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: 16 or 32
Inputs
Download from https://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: 416 or 32
Input Files
02_Heat.rst: Download from https://githubiu.box.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/Amber/amber
- Heat_Restart_File: 02_Heat.rst
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- 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
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- AMBER_Execution_Summary: 03_Prod.info
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- AMBER_Trajectory_file: 03_Prod.mdcrd
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- AMBER_Execution_log: 03_Prod.out
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- 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: 416
Input Files
pdb1y6l-EM-vacuum.tpr: Download from https://githubiu.box.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/GROMACS/GROMMACS
- GROMOS_Coordinate_File: pdb1y6l-EM-vacuum.gro
- Portable_Input_Binary_File: pdb1y6l-EM-vacuum.tpr
Output Files
pdb1y6l-EM-vacuum.tpr.trr
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pdb1y6l-EM-vacuum.gro
GROMACS.oJobID
LAMMPS
- Walltime: 00:30:00 (30 minutes)
- Number of nodes: 1
- Number of processors/cores: 416
Input Files
in.friction: Download from https://githubiu.box.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/LAMMPS/LAMMPS
Friction_Simulation_Input: in.friction
Output Files
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- LAMMPS_Simulation_Log: log.lammps
- LAMMPS.oJobID
ESPRESSO
Parameters
- Walltime: 00:30:00 (30 minutes)
- Number of nodes: 1
- Number of processors/cores: 416
Input Files
Al.sample.in: Download from https://githubiu.box.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/ESPRESSO/Alespresso
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- AI_Pseudopotential_File: Al.sample.in
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- AI_Primitive_Cell: Al.pz-vbc.UPF
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- ESPRESSO_Execution_Log: Al.sample.out
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- 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: 416
Input Files
water.nw: Download from https://githubiu.box.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/NWCHEM/nwchem
- Water_Molecule_Input: water.nw
Output Files
- NWChem_Execution_Log: nwchem_water.out
h2o_freq.b
h2o_freq.drv.hess
...
h2o_freq.zmat NWCHEM.oJobID
Trinity
- Walltime: 00:30:00 (30 minutes)
- Number of nodes: 1
- Number of processors/cores: 416
Input Files
reads.left.fq: Download from https://github.com/SciGaP/XSEDE-Job-Scripts/blob/master/Stampede/Trinity/iu.box.com/trinity
...
- RNA_Seq_Left_Input: reads.left.fq
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- 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
- Walltime: 00:30:00 (30 minutes)
- Number of nodes: 1
- Number of processors/cores: 416
Input Files
AD4_parameters.dat: Download from https://githubiu.box.com/SciGaP/XSEDE-Job-Scripts/blob/master/BigRed2/Autodock/autodock
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Output Files
ind.dlg Autodock.oJobID (nothing interesting)