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Software on the ECC Cluster

Software on the ECC Cluster

The ECC cluster provides a variety of software packages through the Lmod module system, along with additional software installed via Spack. We also support Apptainer for containerized workflows.

Checking Available Software

Using Lmod

The cluster uses Lmod for managing software modules. To see the available software, use:

Command to list available software modules
module avail [XXXXX@ecc-login001]$ module avail ------------------------------------------------------------------------------------------------------------ /opt/ohpc/pub/moduledeps/gnu14 ------------------------------------------------------------------------------------------------------------- mpich/3.4.3-ucx openmpi5/5.0.5 (L) --------------------------------------------------------------------------------------------------------------- /opt/ohpc/pub/modulefiles --------------------------------------------------------------------------------------------------------------- EasyBuild/4.9.4 autotools (L) cmake/3.24.2 gnu14/14.2.0 (L) hwloc/2.11.1 (L) libfabric/1.18.0 (L) ohpc (L) os prun/2.2 (L) spack/0.22.2 ucx/1.17.0 (L) ------------------------------------------------------------------------------------------------------ /share/apps/Intel/intel-oneapi-modulefiles ------------------------------------------------------------------------------------------------------- advisor/latest compiler-intel-llvm/latest compiler/latest dev-utilities/latest dpct/latest intel_ipp_intel64/latest mkl/latest tbb/latest vtune/latest advisor/2025.0 (D) compiler-intel-llvm/2025.0.4 (D) compiler/2025.0.4 (D) dev-utilities/2025.0.0 (D) dpct/2025.0.0 (D) intel_ipp_intel64/2022.0 (D) mkl/2025.0 (D) tbb/2022.0 (D) vtune/2025.0 (D) ccl/latest compiler-rt/latest debugger/latest dnnl/latest dpl/latest intel_ippcp_intel64/latest mpi/latest umf/latest ccl/2021.14.0 (D) compiler-rt/2025.0.4 (D) debugger/2025.0.0 (D) dnnl/3.6.1 (D) dpl/2022.7 (D) intel_ippcp_intel64/2025.0 (D) mpi/2021.14 (D) umf/0.9.1 (D) ------------------------------------------------------------------------------------------------------------------ /share/modulefiles ------------------------------------------------------------------------------------------------------------------- ecc/Miniconda3/25.1.1 ecc/conda/astra-toolbox/2.3.0 ecc/conda/python/3.10 ecc/conda/python/3.13 (D) ecc/cuda/2.8.0_570.86.10 ecc/rclone/v1.69.1 ecc/spack/0.23.1

To load a specific module:

Command to load a software module
module load <software_name>

Additional Software with Spack

For additional software not listed under module avail, use Spack. First, load the Spack environment:

Command to load Spack module
module load ecc/spack/0.23.1

Then check the available software under spack:

