Software environment
On Hábrók a lot of software has been made available. In order to allow multiple versions of software to be available the software is arranged in so-called modules.
module system
By default, only the main modules for getting access to the software stack are loaded: these are named StdEnv and 2023.01 (which denotes the current version of the software stack).
Other than that, no modules for actual applications are loaded by default, which means that the software will not yet be available on the command line prompt. Throughout this page we will use R as an example. Normally the command R should fire up a command line session for R:
[username@habrok ~]$ R -bash: R: command not found [username@habrok ~]$
As you can see R cannot be found. In order to find the options that are available and add the software to our environment we have to make use of the module system. The command module allows for finding and loading software into the environment. For this the command has to be used together with a subcommand to specify the action we want to perform.
The subcommands are:
availfor showing a list of available softwareloadoraddfor loading software into the environmentlistfor showing the currently loaded modulesunloadordelfor unloading a module from the environmentpurgefor unloading all loaded modules from the environmentsavefor saving a set of loaded modules into a configuration for restoring at a later timerestorefor restoring a saved set of modules
module avail
One way to find information about software is to run the command module with the subcommand avail. If we run it without extra arguments we get something like:
[username@habrok ~]$ module avail ---- /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/modules/ai ---- PyTorch/1.12.1-foss-2022a-CUDA-11.7.0 ---- /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/modules/astro ---- astropy/5.1.1-foss-2022a ---- /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/modules/bio ---- angsd/0.940-GCC-11.2.0 BA3-SNPS-autotune/2.1.2-GCC-11.3.0 BamTools/2.5.2-GCC-11.3.0 BayesAss3-SNPs/1.1-GCC-11.3.0 BCFtools/1.15.1-GCC-11.3.0 BEDTools/2.30.0-GCC-11.3.0 BioPerl/1.7.8-GCCcore-11.3.0 Biopython/1.79-foss-2022a BLAST+/2.13.0-gompi-2022a BLAST/2.11.0-Linux_x86_64 ... et cetera...
We can use the spacebar to scroll through the extensive list. As you can see the list contains software packages. For each package one or more versions is available.
In order to bring down the list to certain packages only we can specify an argument to module avail. If we specify 'R', or 'r' as an argument it will show us all packages with an 'r' in its name. This will not help much, so we have to be more precise. A more useful search string would be 'r/3':
[username@habrok ~]$ module avail r/4 -------------------------------------- /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/modules/lang -------------------------------------- R/4.2.1-foss-2022a -------------------------------------- /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/modules/lib --------------------------------------- NSPR/4.34-GCCcore-11.3.0 -------------------------------------- /cvmfs/hpc.rug.nl/versions/2023.01/rocky8/x86_64/amd/zen3/modules/math -------------------------------------- MPFR/4.1.0-GCCcore-11.3.0
Now we can see the actual version(s) of R that is/are available. If multiple versions of the same application are available, only one of them will have '(D)' behind the name, denoting that this is the default versions.
module load/add
In order to load R, we can use the load or equivalent add subcommand for module. Note that we have to be precise with respect to upper- and lowercase now.
[username@habrok ~]$ module load R [username@habrok ~]$ R --version R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License versions 2 or 3. For more information about these matters see https://www.gnu.org/licenses/. [username@habrok ~]$
As can be seen from the last output R version 4.2.1 is now in our environment. If no version is specified the default version of the package is loaded.
CAVEAT Although packages have default versions, these defaults are subject to change without notice. It is therefore better to be explicit in the version that is to be loaded, especially in jobscripts. Otherwise you may find out that jobscripts break when the default suddenly changes.
For loading a specific version the full version has to be specified like:
[username@habrok ~]$ module load R/4.2.1-foss-2022a
module spider
Another way to find out more information about available packages is through module spider. With this subcommand you also have to make sure to use an uppercase R:
[username@habrok ~]$ module spider R
------------------------------------------------------------------------------------------------------------------------------------------------
R: R/4.2.1-foss-2022a
------------------------------------------------------------------------------------------------------------------------------------------------
Description:
R is a free software environment for statistical computing and graphics.
