Difference between revisions of "HPC Software"
From Storrs HPC Wiki
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For 5.1.4-plumed-gsl (the default "gromacs" module), the order of modulefiles should follow this command: | For 5.1.4-plumed-gsl (the default "gromacs" module), the order of modulefiles should follow this command: | ||
$ module load gcc/5.4.0-alt plumed/2-gnu boost/1.61.0-gcc-mpi mpi/openmpi/2.1.0 zlib/1.2.8 fftw/3.3.6-gcc540a gsl gromacs | $ module load gcc/5.4.0-alt plumed/2-gnu boost/1.61.0-gcc-mpi mpi/openmpi/2.1.0 zlib/1.2.8 fftw/3.3.6-gcc540a gsl gromacs | ||
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== How to run == | == How to run == | ||
Revision as of 15:47, 18 April 2019
Contents
Software Guides
- Abaqus Guide - How to use Abaqus FEA 6.12
- CAMx Guide - How to use CAMx with MPI and OMP
- Comsol Guide - How to use COMSOL on the HPC Cluster
- DXA Guide - How to use Dislocation Extraction Algorithm
- Fluent Guide - How to use Fluent of ANSYS
- GPU Mathematica Guide - How to run Wolfram Mathematica with GPU acceleration
- Grace Guide - How to run grace / xmgrace with GUI
- Hadoop Guide - How to use hadoop software
- Intel SDK Guide - How to use Intel Cluster Studio XE 2013 (in progress)
- LAMMPS Guide - How to use LAMMPS
- LS-Dyna Guide - How to use LS-DYNA
- MAPLE Guide - How to use MAPLE on the HPC Cluster
- MATLAB Guide - How to submit MATLAB jobs
- Modules Guide - How to manage and load environment modules
- Motif Guide - How to use Motif on the HPC Cluster
- MPI Guide - A Quick Guide to Programming with MPI
- MPJ Guide - MPJ (Java MPI)
- MPICH2 Guide - How to use MPICH2 on the HPC Cluster
- MVAPICH2 Guide - How to use MVAPICH2 on the HPC Cluster
- NAMD Guide - How to use NAMD on the HPC Cluster
- OpenACC Guide - How to use OpenACC on the HPC Cluster
- OpenMp Usage - how to use OpenMp on the HPC Cluster
- OpenMPI Guide - How to use OpenMPI on the HPC Cluster
- phpbb - How to use phpbb
- Python virtualenv Guide - How to use virtualenv for python
- Qiime Guide - How to use Qiime on the HPC Cluster (in progress)
- R Guide - How to use GNU R on HPC Cluster
- R-LINE Guide - How to use R-LINE on HPC Cluster
- Screenie Guide - How to use Screenie / GNU Screen
- StarCCM Guide - How to use StarCCM (in progress)
- Trinity Guide - How to use the Trinity RNA Sequence Assembler (in progress)
- VASP Guide - How to use VASP
- WINE Guide - How to use WINE on HPC Cluster
- Tensorflow Guide - How to use Tensorflow on HPC Cluster
- Globus(Linux) Guide - How to use Globus command line on HPC Cluster
Other Software Guidelines
BWA
BWA has been compiled to run on the Westmere nodes. When using sbatch, specify --partition=Westmere
$ module load bwa/0.7.5a
GCC
On Westmere nodes which refer to cn01 to cn64.
$ module load gcc/4.7.1
on Sandy Bridge nodes which refer to cn65 to cn104.
$ module load gcc/4.8.2
GEOS-Chem
$ module load intelics/2012.0.032 zlib/1.2.3-ics hdf5/1.8.9-ics netcdf/4.2-ics geos-chem/v9-02
Gromacs
For 5.1.4-plumed-gsl (the default "gromacs" module), the order of modulefiles should follow this command:
$ module load gcc/5.4.0-alt plumed/2-gnu boost/1.61.0-gcc-mpi mpi/openmpi/2.1.0 zlib/1.2.8 fftw/3.3.6-gcc540a gsl gromacs
How to run
When running on Haswell nodes, add
#SBATCH --exclude=cn[65-136,325-343,345-353,355-358,360-364,369-398,400-401],gpu[07-10]
When running on Skylake nodes, add
#SBATCH --exclude=cn[65-136,153-256,265-320,325-328]
Gaussian
$ module load gaussian/g09d01
igraph
$ module load igraph/0.6.5
TrinityRNASeq
$ module load gcc/4.7.1 trinityrnaseq/2013.08.14
