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Sun, 13 Jul 2014 13:59:44 +0000 (UTC) Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit From: smarru@apache.org To: commits@airavata.apache.org Date: Sun, 13 Jul 2014 13:59:44 -0000 Message-Id: <744738c4e036476ba90f078f0b9a8a14@git.apache.org> X-Mailer: ASF-Git Admin Mailer Subject: [1/2] git commit: Updating Identifiers Repository: airavata Updated Branches: refs/heads/master b0618e404 -> 1a223e8c0 Updating Identifiers Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/d83a8441 Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/d83a8441 Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/d83a8441 Branch: refs/heads/master Commit: d83a84416e6785a00cfa558ffa7aad87192ab88b Parents: 16d2d38 Author: Suresh Marru Authored: Sun Jul 13 09:59:29 2014 -0400 Committer: Suresh Marru Committed: Sun Jul 13 09:59:29 2014 -0400 ---------------------------------------------------------------------- .../resources/conf/app-catalog-identifiers.ini | 26 ++++---- .../tools/RegisterSampleApplications.java | 70 ++++++++++---------- 2 files changed, 48 insertions(+), 48 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/d83a8441/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini index 3b3cb85..672a566 100644 --- a/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini +++ b/airavata-api/airavata-client-sdks/airavata-php-sdk/src/main/resources/conf/app-catalog-identifiers.ini @@ -1,14 +1,14 @@ #Apache Airavata Gateway to Airavata Deployment Identifiers -#Sat Jul 12 18:13:37 EDT 2014 -espressoInterfaceId=ESPRESSO_a9c3acd6-4403-445b-b555-d4dbcc53afdb -amberInterfaceId=Amber_26a8a2eb-a5a1-460f-a9c3-9bc5899433b3 -gromacsInterfaceId=GROMACS_c720c8f6-8b70-40be-b228-5f9ea72869f9 -trinityInterfaceId=Trinity_6068b270-157e-4ea0-9ec8-b2757b33a147 -stampedeResourceId=stampede.tacc.xsede.org_3da3cb46-851e-4124-a7bd-37449ca057a8 -bigredResourceId=bigred2.uits.iu.edu_fa40aa10-3703-48c6-a14c-c186d772cd58 -trestlesResourceId=trestles.sdsc.xsede.org_30fb9af6-7cd3-4373-87e4-9987e43cc904 -wrfInterfaceId=WRF_c3c67d74-5e60-4ec6-b50d-9a5d61843296 -autoDockInterfaceId=AutoDock_22c4cbbf-7785-4f96-85c6-8fe8404df6c8 -nwChemInterfaceId=NWChem_574c944e-b376-4e83-9871-96e4c9559a89 -lammpsInterfaceId=LAMMPS_752f3ea6-4ae5-4636-9dba-a6efeb1c4da9 -echoInterfaceId=Echo_c024a9c1-29b2-444d-b523-0729c6679ebb +#Sun Jul 13 09:56:36 EDT 2014 +espressoInterfaceId=ESPRESSO_e13adcc6-5e6f-4660-a206-8ff0dada929f +amberInterfaceId=Amber_7a99cdde-5cc1-423a-8ec9-47eddc809a9a +gromacsInterfaceId=GROMACS_91ce8f05-c895-486e-8fc1-c1480d642754 +trinityInterfaceId=Trinity_9ae8f626-f263-44e1-8106-f18101337aa0 +stampedeResourceId=stampede.tacc.xsede.org_0a91c584-6814-48db-a7e2-723596a66d9f +bigredResourceId=bigred2.uits.iu.edu_815a893b-d0a9-4798-a35f-27ea185a49fb +trestlesResourceId=trestles.sdsc.xsede.org_b39751f9-1d02-4123-a797-41cfc2f050ad +wrfInterfaceId=WRF_2957c31f-bd36-430a-8403-97f87f34958f +autoDockInterfaceId= +nwChemInterfaceId=NWChem_3aa63bba-d86d-4c4b-b3d6-588da6519752 +lammpsInterfaceId=LAMMPS_0646b241-2a94-4de7-8518-1fbfd01b1c83 +echoInterfaceId=Echo_c6e6aaac-7d9d-44fc-aba2-63b5100528e8 http://git-wip-us.apache.org/repos/asf/airavata/blob/d83a8441/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java index ddc4848..781c216 100644 --- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java +++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplications.java @@ -86,10 +86,10 @@ public class RegisterSampleApplications { private static String echoModuleId; private static String amberModuleId; private static String autoDockModuleId; - private static String espressoModuleId; + private static String espressoModuleId = "ESPRESSO_54dc94da-5e2b-4add-b054-41ad88891fdc"; private static String gromacsModuleId = "GROMACS_417271fd-7ac1-4f40-b2a5-ed0908a743eb"; private static String lammpsModuleId; - private static String nwChemModuleId; + private static String nwChemModuleId = "NWChem_edbc318d-4c41-46a7-b216-32bad71eabdd"; private static String trinityModuleId = "Trinity_8af45ca0-b628-4614-9087-c7b73f5f2fb6"; private static