You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@airavata.apache.org by er...@apache.org on 2017/02/15 16:05:06 UTC
airavata-docs git commit: Removed the recipes since admin tutorials
are added.
Repository: airavata-docs
Updated Branches:
refs/heads/master e74b4a145 -> e0a2c13f4
Removed the recipes since admin tutorials are added.
Project: http://git-wip-us.apache.org/repos/asf/airavata-docs/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata-docs/commit/e0a2c13f
Tree: http://git-wip-us.apache.org/repos/asf/airavata-docs/tree/e0a2c13f
Diff: http://git-wip-us.apache.org/repos/asf/airavata-docs/diff/e0a2c13f
Branch: refs/heads/master
Commit: e0a2c13f427e3a24db44ff4bdb7f8b5887430af7
Parents: e74b4a1
Author: Eroma Abeysinghe <er...@gmail.com>
Authored: Wed Feb 15 11:05:02 2017 -0500
Committer: Eroma Abeysinghe <er...@gmail.com>
Committed: Wed Feb 15 11:05:02 2017 -0500
----------------------------------------------------------------------
Application-CookBook.md | 150 +++++++++++--------------------------------
1 file changed, 36 insertions(+), 114 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/airavata-docs/blob/e0a2c13f/Application-CookBook.md
----------------------------------------------------------------------
diff --git a/Application-CookBook.md b/Application-CookBook.md
index 643db25..ae69e4e 100644
--- a/Application-CookBook.md
+++ b/Application-CookBook.md
@@ -1,121 +1,43 @@
-## 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 |
+## Applications to Run in Gateway
+
+### Few Applications Supported by Airavata
+This list contains a sub section of application supported via gateways linked to Airavata.
+We can help you to run these in your own gateway.
+
+| Application | Availability |
+|:----------------- |:------------------------------------- |
+| Abaqus | Comet |
+| Abaqus-6.13-3 | Comet |
+| Abinit | BigRed, Bridges, Comet |
+| Amber_Sander | BigRed, Comet, Stampede |
+| AutoDock | BigRed, Karst |
+| AutoDock_Vina | Comet, Stampede |
+| CP2K | Comet, Stampede |
+| CPMD | Comet |
+| DDSCat | Comet |
+| DFTB+ | Stampede |
+| Gamess | BigRed, Comet, Gordon, Stampede |
+| Gaussian | BigRed. Bridges, Comet, Gordon |
+| Gaussian16 | Bridges |
+| Gromacs | BigRed, Bridges, Comet, Stampede |
+| Lammps | BigRed, Comet, Gordon, Stampede |
+| Molcas | Stampede KNL, Stampede |
+| NEK5000 | BigRed |
+| NWChem | Comet, Stampede |
+| Phasta_P | Stampede |
+| PSI4.0 | Comet |
+| QChem | Comet |
+| Quantum_Espresso | Comet, Bridges, JetStream, Stampede |
+| Tinker_Monte | Stampede |
+| Trinity | Karst |
+| 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 |
+Inputs for all applications currently available in Airavata can be found <a href="https://iu.box.com/s/9ztdby709kso8siachz16svn2y511nn7" target="_blank">Here!</a>
-##### 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 | |
+### Application Configuration
+For sample configurations please refer <a href="/Admin-Tutorials" target="_blank">Admin Tutorials</a>
\ No newline at end of file