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(This is an issue that I ran into and I want to post it on the wiki so others can learn from my mistake. If there's a better way to fix this issue, please let me know.)
(Converting to modules and slurm/centos)
Line 2: Line 2:
For a complete list of all installed software, see [[NodePackageList]]
For a complete list of all installed software, see [[NodePackageList]]


== Toolchains ==
A toolchain is a set of compilers, libraries and applications that are needed to build software. Some software functions better when using specific toolchains.
We provide a good number of toolchains and versions of toolchains make sure your applications will compile and/or run correctly.
These toolchains include (you can run 'module keyword keychain compiler'):
; GCC:    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,...).
; GCCcore:    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,...).
; foss:    GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
; gcccuda:    GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.
; gmvapich2:    GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support.
; gompi:    GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
; gompic:    GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.
; goolfc:    GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
; icc:    C and C++ compiler from Intel
; iccifort:    Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL
; ifort:    Fortran compiler from Intel
; iomkl:    Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.
; iompi:    Intel C/C++ and Fortran compilers, alongside Open MPI.
You can run 'module spider $toolchain' to see the versions we have:
$ module spider iomkl
* iomkl/2017a
* iomkl/2017b
* iomkl/2017beocatb
If you load one of those (module load iomkl/2017b), you can see the other modules and versions of software that it loaded with the 'module list':
$ module list
Currently Loaded Modules:
  1) icc/2017.4.196-GCC-6.4.0-2.28
  2) binutils/2.28-GCCcore-6.4.0
  3) ifort/2017.4.196-GCC-6.4.0-2.28
  4) iccifort/2017.4.196-GCC-6.4.0-2.28
  5) GCCcore/6.4.0
  6) numactl/2.0.11-GCCcore-6.4.0
  7) hwloc/1.11.7-GCCcore-6.4.0
  8) OpenMPI/2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28
  9) iompi/2017b
  10) imkl/2017.3.196-iompi-2017b
  11) iomkl/2017b
As you can see, toolchains can depend on each other. For instance, the iomkl toolchain, depends on iompi, which depends on iccifort, which depend on icc and ifort, which depend on GCCcore which depend on GCC. Hence it is very important that the correct versions of all related software are loaded.
With software we provide, the toolchain used to compile is always specified in the "version" of the software that you want to load.
== Most Commonly Used Software ==
== Most Commonly Used Software ==
=== [http://www.open-mpi.org/ OpenMPI] ===
=== [http://www.open-mpi.org/ OpenMPI] ===
Version 2.0.1
We provide lots of versions, you are most likely better off directly loading a toolchain or application to make sure you get the right version, but you can see the versions we have with 'module spider OpenMPI':


=== [http://www.scilab.org Scilab] ===
* OpenMPI/2.0.2-GCC-6.3.0-2.27
Version 6.0.0
* OpenMPI/2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27
* OpenMPI/2.1.1-GCC-6.4.0-2.28
* OpenMPI/2.1.1-GCC-7.2.0-2.29
* OpenMPI/2.1.1-gcccuda-2017b
* OpenMPI/2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28
* OpenMPI/2.1.1-iccifort-2018.0.128-GCC-7.2.0-2.29


=== [http://www.r-project.org/ R] ===
=== [http://www.r-project.org/ R] ===
Version 3.3.1
We currently provide (module -r spider '^R$'):
* R/3.4.0-foss-2017beocatb-X11-20170314


==== Modules ====
==== Modules ====
Line 18: Line 69:
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">
<syntaxhighlight lang="bash">
module load R
R
R
</syntaxhighlight>
</syntaxhighlight>
Line 32: Line 84:
==== Running R Jobs ====
==== Running R Jobs ====


You cannot submit an R script directly. '<tt>qsub myscript.R</tt>' will result in an error. Instead, you need to make a bash [[AdvancedSGE#Running_from_a_qsub_Submit_Script|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. '<tt>sbatch myscript.R</tt>' will result in an error. Instead, you need to make a bash [[AdvancedSGE#Running_from_a_qsub_Submit_Script|script]] that will call R appropriately. Here is a minimal example. We'll save this as submit-R.sbatch


