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(A note on mpi4py)
(Add OpenMP and fix some formatting)
Line 5: Line 5:
 
=== [http://www.open-mpi.org/ OpenMPI] ===
 
=== [http://www.open-mpi.org/ OpenMPI] ===
 
Version 1.4.3
 
Version 1.4.3
 +
 +
=== [http://openmp.org/wp/ OpenMP] ===
 +
OpenMP isn't really a software package itself. It is a set of directives for C, C++, and Fortran which greatly simplifies parallelizing applications on a single node. There is a good tutorial for OpenMP at [https://computing.llnl.gov/tutorials/openMP/ https://computing.llnl.gov/tutorials/openMP/]
  
 
=== [http://www.scilab.org Scilab] ===
 
=== [http://www.scilab.org Scilab] ===
Line 17: Line 20:
 
==== Installing your own modules ====
 
==== Installing your own modules ====
 
To install your own module, login to Beocat and start R interactively
 
To install your own module, login to Beocat and start R interactively
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
R
 
R
 
</syntaxhighlight>
 
</syntaxhighlight>
 
Then install the package using
 
Then install the package using
<syntaxhighlight lang="rsplus" line>
+
<syntaxhighlight lang="rsplus">
 
install.packages("PACKAGENAME")
 
install.packages("PACKAGENAME")
 
</syntaxhighlight>
 
</syntaxhighlight>
Line 27: Line 30:
  
 
After installing you can test before leaving interactive mode by issuing the command
 
After installing you can test before leaving interactive mode by issuing the command
<syntaxhighlight lang="rsplus" line>
+
<syntaxhighlight lang="rsplus">
 
library("PACKAGENAME")
 
library("PACKAGENAME")
 
</syntaxhighlight>
 
</syntaxhighlight>
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You cannot submit an R script directly. 'qsub myscript.R' will result in an error. Instead, you need to make a bash script that will call R appropriately. Here is a minimal example. We'll save this as submit-R.qsub
 
You cannot submit an R script directly. 'qsub myscript.R' will result in an error. Instead, you need to make a bash script that will call R appropriately. Here is a minimal example. We'll save this as submit-R.qsub
  
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
  #!/bin/bash
 
  #!/bin/bash
 
  # First, lets tell the qsub command which resources we need
 
  # First, lets tell the qsub command which resources we need
Line 59: Line 62:
  
 
Now, to submit your R job, you would type
 
Now, to submit your R job, you would type
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
qsub submit-R.qsub
 
qsub submit-R.qsub
 
</syntaxhighlight>
 
</syntaxhighlight>
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</pre>
 
</pre>
 
If you'll note,  oracle-jdk-bin-1.7 (marked "system-vm") is the default for all users. If you have a custom version set, it will be marked with "user-vm". Now if you wanted to use icedtea-6, you could run the following:
 
If you'll note,  oracle-jdk-bin-1.7 (marked "system-vm") is the default for all users. If you have a custom version set, it will be marked with "user-vm". Now if you wanted to use icedtea-6, you could run the following:
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
eselect java-vm set user 1
 
eselect java-vm set user 1
 
</syntaxhighlight>
 
</syntaxhighlight>
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* [[LinuxBasics#Shells|Change your shell]] to bash
 
* [[LinuxBasics#Shells|Change your shell]] to bash
 
* Make sure ~/.bash_profile exists
 
* Make sure ~/.bash_profile exists
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
if [ ! -f ~/.bash_profile ]; then cp /etc/skel/.bash_profile ~/.bash_profile; fi
 
if [ ! -f ~/.bash_profile ]; then cp /etc/skel/.bash_profile ~/.bash_profile; fi
 
</syntaxhighlight>
 
</syntaxhighlight>
 
* Add a line like <code>source /usr/bin/virtualenvwrapper.sh</code> to your .bash_profile.
 
* Add a line like <code>source /usr/bin/virtualenvwrapper.sh</code> to your .bash_profile.
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
echo "source /usr/bin/virtualenvwrapper.sh" >> ~/.bash_profile
 
echo "source /usr/bin/virtualenvwrapper.sh" >> ~/.bash_profile
 
</syntaxhighlight>
 
</syntaxhighlight>
 
* Show your existing environments
 
* Show your existing environments
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
workon
 
workon
 
</syntaxhighlight>
 
</syntaxhighlight>
 
* Create a virtual environment. Here I will create a default virtual environment called 'test', a python2 virtual environment called 'testp2', a python3 virtual environment called 'testp3', and a pypy environment called testpypy. Note that <code>mkvirtualenv --help</code> has many more useful options.
 