String wrfModuleId; @@ -245,7 +245,7 @@ public class RegisterSampleApplications { registerAmberInterface(); //Registering AutoDock - registerAutoDockInterface(); +// registerAutoDockInterface(); //Registering Espresso registerEspressoInterface(); @@ -304,13 +304,13 @@ public class RegisterSampleApplications { appModules.add(amberModuleId); InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Heat_Restart_File", null, - DataType.URI, null, false, "Heating up the system equilibration stage", null); + DataType.URI, null, false, "Heating up the system equilibration stage - 02_Heat.rst", null); InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("Production_Control_File", null, - DataType.URI, null, false, "Constant pressure and temperature for production stage", null); + DataType.URI, null, false, "Constant pressure and temperature for production stage - 03_Prod.in", null); InputDataObjectType input3 = RegisterSampleApplicationsUtils.createAppInput("Parameter_Topology_File", null, - DataType.URI, null, false, "Parameter and Topology coordinates", null); + DataType.URI, null, false, "Parameter and Topology coordinates - prmtop", null); List applicationInputs = new ArrayList(); applicationInputs.add(input1); @@ -383,20 +383,21 @@ public class RegisterSampleApplications { appModules.add(espressoModuleId); InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("AI_Primitive_Cell", null, - DataType.URI, null, false, "AI_Metal_Input_File", null); + DataType.URI, null, false, "AI_Metal_Input_File - Al.sample.in", null); InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("AI_Pseudopotential_File", null, - DataType.URI, null, false, "Constant pressure and temperature for production stage", null); + DataType.URI, null, false, "Constant pressure and temperature for production stage - Al.pz-vbc.UPF", null); List applicationInputs = new ArrayList(); applicationInputs.add(input1); applicationInputs.add(input2); - OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Echoed_Output", - "", DataType.STRING); + OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("ESPRESSO_Execution_Log",null,DataType.URI); + OutputDataObjectType output2 = RegisterSampleApplicationsUtils.createAppOutput("ESPRESSO_WFC_Binary_file",null,DataType.URI); List applicationOutputs = new ArrayList(); applicationOutputs.add(output1); + applicationOutputs.add(output2); espressoInterfaceId = airavataClient.registerApplicationInterface( RegisterSampleApplicationsUtils.createApplicationInterfaceDescription(espressoName, espressoDescription, @@ -416,10 +417,10 @@ public class RegisterSampleApplications { appModules.add(gromacsModuleId); InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Portable_Input_Binary_File", null, - DataType.URI, null, false, "Coordinates velocities, molecular topology and simulation parameters", null); + DataType.URI, null, false, "Coordinates velocities, molecular topology and simulation parameters - pdb1y6l-EM-vacuum.tpr", null); InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("GROMOS_Coordinate_File", null, - DataType.URI, null, false, "Trajectory Coordinates Molecular Structure in Gromos87 format", null); + DataType.URI, null, false, "Trajectory Coordinates Molecular Structure in Gromos87 format - pdb1y6l-EM-vacuum.gro", null); List applicationInputs = new ArrayList(); applicationInputs.add(input1); @@ -452,7 +453,7 @@ public class RegisterSampleApplications { appModules.add(lammpsModuleId); InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Friction_Simulation_Input", null, - DataType.URI, null, false, "Friction Simulation Input", null); + DataType.URI, null, false, "Friction Simulation Input - in.friction", null); List applicationInputs = new ArrayList(); applicationInputs.add(input1); @@ -480,13 +481,12 @@ public class RegisterSampleApplications { appModules.add(nwChemModuleId); InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Water_Molecule_Input", null, - DataType.URI, null, false, "Water Molecule Input File", null); + DataType.URI, null, false, "Water Molecule Input File - water.nw", null); List applicationInputs = new ArrayList(); applicationInputs.add(input1); - OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("Echoed_Output", - "", DataType.STRING); + OutputDataObjectType output1 = RegisterSampleApplicationsUtils.createAppOutput("NWChem_Execution_Log",null,DataType.URI); List applicationOutputs = new ArrayList(); applicationOutputs.add(output1); @@ -510,10 +510,10 @@ public class RegisterSampleApplications { appModules.add(trinityModuleId); InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("RNA_Seq_Left_Input", null, - DataType.URI, null, false, "RNA-Seq Left Library", null); + DataType.URI, null, false, "RNA-Seq Left Library - reads.left.fq", null); InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("RNA_Seq_Right_Input", null, - DataType.URI, null, false, "RNA-Seq Right Library", null); + DataType.URI, null, false, "RNA-Seq Right Library - reads.right.fq", null); List applicationInputs = new ArrayList(); applicationInputs.add(input1); @@ -545,13 +545,13 @@ public class RegisterSampleApplications { appModules.add(wrfModuleId); InputDataObjectType input1 = RegisterSampleApplicationsUtils.createAppInput("Config_Namelist_File", null, - DataType.URI, null, false, "Namelist Configuration File", null); + DataType.URI, null, false, "Namelist Configuration File - namelist.input", null); InputDataObjectType input2 = RegisterSampleApplicationsUtils.createAppInput("WRF_Initial_Conditions", null, - DataType.URI, null, false, "Initial Conditions File", null); + DataType.URI, null, false, "Initial Conditions File - wrfinput_d01", null); InputDataObjectType input3 = RegisterSampleApplicationsUtils.createAppInput("WRF_Boundary_File", null, - DataType.URI, null, false, "Boundary Conditions File", null); + DataType.URI, null, false, "Boundary Conditions File - wrfbdy_d01", null); List applicationInputs = new ArrayList(); applicationInputs.add(input1); @@ -697,24 +697,24 @@ public class RegisterSampleApplications { //Register AutoDock String autoDockDeployId = airavataClient.registerApplicationDeployment( - RegisterSampleApplicationsUtils.createApplicationDeployment(nwChemModuleId, bigredResourceId, + RegisterSampleApplicationsUtils.createApplicationDeployment(autoDockModuleId, bigredResourceId, "/N/u/cgateway/BigRed2/production/app_wrappers/auto_dock_wrapper.sh", ApplicationParallelismType.MPI, autoDockDescription)); System.out.println("AutoDock on bigredII deployment Id " + autoDockDeployId); - //Register GROMACS - String gromacsAppDeployId = airavataClient.registerApplicationDeployment( - RegisterSampleApplicationsUtils.createApplicationDeployment(gromacsModuleId, bigredResourceId, - "/N/u/cgateway/BigRed2/production/app_wrappers/gromacs_wrapper.sh", ApplicationParallelismType.MPI, - gromacsDescription)); - System.out.println("GROMACS on bigredII deployment Id " + gromacsAppDeployId); - - //Register LAMMPS - String lammpsAppDeployId = airavataClient.registerApplicationDeployment( - RegisterSampleApplicationsUtils.createApplicationDeployment(lammpsModuleId, bigredResourceId, - "/N/u/cgateway/BigRed2/production/app_wrappers/lammps_wrapper.sh", ApplicationParallelismType.MPI, - lammpsDescription)); - System.out.println("LAMMPS on bigredII deployment Id " + lammpsAppDeployId); +// //Register GROMACS +// String gromacsAppDeployId = airavataClient.registerApplicationDeployment( +// RegisterSampleApplicationsUtils.createApplicationDeployment(gromacsModuleId, bigredResourceId, +// "/N/u/cgateway/BigRed2/production/app_wrappers/gromacs_wrapper.sh", ApplicationParallelismType.MPI, +// gromacsDescription)); +// System.out.println("GROMACS on bigredII deployment Id " + gromacsAppDeployId); +// +// //Register LAMMPS +// String lammpsAppDeployId = airavataClient.registerApplicationDeployment( +// RegisterSampleApplicationsUtils.createApplicationDeployment(lammpsModuleId, bigredResourceId, +// "/N/u/cgateway/BigRed2/production/app_wrappers/lammps_wrapper.sh", ApplicationParallelismType.MPI, +// lammpsDescription)); +// System.out.println("LAMMPS on bigredII deployment Id " + lammpsAppDeployId); } catch (TException e) { e.printStackTrace();