Other possible modules matches:
Amber, AmberTools, Arrow, BioPerl, Brotli, CapnProto, DendroPy, FastTree, FreeSurfer, FriBidi, GCCcore, GDRCopy, GObject-Introspection, ...
You will need to load all module(s) on any one of the lines below before the "R/4.2.1-foss-2022a" module is available to load.
2023.01
This module provides the following extensions:
[removed the long output showing all included R libraries>
This command shows some extra information on the package.
module list
In order to find out which modules have been loaded the subcommand list can be used:
[username@habrok ~]$ module list Currently Loaded Modules: 1) 2023.01 (S) 35) X11/20220504-GCCcore-11.3.0 69) LAME/3.100-GCCcore-11.3.0 2) StdEnv (S) 36) gzip/1.12-GCCcore-11.3.0 70) libsndfile/1.1.0-GCCcore-11.3.0 3) GCCcore/11.3.0 37) lz4/1.9.3-GCCcore-11.3.0 71) ICU/71.1-GCCcore-11.3.0 4) zlib/1.2.12-GCCcore-11.3.0 38) zstd/1.5.2-GCCcore-11.3.0 72) Szip/2.1.1-GCCcore-11.3.0 5) binutils/2.38-GCCcore-11.3.0 39) libdrm/2.4.110-GCCcore-11.3.0 73) HDF5/1.12.2-gompi-2022a 6) GCC/11.3.0 40) libglvnd/1.4.0-GCCcore-11.3.0 74) UDUNITS/2.2.28-GCCcore-11.3.0 7) numactl/2.0.14-GCCcore-11.3.0 41) libunwind/1.6.2-GCCcore-11.3.0 75) GSL/2.7-GCC-11.3.0 8) XZ/5.2.5-GCCcore-11.3.0 42) LLVM/14.0.3-GCCcore-11.3.0 76) ATK/2.38.0-GCCcore-11.3.0 9) libxml2/2.9.13-GCCcore-11.3.0 43) Mesa/22.0.3-GCCcore-11.3.0 77) Gdk-Pixbuf/2.42.8-GCCcore-11.3.0 10) libpciaccess/0.16-GCCcore-11.3.0 44) libGLU/9.0.2-GCCcore-11.3.0 78) HarfBuzz/4.2.1-GCCcore-11.3.0 11) hwloc/2.7.1-GCCcore-11.3.0 45) pixman/0.40.0-GCCcore-11.3.0 79) FriBidi/1.0.12-GCCcore-11.3.0 12) OpenSSL/1.1 46) libffi/3.4.2-GCCcore-11.3.0 80) Pango/1.50.7-GCCcore-11.3.0 13) libevent/2.1.12-GCCcore-11.3.0 47) gettext/0.21-GCCcore-11.3.0 81) GTK2/2.24.33-GCCcore-11.3.0 14) UCX/1.12.1-GCCcore-11.3.0 48) PCRE/8.45-GCCcore-11.3.0 82) Ghostscript/9.56.1-GCCcore-11.3.0 15) libfabric/1.15.1-GCCcore-11.3.0 49) GLib/2.72.1-GCCcore-11.3.0 83) JasPer/2.0.33-GCCcore-11.3.0 16) PMIx/4.1.2-GCCcore-11.3.0 50) cairo/1.17.4-GCCcore-11.3.0 84) LittleCMS/2.13.1-GCCcore-11.3.0 17) UCC/1.0.0-GCCcore-11.3.0 51) libreadline/8.1.2-GCCcore-11.3.0 85) ImageMagick/7.1.0-37-GCCcore-11.3.0 18) OpenMPI/4.1.4-GCC-11.3.0 52) Tcl/8.6.12-GCCcore-11.3.0 86) GLPK/5.0-GCCcore-11.3.0 19) OpenBLAS/0.3.20-GCC-11.3.0 53) SQLite/3.38.3-GCCcore-11.3.0 87) nodejs/16.15.1-GCCcore-11.3.0 20) FlexiBLAS/3.2.0-GCC-11.3.0 54) PCRE2/10.40-GCCcore-11.3.0 88) Python/3.10.4-GCCcore-11.3.0 21) FFTW/3.3.10-GCC-11.3.0 55) NASM/2.15.05-GCCcore-11.3.0 89) netCDF/4.9.0-gompi-2022a 22) gompi/2022a 56) libjpeg-turbo/2.1.3-GCCcore-11.3.0 