Available modules¶
Below is the software available in the "Aristotle" institutional cluster. Note that any software or application may be installed in more than one version.
Request for software installation
If you wish to install software that is not listed below you can submit the relevant form.
Sofware and applications lists¶
Available software with gcc/9.4.0 and openmpi/4.1.2
Available software with gcc/9.2.0 and mvapich2/2.3.4
Available software with gcc/9.2.0 and openmpi/3.1.4
Available software with gcc/8.2.0 and openmpi/3.1.4
Available software with gcc/8.2.0 and openmpi/3.1.3
Available software with gcc/7.3.0 and openmpi/3.1.4
Available software with gcc/7.3.0 and openmpi/3.1.3
Available software with gcc/6.4.0 and openmpi/3.1.3
Available software with intel/19.0.5 and intel-mpi/2019.4.243
Available software with intel/19.0.5 and openmpi/3.1.4
Available software with intel/19.0.5 and openmpi/3.1.3
Intro to using modulefiles¶
The software/applications are available when using modulefiles. For example when we login to the cluster, the version of the gcc compiler available is 4.8.5:
# gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
This version is called "system version".
To make another version available in the UI (on the command line) we need to load the corresponding modulefile first, e.g. to use version `9.2.0':
# module load gcc/9.2.0
# gcc --version
gcc (Spack GCC) 9.2.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
We note that in the output of gcc --version the version is 9.2.0 and not the system version (4.8.5). If we want to see which versions of the gcc package/software are available we can run module avail gcc, e.g:
# module avail gcc
------------ /mnt/apps/aristotle/site/share/spack/lmod/linux-centos7-x86_64/Core -------------
gcc/5.5.0 gcc/6.4.0 gcc/7.3.0 gcc/8.2.0 (D) gcc/9.2.0
Where:
D: Default Module
Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the
"keys".
In the output of the last command we notice that the default version is 8.2.0, so if we call module load gcc without specifying a particular version, 8.2.0 will be activated as shown and in the box below:
# module load gcc
# gcc --version
gcc (GCC) 8.2.0
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Modulefiles structure¶
Most software packages that are centrally installed on the cluster are compiled with one or more compilers (e.g., gcc and intel). Similarly (and one level down) a parallel application may have been compiled using more than one mpi implementation (e.g. and with openmpi and with intel-mpi).
Consequently the structure of modulefiles available is hierarchical, meaning the libraries or applications that have been compiled with a given compiler are shown as available with module avail only after we have loaded the given compiler into the environment.
The compilers are at the first level of the hierarchy. After the login the only softwares available for use are:
# module avail
----- /mnt/apps/aristotle/site/share/spack/lmod/linux-centos7-x86_64/Core ------
gcc/5.5.0 gcc/10.2.0
gcc/6.4.0 intel-oneapi-compilers/2022.0.2-sygdcrc
gcc/7.3.0 intel/19.0.5 (D)
gcc/8.2.0 (D) intel/20.0.2
gcc/9.2.0
gcc/9.4.0-eewq4j6
The second level is where most applications are located. To see them as available modulefiles we first need to load a compiler, e.g.:
# module load intel/19.0.5
# module avail
- /mnt/apps/aristotle/site/share/spack/lmod/linux-centos7-x86_64/intel/19.0.5 --
autoconf/2.69 hwloc/1.11.9 openmpi/3.1.2
automake/1.16.1 hwloc/1.11.11 (D) openmpi/3.1.3
axel/2.16.1 jasper/1.900.1 openmpi/3.1.4 (D)