* Create a virtual environment. Here I will create a default virtual environment called 'test', a python2 virtual environment called 'testp2', a python3 virtual environment called 'testp3', and a pypy environment called testpypy. Note that <code>mkvirtualenv --help</code> has many more useful options.
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
  mkvirtualenv -p $(which python2) testp2
 
  mkvirtualenv -p $(which python2) testp2
 
  mkvirtualenv -p $(which python3) testp3
 
  mkvirtualenv -p $(which python3) testp3
Line 144: Line 147:
 
</pre>
 
</pre>
 
* You can now install the python modules you want. This can be done using <tt>pip</tt>.
 
* You can now install the python modules you want. This can be done using <tt>pip</tt>.
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
pip install numpy biopython
 
pip install numpy biopython
 
</syntaxhighlight>
 
</syntaxhighlight>
 
==== Using your virtual environment within a job ====
 
==== Using your virtual environment within a job ====
 
Here is a simple job script using the virtual environment testp2
 
Here is a simple job script using the virtual environment testp2
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
#!/bin/bash
 
#!/bin/bash
 
source /usr/bin/virtualenvwrapper.sh
 
source /usr/bin/virtualenvwrapper.sh
Line 159: Line 162:
  
 
Make sure the following is executed before running <code>pip install numpy</code>
 
Make sure the following is executed before running <code>pip install numpy</code>
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
cp /opt/beocat/numpy/.numpy-site.cfg ~/.numpy-site.cfg
 
cp /opt/beocat/numpy/.numpy-site.cfg ~/.numpy-site.cfg
 
</syntaxhighlight>
 
</syntaxhighlight>
 
==== A note on [http://mpi4py.scipy.org/docs/usrman/index.html mpi4py] ====
 
==== A note on [http://mpi4py.scipy.org/docs/usrman/index.html mpi4py] ====
 
If you are wanting to use mpi with your python script and are using a virtual environment, you will need to send the correct environment variables to all of the mpi processes to make the virtual environment work.
 
If you are wanting to use mpi with your python script and are using a virtual environment, you will need to send the correct environment variables to all of the mpi processes to make the virtual environment work.
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
#!/bin/bash
 
#!/bin/bash
 
# sample mpi4py submit script
 
# sample mpi4py submit script
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** [[LinuxBasics#Shells|Change your shell]] to bash
 
** [[LinuxBasics#Shells|Change your shell]] to bash
 
** Install perlbrew
 
** Install perlbrew
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
curl -L http://install.perlbrew.pl | bash
 
curl -L http://install.perlbrew.pl | bash
 
</syntaxhighlight>
 
</syntaxhighlight>
 
** Make sure that ~/.bash_profile exists
 
** Make sure that ~/.bash_profile exists
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
if [ ! -f ~/.bash_profile ]; then cp /etc/skel/.bash_profile ~/.bash_profile; fi
 
if [ ! -f ~/.bash_profile ]; then cp /etc/skel/.bash_profile ~/.bash_profile; fi
 
</syntaxhighlight>
 
</syntaxhighlight>
 
** Add <code>source ~/perl5/perlbrew/etc/bashrc</code> to ~/.bash_profile
 
** Add <code>source ~/perl5/perlbrew/etc/bashrc</code> to ~/.bash_profile
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
echo "source ~/perl5/perlbrew/etc/bashrc" >> ~/.bash_profile
 
echo "source ~/perl5/perlbrew/etc/bashrc" >> ~/.bash_profile
 
</syntaxhighlight>
 
</syntaxhighlight>
 
** Then source your bash profile
 
** Then source your bash profile
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
source ~/.bash_profile
 
source ~/.bash_profile
 
</syntaxhighlight>
 
</syntaxhighlight>
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</pre>
 
</pre>
 
** In this case the version is 5.16.3, so we run
 
** In this case the version is 5.16.3, so we run
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
perlbrew install -f -n -D usethreads perl-5.16.3
 
