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Difference between revisions of "NewSoftware"
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<strong>09/28/2016 - lammps 30Jul16</strong> | <strong>09/28/2016 - lammps 30Jul16</strong> | ||
− | <pre | + | <pre>module load lammps/[cpu,gpu]/30Jul16 </pre> |
<strong>08/23/2016 - Ansys 17.1 for Linux 6,7</strong> | <strong>08/23/2016 - Ansys 17.1 for Linux 6,7</strong> | ||
− | <pre | + | <pre>module load ansys/17.1 </pre> |
<strong>08/09/2016 - FMRIB Software Library (FSL 5.0.9) for Linux 6,7</strong> | <strong>08/09/2016 - FMRIB Software Library (FSL 5.0.9) for Linux 6,7</strong> | ||
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FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. | FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. | ||
− | <pre | + | <pre>module load fsl/5.0.9</pre> |
<strong>08/02/2016 - Open MPI for Scientific Linux 6,7</strong> | <strong>08/02/2016 - Open MPI for Scientific Linux 6,7</strong> | ||
− | <pre | + | <pre>module load ompi/2.0.0</pre> |
<strong>06/15/2016 - gcc 6.1.0 for Scientific Linux 6,7</strong> | <strong>06/15/2016 - gcc 6.1.0 for Scientific Linux 6,7</strong> | ||
− | <pre | + | <pre>module load gcc/6.1.0</pre> |
<strong>06/15/2016 - gcc 5.4.0 for Scientific Linux 6,7</strong> | <strong>06/15/2016 - gcc 5.4.0 for Scientific Linux 6,7</strong> | ||
− | <pre | + | <pre>module load gcc/5.4.0</pre> |
<strong>06/15/2016 - gcc 5.3.0 for Scientific Linux 6,7</strong> | <strong>06/15/2016 - gcc 5.3.0 for Scientific Linux 6,7</strong> | ||
− | <pre | + | <pre>module load gcc/5.3.0</pre> |
<strong>05/13/2016 - Anaconda python 3.5.1</strong> | <strong>05/13/2016 - Anaconda python 3.5.1</strong> | ||
− | <pre | + | <pre>module load python3</pre> |
<strong>05/13/2016 - Anaconda python 2.7.11</strong> | <strong>05/13/2016 - Anaconda python 2.7.11</strong> | ||
− | <pre | + | <pre>module load python2</pre> |
<strong>03/18/2016 - R 3.2.4</strong> | <strong>03/18/2016 - R 3.2.4</strong> | ||
− | <pre | + | <pre>module load R-Project</pre> |
<strong>02/22/2016 - gcc 5.3.0 for Scientific Linux 7</strong> | <strong>02/22/2016 - gcc 5.3.0 for Scientific Linux 7</strong> | ||
− | <pre | + | <pre>module load gcc5/5.3.0-sl7</pre> |
<strong>02/22/2016 - gcc 5.3.0 for Scientific Linux 6</strong> | <strong>02/22/2016 - gcc 5.3.0 for Scientific Linux 6</strong> | ||
− | <pre | + | <pre>module load gcc5</pre> |
<strong>02/04/2016 - NWchem 6.6</strong> | <strong>02/04/2016 - NWchem 6.6</strong> | ||
− | <pre | + | <pre>module load nwchem</pre> |
<strong>02/03/2016 - Gromacs 5.1.1</strong> | <strong>02/03/2016 - Gromacs 5.1.1</strong> | ||
− | <pre | + | <pre>module load load gromacs/5.1.1</pre> |
<strong>10/19/2015 - Intel Parallel Studio XE Cluster Edition</strong> | <strong>10/19/2015 - Intel Parallel Studio XE Cluster Edition</strong> | ||
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GNU compilers. This installation does not include gfortran. | GNU compilers. This installation does not include gfortran. | ||
− | <pre | + | <pre>module load load gcc5</pre> |
<strong>05/14/2015 - mafTools v01</strong> | <strong>05/14/2015 - mafTools v01</strong> | ||
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Bioinformatics tools for dealing with Multiple Alignment Format (MAf) | Bioinformatics tools for dealing with Multiple Alignment Format (MAf) | ||
− | <pre | + | <pre>module load load maftools</pre> |
<strong>04/17/2015 - R 3.1.2</strong> | <strong>04/17/2015 - R 3.1.2</strong> | ||
− | <pre | + | <pre>module load load R-Project</pre> |
<strong>03/04/2015 - Freefem++</strong> | <strong>03/04/2015 - Freefem++</strong> | ||
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On stheno | On stheno | ||
