Software List

List of software centrally available via the modules tool at the INCD Cirrus HPC and HTC clusters as of March 2020. To request the installation of additional software contact the INCD support helpdesk.

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)

CentOS 7

-------------------------- /cvmfs/sw.el7/modules/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

-------------------------- /cvmfs/sw.el7/modules/soft --------------------------
aster-13.1.0                 hdf5-1.8.16
blat-36.2                    homer-4.8
boost-1.55                   intel/2019
bowtie2-2.3.0                intel/2019.mkl
clang/7.0.0                  intel/2019.mpi
clang/ngspice/30             intel/openmpi/4.0.3
clang/openmpi/4.0.1-test     intel/swan/41.31
cmake/3.11.2                 kallisto-0.43.0
cmake/3.5.2                  macs-1.4.2
conn-R2018b                  matlab/R2018a
cuda                         matlab/R2018b
cuda-10.1                    matlab/R2019b
cuda-10.2                    mpich-3.2
cuda-8.0                     mvapich2-1.8
cuda-9.0                     netcdf/4.6.1
DATK                         netcdf2/4.6.1
fastqc-0.11.5                netcdf-fortran/4.4.4
fftw/3.3.4                   ngspice/30
fftw/3.3.5                   openmpi/2.1.0
gcc-4.8                      openmpi-1.10.2
gcc55/openmpi/4.0.1          parallel/20180622
gcc-5.5                      plumed-2.2.1
gcc63/mpich-3.2              python/3.7.2
gcc63/netcdf/4.6.1           python-2.7.11
gcc63/netcdf-fortran/4.4.4   python-3.5.1
gcc63/ngspice/30             python-3.5.4
gcc63/openmpi/2.1.0          r-3.2.5
gcc63/openmpi-1.10.2         r-3.5.2
gcc63/r-3.4.2                rt
gcc63/schism/5.4.0           sbcl-1.3.4
gcc63/scipion/2.0_2019-04-23 schism/5.4.0
gcc-6.3                      sicer-1.1
gcc-7.3                      star-2.5.2b
gcc74/gromacs/2019.4         trimmomatic-0.33
gcc74/openmpi/4.0.1          udocker/1.1.3
gcc74/plumed/2.5.3           weblogo-2.8.2
gcc-7.4                      wine/4.2
gromacs-4.6.7

CentOS 6

-------------------------- /cvmfs/sw.el6/modules/soft --------------------------
aster-11.5.0               gcc63/openmpi/1.6.3
bcbio                      gcc63/openmpi/1.6.5
bcl2fastq-2.20.0           gcc63/openmpi/2.1.0
bctest                     gcc63/parmetis/3.1
bluefin                    gcc63/r-3.4.2
boost-1.50.0               gcc63/r-3.5.2
boost-1.57.0               gcc63/teste
clang/fftw/3.3.8           gcc-6.3
clang/openmpi/2.1.6        gcc-7.3
clang/openmpi/3.1.3        go/1.6
clang/openmpi/4.0.0        gromacs-4.6.5
clang-3.4.2                gromacs-4.6.7
cmake/2.8.12               gromacs-5.0.4
cmake/3.11.4               gromacs-5.1.3
cmake/3.5.2                hdf5-1.8.16
cmtk-3.2.2                 heasoft/6.24
cp2k-2.6.1-popt            hwloc-1.10.1
cp2k-4.1-psmp              matlab/R2012a
cuda-6.5                   matlab/R2012a.i686
cuda-6.5.14                matlab/R2012b
cuda-7.0.28                matlab/R2013b
cuda-7.5                   matlab/R2018a
cuda-8.0                   metis-4.0.3
cuda-9.0                   metis-5.1.0
cufflinks-2.2.1            miso-0.5.3
DATK                       ml
fermi/11.5.3               modules
fftw-3.3.2                 mpich/3.2
fftw-3.3.4                 nwchem-6.8
fftw-3.3.5                 octave-3.8.2
freesurfer-5.3.0           octave-4.0.2
freesurfer-6.0.0           open64-5.0
gawk/4.2.1                 opencsp-1.0
gcc44/o3                   opencv-2.4.10
gcc44/openmpi/1.10.2       opencv-2.4.9
gcc44/openmpi/1.6.3        openmpi/1.10.2
gcc44/openmpi/1.6.5        openmpi/1.6.3
gcc44/openmpi/2.1.0        openmpi/1.6.5
gcc-4.4                    openmpi/2.1.0
gcc46/openmpi/1.10.2       parallel/20180622
gcc46/openmpi/1.6.3        phy-0.2.2
gcc46/openmpi/1.6.5        plumed-2.2.1
gcc-4.6                    pp-1.6.4
gcc-4.7                    pvm/3.4.6
gcc48/bcl2fastq-2.20.0     python-2.7.11
gcc48/fftw-3.3.4           python-2.7.13
gcc48/fftw-3.3.5           python-2.7.14
gcc48/gcc-4.8.3            python-2.7.8
gcc48/hdf5-1.8.16          python-2.7.9
gcc-4.8                    python-3.5.1
gcc49/mpich/3.2            qt-4.8.6
gcc49/netcdf-4.4.1.1       qt-5.4.1
gcc49/openmpi/2.1.0        r-3.2.4
gcc49/rr                   r-3.4.2
gcc-4.9                    rstudio-0.98.1103
gcc54/netcdf-4.4.1.1       rt
gcc54/openmpi/2.1.0        sbcl-1.3.4
gcc-5.4                    spark-1.4.1
gcc63/bcl2fastq-2.20.0     spark-1.5.0
gcc63/fftw-3.3.7           spark-2.0.0
gcc63/mpich/3.2            subversion-1.9
gcc63/netcdf/4.4.1.1       texlive/2016
gcc63/netcdf/4.6.1         texlive/2018
gcc63/netcdf2/4.6.1        thunder
gcc63/netcdf-fortran/4.4.4 ucont
gcc63/nwchem-6.8           udocker/1.1.3

