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.
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
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 infrastrctures.
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/bob -----------------------------
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)
-------------------- /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