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.
Intel Compilers available
Users can also install software on their own for further information see the section on User Software Installation. Execution of user defined software environments (operating system and libraries) using Linux containers in the HPC and HTC clusters with uDocker and Singularity is also supported.
INCD-Lisbon HPC and HTC cluster (Cirrus-A)
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
- 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 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