− | <pre | + | <pre>module load freefem++</pre> |
On kong and all SL6 AFS clients | On kong and all SL6 AFS clients | ||
− | <pre | + | <pre>module load freefem++-sl6</pre> |
<strong>02/10/2015</strong> - Anaconda Python | <strong>02/10/2015</strong> - Anaconda Python |
Latest revision as of 16:19, 14 October 2020
11/02/2016 - Siesta 4.1-b1
module load siesta
10/10/2016 - Jython 2.7.0
module load jython
Note: it is likely that the default python3 module will not allow the python2 module to load. To circumvent this problem, on Kong create a file ~/.modules with the following 2 lines :
module load sge module load python2
09/28/2016 - lammps 30Jul16
module load lammps/[cpu,gpu]/30Jul16
08/23/2016 - Ansys 17.1 for Linux 6,7
module load ansys/17.1
08/09/2016 - FMRIB Software Library (FSL 5.0.9) for Linux 6,7
FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
module load fsl/5.0.9
08/02/2016 - Open MPI for Scientific Linux 6,7
module load ompi/2.0.0
06/15/2016 - gcc 6.1.0 for Scientific Linux 6,7
module load gcc/6.1.0
06/15/2016 - gcc 5.4.0 for Scientific Linux 6,7
module load gcc/5.4.0
06/15/2016 - gcc 5.3.0 for Scientific Linux 6,7
module load gcc/5.3.0
05/13/2016 - Anaconda python 3.5.1
module load python3
05/13/2016 - Anaconda python 2.7.11
module load python2
03/18/2016 - R 3.2.4
module load R-Project
02/22/2016 - gcc 5.3.0 for Scientific Linux 7
module load gcc5/5.3.0-sl7
02/22/2016 - gcc 5.3.0 for Scientific Linux 6
module load gcc5
02/04/2016 - NWchem 6.6
module load nwchem
02/03/2016 - Gromacs 5.1.1
module load load gromacs/5.1.1
10/19/2015 - Intel Parallel Studio XE Cluster Edition
See "Intel" under "Compilers"
09/22/2015 - GNU gcc 5.2.0
GNU compilers. This installation does not include gfortran.
module load load gcc5
05/14/2015 - mafTools v01
Bioinformatics tools for dealing with Multiple Alignment Format (MAf)
module load load maftools
04/17/2015 - R 3.1.2
module load load R-Project
03/04/2015 - Freefem++
Freefem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D.
On stheno
module load freefem++
On kong and all SL6 AFS clients
module load freefem++-sl6
02/10/2015 - Anaconda Python
Enterprise-ready Python distribution for large-scale data processing, predictive analytics, and scientific computing.
To use anaconda :
module load anaconda
Note that anaconda includes openmpi and the mpi4py python module.
Example python script using mpy4py
#!/afs/cad/linux/anaconda-2.1.0/anaconda/bin/python from mpi4py import MPI comm = MPI.COMM_WORLD size = comm.Get_size() rank = comm.Get_rank() if rank == 0: data = [(x+1)**x for x in range(size)] print 'we will be scattering:',data else: data = None data = comm.scatter(data, root=0) data += 1 print 'rank',rank,'has data:',data newData = comm.gather(data,root=0) if rank == 0: print 'master:',newData
Sample submit script for the mpi4py python script
#!/bin/sh # # EXAMPLE OMPI SCRIPT FOR SGE # Modified by Gwolosh from Basement Supercomputing 1/2/2006 DJE # To use, change "OMPI_JOB", "NUMBER_OF_CPUS", # "OMPI_PROGRAM_NAME" and "UCID" to real values. # # Your job name #$ -N OMPI_JOB # # Use current working directory #$ -cwd # # Join stdout and stderr #$ -j y # # pe request for OMPI. Set your number of processors here. # Make sure you use the "ompi" parallel environment. #$ -pe ompi NUMBER_OF_CPUS # email beginning and end of job #$ -m be #$ -M UCID@njit.edu # # Run job through bash shell #$ -S /bin/bash # #Generate an machine file echo "Got $NSLOTS processors." echo $PE_HOSTFILE machines=$TMPDIR/machines touch $machines cat $PE_HOSTFILE | awk ' {print $1} ' >> $machines # For reporting only cat $machines # # Use full pathname to make sure we are using the right mpiexec /afs/cad/linux/anaconda-2.1.0/anaconda/bin/mpiexec -f $machines -np $NSLOTS /full/path/to/OMPI_PROGRAM_NAME