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Posted to commits@airavata.apache.org by ch...@apache.org on 2016/02/26 22:57:37 UTC
airavata git commit: adding parallelism types
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 <ch...@apache.org>
Authored: Fri Feb 26 17:00:25 2016 -0500
Committer: Chathuri Wimalasena <ch...@apache.org>
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;