------------------------- /cvmfs/sw.el6/modules/gcc44 --------------------------
gcc44/abyss-1.3.6    gcc44/gromacs-4.6.3  gcc44/opencv-2.4.9
gcc44/esys-2.2.2     gcc44/gromacs-4.6.5  gcc44/parmetis-3.1
gcc44/fftw-3.3.2     gcc44/gromacs-5.0.4  gcc44/pvm-3.4.6
gcc44/fftw-3.3.4     gcc44/hdf5-1.8.14    gcc44/python-2.7.8
gcc44/gcc-4.4        gcc44/MITSIMLab_sl5  gcc44/selfe-3.1dc
gcc44/gerris-121130  gcc44/mvapich2-1.8   gcc44/yade-1.5.0
gcc44/gerris-130802  gcc44/netcdf-4.1.3
gcc44/gromacs-4.5.5  gcc44/netcdf-4.3.3.1

------------------------- /cvmfs/sw.el6/modules/gcc46 --------------------------
gcc46/abyss-1.3.6   gcc46/gromacs-4.5.5 gcc46/parmetis-3.1
gcc46/esys-2.2.2    gcc46/gromacs-4.6.3 gcc46/pvm-3.4.6
gcc46/fftw-3.3.2    gcc46/gromacs-4.6.5 gcc46/selfe-3.1dc
gcc46/fftw-3.3.4    gcc46/gromacs-5.0.4 gcc46/velvet-1.2.10
gcc46/gcc-4.6.3     gcc46/MITSIMLab_sl5 gcc46/yade-1.5.0
gcc46/gerris-121130 gcc46/mvapich2-1.8
gcc46/gerris-130802 gcc46/netcdf-4.1.3

------------------------- /cvmfs/sw.el6/modules/gcc47 --------------------------
gcc47/abyss-1.3.6     gcc47/gerris-121130   gcc47/openmpi-1.6.5
gcc47/boost-1.55.0    gcc47/gerris-130802   gcc47/parmetis-3.1
gcc47/boost-1.57.0    gcc47/gromacs-4.6.3   gcc47/petsc-3.4.2
gcc47/cufflinks-2.2.1 gcc47/gromacs-4.6.5   gcc47/pvm-3.4.6
gcc47/esys-2.2.2      gcc47/gromacs-5.0.4   gcc47/samtools-0.1.19
gcc47/fftw-3.3.2      gcc47/mvapich2-1.8    gcc47/samtools-1.2
gcc47/fftw-3.3.4      gcc47/netcdf-4.1.3    gcc47/selfe-3.1dc
gcc47/gcc-4.7.1       gcc47/openmpi-1.6.3   gcc47/vasp-5.3.13

-------------------------- /cvmfs/sw.el6/modules/RNA ---------------------------
bedtools-2.26.0  cufflinks-2.2.1  kallisto-0.43.0  start-2.5.2b
blat-36.2        fastqc-0.11.5    macs-1.4.2       tophat-2.1.1
bowtie2-2.2.4    hisat2-2.0.5     samtools-1.3.1   trimmomatic-0.33
bowtie2-2.3.0    homer-4.8        sicer-1.1        weblog-2.8.2

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