90) GEOS/3.10.3-GCC-11.3.0 23) FFTW.MPI/3.3.10-gompi-2022a 57) jbigkit/2.1-GCCcore-11.3.0 91) nlohmann_json/3.10.5-GCCcore-11.3.0 24) ScaLAPACK/2.2.0-gompi-2022a-fb 58) libdeflate/1.10-GCCcore-11.3.0 92) PROJ/9.0.0-GCCcore-11.3.0 25) foss/2022a 59) LibTIFF/4.3.0-GCCcore-11.3.0 93) libgeotiff/1.7.1-GCCcore-11.3.0 26) bzip2/1.0.8-GCCcore-11.3.0 60) Java/11.0.16 94) pybind11/2.9.2-GCCcore-11.3.0 27) expat/2.4.8-GCCcore-11.3.0 61) Tk/8.6.12-GCCcore-11.3.0 95) SciPy-bundle/2022.05-foss-2022a 28) libpng/1.6.37-GCCcore-11.3.0 62) cURL/7.83.0-GCCcore-11.3.0 96) libtirpc/1.3.2-GCCcore-11.3.0 29) Brotli/1.0.9-GCCcore-11.3.0 63) GMP/6.2.1-GCCcore-11.3.0 97) HDF/4.2.15-GCCcore-11.3.0 30) freetype/2.12.1-GCCcore-11.3.0 64) NLopt/2.7.1-GCCcore-11.3.0 98) GDAL/3.5.0-foss-2022a 31) ncurses/6.3-GCCcore-11.3.0 65) libogg/1.3.5-GCCcore-11.3.0 99) MPFR/4.1.0-GCCcore-11.3.0 32) util-linux/2.38-GCCcore-11.3.0 66) FLAC/1.3.4-GCCcore-11.3.0 100) libgit2/1.4.3-GCCcore-11.3.0 33) fontconfig/2.14.0-GCCcore-11.3.0 67) libvorbis/1.3.7-GCCcore-11.3.0 101) R/4.2.1-foss-2022a 34) xorg-macros/1.19.3-GCCcore-11.3.0 68) libopus/1.3.1-GCCcore-11.3.0
As you can see not only R itself has been loaded, but also a lot of other modules. These modules are all the tools and libraries this version of R depends on.
One of the issues that you will probably encounter is that if you want to use different modules, and load these, that you run into conflicts with respect to the underlying dependencies. More on this later.
module del/unload
In order to unload a certain module from the environment the unload or equivalent del subcommand can be used:
[username@habrok ~]$ module unload R [username@habrok ~]$ module list Currently Loaded Modules: 1) 2023.01 (S) 35) X11/20220504-GCCcore-11.3.0 69) LAME/3.100-GCCcore-11.3.0 2) StdEnv (S) 36) gzip/1.12-GCCcore-11.3.0 70) libsndfile/1.1.0-GCCcore-11.3.0 3) GCCcore/11.3.0 37) lz4/1.9.3-GCCcore-11.3.0 71) ICU/71.1-GCCcore-11.3.0 4) zlib/1.2.12-GCCcore-11.3.0 38) zstd/1.5.2-GCCcore-11.3.0 72) Szip/2.1.1-GCCcore-11.3.0 5) binutils/2.38-GCCcore-11.3.0 39) libdrm/2.4.110-GCCcore-11.3.0 73) HDF5/1.12.2-gompi-2022a 6) GCC/11.3.0 40) libglvnd/1.4.0-GCCcore-11.3.0 74) UDUNITS/2.2.28-GCCcore-11.3.0 7) numactl/2.0.14-GCCcore-11.3.0 41) libunwind/1.6.2-GCCcore-11.3.0 75) GSL/2.7-GCC-11.3.0 8) XZ/5.2.5-GCCcore-11.3.0 42) LLVM/14.0.3-GCCcore-11.3.0 76) ATK/2.38.0-GCCcore-11.3.0 9) libxml2/2.9.13-GCCcore-11.3.0 43) Mesa/22.0.3-GCCcore-11.3.0 77) Gdk-Pixbuf/2.42.8-GCCcore-11.3.0 10) libpciaccess/0.16-GCCcore-11.3.0 44) libGLU/9.0.2-GCCcore-11.3.0 78) HarfBuzz/4.2.1-GCCcore-11.3.0 