<syntaxhighlight lang="bash">
<syntaxhighlight lang="bash">
  #!/bin/bash
  #!/bin/bash
  #$ -l mem=1G
  #SBATCH --mem-per-cpu=1G
  # Now we tell qsub how long we expect our work to take: 15 minutes (H:MM:SS)
  # Now we tell qsub how long we expect our work to take: 15 minutes (D-H:MM:SS)
  #$ -l h_rt=0:15:00
  #SBATCH --time=0-0:15:00
   
   
  # Now lets do some actual work. This starts R and loads the file myscript.R
  # Now lets do some actual work. This starts R and loads the file myscript.R
  R --no-save -q < myscript.R
  module load R
R --no-save -q < myscript.R
  </syntaxhighlight>
  </syntaxhighlight>


Now, to submit your R job, you would type
Now, to submit your R job, you would type
<syntaxhighlight lang="bash">
<syntaxhighlight lang="bash">
qsub submit-R.qsub
sbatch submit-R.sbatch
</syntaxhighlight>
</syntaxhighlight>


=== [http://www.java.com/ Java] ===
=== [http://www.java.com/ Java] ===
We support 4 versions of the Java VM on Beocat. [[wikipedia:IcedTea|IcedTea]] 7 and 8 (based on [[wikipedia:OpenJDK|OpenJDK]]), Oracle JDK 1.7 (Java 7), and Oracle JDK 1.8 (Java 8).
We currently provide (module spider Java):
 
* Java/1.8.0_131
We allow each user to select his or her Java version individually. If you do not select one, we default to IcedTea 8. This was changed from Oracle JDK 1.7 on May 29, 2015 due to a EOL notice from Oracle.
* Java/1.8.0_144
 
==== Selecting your Java version ====
First, lets list the available versions. This can be done with the command <code>eselect java-vm list</code>
<pre>
% eselect java-vm list
Available Java Virtual Machines:
  [1]  icedtea-bin-7
  [2]  icedtea-bin-8  system-vm
  [3]  oracle-jdk-bin-1.7
  [4]  oracle-jdk-bin-1.8
</pre>
If you'll note,  icedtea-bin-8 (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-7, you could run the following:
<syntaxhighlight lang="bash">
eselect java-vm set user 1
</syntaxhighlight>
Now, we see the difference when running the above command
<pre>
% eselect java-vm list
Available Java Virtual Machines:
  [1]  icedtea-bin-7 user-vm
  [2]  icedtea-bin-8  system-vm
  [3]  oracle-jdk-bin-1.7
  [4]  oracle-jdk-bin-1.8
</pre>
To verify you are seeing the correct java, you can run <code>java -version</code>
<pre>
% java -version
java version "1.7.0_121"
OpenJDK Runtime Environment (IcedTea 2.6.8) (Gentoo icedtea-7.2.6.8)
OpenJDK 64-Bit Server VM (build 24.121-b00, mixed mode)
</pre>


=== [http://www.python.org/about/ Python] ===
=== [http://www.python.org/about/ Python] ===
We currently provide (module spider Python)
* Python/2.7.13-foss-2017beocatb
* Python/2.7.13-GCCcore-7.2.0-bare
* Python/2.7.13-iomkl-2017a
* Python/2.7.13-iomkl-2017beocatb
* Python/3.6.3-foss-2017b
* Python/3.6.3-foss-2017beocatb
* Python/3.6.3-iomkl-2017beocatb


We have several versions of Python available:
If you need modules that we do not have installed, you should use [https://virtualenv.pypa.io/en/stable/userguide/ virtualenv] to setup a virtual python environment in your home directory. This will let you install python modules as you please.
* [http://docs.python.org/2.7/ CPython 2.7]
* [http://docs.python.org/3.4/ CPython 3.4]
* [http://pypy.org/ PyPy 5.4.1] (Python 2.7.10)
* [http://pypy.org/ PyPy3 5.5.0-alpha0] (Python 3.3.5)
 
For the uninitiated PyPy provides [[wikipedia:Just-in-time_compilation|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 or pypy as you would any other application.
 
