Software List []

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==== Software List ====


^  Name  ^  Version  ^  Installation  ^  Module  ^ note ^
^  LIBRERIE  ^^^^^
| gsl       | 1.15-13           | rpm | no  | https://www.gnu.org/software/gsl/ |
| gsl-gnu-ohpc       | 2.2.1           | rpm | gnu gsl   | 
| boost     | 1.53.0             | rpm | no   |
| fftw     | 3.3.3     | rpm | no   | http://www.fftw.org/ |
| lapack   | 3.4.2    | rpm | no   | http://www.netlib.org/lapack/ |
| scalapack-gnu-openmpi-ohpc   | 2.0.2     | rpm   | gnu openmpi scalapack | http://www.netlib.org/scalapack/  | 
| hdf5     | 1.8.12     | rpm  | no | https://support.hdfgroup.org/HDF5/ |
| hdf5-gnu-ohpc    | 1.8.17     | rpm  | gnu hdf5  | 
| phdf5-gnu--openmpi-ohpc    | 1.8.17     | rpm  | gnu openmpi phdf5  | https://support.hdfgroup.org/HDF5/PHDF5/ |
| atlas    | 3.10.1   | rpm   | no  |
| blas    | 3.4.2   | rpm   | no  | http://www.netlib.org/blas/ |
| openblas    | 0.2.19   | rpm   | no  | http://www.netlib.org/blas/ |
| openblas-gnu-ohpc   | 0.2.19   | rpm   | gnu openblas  |
| gmp     | 6.0.0   | rpm  | no  | https://gmplib.org/ |
| cuDNN   | 6.0.21  | nvidia  | no  | https://developer.nvidia.com/cudnn |
^  Compilers, Debuggers, Profilers  ^^^^^
| group install "Development Tools”   | 4.8.5  | rpm  | no  | gcc/gfortran/g++ 4.8.5   |
| gnu-compilers-ohpc | 5.4.0  | rpm  | gnu  | gcc/gfortran/g++   5.4.0   |
| openmpi-gnu-ohpc    | 1.10.4  | rpm   | gnu openmpi   | 
| [[.:priv:cluster:softwareapplicativo:intel | INTEL ]]   | 16.0.3  | /hpc/share | intel  | https://software.intel.com/en-us/intel-compilers |
| [[.:priv:cluster:softwareapplicativo:intel | INTEL MPI ]]   | 5.1.3 | /hpc/share | intel intelmpi   |
| [[.:priv:cluster:softwareapplicativo:pgi | PGI ]] | 16.10 Community | /hpc/share | pgi  | http://www.pgroup.com/products/community.htm |
| [[.:priv:cluster:softwareapplicativo:pgi | openmpi /PGI ]] | 1.10.2 /PGI2016 | /hpc/share | pgi openmpi | 
| CUDA     | 8.0.61 | /hpc/share  | cuda  | https://developer.nvidia.com/about-cuda |
| openjdk  | 1.8.0  | rpm   | no  | java  |
| python   | 2.7.5  | rpm   | no  | https://www.python.org/ |
| python   | 3.6.3 | | gnu phyton | https://www.python.org/ |
| numpy   | 1.7.1  | rpm   | no  | http://www.numpy.org/ |
| python-numpy-gnu-ohpc   | 1.11.1  | rpm   | gnu numpy  |
| scipy  | 0.12.1  | rpm   | no  | https://www.scipy.org/ |
| python-scipy-gnu-openmpi-ohpc  | 0.18.0  | rpm   | gnu openmpi scipy  |
| gdb  | 7.6.1  | rpm   | no  | GNU Debugger  | 
| valgrind     | 3.11.0   | rpm  | no  | http://valgrind.org/  |
| valgrind-ohpc     | 3.11.0   | rpm  | valgrind  |  |
^  APPLICATIONS / TOOLS  ^^^^^
| [[.:priv:cluster:softwareapplicativo:Crystal14 ]]  | 1.04           | /hpc/share | crystal14/1.0.4 (todo) |  
| Matlab     | R2011a   | /hpc/share   | matlab/R2011a  |
