From Beocat
Revision as of 16:07, 31 January 2018 by Mozes (talk | contribs) (→‎R)
Jump to: navigation, search

Drinking from the Firehose

For a complete list of all installed modules, see ModuleList

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

Packages

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 R Packages

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=301"