# Software List List of software centrally available via the modules tool at the INCD Cirrus HPC and HTC clusters as of **August 2022**. Full list changes and to request the installation of additional software contact the INCD support **[helpdesk](/books/user-support/page/helpdesk)**. **Intel Compilers available** Users can also install software on their own for further information see the section on **[User Software Installation](https://wiki.incd.pt/books/software/chapter/user-software-installation)**. Execution of user defined software environments (operating system and libraries) using Linux containers in the HPC and HTC clusters with **[uDocker](https://github.com/indigo-dc/udocker)** and **[Singularity](https://sylabs.io/docs/)** is also supported. ### INCD-Lisbon HPC and HTC cluster (Cirrus-A) #### AlmaLinux 8 ``` [jpina@cirrus01 ~]$ module avail --------------------------------------------------------------------------------------------------------------- /cvmfs/sw.el8/modules/hpc/main --------------------------------------------------------------------------------------------------------------- R/4.4.3 (D) gcc-11.3 gcc-8.5 julia/1.9.4 julia/1.11.4 (D) matlab-runtime/9.0.1 python/3.7 python/3.11 (D) spack/0.19.1 udocker/1.3.16 aoc-4.0.0 gcc-13.2 intel/oneapi/2023 julia/1.10.5 matlab-runtime/R2016a matlab-runtime/24.1 (D) python/3.8 qgis/3.40.5 spack/0.21.1 (D) udocker/1.3.17 (D) bazelisk/1.22.0 gcc-14.1 julia/1.6.7 julia/1.11.0 matlab-runtime/R2024a opam python/3.10 qgis/3.44.2 (D) spark/3.1.1 -------------------------------------------------------------------------------------------------------------- /cvmfs/sw.el8/modules/hpc/aoc40 --------------------------------------------------------------------------------------------------------------- aoc40/R/4.2.2 aoc40/gromacs/2023 aoc40/libs/blas/3.11.0 aoc40/libs/gsl/2.7 aoc40/libs/jemalloc/5.3.0 aoc40/libs/libpng/1.6.39 aoc40/libs/openblas/0.3.21 aoc40/openmpi/4.1.4 aoc40/gamess/2023-R2 aoc40/libs/aocl/4.0 aoc40/libs/fftw/3.3.10 aoc40/libs/hdf5/1.14.0 aoc40/libs/lapack/3.11.0 aoc40/libs/nlopt/2.7.1 aoc40/mvapich2/2.3.7 -------------------------------------------------------------------------------------------------------------- /cvmfs/sw.el8/modules/hpc/gcc85 --------------------------------------------------------------------------------------------------------------- gcc85/R/4.2.2 gcc85/libs/gsl/2.7 gcc85/libs/lapack/3.11.0 gcc85/libs/openblas/0.3.21 gcc85/netcdf-cxx/4.2 gcc85/openfoam-org/11 gcc85/plumed/2.9.0 gcc85/libs/blas/3.11.0 gcc85/libs/hdf5/1.14.0 gcc85/libs/libpng/1.6.39 gcc85/mvapich2/2.3.7 gcc85/netcdf-cxx4/4.3.1 gcc85/openfoam/2306 gcc85/spin/6.5.1 gcc85/libs/fftw/3.3.10 gcc85/libs/jemalloc/5.3.0 gcc85/libs/nlopt/2.7.1 gcc85/netcdf-c/4.9.0 gcc85/netcdf-fortran/4.6.0 gcc85/openmpi/4.1.4 -------------------------------------------------------------------------------------------------------------- /cvmfs/sw.el8/modules/hpc/gcc11 --------------------------------------------------------------------------------------------------------------- gcc11/R/4.2.2 gcc11/gromacs/2022.5 gcc11/libs/boost/1.80.0 gcc11/libs/jemalloc/5.3.0 gcc11/libs/openblas/0.3.21 gcc11/netcdf-cxx4/4.3.1 gcc11/openfoam-org/10 (D) gcc11/paraview/5.10.1 gcc11/slim/4.2.2 gcc11/cp2k/2023.1 gcc11/gromacs/2023 (D) gcc11/libs/fftw/3.3.10 gcc11/libs/lapack/3.11.0 gcc11/mvapich2/2.3.7 gcc11/netcdf-fortran/4.6.0 gcc11/openfoam/2012 gcc11/pfft/1.0.8 gcc11/slim/5.0 (D) gcc11/gromacs/2020.4 