Difference between revisions of "Accessing software"
From ALICE Documentation
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4) slurm/18.08.4 8) ncurses/6.1-GCCcore-8.2.0 12) XZ/5.2.4-GCCcore-8.2.0 | 4) slurm/18.08.4 8) ncurses/6.1-GCCcore-8.2.0 12) XZ/5.2.4-GCCcore-8.2.0 | ||
| − | <br />The command <code>module purge</code> | + | <br />The command <code>module purge</code> unloads everything at once. |
[deuler@nodelogin01 ~]$ module purge | [deuler@nodelogin01 ~]$ module purge | ||
[deuler@nodelogin01 ~]$ module list | [deuler@nodelogin01 ~]$ module list | ||
Revision as of 09:58, 12 July 2019
Before we start using individual software packages, we need to understand why multiple versions of software are available on HPC systems and why users need to have a way to control which version they are using. The three biggest factors are:
- software incompatibilities;
- versioning;
- dependencies.
Software incompatibility is a major headache for programmers. Sometimes the presence (or absence) of a software package will break others that depend on it. Two of the most famous examples are Python 2 and 3 and C compiler versions. Python 3 famously provides a python command that conflicts with that provided by Python 2. Software compiled against a newer version of the C libraries and then used when they are not present will result in a nasty 'GLIBCXX_3.4.20' not found error, for instance.
Software versioning is another common issue. A team might depend on a certain package version for their research project - if the software version was to change (for instance, if a package was updated), it might affect their results. Having access to multiple software versions allow a set of researchers to prevent software versioning issues from affecting their results.
Dependencies are where a particular software package (or even a particular version) depends on having access to another software package (or even a particular version of another software package). For example, the VASP materials science software may depend on having a particular version of the FFTW (Fastest Fourier Transform in the West) software library available for it to work.
Contents
Environment modules
Environment modules are the solution to these problems. A module is a self-contained description of a software package - it contains the settings required to run a software package and, usually, encodes required dependencies on other software packages.
There are a number of different environment module implementations commonly used on HPC systems: the two most common are TCL modules and Lmod. Both of these use similar syntax and the concepts are the same so learning to use one will allow you to use whichever is installed on the system you are using. In both implementations the module command is used to interact with environment modules. An additional subcommand is usually added to the command to specify what you want to do. For a list of subcommnands you can use module -h or module help. As for all commands, you can access the full help on the man pages with man module.
