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
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-Minho HPC and HTC cluster (Cirrus-B)
CentOS 7
----------------------------- /etc/modulefiles/LIP -----------------------------
atlasSetup geant/4.10.02.p01 pythia/8.2.15
clhep/2.2.0.8 geant/4.10.03 pythia/8.2.35
clhep/2.3.1.1 geant/4.10.05.p01 pythia/8.2.40
clhep/2.3.2.2 geant/4.10.06 root/5.34.36
clhep/2.3.4.3 geant/4.10.06.p01 root/6.04.02
clhep/2.4.1.3 hepmc/2.6.9 root/6.08.00
delphes/3.4.1 heptoptagger/2.0 root/6.10.02
delphes/3.4.2pre10 lhapdf/6.1.6 root/6.12.06
delphes/3.4.2pre15 lhapdf/6.2.3 root/6.14.06
fastjet/3.3.0 madgraph/2.6.0 root/6.16.00
fluka/2011.2x.7 madgraph/2.6.1 root/6.18.04
gcc74/clhep/2.4.1.3 pythia/6.4.26 topas/3.3.beta1
gcc74/geant/4.10.05.p01 pythia/6.4.28 xroot/4.3.0
----------------------------- /etc/modulefiles/Cirrus -----------------------------
aster-13.1.0 intel/gromacs/2019.3-fftw3
blat-36.2 intel/gromacs/2019.4
boost-1.55 intel/openfoam/1906
bowtie2-2.3.0 intel/openmpi/1.10.7
clang/7.0.0 intel/openmpi/4.0.1
clang/ngspice/30 intel/plumed/2.5.2
cmake/3.11.2 kallisto-0.43.0
conn-R2018b macs-1.4.2
DATK matlab/R2018a
fastqc-0.11.5 matlab/R2018b
fftw-3.3.5 matlab/R2019b
gcc-4.8 mpich-3.2
gcc63/fftw/3.3.8 mvapich2-1.8
gcc63/gromacs/2019.3 netcdf/4.6.1
gcc63/gromacs/2019.4 netcdf/4.6.1-teste
gcc63/mpich-3.2 netcdf-fortran/4.4.4
gcc63/netcdf/4.6.1 netcdf-fortran/4.4.4-teste
gcc63/netcdf-fortran/4.4.4 ngspice/30
gcc63/ngspice/30 openmpi/1.10.7
gcc63/openfoam/1906 openmpi/4.0.1
gcc63/openmpi/1.10.7 papi/5.7.0
gcc63/openmpi/3.1.4 parallel/20180622
gcc63/openmpi/4.0.1 plumed-2.2.1
gcc63/plumed/2.5.2 python/2.7.11
gcc63/r-3.4.2 python/3.7.2
gcc63/schism/5.4.0 r-3.5.2
gcc63/teste/0.9.1 rt
gcc-6.3 sbcl-1.3.4
gcc-7.3 schism/5.4.0
gromacs-4.6.7 sicer-1.1
hdf5-1.8.16 star-2.5.2b
homer-4.8 trimmomatic-0.33
intel/2019 udocker/1.1.1
intel/2019.mkl weblogo-2.8.2
intel/2019.mpi wine/4.2
intel/gromacs/2019.3
ISEC-Coimbra HPC cluster (Cirrus-C)
CentOS 7
-------------------- /usr/global/Modules/3.2.10/modulefiles --------------------
AddMyPrivateModulesDirectory
Compilers/GCC/4.8.5
Compilers/GCC/4.9.3
Compilers/GCC/5.4.0
Compilers/GCC/6.1.0
Compilers/Intel/2016.3.210
Compilers/Intel/2016.3.210-optimize
Compilers/Java/jre-1.8.0_221
Compilers/Python/3.7.4-with_GCC_4.8.5
Libraries/BLAS/3.8.0-with_GCC_4.8.5
Libraries/BLAS/3.8.0-with_GCC_4.9.3
Libraries/BLAS/3.8.0-with_GCC_5.4.0
Libraries/BLAS/3.8.0-with_GCC_6.1.0
Libraries/BLAS/3.8.0-with_Intel_2016.3.210
Libraries/BLAS/3.8.0-with_OpenMPI_4.0.2-with_GCC_4.8.5
Libraries/BOOST/1.66.0-with_GCC_6.1.0
Libraries/CLHEP/2.0.4.2-with_GCC_4.8.5
Libraries/CLHEP/2.4.1.0-with_GCC_4.8.5
Libraries/GNU/CLooG/0.16.1-with_isl_bundled-with_gmp_bundled
Libraries/GNU/CLooG/0.18.0-with_isl_0.11.1-with_gmp_6.1.0
Libraries/GNU/CLooG/0.18.1-with_isl_0.12.2-with_gmp_6.1.0
Libraries/GNU/GMP/4.3.2
Libraries/GNU/GMP/6.1.0
Libraries/GNU/ISL/0.11.1-with_gmp_6.1.0
Libraries/GNU/ISL/0.12.2-with_gmp_6.1.0
Libraries/GNU/ISL/0.14-with_gmp_6.1.0
Libraries/GNU/ISL/0.16-with_gmp_6.1.0
Libraries/GNU/MPC/0.8.1-with_mpfr_2.4.2-with_gmp_4.3.2
Libraries/GNU/MPC/1.0.3-with_mpfr_3.1.4-with_gmp_6.1.0
Libraries/GNU/MPFR/3.1.4-with_gmp_6.1.0
Libraries/HDF5/1.10.5-with_GCC_4.8.5