perlbrew install -f -n -D usethreads perl-5.16.3
 
</syntaxhighlight>
 
</syntaxhighlight>
 
** To temporarily use the new version of perl in the current shell, we now run
 
** To temporarily use the new version of perl in the current shell, we now run
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
perlbrew use perl-5.16.3
 
perlbrew use perl-5.16.3
 
</syntaxhighlight>
 
</syntaxhighlight>
 
** To switch versions of perl for every new login or job, run
 
** To switch versions of perl for every new login or job, run
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
perlbrew switch perl-5.16.3
 
perlbrew switch perl-5.16.3
 
</syntaxhighlight>
 
</syntaxhighlight>
 
** You can reverse this switch with
 
** You can reverse this switch with
<syntaxhighlight lang="bash" line>
+
<syntaxhighlight lang="bash">
 
perlbrew switch-off
 
perlbrew switch-off
 
</syntaxhighlight>
 
</syntaxhighlight>

Revision as of 10:59, 9 July 2014

Drinking from the Firehose

For a complete list of all installed software, see NodePackageList

Most Commonly Used Software

OpenMPI

Version 1.4.3

OpenMP

OpenMP isn't really a software package itself. It is a set of directives for C, C++, and Fortran which greatly simplifies parallelizing applications on a single node. There is a good tutorial for OpenMP at https://computing.llnl.gov/tutorials/openMP/

Scilab

Version 5.4.0

R

Version 3.0.3

Modules

We provide a small number of R modules installed by default, these are generally modules that are needed by more than one person.

Installing your own modules

To install your own module, login to Beocat and start R interactively

R

Then install the package using

install.packages("PACKAGENAME")

Follow the prompts. Note that there is a CRAN mirror at KU - it will be listed as "USA (KS)".

After installing you can test before leaving interactive mode by issuing the command

library("PACKAGENAME")

Running R Jobs

You cannot submit an R script directly. 'qsub myscript.R' will result in an error. Instead, you need to make a bash script that will call R appropriately. Here is a minimal example. We'll save this as submit-R.qsub

 #!/bin/bash
 # First, lets tell the qsub command which resources we need
 # lets start with memory (in this case I ask for 1 gigabyte).
 # For help on these, see [[SGEBasics]]
 
 #$ -l mem=1G
 # Now we tell qsub how long we expect our work to take: 15 minutes (H:MM:SS)
 
 #$ -l h_rt=0:15:00
 
 # Lets output a little useful information This will put something like "Starting the job at: Thu Jan 26 10:43:26 CST 2012" in your output file
 echo -n "Starting the job at: "
 date
 
 # Now lets do some actual work. A lot of our users use R, so we'll go over that
 # This starts R and loads the file myscript.R
 R --no-save -q < myscript.R
 
 # like before, this is just useful information
 echo -n "Ending the job at: "
 date

Now, to submit your R job, you would type

qsub submit-R.qsub

Java

Versions 1.6 and 1.7

We support 4 versions of the Java VM on Beocat. IcedTea 6 and 7 (based on OpenJDK), Sun JDK 1.6 (Java 6), and Oracle JDK 1.7 (Java 7).

We allow each user to select his or her Java version individually. If you do not select one, we default to Sun JDK 1.7.

Selecting your Java version

First, lets list the available versions. This can be done with the command eselect java-vm list

% eselect java-vm list
Available Java Virtual Machines:
  [1]   icedtea-bin-6
  [2]   icedtea-bin-7
  [3]   oracle-jdk-bin-1.7  system-vm
  [4]   sun-jdk-1.6

If you'll note, oracle-jdk-bin-1.7 (marked "system-vm") is the default for all users. If you have a custom version set, it will be marked with "user-vm". Now if you wanted to use icedtea-6, you could run the following:

eselect java-vm set user 1

Now, we see the difference when running the above command

% eselect java-vm list
Available Java Virtual Machines:
  [1]   icedtea-bin-6  user-vm
  [2]   icedtea-bin-7
  [3]   oracle-jdk-bin-1.7  system-vm
  [4]   sun-jdk-1.6

To verify you are seeing the correct java, you can run java -version

% java -version
java version "1.6.0_27"
OpenJDK Runtime Environment (IcedTea6 1.12.7) (Gentoo build 1.6.0_27-b27)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

Python

We have several versions of Python available:

For the uninitiated PyPy provides just-in-time compilation for python code. While it doesn't support all modules, code which does run under PyPy can see a significant performance increase.

