Repository: airavata Updated Branches: refs/heads/develop d66d16980 -> 833de75a3
adding parallelism types Project: http://git-wip-us.apache.org/repos/asf/airavata/repo Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/833de75a Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/833de75a Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/833de75a Branch: refs/heads/develop Commit: 833de75a3e27621bc151f6cc6bae39b47e101c7a Parents: d66d169 Author: Chathuri Wimalasena <[email protected]> Authored: Fri Feb 26 17:00:25 2016 -0500 Committer: Chathuri Wimalasena <[email protected]> Committed: Fri Feb 26 17:00:25 2016 -0500 ---------------------------------------------------------------------- .../client/samples/RegisterSampleData.java | 2 +- .../tools/RegisterOGCEUS3Application.java | 2 +- .../tools/RegisterSampleApplications.java | 2 +- .../tools/RegisterSampleApplicationsUtils.java | 2 +- .../client/tools/RegisterUS3Application.java | 2 +- .../apache/airavata/gfac/core/GFacUtils.java | 28 +++++--------------- .../task/utils/bes/ApplicationProcessor.java | 2 +- .../catalog/impl/ApplicationDeploymentImpl.java | 2 +- .../ApplicationRegister.java | 2 +- 9 files changed, 14 insertions(+), 30 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/airavata/blob/833de75a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/RegisterSampleData.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/RegisterSampleData.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/RegisterSampleData.java index 557b208..c737695 100644 --- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/RegisterSampleData.java +++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/samples/RegisterSampleData.java @@ -24,7 +24,6 @@ package org.apache.airavata.client.samples; import org.apache.airavata.api.Airavata; import org.apache.airavata.api.client.AiravataClientFactory; import org.apache.airavata.client.tools.RegisterSampleApplicationsUtils; -import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType; import org.apache.airavata.model.appcatalog.computeresource.ComputeResourceDescription; import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionInterface; import org.apache.airavata.model.appcatalog.computeresource.JobSubmissionProtocol; @@ -39,6 +38,7 @@ import org.apache.airavata.model.application.io.OutputDataObjectType; import org.apache.airavata.model.data.movement.DataMovementInterface; import org.apache.airavata.model.data.movement.DataMovementProtocol; import org.apache.airavata.model.error.AiravataClientException; +import org.apache.airavata.model.parallelism.ApplicationParallelismType; import org.apache.airavata.model.security.AuthzToken; import org.apache.airavata.model.workspace.Gateway; import org.apache.thrift.TException; http://git-wip-us.apache.org/repos/asf/airavata/blob/833de75a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterOGCEUS3Application.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterOGCEUS3Application.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterOGCEUS3Application.java index 6ed6a78..b95cdd7 100644 --- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterOGCEUS3Application.java +++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterOGCEUS3Application.java @@ -23,7 +23,6 @@ package org.apache.airavata.client.tools; import org.apache.airavata.api.Airavata; import org.apache.airavata.api.client.AiravataClientFactory; -import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType; import org.apache.airavata.model.appcatalog.computeresource.*; import org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference; import org.apache.airavata.model.appcatalog.gatewayprofile.GatewayResourceProfile; @@ -34,6 +33,7 @@ import org.apache.airavata.model.data.movement.DMType; import org.apache.airavata.model.data.movement.SCPDataMovement; import org.apache.airavata.model.data.movement.SecurityProtocol; import org.apache.airavata.model.error.AiravataClientException; +import org.apache.airavata.model.parallelism.ApplicationParallelismType; import org.apache.airavata.model.security.AuthzToken; import org.apache.thrift.TException; import org.slf4j.Logger; http://git-wip-us.apache.org/repos/asf/airavata/blob/833de75a/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 836c88d..7c2a648 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 @@ -24,7 +24,6 @@ import org.apache.airavata.api.Airavata; import org.apache.airavata.api.client.AiravataClientFactory; import org.apache.airavata.client.samples.CreateLaunchExperiment; import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription; -import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType; import org.apache.airavata.model.appcatalog.appdeployment.CommandObject; import org.apache.airavata.model.appcatalog.computeresource.