XSEDE14 Gateway Tutorial Application Input Files and Parameters

All inputs files are taken from public tutorials. See https://github.com/SciGaP/XSEDE-Job-Scripts/ for sources.

WRF

Parameters

Walltime: 00:30:00 (30 minutes)
Number of nodes: 1
Number of processors/cores: 4

Inputs

namelist.input - https://raw.github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/WRF/namelist.input

wrfbdy_d01 - https://raw.github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/WRF/wrfbdy_d01

wrfinput_d01 - https://raw.github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/WRF/wrfinput_d01

Outputs

AMBER

Parameters

Walltime: 00:30:00 (30 minutes)
Number of nodes: 1
Number of processors/cores: 4

Input Files

02_Heat.rst: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/Amber/02_Heat.rst

03_Prod.in: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/Amber/03_Prod.in

prmtop: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/Amber/prmtop

Output Files

03_Prod.info

03_Prod.mdcrd

03_Prod.out

03_Prod.rst

Amber.oJobID (nothing interesting)

GROMACS

Parameters

Walltime: 00:30:00 (30 minutes)
Number of nodes: 1
Number of processors/cores: 4

Input Files

pdb1y6l-EM-vacuum.tpr: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/GROMACS/pdb1y6l-EM-vacuum.tpr

Output Files

pdb1y6l-EM-vacuum.tpr.trr

pdb1y6l-EM-vacuum.tpr.edr

pdb1y6l-EM-vacuum.tpr.log

pdb1y6l-EM-vacuum.gro

GROMACS.oJobID

LAMMPS

Parameters

Walltime: 00:30:00 (30 minutes)
Number of nodes: 1
Number of processors/cores: 4

Input Files

in.friction: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/LAMMPS/in.friction

Output Files

log.lammps

LAMMPS.oJobID

ESPRESSO

Parameters

Walltime: 00:30:00 (30 minutes)
Number of nodes: 1
Number of processors/cores: 4

Input Files

Al.sample.in: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/ESPRESSO/Al.sample.in

Al.pz-vbc.UPF: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/ESPRESSO/Al.pz-vbc.UPF

Output Files

Al.sample.out

Al_exc3.save/ (directory)

Al_exc3.wfc1

Al_exc3.wfc2

Al_exc3.wfc3

Al_exc3.wfc4 ESPRESSO.oJobID (nothing)

NWCHEM

Parameters

Walltime: 00:30:00 (30 minutes)
Number of nodes: 1
Number of processors/cores: 4

Input Files

water.nw: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/NWCHEM/water.nw

Output Files

h2o_freq.b

h2o_freq.drv.hess

h2o_freq.mp2nos

h2o_freq.b^-1

h2o_freq.fd_ddipole

h2o_freq.nmode

h2o_freq.c

h2o_freq.hess

h2o_freq.p

h2o_freq.db

h2o_freq.movecs

h2o_freq.zmat NWCHEM.oJobID

Trinity

Parameters

Walltime: 00:30:00 (30 minutes)
Number of nodes: 1
Number of processors/cores: 4

Input Files

reads.left.fq: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/Trinity/reads.left.fq

reads.right.fq: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/Trinity/reads.right.fq

Output Files

Trinity: Everything under the specified Output directory

Trinity.fasta (most interesting maybe)

Trinity.oJobID

Example Output Directory Contents

both.fa                         jellyfish.kmers.fa
both.fa.read_count              scaffolding_entries.sam
bowtie.nameSorted.sam           target.1.ebwt
bowtie.nameSorted.sam.finished  target.2.ebwt
bowtie.out.finished             target.3.ebwt
chrysalis                       target.4.ebwt
inchworm.K25.L25.fa             target.fa
inchworm.K25.L25.fa.finished    target.fa.finished
inchworm.kmer_count             target.rev.1.ebwt
iworm_bundle_file_listing.txt   target.rev.2.ebwt
iworm_scaffolds.txt             Trinity.fasta
iworm_scaffolds.txt.finished    Trinity.timing
jellyfish.1.finished