If, however, you need modules that we do not have installed, you should use [http://www.doughellmann.com/projects/virtualenvwrapper/ 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 ====
==== Setting up your virtual environment ====
* [[LinuxBasics#Shells|Change your shell]] to bash
* Make sure ~/.bash_profile exists
<syntaxhighlight lang="bash">
<syntaxhighlight lang="bash">
if [ ! -f ~/.bash_profile ]; then cp /etc/skel/.bash_profile ~/.bash_profile; fi
# Load Python
module load Python/3.6.3-iomkl-2017beocatb
</syntaxhighlight>
</syntaxhighlight>
* Add a line like <code>source /usr/bin/virtualenvwrapper.sh</code> to your .bashrc.
* Create a location for your virtual environments (optional, but helps keep things organized)
<syntaxhighlight lang="bash">
<syntaxhighlight lang="bash">
echo "source /usr/bin/virtualenvwrapper.sh" >> ~/.bashrc
mkdir ~/virtualenvs
cd ~/virtualenvs
</syntaxhighlight>
</syntaxhighlight>
* '''''CRITICAL:''''' Logout, and then log back in
* Create a virtual environment. Here I will create a default virtual environment called 'test'. Note that <code>virtualenv --help</code> has many more useful options.
* Show your existing environments
<syntaxhighlight lang="bash">
<syntaxhighlight lang="bash">
workon
virtualenv test
</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.
<syntaxhighlight lang="bash">
mkvirtualenv -p $(which python2) testp2
mkvirtualenv -p $(which python3) testp3
mkvirtualenv -p $(which pypy) testpypy
</syntaxhighlight>
</syntaxhighlight>
* Lets look at our virtual environments
* Lets look at our virtual environments
<pre>
<pre>
%workon
% ls ~/virtualenvs
testp2
test
testp3
testpypy
</pre>
</pre>
* Activate one of these
* Activate one of these
<pre>
<pre>
%workon testp2
%source ~/virtualenvs/test/bin/activate
</pre>
</pre>
* You can now install the python modules you want. This can be done using <tt>pip</tt>.
* You can now install the python modules you want. This can be done using <tt>pip</tt>.
Line 140: Line 151:
<syntaxhighlight lang="bash">
<syntaxhighlight lang="bash">
#!/bin/bash
#!/bin/bash
source /usr/bin/virtualenvwrapper.sh
module load Python/3.6.3-iomkl-2017beocatb
workon testp2
source ~/virtualenvs/test/bin/activate
~/path/to/your/python/script.py
python ~/path/to/your/python/script.py
</syntaxhighlight>
==== A note on [http://mpi4py.scipy.org/docs/usrman/index.html mpi4py] ====
If you are wanting to use mpi with your python script and are using a virtual environment, you will need to send the correct environment variables to all of the mpi processes to make the virtual environment work.
<syntaxhighlight lang="bash">
#!/bin/bash
# sample mpi4py submit script
source /usr/bin/virtualenvwrapper.sh
workon testp2
# figure out the location of the python interpreter in the virtual environment
PYTHON_BINARY=$(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
</syntaxhighlight>
</syntaxhighlight>
If you are using comm.send and comm.recv for communication with python objects and receive an output message like the one below, you will need to use [https://support.beocat.ksu.edu/BeocatDocs/index.php/AdvancedSGE#Infiniband infiniband] to allow MPI to communicate properly.
<syntaxhighlight lang="xml">
--------------------------------------------------------------------------
[[33053,1],52]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:


Module: OpenFabrics (openib)
=== [http://www.perl.org/ Perl] ===
  Host: host
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.


Another transport will be used instead, although this may result in
If you need a newer version (or threads), just load one we provide in our modules (module spider Perl):
lower performance.
* Perl/5.26.0-foss-2017beocatb
--------------------------------------------------------------------------
* Perl/5.26.0-iompi-2017beocatb
</syntaxhighlight>