*; import org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference; @@ -37,6 +36,7 @@ import org.apache.airavata.model.data.movement.DataMovementProtocol; import org.apache.airavata.model.data.movement.SCPDataMovement; import org.apache.airavata.model.data.movement.SecurityProtocol; import org.apache.airavata.model.error.AiravataClientException; +import org.apache.airavata.model.parallelism.ApplicationParallelismType; import org.apache.airavata.model.security.AuthzToken; import org.apache.thrift.TException; import org.slf4j.Logger; http://git-wip-us.apache.org/repos/asf/airavata/blob/833de75a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplicationsUtils.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplicationsUtils.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplicationsUtils.java index dfe6b80..202b9a0 100644 --- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplicationsUtils.java +++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterSampleApplicationsUtils.java @@ -23,7 +23,6 @@ package org.apache.airavata.client.tools; import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription; import org.apache.airavata.model.appcatalog.appdeployment.ApplicationModule; -import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType; import org.apache.airavata.model.appcatalog.appdeployment.CommandObject; import org.apache.airavata.model.appcatalog.appinterface.*; import org.apache.airavata.model.appcatalog.computeresource.*; @@ -33,6 +32,7 @@ import org.apache.airavata.model.application.io.InputDataObjectType; import org.apache.airavata.model.application.io.OutputDataObjectType; import org.apache.airavata.model.data.movement.DataMovementInterface; import org.apache.airavata.model.data.movement.DataMovementProtocol; +import org.apache.airavata.model.parallelism.ApplicationParallelismType; import java.util.List; import java.util.Map; http://git-wip-us.apache.org/repos/asf/airavata/blob/833de75a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterUS3Application.java ---------------------------------------------------------------------- diff --git a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterUS3Application.java b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterUS3Application.java index 9523389..20c5474 100644 --- a/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterUS3Application.java +++ b/airavata-api/airavata-client-sdks/java-client-samples/src/main/java/org/apache/airavata/client/tools/RegisterUS3Application.java @@ -23,7 +23,6 @@ package org.apache.airavata.client.tools; import org.apache.airavata.api.Airavata; import org.apache.airavata.api.client.AiravataClientFactory; -import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType; import org.apache.airavata.model.appcatalog.computeresource.*; import org.apache.airavata.model.appcatalog.gatewayprofile.ComputeResourcePreference; import org.apache.airavata.model.appcatalog.gatewayprofile.GatewayResourceProfile; @@ -34,6 +33,7 @@ import org.apache.airavata.model.data.movement.DMType; import org.apache.airavata.model.data.movement.SCPDataMovement; import org.apache.airavata.model.data.movement.SecurityProtocol; import org.apache.airavata.model.error.AiravataClientException; +import org.apache.airavata.model.parallelism.ApplicationParallelismType; import org.apache.airavata.model.security.AuthzToken; import org.apache.thrift.TException; import org.slf4j.Logger; http://git-wip-us.apache.org/repos/asf/airavata/blob/833de75a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java index 1325659..aa44fc6 100644 --- a/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java +++ b/modules/gfac/gfac-core/src/main/java/org/apache/airavata/gfac/core/GFacUtils.java @@ -596,33 +596,17 @@ public class GFacUtils { } ApplicationParallelismType parallelism = appDepDescription.getParallelism(); + Map<ApplicationParallelismType, String> parallelismPrefix = processContext.getResourceJobManager().getParallelismPrefix(); if (parallelism != null) { if (parallelism != ApplicationParallelismType.SERIAL) { - // FIXME this needs to be fixed once parallaliasation retrieved by app catalog - if (appDepDescription.getComputeHostId().contains("stampede")){ - jobDescriptor.setJobSubmitter("ibrun"); - }else if (appDepDescription.getComputeHostId().contains("bigred2")){ - if (parallelism == ApplicationParallelismType.CRAY_MPI){ - if (processModel.getApplicationInterfaceId().contains("Lammps")){ - jobDescriptor.setJobSubmitter("aprun -N 1 -n"); - }else { - jobDescriptor.setJobSubmitter("aprun -n"); - } - }else if (parallelism == ApplicationParallelismType.CCM){ - jobDescriptor.setJobSubmitter("ccmrun"); + if (parallelismPrefix != null){ + String parallelismCommand = parallelismPrefix.get(parallelism); + if (parallelismCommand != null){ + jobDescriptor.setJobSubmitter(parallelismCommand); }else { - jobDescriptor.setJobSubmitter("aprun -n"); + throw new GFacException("Parallelism prefix is not defined for given parallelism type " + parallelism + ".. Please define the parallelism prefix at App Catalog"); } - }else if (appDepDescription.getComputeHostId().contains("comet")){ - jobDescriptor.setJobSubmitter("mpiexec"); - }else if (appDepDescription.getComputeHostId().contains("gordon")){ - jobDescriptor.setJobSubmitter(" mpirun_rsh -hostfile $PBS_NODEFILE -np"); - }else if (appDepDescription.getComputeHostId().contains("alamo")){ - jobDescriptor.setJobSubmitter("mpirun -np"); - }else { - jobDescriptor.setJobSubmitter("ibrun"); } - } } return jobDescriptor; http://git-wip-us.apache.org/repos/asf/airavata/blob/833de75a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/utils/bes/ApplicationProcessor.java ---------------------------------------------------------------------- diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/utils/bes/ApplicationProcessor.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/utils/bes/ApplicationProcessor.java index b17b92e..d9ef7e2 100644 --- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/utils/bes/ApplicationProcessor.java +++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/utils/bes/ApplicationProcessor.java @@ -23,8 +23,8 @@ package org.apache.airavata.gfac.impl.task.utils.bes; import org.apache.airavata.gfac.core.context.ProcessContext; import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription; -import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType; import org.apache.airavata.model.application.io.InputDataObjectType; +import org.apache.airavata.model.parallelism.ApplicationParallelismType; import org.ggf.schemas.jsdl.x2005.x11.jsdl.ApplicationType; import org.ggf.schemas.jsdl.x2005.x11.jsdl.JobDefinitionType; import org.ggf.schemas.jsdl.x2005.x11.jsdlPosix.FileNameType; http://git-wip-us.apache.org/repos/asf/airavata/blob/833de75a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/impl/ApplicationDeploymentImpl.java ---------------------------------------------------------------------- diff --git a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/impl/ApplicationDeploymentImpl.java b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/impl/ApplicationDeploymentImpl.java index 3cb219e..9d49f0a 100644 --- a/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/impl/ApplicationDeploymentImpl.java +++ b/modules/registry/registry-core/src/main/java/org/apache/airavata/registry/core/app/catalog/impl/ApplicationDeploymentImpl.java @@ -22,9 +22,9 @@ package org.apache.airavata.registry.core.app.catalog.impl; import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription; -import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType; import org.apache.airavata.model.appcatalog.appdeployment.CommandObject; import org.apache.airavata.model.appcatalog.appdeployment.SetEnvPaths; +import org.apache.airavata.model.parallelism.ApplicationParallelismType; import org.apache.airavata.registry.core.app.catalog.resources.*; import org.apache.airavata.registry.core.app.catalog.util.AppCatalogThriftConversion; import org.apache.airavata.registry.cpi.AppCatalogException; http://git-wip-us.apache.org/repos/asf/airavata/blob/833de75a/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ApplicationRegister.java ---------------------------------------------------------------------- diff --git a/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ApplicationRegister.java b/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ApplicationRegister.java index 76a9db0..5fa6ad3 100644 --- a/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ApplicationRegister.java +++ b/modules/test-suite/multi-tenanted-airavata/src/main/java/org/apache/airavata/testsuite/multitenantedairavata/ApplicationRegister.java @@ -24,12 +24,12 @@ package org.apache.airavata.testsuite.multitenantedairavata; import org.apache.airavata.api.Airavata; import org.apache.airavata.model.appcatalog.appdeployment.ApplicationDeploymentDescription; import org.apache.airavata.model.appcatalog.appdeployment.ApplicationModule; -import org.apache.airavata.model.appcatalog.appdeployment.ApplicationParallelismType; import org.apache.airavata.model.appcatalog.appdeployment.CommandObject; import org.apache.airavata.model.appcatalog.appinterface.ApplicationInterfaceDescription; import org.apache.airavata.model.application.io.DataType; import org.apache.airavata.model.application.io.InputDataObjectType; import org.apache.airavata.model.application.io.OutputDataObjectType; +import org.apache.airavata.model.parallelism.ApplicationParallelismType; import org.apache.airavata.model.security.AuthzToken; import org.apache.airavata.model.workspace.Gateway; import org.apache.airavata.testsuite.multitenantedairavata.utils.FrameworkUtils;
