Difference between revisions of "HPC Software"
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module load fluent | module load fluent | ||
Next, with an input script foo.txt, run | Next, with an input script foo.txt, run | ||
| − | bsub fluent 3d -g -i | + | bsub -n $nprocs -Is fluent 3d -t$nprocs -g -i journal-file -lsf |
foo.txt must refer to a .cas input file. 3d is one of | foo.txt must refer to a .cas input file. 3d is one of | ||
2d 2ddp_host 2d_host 3d 3ddp_host 3d_host | 2d 2ddp_host 2d_host 3d 3ddp_host 3d_host | ||
2ddp 2ddp_node 2d_node 3ddp 3ddp_node 3d_node | 2ddp 2ddp_node 2d_node 3ddp 3ddp_node 3d_node | ||
| + | $nprocs indicates the number of cores you need to run the job. Two $nprocs must be the same number. -g indicates no gui. For example, to start a job with 12 cores: | ||
| + | bsub -n 12 -Is fluent 3d -t12 -g -i journal-file -lsf | ||
===GCC=== | ===GCC=== | ||
Revision as of 14:21, 22 July 2014
- List of software installed on the HORNET cluster
Contents
Software Guides
- Abaqus Guide - How to use Abaqus FEA 6.12
- Comsol Guide - How to use COMSOL on Hornet Cluster
- DXA Guide - How to use Dislocation Extraction Algorithm
- 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)
- LS-Dyna Guide - How to use LS-DYNA
- MAPLE Guide - How to use MAPLE on Hornet cluster
- MATLAB Guide - How to submit MATLAB jobs
- Modules Guide - How to manage and load environment modules
- MPI Guide - A Quick Guide to Programming with MPI
- MPJ Guide - MPJ (Java MPI)
- MPICH2 Guide - How to use MPICH2 on the Hornet cluster
- NAMD Guide - How to use NAMD on the Hornet cluster
- OpenACC Guide - How to use OpenACC on the Hornet cluster
- OpenMp Usage - how to use OpenMp on the Hornet cluster
- phpbb - How to use phpbb
- Python virtualenv Guide - How to use virtualenv for python
- Qiime Guide - How to use Qiime on the Hornet cluster (in progress)
- R Guide - How to use GNU R on Hornet 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
Other Software Guidelines
BWA
BWA is only available in the Westmere nodes. i.e. hornet-login1.engr.uconn.edu and hornet.engr.uconn.edu
$ module load bwa/0.7.5a
fluent
First load the fluent module
module load fluent
Next, with an input script foo.txt, run
bsub -n $nprocs -Is fluent 3d -t$nprocs -g -i journal-file -lsf
foo.txt must refer to a .cas input file. 3d is one of
2d 2ddp_host 2d_host 3d 3ddp_host 3d_host 2ddp 2ddp_node 2d_node 3ddp 3ddp_node 3d_node
$nprocs indicates the number of cores you need to run the job. Two $nprocs must be the same number. -g indicates no gui. For example, to start a job with 12 cores:
bsub -n 12 -Is fluent 3d -t12 -g -i journal-file -lsf
GCC
On Westmere nodes which refer to cn01 to cn64. Login node: hornet.engr.uconn.edu or hronet-login1.engr.uconn.edu
$ module load gcc/4.7.1
on Sandy Bridge nodes which refer to cn65 to cn104. Login node: hornet-login1.engr.uconn.edu
$ 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 4.6.5 with plumed on the Westmere nodes (hornet.engr.uconn.edu). The order of modulefiles should follow this command.
$ module load gcc/4.7.1 intelcis/2013.1.039-full gromacs/4.6.5-plumed
Gaussian
$ module load gaussian/g09d01
igraph
$ module load igraph/0.6.5
LAMMPS
$ module load lammps/23Sep13
motif
$ module load motif/2.3.4
R-LINE
$ module load rline/1.2
Then run:
$ RLINE
TrinityRNASeq
$ module load gcc/4.7.1 trinityrnaseq/2013.08.14
WINE
WINE is used to execute windows application on linux, but we do not recommend user to do so. You can send email to hpchelp@engr.uconn.edu to request installation of software in linux for help.
To load WINE,
$ module load wine/1.1.27-withoutX