gcc11/keras/2.10.0 gcc11/libs/gsl/2.7 gcc11/libs/libpng/1.6.39 gcc11/netcdf-c/4.9.0 gcc11/ngspice/37 gcc11/openfoam/2206 (D) gcc11/plumed/2.8.0 gcc11/gromacs/2021.4 gcc11/libs/blas/3.11.0 gcc11/libs/hdf5/1.14.0 gcc11/libs/nlopt/2.7.1 gcc11/netcdf-cxx/4.2 gcc11/openfoam-org/2.4.0 gcc11/openmpi/4.1.4 gcc11/plumed/2.9.0 (D) -------------------------------------------------------------------------------------------------------------- /cvmfs/sw.el8/modules/hpc/gcc13 --------------------------------------------------------------------------------------------------------------- gcc13/arpack/3.9.1 gcc13/brams/6.0.0 gcc13/foam-extend/4.1 gcc13/libs/hdf5/1.14.3 gcc13/netcdf-c/4.9.2 gcc13/openfoam/2206 gcc13/openmpi/4.1.6 gcc13/spooles/2.2 gcc13/xbeach/1.24.6057 gcc13/blas/3.12.0 gcc13/calculix/2.20 gcc13/gromacs/2020.4 gcc13/mooring gcc13/netcdf-fortran/4.6.1 gcc13/openfoam/2306 gcc13/petsc/3.22 gcc13/vtk/9.4.1 gcc13/xbeach/1.24.6088M (D) gcc13/boost/1.86.0 gcc13/eigen3/3.4.0 gcc13/lapack/3.12.0 gcc13/mvapich2/2.3.7 gcc13/openblas/0.3.28 gcc13/openfoam/2406 (D) gcc13/precice/3.1.2 gcc13/xbeach/1.23.5960 -------------------------------------------------------------------------------------------------------------- /cvmfs/sw.el8/modules/hpc/intel --------------------------------------------------------------------------------------------------------------- gmxMMPBSA/1.6.3 intel/libs/blas/3.11.0 intel/libs/hdf5/1.14.0 intel/libs/lapack/3.11.0 intel/mvapich2/2.3.7 intel/netcdf-cxx4/4.3.1 intel/openfoam-org/11 intel/openmpi/4.1.4 intel/castep/24.1 intel/libs/fftw/3.3.10 intel/libs/hdf5/1.14.3 (D) intel/libs/libpng/1.6.39 intel/netcdf-c/4.9.2 intel/netcdf-fortran/4.6.1 intel/openfoam/2306 intel/openmpi/4.1.6 (D) intel/gamess/2023-R2 intel/libs/gsl/2.7 intel/libs/jemalloc/5.3.0 intel/libs/nlopt/2.7.1 intel/netcdf-cxx/4.2 intel/nwchem/nwchem-7.2.2 intel/openfoam/2506 (D) ----------------------------------------------------------------------------------------------------------------- /cvmfs/sw.el8/modules/gpu ------------------------------------------------------------------------------------------------------------------ cuda/10.2 cuda/11.2 cuda/11.8 cuda/12.1 cuda/12.6 (D) nvhpc-byo-compiler/23.1 nvhpc-nompi/23.1 nvhpc/23.1 tensorflow/2.14.0 tensorflow/2.18.0 tensorflow/2.19.0 (D) ----------------------------------------------------------------------------------------------------------------- /cvmfs/sw.el8/modules/bio ------------------------------------------------------------------------------------------------------------------ R/4.2.2 bcftools/1.8 bowtie2/2.5.1 (D) fastqc/0.11.9 grenepipe/0.14.0 igv/2.12.3 orca/6.0.1 raxml/8.2.12 star/2.7.6a trinity/2.14.0 R/4.4.3 beagle/5.4 bwa/0.7.17 fastqc/0.12.1 (D) grenepipe/0.15.0 (D) iqtree2/2.1.2 orca/shared/5.0.4 salmon/1.10.3 star/2.7.10b (D) vcftools/0.1.14 admixture/1.3.0 bismark/0.23.0 chimera/1.18 figtree/0.12.1 hisat2/2.2.1 iqtree2/2.2.2 (D) orca/static/5.0.4 samtools/1.8 stringtie/3.0.0 vcftools/0.1.16 (D) alphafold/2.3.2 bismark/0.24.1 (D) chromopainter/0.0.4 figtree/1.4.3 (D) hmmer/3.3.2 jellyfish/2.3.1 picard/3.1.1 samtools/1.17 (D) suitesparse/7.8.2 vina-gpu/2.1 alphapulldown/2.0.1 blast-plus/2.12.0 cutadapt/4.4 finestructure/4.1.1 hmmer/3.4 (D) kallisto/0.50.1 plink/1.07 sickle/1.33 transdecoder/5.5.0 autodock-gpu-develop/11.3.0 blast-plus/2.14.1 (D) eigensoft/8.0.0 freebayes/1.3.6 htslib/1.8 mrbayes/3.2.7a plink2/2.00a4.3 sratoolkit/3.0.0 transdecoder/5.7.1 (D) autodock-vina/1.2.3 