11) hwloc/2.7.1-GCCcore-11.3.0 45) pixman/0.40.0-GCCcore-11.3.0 79) FriBidi/1.0.12-GCCcore-11.3.0 12) OpenSSL/1.1 46) libffi/3.4.2-GCCcore-11.3.0 80) Pango/1.50.7-GCCcore-11.3.0 13) libevent/2.1.12-GCCcore-11.3.0 47) gettext/0.21-GCCcore-11.3.0 81) GTK2/2.24.33-GCCcore-11.3.0 14) UCX/1.12.1-GCCcore-11.3.0 48) PCRE/8.45-GCCcore-11.3.0 82) Ghostscript/9.56.1-GCCcore-11.3.0 15) libfabric/1.15.1-GCCcore-11.3.0 49) GLib/2.72.1-GCCcore-11.3.0 83) JasPer/2.0.33-GCCcore-11.3.0 16) PMIx/4.1.2-GCCcore-11.3.0 50) cairo/1.17.4-GCCcore-11.3.0 84) LittleCMS/2.13.1-GCCcore-11.3.0 17) UCC/1.0.0-GCCcore-11.3.0 51) libreadline/8.1.2-GCCcore-11.3.0 85) ImageMagick/7.1.0-37-GCCcore-11.3.0 18) OpenMPI/4.1.4-GCC-11.3.0 52) Tcl/8.6.12-GCCcore-11.3.0 86) GLPK/5.0-GCCcore-11.3.0 19) OpenBLAS/0.3.20-GCC-11.3.0 53) SQLite/3.38.3-GCCcore-11.3.0 87) nodejs/16.15.1-GCCcore-11.3.0 20) FlexiBLAS/3.2.0-GCC-11.3.0 54) PCRE2/10.40-GCCcore-11.3.0 88) Python/3.10.4-GCCcore-11.3.0 21) FFTW/3.3.10-GCC-11.3.0 55) NASM/2.15.05-GCCcore-11.3.0 89) netCDF/4.9.0-gompi-2022a 22) gompi/2022a 56) libjpeg-turbo/2.1.3-GCCcore-11.3.0 90) GEOS/3.10.3-GCC-11.3.0 23) FFTW.MPI/3.3.10-gompi-2022a 57) jbigkit/2.1-GCCcore-11.3.0 91) nlohmann_json/3.10.5-GCCcore-11.3.0 24) ScaLAPACK/2.2.0-gompi-2022a-fb 58) libdeflate/1.10-GCCcore-11.3.0 92) PROJ/9.0.0-GCCcore-11.3.0 25) foss/2022a 59) LibTIFF/4.3.0-GCCcore-11.3.0 93) libgeotiff/1.7.1-GCCcore-11.3.0 26) bzip2/1.0.8-GCCcore-11.3.0 60) Java/11.0.16 94) pybind11/2.9.2-GCCcore-11.3.0 27) expat/2.4.8-GCCcore-11.3.0 61) Tk/8.6.12-GCCcore-11.3.0 95) SciPy-bundle/2022.05-foss-2022a 28) libpng/1.6.37-GCCcore-11.3.0 62) cURL/7.83.0-GCCcore-11.3.0 96) libtirpc/1.3.2-GCCcore-11.3.0 29) Brotli/1.0.9-GCCcore-11.3.0 63) GMP/6.2.1-GCCcore-11.3.0 97) HDF/4.2.15-GCCcore-11.3.0 30) freetype/2.12.1-GCCcore-11.3.0 64) NLopt/2.7.1-GCCcore-11.3.0 98) GDAL/3.5.0-foss-2022a 31) ncurses/6.3-GCCcore-11.3.0 65) libogg/1.3.5-GCCcore-11.3.0 99) MPFR/4.1.0-GCCcore-11.3.0 32) util-linux/2.38-GCCcore-11.3.0 66) FLAC/1.3.4-GCCcore-11.3.0 100) libgit2/1.4.3-GCCcore-11.3.0 33) fontconfig/2.14.0-GCCcore-11.3.0 67) libvorbis/1.3.7-GCCcore-11.3.0 34) xorg-macros/1.19.3-GCCcore-11.3.0 68) libopus/1.3.1-GCCcore-11.3.0
As you can see R has been removed from the environment. This is not true, however, for the dependencies that were loaded as well. In most cases the unload or del subcommand is therefore not very useful.
module purge
In order to completely clear the list of loaded modules the subcommand purge must be used. This is an effective way of making sure all modules are gone, before loading a new package.