On login you may start out with a default set of modules loaded or you may start out with an empty environment, this depends on the setup of the system you are using.
List currently loaded modules
The module list command shows which modules you currently have loaded in your environment. If you have no modules loaded, you will see a message telling you so
[remote]$ module list
No Modulefiles Currently Loaded.
List available modules
To see the available modules, use module avail
[deuler@nodelogin01 ~]$ module avail
------------------------------------------------ /cm/shared/easybuild/modules/all ------------------------------------------------- Autoconf/2.69-GCCcore-6.4.0 binutils/2.31.1-GCCcore-8.2.0 Autoconf/2.69-GCCcore-8.2.0 (D) binutils/2.31.1 (D) Automake/1.15.1-GCCcore-6.4.0 bzip2/1.0.6-GCCcore-6.4.0 Automake/1.16.1-GCCcore-8.2.0 (D) bzip2/1.0.6-GCCcore-8.2.0 (D) Autotools/20170619-GCCcore-6.4.0 expat/2.2.5-GCCcore-6.4.0 Autotools/20180311-GCCcore-8.2.0 (D) flex/2.6.3 Bison/3.0.4-GCCcore-6.4.0 flex/2.6.4-GCCcore-6.4.0 Bison/3.0.4 flex/2.6.4-GCCcore-8.2.0 Bison/3.0.5-GCCcore-6.4.0 flex/2.6.4 (D) Bison/3.0.5-GCCcore-8.2.0 fontconfig/2.12.6-GCCcore-6.4.0 Bison/3.0.5 (D) foss/2018a Docutils/0.9.1-foss-2018a-Python-2.7.14 foss/2019a (D) EasyBuild/3.9.2 freetype/2.9-GCCcore-6.4.0 FFTW/3.3.7-gompi-2018a gettext/0.19.8.1-GCCcore-6.4.0 FFTW/3.3.8-gompi-2019a (D) gettext/0.19.8.1 (D) GCC/6.4.0-2.28 gompi/2018a GCC/8.2.0-2.31.1 (D) gompi/2019a (D) GCCcore/6.4.0 gperf/3.1-GCCcore-6.4.0 GCCcore/8.2.0 (D) h5py/2.7.1-foss-2018a-Python-2.7.14 GMP/6.1.2-GCCcore-6.4.0 help2man/1.47.4-GCCcore-6.4.0 GMP/6.1.2-GCCcore-8.2.0 (D) help2man/1.47.4 GSL/2.4-GCCcore-6.4.0 help2man/1.47.7-GCCcore-8.2.0 (D) HDF5/1.8.20-foss-2018a hwloc/1.11.8-GCCcore-6.4.0 HDF5/1.10.1-foss-2018a (D) hwloc/1.11.11-GCCcore-8.2.0 (D) M4/1.4.17 intltool/0.51.0-GCCcore-6.4.0-Perl-5.26.1 M4/1.4.18-GCCcore-6.4.0 libffi/3.2.1-GCCcore-6.4.0 M4/1.4.18-GCCcore-8.2.0 libffi/3.2.1-GCCcore-8.2.0 (D) M4/1.4.18 (D) libpciaccess/0.14-GCCcore-6.4.0 MPFR/4.0.1-GCCcore-6.4.0 libpciaccess/0.14-GCCcore-8.2.0 (D) OpenBLAS/0.2.20-GCC-6.4.0-2.28 libpng/1.6.34-GCCcore-6.4.0 OpenBLAS/0.3.5-GCC-8.2.0-2.31.1 (D) libreadline/7.0-GCCcore-6.4.0 OpenMPI/2.1.2-GCC-6.4.0-2.28 libreadline/8.0-GCCcore-8.2.0 (D) OpenMPI/3.1.3-GCC-8.2.0-2.31.1 (D) libtool/2.4.6-GCCcore-6.4.0 Perl/5.26.1-GCCcore-6.4.0 libtool/2.4.6-GCCcore-8.2.0 (D) Python/2.7.14-foss-2018a libxml2/2.9.4-GCCcore-6.4.0 Python/2.7.15-GCCcore-8.2.0 libxml2/2.9.7-GCCcore-6.4.0 Python/3.7.2-GCCcore-8.2.0 (D) libxml2/2.9.8-GCCcore-8.2.0 (D) SQLite/3.21.0-GCCcore-6.4.0 matplotlib/2.1.2-foss-2018a-Python-2.7.14 SQLite/3.27.2-GCCcore-8.2.0 (D) mpi4py/3.0.0-foss-2018a-Python-2.7.14 ScaLAPACK/2.0.2-gompi-2018a-OpenBLAS-0.2.20 ncurses/6.0-GCCcore-6.4.0 ScaLAPACK/2.0.2-gompi-2019a-OpenBLAS-0.3.5 (D) ncurses/6.0 SciPy-bundle/2019.03-foss-2019a ncurses/6.1-GCCcore-8.2.0 (D) Szip/2.1.1-GCCcore-6.4.0 numactl/2.0.11-GCCcore-6.4.0 Tcl/8.6.8-GCCcore-6.4.0 numactl/2.0.12-GCCcore-8.2.0 (D) Tcl/8.6.9-GCCcore-8.2.0 (D) pip/19.1.1-foss-2018a-Python-2.7.14 Tk/8.6.8-foss-2018a pkg-config/0.29.2-GCCcore-6.4.0 Tkinter/2.7.14-foss-2018a-Python-2.7.14 pkgconfig/1.3.1-foss-2018a-Python-2.7.14 