| Matlab     | R2017a   | /hpc/share   | matlab/R2017a (default)  |
| FSDA       | | /hpc/share | toolkit di matlab/R2017a | http://www.riani.it/MATLAB/FSDA/index.html|
| Octave    | 3.8.2   | rpm        | no    | https://www.gnu.org/software/octave/  |
| [[.:priv:cluster:softwareapplicativo:R]]       | 3.3.3   | module     |  gnu R_base/3.3.2  | https://www.r-project.org/  |
| [[.:priv:cluster:softwareapplicativo:QE]]        | 5.4.0  | rpm  | no | http://www.quantum-espresso.org/    |
| [[.:priv:cluster:softwareapplicativo:Gromacs ]]  | 4.5.7, 5.1.4 | /hpc/share  | no  | http://www.gromacs.org/ |
| [[.:priv:cluster:softwareapplicativo:Gaussian ]]  | 09, 16  | /hpc/share |  | http://gaussian.com/   |
| [[.:priv:cluster:softwareapplicativo:Amber ]]  | 11  | /hpc/share |  | http://ambermd.org/ |
| [[.:priv:cluster:softwareapplicativo:Schrodinger ]]  | 2017 | /hpc/share |  |   |
| [[.:priv:cluster:softwareapplicativo:Abaqus ]]  | 2017, 2018  | /hpc/share |  | https://en.wikipedia.org/wiki/Abaqus |
| [[.:priv:cluster:softwareapplicativo:Emboss ]]  | 6.6.0  | /hpc/share |  | http://emboss.sourgeforge.net  |
| [[.:priv:cluster:softwareapplicativo:Itpp ]]  | 4.4.1  | /hpc/share |  | http://itpp.sourceforge.net  |
| [[.:priv:cluster:softwareapplicativo:AutoDock ]]  | 4.2.6 | /hpc/share  |    |
| [[.:priv:cluster:softwareapplicativo:fds ]] | 6.5.3 | /hpc/share | | https://github.com/firemodels/fds/wiki |
| [[.:priv:cluster:softwareapplicativo:sentaurus ]] | 2017.09 | /hpc/share | sentaurus| |
| [[.:priv:cluster:softwareapplicativo: Samtools]] | 1.6 | /hpc/share | |http://www.htslib.org/ |
| [[.:priv:cluster:softwareapplicativo: Star]] | 2.5.3a | /hpc/share | |https://github.com/alexdobin/STAR |
| [[.:priv:cluster:softwareapplicativo: Bedtools ]] | 2.25.0 | /hpc/share | | http://bedtools.readthedocs.io/en/latest/ |
| [[.:priv:cluster:softwareapplicativo: Bowtie ]] | 1.2.2 | /hpc/share | | http://bowtie-bio.sourceforge.net/index.shtml |
| [[.:priv:cluster:softwareapplicativo: Bowtie2 ]] | 2.3.3.1 | /hpc/share | | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| [[.:priv:cluster:softwareapplicativo: tensorflow-gpu ]] |  | module | gnu python/3.6.3 cuda | https://www.tensorflow.org |
| [[.:priv:cluster:softwareapplicativo: keras ]] |  | module |gnu python/3.6.3 cuda| https://keras.io/ |
| [[.:priv:cluster:softwareapplicativo: qiime ]] |  | virtualenv  | | http://qiime.org/ |
| [[.:priv:cluster:softwareapplicativo: flash ]] |  | module | | |
| [[.:priv:cluster:softwareapplicativo: prinseq ]] |  | module | |  |
| [[.:priv:cluster:softwareapplicativo: espresso md ]] |  | virtualenv | | http://espressomd.org/wordpress/|
| [[.:priv:cluster:softwareapplicativo: namd ]] |  | module  | | http://www.ks.uiuc.edu/Research/namd/|
| [[.:priv:cluster:softwareapplicativo: plumed ]] |  | module  | | http://www.plumed.org/|
| [[.:priv:cluster:softwareapplicativo: mpi4py ]] |  | rpm ohpc  | | |