If you just need python and its default modules, you can use python2 python3 pypy-c1.9 or pypy-c2.0 as you would any other application.

If, however, you need modules that we do not have installed, you should use virtualenvwrapper to setup a virtual python environment in your home directory. This will let you install python modules as you please.

Setting up your virtual environment

if [ ! -f ~/.bash_profile ]; then cp /etc/skel/.bash_profile ~/.bash_profile; fi
  • Add a line like source /usr/bin/virtualenvwrapper.sh to your .bash_profile.
echo "source /usr/bin/virtualenvwrapper.sh" >> ~/.bash_profile
  • Show your existing environments
workon
  • Create a virtual environment. Here I will create a default virtual environment called 'test', a python2 virtual environment called 'testp2', a python3 virtual environment called 'testp3', and a pypy environment called testpypy. Note that mkvirtualenv --help has many more useful options.
 mkvirtualenv -p $(which python2) testp2
 mkvirtualenv -p $(which python3) testp3
 mkvirtualenv -p $(which pypy-c2.0) testpypy
  • Lets look at our virtual environments
%workon
testp2
testp3
testpypy
  • Activate one of these
%workon testp2
  • You can now install the python modules you want. This can be done using pip.
pip install numpy biopython

Using your virtual environment within a job

Here is a simple job script using the virtual environment testp2

#!/bin/bash
source /usr/bin/virtualenvwrapper.sh
workon testp2
~/path/to/your/python/script.py

A note on NumPy

NumPy is a commonly-used Python package.

Make sure the following is executed before running pip install numpy

cp /opt/beocat/numpy/.numpy-site.cfg ~/.numpy-site.cfg

A note on mpi4py

If you are wanting to use mpi with your python script and are using a virtual environment, you will need to send the correct environment variables to all of the mpi processes to make the virtual environment work.

#!/bin/bash
# sample mpi4py submit script
source /usr/bin/virtualenvwrapper.sh
workon testp2
# figure out the location of the python interpreter in the virtual environment
PYTHON_BINARY=$(which python)
# mpirun the python interpreter within the virtual environment
# if you don't use the interpreter within the virtual environment, i.e. just using 'python'
# the system python interpreter (without access to your other modules) will be used.
mpirun ${PYTHON_BINARY} ~/path/to/your/mpi-enabled/python/script.py

Perl

The system-wide version of perl is tracking the stable releases of perl. Unfortunately there are some features that we do not include in the system distribution of perl, namely threads.

Getting Perl with threads

curl -L http://install.perlbrew.pl | bash
    • Make sure that ~/.bash_profile exists
if [ ! -f ~/.bash_profile ]; then cp /etc/skel/.bash_profile ~/.bash_profile; fi
    • Add source ~/perl5/perlbrew/etc/bashrc to ~/.bash_profile
echo "source ~/perl5/perlbrew/etc/bashrc" >> ~/.bash_profile
    • Then source your bash profile
source ~/.bash_profile
  • Now, install perl with threads within perlbrew
    • Find the current Perl version.
% perl -version

This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux
(with 22 registered patches, see perl -V for more detail)
(...several more lines deleted)
    • In this case the version is 5.16.3, so we run
perlbrew install -f -n -D usethreads perl-5.16.3
    • To temporarily use the new version of perl in the current shell, we now run
perlbrew use perl-5.16.3
    • To switch versions of perl for every new login or job, run
perlbrew switch perl-5.16.3
    • You can reverse this switch with
perlbrew switch-off

Installing my own software

Installing and maintaining software for the many different users of Beocat would be very difficult, if not impossible. For this reason, we don't generally install user-run software on our cluster. Instead, we ask that you install it into your home directories.

In many cases, the software vendor or support site will incorrectly assume that you are installing the software system-wide or that you need 'sudo' access.

As a quick example of installing software in your home directory, we have a sample video on our Training Videos page. If you're still having problems or questions, please contact support as mentioned on our Main Page.