On eRI we make software available using environment modules, sometime also referred to as lmod. This article describes how to use the module command to find, load and purge software.
Environment Modules
Modules are a convenient way to provide access to applications on the cluster. They prepare the environment you need to run an application.
For a full list of module commands run man module or visit the lmod documentation here.
| Lists all available modules. |
| Searches available modules for [module name] |
| Shows information about [module name] |
| Loads [module name] |
| Lists currently loaded modules. |
| Purge (remove) all modules from your environment |
For example, if you want to use the R programming language you would:
...
This will load all of the software and dependencies required to run Rversion 4.3.2. To see the list of software loaded when you run the above command you can run the module list command:
| Code Block |
|---|
...
ASReml/4.2.1.206 SQLite/3.42.0-GCCcore-12.3.0 (L) Apptainer/1.2.5 SWIG/3.0.8 Arrow/14.0.1-GCC-12.3.0 (L) ScaLAPACK/2.2.0-gompi-2023a-fb (L) BCL-Convert/4.2.4 Szip/2.1.1-GCCcore-12.3.0 (L) BLASTDB/2024-04 Tcl/8.6.10-GCCcore-12.3.0 BLIS/0.9.0-GCC-12.3.0 |
...
TeXLive/2022 BLIS/4.1-GCC-12.3.0-amd (D) Tk/8.6.10-GCCcore-12.3.0 Boost/1.83.0-GCC-12.3.0 UCC/1.2.0-GCCcore-12.3.0 (L) |
...
CMake/3.27.7 UCX/1.14.1-GCCcore-12.3.0 (L) CUDA/11.8.0 UDUNITS/2.2.28-GCCcore-12.3.0 (L) Canu/2.2-GCC-12.3.0 XZ/5.4.2-GCCcore-12.3.0 |
...
(L) EasyBuild/4.8.1 ZeroMQ/4.3.5-GCCcore-12.3.0 EasyBuild/4.9.2 (D) ant/1.10.9-Java-17 FFTW.MPI/3.3.10-gompi-2023a (L) binutils/2.40-GCCcore-12.3.0 (L) FFTW/3.3.10-GCC-12.3.0 (L) binutils/2.40 (D) FlexiBLAS/3.3.1-GCC-12.3.0 (L) bzip2/1.0.8-GCCcore-12.3.0 |
...
(L) |
...
FriBidi/1 |
...
.0.12-GCC-12.3.0 cURL/8.3.0-GCCcore-12.3.0 |
...
(L) GCC/12.3.0 |
...
(L) cuDNN/8.6.0.163-CUDA-11.8.0 GCCcore/12.3.0 (L) expat/2.5.0-GCCcore-12.3.0 (L) GDAL/3.6.4-gompi-2023a (L) fontconfig/2.14.2-GCCcore-12.3.0 GEOS/3.11.3-GCC-12.3.0 |
...
(L) foss/2023a (L) GLib/2.78.1-GCC-12.3.0 freetype/2.13.2-GCCcore-12.3.0 |
...
|
...
GMP/6.2.1-GCCcore-12.3.0 (L) gettext/0.21-GCCcore-12.3.0 |
...
Go/1.22.3 gompi/2023a (L) HDF5/1.14.3-gompi-2023a (L) gperf/3.1 HarfBuzz/4.4.1-GCC-12.3.0 gquery-dev/0.7.0 IGV/2.17.4 gquery-dev/0.8.1 IRkernel/1.3.2-foss-2023a-R-4.3.2 gquery-dev/0.9.0 IRkernel/1.3.2-foss-2023a-R-4.3.3 (D) gquery-dev/0.9.1 Java/17 gquery-dev/0.9.2 (D) Java/20.0.2 (L,D) gquery-test/0.8.1 Julia/1.10.1-GCC-12.3.0-VTune gquery-test/0.9.0 JupyterLab/2023.11.0-foss-2023a-3.6.3 gquery-test/0.9.1 JupyterLab/2024.05.0-foss-2023a-4.2.0 (D) gquery-test/0.9.2 (D) KEALib/1.5.2-gompi-2023a (L) gquery/0.8.1 LLVM/14.0.6-GCC-12.3.0-static gquery/0.9.0 LibTIFF/4.4.0-GCCcore-12.3.0 gquery/0.9.1 LibTIFF/4.5.1-GCCcore-12.3.0 (L,D) gquery/0.9.2 (D) Meson/0.62.1 graphite2/1.3.14 Miniconda3/23.10.0-1 json-c/0.17-GCC-12.3.0 (L) NASM/2.15.05 libKML/1.3.0.2017-GCC-12.3.0 |
...
