium's wrappers (instead of OpenGL? wrappers) will work. What is written, however, runs very nicely.
- Movie and video playback is slightly constricted to the ratio initially set out in the sage.conf file. Resizing a window through the GUI is guesswork (no way to tell the new ratio until you've resized); you can run 'resize [app num] [posX] [posY] [sizeX] [sizeY]' from command line after 'fsConsole', but this is tedious at best. The other alternative is either creating a bunch of different launcher for the same app with different ratios or pre-converting all videos/images to a certain ratio (neither of which is particularly desirable).
What remains to be tested?
In order of highest priority then ease:
- Sun's new optimized cluster.
- Noodle
- "Stereo" display (true stereo not testable, due to the use of LCD screens)
- Previously unthought of optimizations(?)
VNCBanksy
Banksy uses OSXVNC to provide VNC connections for clients. While it is a fully functional client, it requires that every user desiring remote access be physically logged into the machine using fast-user switching. At the time of writing, no better solution has been found; OSX 10.5 is slated to offer full Unix support (unlike the obfuscating layers they're adding on top of it now), so we will hopefully be able to implement a better solution then. The procedure is straightforward:
- Fast-switch to Administrator (click on the name of whoever's logged in in the upper right hand corner) -- standard root pw.
- Apple > System Preferences > Accounts > Create a local account (here: "joe") for the user that doesn't conflict with the NIS logon (we've had a hard enough time with NIS in the past)
- Performance boosts:
- Set the user's background to a solid grey, white, or black (set under Sys Prefs).
- Set the font scheme (Sys Prefs > Appearances) to Default (CRT).
- Make a copy of the OSXVNC application residing on root's desktop onto the new user's desktop (/Users/joe/Desktop). To make sure all of the application files are copied, you'll have to do a visual drag and drop, not a 'cp'.
- Run OSXVNC under joe's account, click and hold on the icon in the Dock, and set OSXVNC to open at login.
- Explicitly set joe's port. As of the last account creation (10.26.06 - 17:14), the next available port is 5904.
- Configure the second tab for desktop sharing, etc. on a case by case basis. Defaults should be fine.
- In the last tab, configure as a startup item.
- Restart the VNC server.
When you contact the new user, make sure to inform him or her of three things:
- If the machine crashes or is rebooted, a member of the sysadm team needs to be notified so they can log everybody in.
- When they wish to terminate their session, they need to close their VNC viewer rather than clicking Apple > Logout. The latter action requires that a member of the sysadm team logs them physically before they can VNC again. This also means that they should close whatever resources they aren't using before logging out, because this is equivalent to a VNC session suspension.
- Tell them to connect using either the Zlib or Hextile compression settings from their VNC viewer. These two provide the best compression/refresh rate ratio over a LAN.
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WebStatistics
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SystemSetup
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26 Oct 2009 - 18:27 - r1.23
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Workstation Installation Procedures Note: Not all steps are always applicable For all machines: Choose machine name from http://www.the-artists.org. Be sure that ...
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LONI Infrastructure Home Old Pages Looking for the old homepage? Click here. Weekly SysAdmin Notes Notes from each Systems Administration team meeting. Help for ...
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How to use the Star-P Software to Parallel Process on the Cranium Cluster Star-P software allows users performing scientific, engineering or analytical computation ...
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How-to Guides This is an area to post How-to guides on implementations we've done. This is seperate from Standard Operating Procedure (SOP) guides, which state authoritatively ...
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Windows XP Use the LONI VLK key for Windows XP SP2. The first five letters should be QXT34. When prompted, set the Administrator's account to the standard workstations ...
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NodeList
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19 Jun 2009 - 21:33 - NEW
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Special List for the Cranium's Compute Nodes This page described the different lists used by agentSmith to monitor the entire Cranium cluster. agentSmith uses three ...
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21 May 2009 - 01:38 - r1.6
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Yum Server Installation 1. install a linux os (red hat) make sure you have apache or some other webserver is installed 2. install the svn mrepo from http://dag.wieers ...