[username@habrok ~]$ module purge The following modules were not unloaded: (Use "module --force purge" to unload all): 1) 2023.01 2) StdEnv [username@habrok ~]$ module list Currently Loaded Modules: 1) 2023.01 (S) 2) StdEnv (S) Where: S: Module is Sticky, requires --force to unload or purge [username@habrok ~]$
Note that, even with purge, it will not unload the two default modules StdEnv and 2023.01, as you will lose access to all modules in that case. If you do really want to unload those ones as well, you can use module –force purge. In order to regain access to the modules of the 2023.01 software stack later on, you can use module load 2023.01.
module save
If you have a set of modules that you need to use more often, you can save this set into a configuration which is stored for reuse later. This can be done using the subcommand restore.
[username@habrok ~]$ module load BLAST+/2.13.0-gompi-2022a [username@habrok ~]$ module load Stacks/2.62-foss-2022a [username@habrok ~]$ module save my_favorite_modules Saved current collection of modules to: "my_favorite_modules" [username@habrok ~]$
module restore
In order to restore a set of saved modules into the environment the subcommand restore has to be used:
[username@habrok ~]$ module purge The following modules were not unloaded: (Use "module --force purge" to unload all): 1) 2023.01 2) StdEnv [username@habrok ~]$ module list Currently Loaded Modules: 1) 2023.01 (S) 2) StdEnv (S) Where: S: Module is Sticky, requires --force to unload or purge [username@habrok ~]$ module restore my_favorite_modules Restoring modules from user's my_favorite_modules [username@habrok ~]$ module list Currently Loaded Modules: 1) 2023.01 (S) 13) libevent/2.1.12-GCCcore-11.3.0 25) libpng/1.6.37-GCCcore-11.3.0 2) StdEnv (S) 14) UCX/1.12.1-GCCcore-11.3.0 26) NASM/2.15.05-GCCcore-11.3.0 3) GCCcore/11.3.0 15) libfabric/1.15.1-GCCcore-11.3.0 27) libjpeg-turbo/2.1.3-GCCcore-11.3.0 4) zlib/1.2.12-GCCcore-11.3.0 16) PMIx/4.1.2-GCCcore-11.3.0 28) LMDB/0.9.29-GCCcore-11.3.0 5) binutils/2.38-GCCcore-11.3.0 17) UCC/1.0.0-GCCcore-11.3.0 29) BLAST+/2.13.0-gompi-2022a 6) GCC/11.3.0 18) OpenMPI/4.1.4-GCC-11.3.0 30) OpenBLAS/0.3.20-GCC-11.3.0 7) numactl/2.0.14-GCCcore-11.3.0 19) gompi/2022a 31) FlexiBLAS/3.2.0-GCC-11.3.0 8) XZ/5.2.5-GCCcore-11.3.0 20) bzip2/1.0.8-GCCcore-11.3.0 32) FFTW/3.3.10-GCC-11.3.0 9) libxml2/2.9.13-GCCcore-11.3.0 21) PCRE/8.45-GCCcore-11.3.0 33) FFTW.MPI/3.3.10-gompi-2022a 10) libpciaccess/0.16-GCCcore-11.3.0 22) ICU/71.1-GCCcore-11.3.0 34) ScaLAPACK/2.2.0-gompi-2022a-fb 11) hwloc/2.7.1-GCCcore-11.3.0 23) Boost/1.79.0-GCC-11.3.0 35) foss/2022a 12) OpenSSL/1.1 24) GMP/6.2.1-GCCcore-11.3.0 36) Stacks/2.62-foss-2022a [username@habrok ~]$
Next section: Transferring data