bison/3.4.2 libjpeg-turbo/1.5.90 openssl/1.0.2o
boost/1.70.0 libpng/1.6.34 openssl/1.1.1d (D)
bzip2/1.0.8 libpng/1.6.37 (D) perl/5.26.2
cgal/4.13 libtool/2.4.6 perl/5.30.0 (D)
cmake/3.9.6 libxml2/2.9.8 pkgconf/1.4.2
cmake/3.12.3 libxml2/2.9.9 (D) pkgconf/1.6.3 (D)
cmake/3.15.4 (D) m4/1.4.18 python/3.3.5
curl/7.63.0 miniconda2/4.5.11 readline/7.0
diffutils/3.6 miniconda3/4.5.11 readline/8.0 (D)
diffutils/3.7 (D) mpfr/4.0.2 slurm/17-11-8-1
expat/2.2.9 nasm/2.13.03 sqlite/3.30.1
fontsproto/2.1.3 ncurses/6.1 tar/1.32
gmake/4.2.1 numactl/2.0.11 xz/5.2.4
gmp/6.1.2 numactl/2.0.12 (D) zlib/1.2.11
help2man/1.47.11 openblas/0.3.7
----- /mnt/apps/aristotle/site/share/spack/lmod/linux-centos7-x86_64/Core ------
gcc/5.5.0 gcc/10.2.0
gcc/6.4.0 intel-oneapi-compilers/2022.0.2-sygdcrc
gcc/7.3.0 intel/19.0.5 (D)
gcc/8.2.0 (D) intel/20.0.2
gcc/9.2.0
gcc/9.4.0-eewq4j6
Some parallel applications (using one mpi library) are located at the third level, e.g. the libraries hdf5:
# module load openmpi/3.1.3
# module avail
------ /mnt/apps/aristotle/site/share/spack/lmod/linux-centos7-x86_64/openmpi/3.1.3-q4h4qu4/intel/19.0.5.281 -------
hdf5/1.8.19 hdf5/1.10.4 (D) netcdf-fortran/4.4.4 netcdf/4.6.1 regcm/4.4.5.11 regcm/4.7.0 (D)
------------------- /mnt/apps/aristotle/site/share/spack/lmod/linux-centos7-x86_64/intel/19.0.5 --------------------
autoconf/2.69 fontsproto/2.1.3 miniconda2/4.5.11 perl/5.30.0 (D)
automake/1.16.1 gmake/4.2.1 miniconda3/4.5.11 pkgconf/1.4.2
axel/2.16.1 gmp/6.1.2 mpfr/4.0.2 pkgconf/1.6.3 (D)
bison/3.4.2 help2man/1.47.11 nasm/2.13.03 python/3.3.5
boost/1.70.0 hwloc/1.11.9 ncurses/6.1 readline/7.0
bzip2/1.0.8 hwloc/1.11.11 (D) numactl/2.0.11 readline/8.0 (D)
cgal/4.13 jasper/1.900.1 numactl/2.0.12 (D) slurm/17-11-8-1
cmake/3.9.6 libjpeg-turbo/1.5.90 openblas/0.3.7 sqlite/3.30.1
cmake/3.12.3 libpng/1.6.34 openmpi/3.1.2 tar/1.32
cmake/3.15.4 (D) libpng/1.6.37 (D) openmpi/3.1.3 (L) xz/5.2.4
curl/7.63.0 libtool/2.4.6 openmpi/3.1.4 (D) zlib/1.2.11
diffutils/3.6 libxml2/2.9.8 openssl/1.0.2o
diffutils/3.7 (D) libxml2/2.9.9 (D) openssl/1.1.1d (D)
expat/2.2.9 m4/1.4.18 perl/5.26.2
----------------------- /mnt/apps/aristotle/site/share/spack/lmod/linux-centos7-x86_64/Core ------------------------
gcc/5.5.0 gcc/6.4.0 gcc/7.3.0 gcc/8.2.0 (D) gcc/9.2.0 intel/19.0.5 (L)
Using spider¶
To see which modulefiles we need to load first in order to make an application available in the UI we can use the command module spider. E.g. to see which options are available to "load" the fftw (Fastest Fourier Transform in the West) library we can run the following command:
# module spider fftw/3.3.8
-------------------------------------------------------------------------------------------
fftw: fftw/3.3.8
-------------------------------------------------------------------------------------------
You will need to load all module(s) on any one of the lines below before the "fftw/3.3.8" m
odule is available to load.
gcc/6.4.0 openmpi/3.1.3
gcc/7.3.0 openmpi/3.1.3
gcc/8.2.0 openmpi/3.1.3
gcc/9.2.0 openmpi/3.1.4
Help:
FFTW is a C subroutine library for computing the discrete Fourier
transform (DFT) in one or more dimensions, of arbitrary input size, and
of both real and complex data (as well as of even/odd data, i.e. the
discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which
is free software, should become the FFT library of choice for most
applications.
We see that the configured library (fftw/3.3.8) is installed four times and to bring it into the UI we need to first load a combination of gcc and openmpi, e.g:
# module load gcc/9.2.0 openmpi/3.1.4
# module load fftw/3.3.8