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Disabled Cranium Production Nodes (Hardware and Testing) This page is meant to serve as formal notification of disabled nodes, which we do on a near-daily basis. ...
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LONI Grid Computing Notes To facilitate the submission and execution of compute jobs in this heterogeneous compute environment, SUN's Grid Engine (SGE) is used to ...
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LONIssh
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LONI SSH Gateways SSH is short for Secure Shell. It provides a secure, encrypted method of transmitting information over TCP/IP to ensure the confidentiality, integrity ...
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Accessing the LONI Network Remotely SSH SSH is short for Secure Shell. It provides a secure, encrypted method of transmitting information over TCP/IP to ensure the ...
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UsingFTP
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19 Nov 2008 - 00:10 - r1.4
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How to Create Directories/Files on the FTP Server The LONI FTP Server is frost. It uses anonymous ftp connections and the access control method is by knowing the ...
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PFX2PEM
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29 Oct 2008 - 01:00 - NEW
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DavidHasson
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1) Export from windows: From IIS Admin: From Certificates Snap-in (run- mmc.exe, add- certificates, computer store, local machine) 2) openssl pkcs12 in c:\certs\yourcert ...
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28 Aug 2008 - 02:03 - r1.4
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How to configure Mantis to use LDAP as authentication method Download the latest stable Mantis version from this link on dev-mantis:/tmp, tar C /usr/local/apache2 ...
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26 Aug 2008 - 22:02 - r1.3
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Old Infrastructure Home Page Systems Administration FAQs ComputerCenterSchema A brief description about the LONI Computer Center GridComputing How to submit command ...
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AgentSmith
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14 Aug 2008 - 03:09 - r1.4
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Monitoring and Diagnosing the Cerebro cluster with agentSmith This application is a Perl script which monitors, diagnoses and provides defined solutions to the Cranium ...
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JonathanPierce 07 Aug 2008 first rev, no permissions second rev, adding correct permissions third rev, now i messed things up horribly Set ALLOWTOPICVIEW Main.TwinGeneticsGroup ...
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24 Jul 2008 - 17:16 - r1.2
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Configureation page for the Sun 3510. To access the 3510 telnet to 10.0.129.199. The password is the default password using 3510. For configuration settings please ...
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ChangeLogs
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Change Logs Major Recent Changes Network Hardware General Network Changes loni-core-1 loni-fwsm loni-core-2 loni-sw-1 loni-sw-2 nrb-r19-tor1 loni-sw-4 loni-sw-5 loni ...
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ACSLS
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ACSLS Management Log in as or su to ACSSA for cmd proc: ssh acssa@acsls-1.loni.ucla.edu or su acssa Bring CAP or other device offline and back online (in this case ...
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Apache
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26 Jun 2006 - 21:47 - NEW
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Install Apache 2.0.58: cd /tmp wget http://apache.mirrormax.net/httpd/httpd-2.0.58.tar.gz sudo tar xvzf httpd-2.0.58.tar.gz cd httpd-2.0.58 sudo ./configure prefix ...
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05 May 2009 - 10:48 - r1.33
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Disabled Cranium Production Nodes (Hardware and Testing) This page is meant to serve as formal notification of disabled nodes, which we do on a near-daily basis. ...
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01 Feb 2007 - 21:24 - r1.3
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Configuring your Email client for IMAP To access your access your email via IMAP you must configure your email client to use SSL. When configuring your server settings ...
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GettingOnline
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19 Mar 2009 - 02:10 - r1.27
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DavidHasson
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Accessing the LONI Network Remotely SSH SSH is short for Secure Shell. It provides a secure, encrypted method of transmitting information over TCP/IP to ensure the ...
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GridComputing
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01 May 2009 - 23:29 - r1.32
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RicoMagsipoc
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LONI Grid Computing Notes To facilitate the submission and execution of compute jobs in this heterogeneous compute environment, SUN's Grid Engine (SGE) is used to ...
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