Command output showing available modules after loading Spack
module avail [@ecc-login001]$module avail ------------------------------------------------------------------------------------------ /share/apps/spack/0.23.1/share/spack/lmod/linux-rocky9-x86_64/Core ------------------------------------------------------------------------------------------- apptainer/1.3.6-m6hnups ed/1.4-d75cfoj go-bootstrap/1.22.12-xvd4k4k libsigsegv/2.14-spllta5 ncurses/6.5-z2573q4 py-setuptools/75.8.0-4dxxr3z texinfo/7.1-iyakqqc autoconf-archive/2023.02.20-ahlsld7 elfutils/0.192-q5d3m4s go-md2man/2.0.4-ftvpvie libtool/2.4.7-2svv5hd nghttp2/1.65.0-v2gd5mh py-wheel/0.41.2-4cdx5b6 unzip/6.0-ebi33lt autoconf/2.72-zy6mwqs expat/2.6.4-lcbmurn go/1.24.1-2jd2nwt libxcrypt/4.4.35-jcn5b6x ninja/1.12.1-kzm7xfa python-venv/1.0-kwpudmz util-linux-uuid/2.40.2-zk24zrc automake/1.16.5-fkyrakr findutils/4.10.0-yvvjv5v gocryptfs/2.5.1-v2gymf4 libxml2/2.13.5-7g525gy openjdk/21.0.0_35-7nsiyk5 python/3.13.2-wffxwpz wget/1.24.5-garqeqe bash/5.2-hongnnw fuse-overlayfs/1.14-ititwgk gperf/3.1-j763b46 lmod/8.7.55-tp6ijtl openssl/3.4.0-lxrxzsd re2c/3.1-xgejedw xz/5.6.3-k5f73ju bc/1.07.1-ne47k3j gawk/5.3.1-q5vwnhj grep/3.11-xrgztxr lua-luafilesystem/1.8.0-m5guucv p7zip/17.05-ouotjju readline/8.2-lwudtej zlib-ng/2.2.3-sxmihjh berkeley-db/18.1.40-j2xirp7 gcc-runtime/14.2.0-b5th2zu libbsd/0.12.2-uw46wao lua-luaposix/36.1-ortpxco patch/2.7.6-toq5cve sed/4.9-xxiyao4 zstd/1.5.6-hqwwnoo bzip2/1.0.8-egdsitg gdbm/1.23-el5472r libffi/3.4.6-2kgdjpd lua/5.4.6-rnkjraq pcre2/10.44-yeggcq2 sqlite/3.46.0-bly5z3p ca-certificates-mozilla/2025-02-25-qvj4bzn gettext/0.23.1-72hd44g libfuse/3.16.2-jbrwmmg lz4/1.10.0-zj2ikmx perl/5.40.0-guz5eqa squashfs/4.6.1-4o52ihm conmon/2.1.12-ylepixw glib/2.82.5-xkmtvca libgpg-error/1.51-c53uidd lzo/2.10-r7o3guq pigz/2.8-ujmrllr squashfuse/0.5.2-uftfvbu curl/8.11.1-qp6lw6o glibc/2.34-p655cco libiconv/1.17-fwcdydv m4/1.4.19-vpjm4dl pkgconf/2.3.0-4b7jgan sshfs/3.7.1-g5xtfg2 diffutils/3.10-zpcrnp4 gmake/4.4.1-dt27iqy libmd/1.1.0-wpow76p meson/1.7.0-s2mdkp3 py-cython/3.0.11-hnwne7a tar/1.35-ijj6cx7 e2fsprogs/1.47.1-bsrw3yg gmp/6.3.0-iuzvzxr libseccomp/2.6.0-btjoyag mpfr/4.2.1-hceguny py-pip/24.3.1-kvdh2at tcl/8.6.12-wmwtihr ------------------------------------------------------------------------------------------------------------ /opt/ohpc/pub/moduledeps/gnu14 ------------------------------------------------------------------------------------------------------------- mpich/3.4.3-ucx openmpi5/5.0.5 (L) --------------------------------------------------------------------------------------------------------------- /opt/ohpc/pub/modulefiles --------------------------------------------------------------------------------------------------------------- EasyBuild/4.9.4 autotools (L) cmake/3.24.2 gnu14/14.2.0 (L) hwloc/2.11.1 (L) libfabric/1.18.0 (L) ohpc (L) os prun/2.2 (L) spack/0.22.2 ucx/1.17.0 (L) ------------------------------------------------------------------------------------------------------ /share/apps/Intel/intel-oneapi-modulefiles ------------------------------------------------------------------------------------------------------- advisor/latest compiler-intel-llvm/latest compiler/latest dev-utilities/latest dpct/latest intel_ipp_intel64/latest mkl/latest tbb/latest vtune/latest advisor/2025.0 (D) compiler-intel-llvm/2025.0.4 (D) compiler/2025.0.4 (D) dev-utilities/2025.0.0 (D) dpct/2025.0.0 (D) intel_ipp_intel64/2022.0 (D) mkl/2025.0 (D) tbb/2022.0 (D) vtune/2025.0 (D) ccl/latest compiler-rt/latest debugger/latest dnnl/latest dpl/latest intel_ippcp_intel64/latest mpi/latest umf/latest ccl/2021.14.0 (D) compiler-rt/2025.0.4 (D) debugger/2025.0.0 (D) dnnl/3.6.1 (D) dpl/2022.7 (D) intel_ippcp_intel64/2025.0 (D) mpi/2021.14 (D) umf/0.9.1 (D) ------------------------------------------------------------------------------------------------------------------ /share/modulefiles ------------------------------------------------------------------------------------------------------------------- ecc/Miniconda3/25.1.1 ecc/conda/astra-toolbox/2.3.0 ecc/conda/python/3.10 ecc/conda/python/3.13 (D) ecc/cuda/2.8.0_570.86.10 ecc/rclone/v1.69.1 ecc/spack/0.23.1 (L)

 

Using Conda for Environment Management

We provide Miniconda via Lmod, allowing users to create and manage their own Conda environments.

Loading Conda

To enable Conda, load the Miniconda module:

Command to load Miniconda module
module load ecc/Miniconda3/25.1.1

Creating and Using Conda Environments

To create a new Conda environment:

Command to create a new Conda environment
conda create --name myenv python=3.9

Activate your environment:

Command to activate a Conda environment
conda activate myenv

To install additional packages in your conda env:

Command to install packages in Conda environment
conda install numpy pandas scipy

To deactivate your environment:

Command to deactivate a Conda environment
conda deactivate

Installing Packages in Your Home Directory

By default, Conda environments are stored in ~/.conda/envs/. If you need to install packages in a specific location due to storage constraints, you can specify a different environment location:

Commands to create and activate Conda environment in custom location
conda create --prefix /path/to/custom/env python=3.9 conda activate /path/to/custom/env

Using Apptainer (Containerized Workflows)

The ECC cluster supports Apptainer (formerly Singularity). If you previously used Singularity, you should now transition to Apptainer.

Loading Apptainer

To use Apptainer, first load Spack, then load the Apptainer module:

Commands to load Spack and Apptainer modules
module load ecc/spack/0.23.1 module load apptainer/1.3.6-m6hnups

Once loaded, you can use Apptainer as you would use Singularity.

Example Slurm Job Submission Scripts

For reference, for example, Slurm job submission scripts are available at:

Path to example Slurm job scripts directory
/share/examples/ecc/

These scripts include templates for running jobs with modules, Spack, and Apptainer.

If you need additional software or support, please contact the ECC support team by opening a ticket at https://ukyrcd.atlassian.net/servicedesk/customer/portal/4/group/14/create/49

 

Center for Computational Sciences