bowtie2/2.4.2 evigene/23.7.15 gatk/4.5.0.0 htslib/1.17 (D) openbabel/3.0.0 popoolation2/1.201 stAIcalc trimgalore/0.6.10 ----------------------------------------------------------------------------------------------------------------- /cvmfs/sw.el8/modules/LIP ------------------------------------------------------------------------------------------------------------------ gcc11/geant/4.10.7.3 gcc11/topas/3.9 gcc85/gdcm/2.8.9 gcc85/geant/4.10.7.3 gcc85/root/6.24.06 gcc85/root/6.28.10 gcc85/root/6.30.04 (D) madgraph/2.9.14 ``` * If software required not listed please ask INCD support #### Access and Middleware Besides conventional login using SSH, the cirrus-A computing resources can be accessed via middleware using the [Unified Middleware Distribution](https://wiki.egi.eu/wiki/Middleware) through the EGI and IBERGRID distributed computing infrastructures. ### INCD-D HPC and HTC cluster (Cirrus-D) #### Almalinux 8 ``` [jpina@cirrus01 ~]$ module avail ------------------------------------------------------------------------------ /cvmfs/sw.el7/modules/hpc ------------------------------------------------------------------------------ DATK gcc-6.3 gcc83/gromacs/2021.2 intel/openfoam/1906 python-2.7.11 aoc22/libs/openblas/0.3.10 gcc-7.3 gcc83/iqtree2/2.1.3 intel/openfoam/2012 python-3.5.1 aoc22/openmpi/4.0.3 gcc-7.4 gcc83/libs/gsl/2.6 intel/openfoam/2112 (D) python-3.5.4 aocc/2.2.0 gcc-7.5 gcc83/mvapich2/2.3.5 intel/openmpi/4.0.3 python/3.7.2 aocl/2.2 gcc-8.3 gcc83/nlopt/2.6.2 intel/openmpi/4.1.1 (D) python/3.9.12 (D) aster-13.1.0 gcc55/openmpi/4.0.3 gcc83/openmpi/4.0.3 intel/swan/41.31 r-3.2.5 autodock/4.2.6 gcc63/fftw/3.3.9 gcc83/openmpi/4.1.1 (D) kallisto-0.43.0 r-3.5.2 beast/1.10.4 gcc63/libs/blas/3.9.0 gcc83/prover9/2009-11A libs/32/jemalloc/5.3.0 r-3.6.3 blat-36.2 gcc63/libs/gsl/2.6 git/2.9.5 libs/blas/3.9.0 r-4.0.2 boost-1.55 gcc63/libs/lapack/3.9.0 gromacs-4.6.7 libs/gsl/2.6 sbcl-1.3.4 bowtie2-2.3.0 gcc63/libs/libpng/1.6.37 hdf4/4.2.15 libs/jemalloc/5.3.0 sicer-1.1 clang/7.0.0 gcc63/libs/openblas/0.3.10 hdf5-1.8.16 libs/lapack/3.9.0 star-2.5.2b clang/ngspice/30 gcc63/mpich-3.2 hdf5/1.12.0 libs/libpng/1.6.37 tensorflow/2.4.1 clang/openmpi/4.0.3 gcc63/mvapich2/2.3.5 homer-4.8 libs/openblas/0.3.10 tensorflow/2.7.0 (D) cmake/3.5.2 gcc63/netcdf-fortran/4.4.4 hwloc/2.1.0 macs-1.4.2 trimmomatic-0.33 cmake/3.11.2 gcc63/netcdf-fortran/4.5.2 (D) intel/2019 matlab/R2018a udocker/1.1.3 cmake/3.17.3 gcc63/netcdf/4.6.1 intel/2020 matlab/R2018b udocker/1.1.4 cmake/3.20.3 (D) gcc63/netcdf/4.7.4 (D) intel/gromacs/2021.5 matlab/R2019b (D) udocker/1.1.7 conn-R2018b gcc63/ngspice/34 intel/hdf4/4.2.15 mpich-3.2 udocker/alphafold/2.1.1 cuda gcc63/openmpi/1.10.7 intel/hdf5/1.12.0 mvapich2/2.3.5 udocker/tensorflow/cpu/2.4.1 cuda-10.2 gcc63/openmpi/2.1.0 intel/libs/libpng/1.6.37 netcdf-fortran/4.5.2 udocker/tensorflow/gpu/2.4.1 cuda-11.2 gcc63/openmpi/4.0.3 intel/libs/openblas/0.3.10 netcdf/4.7.4 view3dscene/3.18.0 elsa/1.0.2 gcc63/openmpi/4.1.1 (D) intel/mvapich2/2.3.5 nlopt/2.6.2 (D) vim/8.2 fastqc-0.11.5 gcc63/r-3.4.2 intel/netcdf-fortran/4.5.2 openmpi/1.10.7 weblogo-2.8.2 fftw/3.3.4 gcc63/schism/5.4.0 intel/netcdf/4.7.4 openmpi/2.1.0 wine/4.2 fftw/3.3.5 (D) gcc63/xbeach/1.23.5527 intel/oneapi/2021.3 openmpi/4.0.3 ww3/6.07.1 freewrl/4.4.0 gcc74/gromacs/2019.4 intel/oneapi/2022.1 (D) openmpi/4.1.1 (D) gcc-4.8 gcc74/openmpi/4.0.3 intel/openfoam/5.0 parallel/20180622 gcc-5.5 gcc74/plumed/2.5.3 intel/openfoam/8.0 plumed/2.2.1 ```