==== A note on [http://www.scipy.org/ scipy] ====
SciPy requires numpy, unfortunately it doesn't properly define a dependency on numpy, so you just have to install it first.
<syntaxhighlight lang="bash">
source /usr/bin/virtualenvwrapper.sh
workon testp2
pip install numpy
# now scipy needs lapack and it doesn't detect the system one. lets fix it
export LAPACK=/usr/lib/libreflapack.so
export BLAS=/usr/lib/libopenblas_openmp.so
pip install scipy
</syntaxhighlight>
=== [http://www.perl.org/ 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.
==== Submitting a job with Perl ====
==== Submitting a job with Perl ====
Much like R (above), you cannot simply '<tt>qsub myProgram.pl</tt>', but you must create a [[AdvancedSGE#Running_from_a_qsub_Submit_Script|submit script]] which will call perl. Here is an example:
Much like R (above), you cannot simply '<tt>sbatch myProgram.pl</tt>', but you must create a [[AdvancedSlurm#Running_from_a_sbatch_Submit_Script|submit script]] which will call perl. Here is an example:
<syntaxhighlight lang="bash">
<syntaxhighlight lang="bash">
#!/bin/bash
#!/bin/bash
#$ -l mem=1G
#SBATCH --mem-per-cpu=1G
# Now we tell qsub how long we expect our work to take: 15 minutes (H:MM:SS)
# Now we tell qsub how long we expect our work to take: 15 minutes (H:MM:SS)
#$ -l h_rt=0:15:00
#SBATCH --time=0-0:15:00
# Now lets do some actual work.  
# Now lets do some actual work.  
module load Perl
perl /path/to/myProgram.pl
perl /path/to/myProgram.pl
</syntaxhighlight>
==== Getting Perl with threads ====
* Setup perlbrew
** [[LinuxBasics#Shells|Change your shell]] to bash
** Install perlbrew
<syntaxhighlight lang="bash">
curl -L http://install.perlbrew.pl | bash
</syntaxhighlight>
** Make sure that ~/.bash_profile exists
<syntaxhighlight lang="bash">
if [ ! -f ~/.bash_profile ]; then cp /etc/skel/.bash_profile ~/.bash_profile; fi
</syntaxhighlight>
** Add <code>source ~/perl5/perlbrew/etc/bashrc</code> to ~/.bash_profile
<syntaxhighlight lang="bash">
echo "source ~/perl5/perlbrew/etc/bashrc" >> ~/.bash_profile
</syntaxhighlight>
** Then source your bash profile
<syntaxhighlight lang="bash">
source ~/.bash_profile
</syntaxhighlight>
* Now, install perl with threads within perlbrew
** Find the current Perl version.
<pre>
% 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)
</pre>
** In this case the version is 5.16.3, so we run
<syntaxhighlight lang="bash">
perlbrew install -f -n -D usethreads perl-5.16.3
</syntaxhighlight>
** To temporarily use the new version of perl in the current shell, we now run
<syntaxhighlight lang="bash">
perlbrew use perl-5.16.3
</syntaxhighlight>
** To switch versions of perl for every new login or job, run
<syntaxhighlight lang="bash">
perlbrew switch perl-5.16.3
</syntaxhighlight>
** You can reverse this switch with
<syntaxhighlight lang="bash">
perlbrew switch-off
</syntaxhighlight>
</syntaxhighlight>


Revision as of 10:14, 10 January 2018

Drinking from the Firehose

For a complete list of all installed software, see NodePackageList


Toolchains

A toolchain is a set of compilers, libraries and applications that are needed to build software. Some software functions better when using specific toolchains.

We provide a good number of toolchains and versions of toolchains make sure your applications will compile and/or run correctly.

These toolchains include (you can run 'module keyword keychain compiler'):

GCC
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,...).
GCCcore
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,...).
foss
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
gcccuda
GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.
gmvapich2
GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support.
gompi
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
gompic
GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.
goolfc
GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
icc
C and C++ compiler from Intel
iccifort
Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL
ifort
Fortran compiler from Intel
iomkl
Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.
iompi
Intel C/C++ and Fortran compilers, alongside Open MPI.