X11/20180131-GCCcore-6.4.0 scikit-learn/0.20.3-foss-2019a XML-Parser/2.44_01-GCCcore-6.4.0-Perl-5.26.1 wheel/0.32.0-foss-2018a-Python-2.7.14 XZ/5.2.3-GCCcore-6.4.0 xorg-macros/1.19.1-GCCcore-6.4.0 XZ/5.2.4-GCCcore-8.2.0 (D) xorg-macros/1.19.2-GCCcore-8.2.0 (D) amuse-framework/12.0.0-foss-2018a-Python-2.7.14 zlib/1.2.11-GCCcore-6.4.0 amuse/12.0.0-foss-2018a-Python-2.7.14 zlib/1.2.11-GCCcore-8.2.0 binutils/2.28-GCCcore-6.4.0 zlib/1.2.11 (D) binutils/2.28 ------------------------------------------------------ /cm/local/modulefiles ------------------------------------------------------ cluster-tools/8.2 cmd dot gcc/8.2.0 (L) lua/5.3.5 module-info openldap python36 cm-cloud-copy/8.2 cmsub freeipmi/1.6.2 ipmitool/1.8.18 module-git null python2 shared (L) ----------------------------------------------------- /usr/share/modulefiles ------------------------------------------------------ DefaultModules (L) ----------------------------------------------------- /cm/shared/modulefiles ------------------------------------------------------ blacs/openmpi/gcc/64/1.1patch03 globalarrays/openmpi/gcc/64/5.7 mvapich2/gcc/64/2.3 blas/gcc/64/3.8.0 hdf5/1.10.1 netcdf/gcc/64/4.6.1 bonnie++/1.97.3 hdf5_18/1.8.20 netperf/2.7.0 cm-pmix3/3.0.2 hpl/2.2 openblas/dynamic/0.2.20 default-environment hwloc/1.11.11 openmpi/gcc/64/1.10.7 fftw2/openmpi/gcc/64/double/2.1.5 intel-tbb-oss/ia32/2019_20180718oss scalapack/openmpi/gcc/64/2.0.2 fftw2/openmpi/gcc/64/float/2.1.5 intel-tbb-oss/intel64/2019_20180718oss sge/2011.11p1 fftw3/openmpi/gcc/64/3.3.8 iozone/3_482 slurm/18.08.4 (L) gcc6/6.5.0 lapack/gcc/64/3.8.0 gdb/8.2 mpich/ge/gcc/64/3.3 Where: L: Module is loaded D: Default Module Module defaults are chosen based on Find First Rules due to Name/Version/Version modules found in the module tree. See https://lmod.readthedocs.io/en/latest/060_locating.html for details. Use "module spider" to find all possible modules. Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys"
Load modules
To load a software module, use module load. In the example below, we will use Python 3.
Initially, Python 3 is not loaded. We can test this by using the command which that looks for programs the same way that Bash does. We can use it to tell us where a particular piece of software is stored.
[deuler@nodelogin01 ~]$ which python3/usr/bin/which: no python3 in (/cm/shared/apps/slurm/18.08.4/sbin:/cm/shared/apps/slurm/18.08.4/bin:/cm/local/apps/gcc/8.2.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/deuler/.local/bin:/home/deuler/bin)
We can load the python3 command with module load:
[deuler@nodelogin01 ~]$module load Python/3.7.2-GCCcore-8.2.0[deuler@nodelogin01 ~]$ which python3
/cm/shared/easybuild/software/Python/3.7.2-GCCcore-8.2.0/bin/python3
So what just happened? To understand the output, first we need to understand the nature of the $PATH environment variable. $PATH is a special environment variable that controls where a Linux operating system (OS) looks for software. Specifically $PATH is a list of directories (separated by :) that the OS searches through for a command. As with all environment variables, we can print it using echo.