Libraries/HDF5/1.10.5-with_OpenMPI_4.0.1-with_GCC_4.8.5
Libraries/Intel/daal-2016.3.210
Libraries/Intel/ipp-2016.3.210
Libraries/Intel/mkl-2016.3.210
Libraries/Intel/tbb-2016.3.210
Libraries/LAPACK/3.8.0-with_BLAS_3.6.0-with_GCC_4.8.5
Libraries/LAPACK/3.8.0-with_BLAS_3.6.0-with_GCC_4.9.3
Libraries/LAPACK/3.8.0-with_BLAS_3.6.0-with_GCC_5.4.0
Libraries/LAPACK/3.8.0-with_BLAS_3.6.0-with_GCC_6.1.0
Libraries/LAPACK/3.8.0-with_BLAS_3.6.0-with_Intel_2016.3.210
Libraries/LAPACK/3.8.0-with_BLAS_3.6.0-with_Intel_2016.3.210-optimize
Libraries/Mellanox/hcoll
Libraries/Mellanox/mxm
Libraries/Mellanox/sharp
MPI/IntelMPI/2019.6.166-with_GCC_4.8.5
MPI/IntelMPI/2019.6.166-with_GCC_4.9.3
MPI/IntelMPI/2019.6.166-with_GCC_5.4.0
MPI/IntelMPI/2019.6.166-with_GCC_6.1.0
MPI/IntelMPI/2019.6.166-with_Intel_2016.3.210
MPI/MPICH2/3.3.2-with_GCC_4.8.5-hydra
MPI/MPICH2/3.3.2-with_GCC_4.8.5-slurm
MPI/MPICH2/3.3.2-with_GCC_4.9.3-hydra
MPI/MPICH2/3.3.2-with_GCC_4.9.3-slurm
MPI/MPICH2/3.3.2-with_GCC_5.4.0-hydra
MPI/MPICH2/3.3.2-with_GCC_5.4.0-slurm
MPI/MPICH2/3.3.2-with_GCC_6.1.0-hydra
MPI/MPICH2/3.3.2-with_GCC_6.1.0-slurm
MPI/MPICH2/3.3.2-with_Intel_2016.3.210-hydra
MPI/MPICH2/3.3.2-with_Intel_2016.3.210-slurm
MPI/MVAPICH2/2.3.3-with_GCC_4.8.5
MPI/MVAPICH2/2.3.3-with_GCC_4.9.3
MPI/MVAPICH2/2.3.3-with_GCC_5.4.0
MPI/MVAPICH2/2.3.3-with_GCC_6.1.0
MPI/OpenMPI/4.0.2-Mellanox_Provided-with_GCC_4.8.5
MPI/OpenMPI/4.0.2-Mellanox_Provided-with_GCC_4.9.3
MPI/OpenMPI/4.0.2-Mellanox_Provided-with_GCC_5.4.0
MPI/OpenMPI/4.0.2-Mellanox_Provided-with_GCC_6.1.0
MPI/OpenMPI/4.0.2-with_GCC_4.8.5
MPI/OpenMPI/4.0.2-with_GCC_4.9.3
MPI/OpenMPI/4.0.2-with_GCC_5.4.0
MPI/OpenMPI/4.0.2-with_GCC_6.1.0
MPI/OpenMPI/4.0.2-with_Intel_2016.3.210
Programs/bison/3.4.2-with_GCC_4.8.5
Programs/comsol-5.2a
Programs/flex/2.6.4-with_GCC_4.8.5
Programs/geant4/9.2.p04-with_CLHEP_2.0.4.2-with_GCC_4.8.5
Programs/gromacs/2019.3/with_OpenMPI_4.0.1-with_GCC_4.8.5
Programs/matlab-R2016a
Programs/matlab-R2016a-Runtime
Programs/R/3.4.3-with_GCC_6.1.0-with_BLAS_3.6.0
Programs/R/3.4.3-with_GCC_6.1.0-with_MKL_2016.3.210_sequential-dynamic
Programs/R/3.4.3-with_GCC_6.1.0-with_MKL_2016.3.210_threaded-dynamic
Programs/R/studio
taskfarm
Taskfarmers/taskfarm-with_MPICH_3.2-with_GCC_4.8.5
Taskfarmers/taskfarm-with_MPICH_3.2-with_GCC_4.9.3
Taskfarmers/taskfarm-with_MPICH_3.2-with_GCC_5.4.0
Taskfarmers/taskfarm-with_MPICH_3.2-with_GCC_6.1.0
Taskfarmers/taskfarm-with_MPICH_3.2-with_Intel_2016.3.210
Taskfarmers/taskfarm-with_MPICH_3.2-with_Intel_2016.3.210-optimize
Taskfarmers/taskfarm-with_MVAPICH2_2.2-with_GCC_4.8.5
Taskfarmers/taskfarm-with_MVAPICH2_2.2-with_GCC_4.9.3
Taskfarmers/taskfarm-with_MVAPICH2_2.2-with_GCC_5.4.0
Taskfarmers/taskfarm-with_MVAPICH2_2.2-with_GCC_6.1.0
Taskfarmers/taskfarm-with_MVAPICH2_2.2-with_Intel_2016.3.210
Taskfarmers/taskfarm-with_MVAPICH2_2.2-with_Intel_2016.3.210-optimize
Taskfarmers/taskfarm-with_OpenMPI_2.0.1-with_GCC_4.8.5
Taskfarmers/taskfarm-with_OpenMPI_2.0.1-with_GCC_4.9.3
Taskfarmers/taskfarm-with_OpenMPI_2.0.1-with_GCC_5.4.0
Taskfarmers/taskfarm-with_OpenMPI_2.0.1-with_GCC_6.1.0
Taskfarmers/taskfarm-with_OpenMPI_2.0.1-with_Intel_2016.3.210
Taskfarmers/taskfarm-with_OpenMPI_2.0.1-with_Intel_2016.3.210-optimize
Visualization/view3dscene