You can run 'module spider $toolchain' to see the versions we have: 

$ module spider iomkl
  • iomkl/2017a
  • iomkl/2017b
  • iomkl/2017beocatb

If you load one of those (module load iomkl/2017b), you can see the other modules and versions of software that it loaded with the 'module list': 

$ module list
Currently Loaded Modules:
  1) icc/2017.4.196-GCC-6.4.0-2.28
  2) binutils/2.28-GCCcore-6.4.0
  3) ifort/2017.4.196-GCC-6.4.0-2.28
  4) iccifort/2017.4.196-GCC-6.4.0-2.28
  5) GCCcore/6.4.0
  6) numactl/2.0.11-GCCcore-6.4.0
  7) hwloc/1.11.7-GCCcore-6.4.0
  8) OpenMPI/2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28
  9) iompi/2017b
 10) imkl/2017.3.196-iompi-2017b
 11) iomkl/2017b

As you can see, toolchains can depend on each other. For instance, the iomkl toolchain, depends on iompi, which depends on iccifort, which depend on icc and ifort, which depend on GCCcore which depend on GCC. Hence it is very important that the correct versions of all related software are loaded.

With software we provide, the toolchain used to compile is always specified in the "version" of the software that you want to load.

Most Commonly Used Software

OpenMPI

We provide lots of versions, you are most likely better off directly loading a toolchain or application to make sure you get the right version, but you can see the versions we have with 'module spider OpenMPI':

  • OpenMPI/2.0.2-GCC-6.3.0-2.27
  • OpenMPI/2.0.2-iccifort-2017.1.132-GCC-6.3.0-2.27
  • OpenMPI/2.1.1-GCC-6.4.0-2.28
  • OpenMPI/2.1.1-GCC-7.2.0-2.29
  • OpenMPI/2.1.1-gcccuda-2017b
  • OpenMPI/2.1.1-iccifort-2017.4.196-GCC-6.4.0-2.28
  • OpenMPI/2.1.1-iccifort-2018.0.128-GCC-7.2.0-2.29

R

We currently provide (module -r spider '^R$'):

  • R/3.4.0-foss-2017beocatb-X11-20170314

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 

module load R
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. 'sbatch 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.sbatch 

 #!/bin/bash
 #SBATCH --mem-per-cpu=1G
 # Now we tell qsub how long we expect our work to take: 15 minutes (D-H:MM:SS)
 #SBATCH --time=0-0:15:00
 
 # Now lets do some actual work. This starts R and loads the file myscript.R
 module load R
R --no-save -q < myscript.R

Now, to submit your R job, you would type 

sbatch submit-R.sbatch

Java

We currently provide (module spider Java):

  • Java/1.8.0_131
  • Java/1.8.0_144

Python

We currently provide (module spider Python)

  • Python/2.7.13-foss-2017beocatb
  • Python/2.7.13-GCCcore-7.2.0-bare
  • Python/2.7.13-iomkl-2017a
  • Python/2.7.13-iomkl-2017beocatb
  • Python/3.6.3-foss-2017b
  • Python/3.6.3-foss-2017beocatb
  • Python/3.6.3-iomkl-2017beocatb

If you need modules that we do not have installed, you should use virtualenv 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

# Load Python
module load Python/3.6.3-iomkl-2017beocatb
  • Create a location for your virtual environments (optional, but helps keep things organized)
mkdir ~/virtualenvs
cd ~/virtualenvs
  • Create a virtual environment. Here I will create a default virtual environment called 'test'. Note that virtualenv --help has many more useful options.
virtualenv test
  • Lets look at our virtual environments
% ls ~/virtualenvs
test
  • Activate one of these
%source ~/virtualenvs/test/bin/activate
  • 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
module load Python/3.6.3-iomkl-2017beocatb
source ~/virtualenvs/test/bin/activate
python ~/path/to/your/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.

If you need a newer version (or threads), just load one we provide in our modules (module spider Perl):

  • Perl/5.26.0-foss-2017beocatb
  • Perl/5.26.0-iompi-2017beocatb

Submitting a job with Perl

Much like R (above), you cannot simply 'sbatch myProgram.pl', but you must create a submit script which will call perl. Here is an example: 

#!/bin/bash
#SBATCH --mem-per-cpu=1G
# Now we tell qsub how long we expect our work to take: 15 minutes (H:MM:SS)
#SBATCH --time=0-0:15:00
# Now lets do some actual work. 
module load Perl
perl /path/to/myProgram.pl

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.

Retrieved from "https://support.beocat.ksu.edu/BeocatDocs/index.php?title=Installed_software&oldid=291"