[remote]$ echo $PATH
/cm/shared/easybuild/software/Python/3.7.2-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/XZ/5.2.4-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/SQLite/3.27.2-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/Tcl/8.6.9-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/libreadline/8.0-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/ncurses/6.1-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/bzip2/1.0.6-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/GCCcore/8.2.0/bin:/cm/shared/apps/slurm/18.08.4/sbin:/cm/shared/apps/slurm/18.08.4/bin:/cm/local/apps/gcc/8.2.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/deuler/.local/bin:/home/deuler/bin
You’ll notice a similarity to the output of the which command. In this case, there’s only one difference: the /cm/shared/easybuild/software/Python/3.7.2-GCCcore-8.2.0/bin directory at the beginning. When we used module load Python/3.7.2-GCCcore-8.2.0, it added this directory to the beginning of our $PATH. Let’s examine what is there:
[deuler@nodelogin01 ~]$ \ls /cm/shared/easybuild/software/Python/3.7.2-GCCcore-8.2.0/bin
2to3 futurize pip pytest python3-config rst2odt_prepstyles.py sphinx-apidoc 2to3-3.7 idle3 pip3 py.test pyvenv rst2odt.py sphinx-autogen chardetect idle3.7 pip3.7 python pyvenv-3.7 rst2pseudoxml.py sphinx-build cygdb netaddr pybabel python3 rst2html4.py rst2s5.py sphinx-quickstart cython nosetests __pycache__ python3.7 rst2html5.py rst2xetex.py tabulate cythonize nosetests-3.7 pydoc3 python3.7-config rst2html.py rst2xml.py virtualenv easy_install pasteurize pydoc3.7 python3.7m rst2latex.py rstpep2html.py wheel easy_install-3.7 pbr pygmentize python3.7m-config rst2man.py runxlrd.py
Taking this to its conclusion, module load adds software to your $PATH. It “loads” software. A special note on this, depending on which version of the module program that is installed at your site, module load may also load required software dependencies.
[deuler@nodelogin01 ~]$ module list
Currently Loaded Modules: 1) shared 5) GCCcore/8.2.0 9) libreadline/8.0-GCCcore-8.2.0 13) GMP/6.1.2-GCCcore-8.2.0 2) DefaultModules 6) bzip2/1.0.6-GCCcore-8.2.0 10) Tcl/8.6.9-GCCcore-8.2.0 14) libffi/3.2.1-GCCcore-8.2.0 3) gcc/8.2.0 7) zlib/1.2.11-GCCcore-8.2.0 11) SQLite/3.27.2-GCCcore-8.2.0 15) Python/3.7.2-GCCcore-8.2.0 4) slurm/18.08.4 8) ncurses/6.1-GCCcore-8.2.0 12) XZ/5.2.4-GCCcore-8.2.0
Unload modules
The command module unload “un-loads” a module along with its dependencies. For the above example:
[deuler@nodelogin01 ~]$ module unload Python/3.7.2-GCCcore-8.2.0 [deuler@nodelogin01 ~]$ module list
Currently Loaded Modules: 1) shared 5) GCCcore/8.2.0 9) libreadline/8.0-GCCcore-8.2.0 13) GMP/6.1.2-GCCcore-8.2.0 2) DefaultModules 6) bzip2/1.0.6-GCCcore-8.2.0 10) Tcl/8.6.9-GCCcore-8.2.0 14) libffi/3.2.1-GCCcore-8.2.0 3) gcc/8.2.0 7) zlib/1.2.11-GCCcore-8.2.0 11) SQLite/3.27.2-GCCcore-8.2.0 4) slurm/18.08.4 8) ncurses/6.1-GCCcore-8.2.0 12) XZ/5.2.4-GCCcore-8.2.0
The command module purge unloads everything at once.
[deuler@nodelogin01 ~]$ module purge [deuler@nodelogin01 ~]$ module list
No modules loaded