(L) NLopt/2.7.1-GCC-12.3.0 (L) libffi/3.4.6 NanoPlot/1.43.0-foss-2023a-Python-3.11.6 libgd/2.3.3-GCCcore-12.3.0 Nextflow/24.04.2 libgeotiff/1.7.1-GCC-12.3.0-PROJ-9.3.0 (L) Ninja/1.11.1 libgit2/1.6.4-GCC-12.3.0 (L) OpenBLAS/0.3.23-GCC-12.3.0 |
...
(L) libjpeg-turbo/2.1.5.1-GCCcore-12.3.0 |
...
(L) |
...
OpenJPEG/2.5.0-GCCcore-12.3.0 (L) libpng/1.6.40-GCCcore-12.3.0 (L) OpenMPI/4.1.5-GCC-12.3.0 |
...
(L) |
...
libreadline/8.2-GCCcore-12.3.0 (L) OpenSSL/1.1 (L) libxml2/2.11.4-GCCcore-12.3.0 (L) OpenSSL/3.3.1-GCCcore-12.3.0 (D) libxslt/1.1.38-GCCcore-12.3.0 PCRE2/10.42-GCCcore-12.3.0 (L) lz4/1.9.4-GCCcore-12.3.0 (L) PROJ/9.3.0-GCC-12.3.0 |
...
(L) nanoget/1.19.3-foss-2023a-Python-3.11.6 |
...
Perl/5.38.2-GCC-12.3.0 ncurses/6.4-GCCcore-12.3.0 (L) PostgreSQL/14.12-GCC-12.3.0 netCDF/4.9.2-gompi-2023a (L) Python/3.11.6-foss-2023a |
...
nodejs/18.18.2-GCCcore-12.3.0 |
...
(L) |
...
R-Geo/4.3.2-foss-2023a nullarbor/2.0.20191013 R/4.3.2-foss-2023a |
...
(D) numactl/2. |
...
0. |
...
16-GCCcore-12.3.0 |
...
(L) R/4.3.3-foss-2023a pixman/0.42.2-GCC-12.3.0 R/4.4.0-foss-2023a snakemake/7.32.3-foss-2023a-Python-3.11.6 R/4.4.1-foss-2023a (L) snakemake/8.14.0-foss-2023a-Python-3.11.6 (D) RStudio-Server/2023.12.0-369 snappy/1.1.10-GCCcore-12.3.0 |
...
(L) RStudio-Server/2024.04.2-764 (D) yaml-cpp/0.8.0-GCC-12.3.0 |
...
|
...
Rust/1.73.0 |
...
-GCC-12.3.0 |
...
zlib/1.2.13-GCCcore-12.3.0 (L) SAMtools/0.1.19-GCCcore-12.3.0 |
...
zlib/1.2.13 (D) SOCI/4.0.3-GCC-12.3.0 |
...
|
...
zstd/1.5. |
...
5-GCCcore-12.3.0 |
...
(L) |
...
SPAdes/4. |
...
0. |
...
0-foss-2023a-Python-3.11.6 |
Working with containers
Singularity
Available as Apptainer and aliasing enabled, both apptainer --version and singularity --version will work. There are NeSI/Mahuika based notes on building containers HERE
Example
| Code Block |
|---|
# QIIME1 module purge module |
...
load |
...
Apptainer/ |
...
1.2.5
# recent Apptainer modules set APPTAINER_BIND, which typically breaks
# container builds, so unset it here
unset APPTAINER_BIND
# create a build and cache directory on scratch storage
export APPTAINER_CACHEDIR="/agr/scratch/projects/<YOURPROJECT>/$USER/apptainer_cache"
export APPTAINER_TMPDIR="/agr/scratch/projects/<YOURPROJECT>/$USER/apptainer_tmpdir"
mkdir -p $APPTAINER_CACHEDIR $APPTAINER_TMPDIR
setfacl -b $APPTAINER_TMPDIR
# pull the container
apptainer pull docker://mgrast/qiime:1.0
# execute the container
apptainer exec qiime_1.0.sif align_seqs.py -h |