Application Cookbook Recipes

Apache Airavata Applications and Available Resource List

Application	Resource List
Abinit	BigRed2
Amber_Sander	BigRed2, Stampede, Comet
AutoDock	BigRed2
CP2K	BigRed2
Echo	BigRed2, Stampede, Comet
Gamess	BigRed2, Gordon
Gaussian	BigRed2, Comet, Gordon
Gromacs	BigRed2, Stampede
Lammps	BigRed2, Stampede, Comet
NEK5000	BigRed2
NWChem	Stampede, Comet
Phasta_P	Stampede
Quantum_Espresso	Stampede, Comet
Tinker_Monte	Stampede
WRF	Stampede

Application Inputs

Inputs for all applications currently available in Airavata can be found in https://iu.box.com/s/9ztdby709kso8siachz16svn2y511nn7

Sample Application Recipes

Abinit

Module

• Name: Abinit
• Description: A package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT)

Interface

• Inputs:
  • Pspgth-Input-File
  • Tbase-Input-File-1
  • Tbase-Input-File-2
• Outputs:
  • Application-Out
  • Standard-Error
  • Standard-Out

Deployment

Resource	Executable Path	Application Parallelism	Module Load Commands
bigred2.uits.iu.edu	/N/soft/cle4/abinit/cpu/7.6.4/bin/abinit	CRAY_MPI	module swap PrgEnv-cray/5.2.40 PrgEnv-gnu/5.2.40; module load netcdf fftw abinit

Amber_sander

• Name: Amber_Sander
• Description: Assisted Model Building with Energy Refinement MD Package
• Inputs:
  • Heat-Restart-File
  • Parameter-Topology-File
  • Production-Control-File
• Outputs:
  • Amber-Execution-log
  • Amber-Execution-Summary
  • Amber-Restart-File
  • Amber-Trajectory-File
  • Standard-Error
  • Standard-Out
• Deployment

Resource	Executable Path	Application Parallelism	Module Load Commands
bigred2.uits.iu.edu	/N/soft/cle4/amber/gnu/mpi/12/amber12/bin/sander.MPI -O	MPI	module load amber/gnu/mpi/12; module swap PrgEnv-cray PrgEnv-gnu
stampede.tacc.xsede.org	/opt/apps/intel13/mvapich2_1_9/amber/12.0/bin/sander.MPI -O	MPI	module load amber
comet.sdsc.edu	/opt/amber/bin/sander.MPI	MPI	module load amber

AutoDock

• Name: AutoDock
• Description: AutoDock suite of automated docking tools
• Inputs:
  • HSG1-Maps-FLD
  • Input-File-DAT
  • Input-File-DPF
• Outputs:
  • Standard-Error
  • Standard-Out
• Deployment

Resource	Executable Path	Application Parallelism	Module Load Commands
bigred2.uits.iu.edu	/N/soft/cle4/autodock/4.2/bin/autodock4	MPI	module load autodock/4.2

CP2K

• Name: CP2K
• Description: CP2K Test Application Module
• Inputs:
  • Input-File-INP
• Outputs:
  • CP2K-Application-Output
  • Standard-Error
  • Standard-Out
• Deployment

Resource	Executable Path	Application Parallelism	Module Load Commands
comet.sdsc.edu	/opt/cp2k/bin/cp2k.popt	MPI	module load cp2k

Echo

• Name: CP2K
• Description: A Simple Echo Application
• Inputs:
  • Input-to-Echo
• Outputs:
  • Standard-Error
  • Standard-Out
• Deployment

Resource	Executable Path	Application Parallelism	Module Load Commands
bigred2.uits.iu.edu	/N/u/seagrid/BigRed2/production/app_wrappers/echo_wrapper.sh	SERIAL
stampede.tacc.xsede.org	/home1/02731/scigap/apps/echo_wrapper.sh	SERIAL
comet.sdsc.edu	/home/scigap/apps/echo_wrapper.sh	SERIAL