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

AMBER

Table of Contents

WRF

Parameters

• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 16 or 32

Inputs

Download from 02_Heat.rst: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/Amber/iu.box.com/wrf

• Config_Namelist_File: namelist.input 
• WRF_Boundary_File: wrfbdy_d01
• WRF_Initial_Conditions: wrfinput_d01 

Outputs

AMBER

Parameters

• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 16 or 32

Input Files

Download from https://iu.box.com/amber

• Heat_Restart_File: 02_Heat.rst

...

• Parameter_Topology_File: prmtop
• Production_Control_File: 03_Prod.in

...

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

Output Files

• AMBER_Execution_Summary: 03_Prod.info
• AMBER_Trajectory_file: 03_Prod.mdcrd
• AMBER_Execution_log: 03_Prod.out
• AMBER_Restart_file: 03_Prod.rst
• Amber.oJobID (nothing interesting)

GROMACS

Parameters

• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 16

Input Files

Download from https://iu.box.com/GROMMACS

• GROMOS_Coordinate_File: pdb1y6l-EM-vacuum.gro
• Portable_Input_Binary_File: pdb1y6l-EM-vacuum.tpr

Output Files

...

pdb1y6l-EM-vacuum.tpr: .trr

pdb1y6l-EM-vacuum.tpr.edr

https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/GROMACS/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: 16

Input Files

Download from in.friction: https://githubiu.box.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/LAMMPS/LAMMPS

• Friction_Simulation_Input: in.friction

ESPRESSO

Output Files

• LAMMPS_Simulation_Log: log.lammps
• LAMMPS.oJobID

ESPRESSO

Parameters

• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 16

Input Files

Download from Al.sample.in: https://githubiu.box.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/ESPRESSO/Alespresso

• AI_Pseudopotential_File: Al.sample.in

...

• AI_Primitive_Cell: Al.pz-vbc.UPF

...

• Output Files

• ESPRESSO_Execution_Log: Al.sample.out
• ESPRESSO_WFC_Binary_file: 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: 16

Input Files

Download from https://iu.box.com/nwchem

• Water_Molecule_Input: water.nw

Output Files

• NWChem_Execution_Log: nwchem_water.out

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: 16

Input Files

Download from https://iu.box.com/trinity

• RNA_Seq_Left_Input: reads.left.fq
• RNA_Seq_Right_Input: reads.right.fq

Output Files

• Trinity_Execution_Log: Trinity - Everything under the specified Output directory
• Trinity_FASTA_File: 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

Autodock

Parameters

• Walltime: 00:30:00 (30 minutes)
• Number of nodes: 1
• Number of processors/cores: 16

Input Files

Download from https://iu.box.com/autodock

NWCHEM

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

Trinity

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

Autodock

AD4_parameters.dat: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/BigRed2/Autodock/AD4_parameters.dat

hsg1.A.map: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/BigRed2/Autodock/hsg1.A.map

hsg1.C.map: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/BigRed2/Autodock/hsg1.C.map

hsg1.d.map: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/BigRed2/Autodock/hsg1.d.map

hsg1.e.map: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/BigRed2/Autodock/hsg1.e.map

hsg1.HD.map: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/BigRed2/Autodock/hsg1.HD.map

...

• AD4_parameters.dat
• hsg1.A.map
• hsg1.C.map
• hsg1.d.map
• hsg1.e.map
• hsg1.HD.map

• hsg1.maps.fld
• hsg1.NA.map

...

• hsg1.N.map

...

• hsg1.OA.map

...

• ind.dpf
• ind.pdbqt

Output Files

ind.dlg Autodock.oJobID (nothing interesting): https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/BigRed2/Autodock/ind.dpfind.pdbqt: https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/BigRed2/Autodock/ind.pdbqt