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Posted to commits@airavata.apache.org by sh...@apache.org on 2016/11/02 23:07:19 UTC
airavata git commit: Improved aurora job submission task to use
application deployment and delegated datastaging to framework
Repository: airavata
Updated Branches:
refs/heads/develop ea5fc9bae -> 4cafd7a5c
Improved aurora job submission task to use application deployment and delegated datastaging to framework
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/4cafd7a5
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/4cafd7a5
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/4cafd7a5
Branch: refs/heads/develop
Commit: 4cafd7a5cf51b069537e7bbe745de56c396d7406
Parents: ea5fc9b
Author: Shameera Rathnayaka <sh...@gmail.com>
Authored: Wed Nov 2 19:07:14 2016 -0400
Committer: Shameera Rathnayaka <sh...@gmail.com>
Committed: Wed Nov 2 19:07:14 2016 -0400
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.../apache/airavata/gfac/impl/task/AuroraJobSubmission.java | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
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http://git-wip-us.apache.org/repos/asf/airavata/blob/4cafd7a5/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/AuroraJobSubmission.java
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diff --git a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/AuroraJobSubmission.java b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/AuroraJobSubmission.java
index f51503d..0941c85 100644
--- a/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/AuroraJobSubmission.java
+++ b/modules/gfac/gfac-impl/src/main/java/org/apache/airavata/gfac/impl/task/AuroraJobSubmission.java
@@ -85,11 +85,12 @@ public class AuroraJobSubmission implements JobSubmissionTask{
// only autodoc vina
String workingDir = taskContext.getWorkingDir();
// ProcessBean proc1 = new ProcessBean("process_1", "mkdir -p " + workingDir, false);
- ProcessBean proc2 = new ProcessBean("process_2", "cp -rf /home/centos/efs-mount-point/autodock-vina/* " + workingDir , false);
- ProcessBean proc3 = new ProcessBean("process_3", "cd " + workingDir + " && ./vina_screenM.sh", false);
+// ProcessBean proc2 = new ProcessBean("process_2", "cp -rf /home/centos/efs-mount-point/autodock-vina/* " + workingDir , false);
+ String executablePath = processContext.getApplicationDeploymentDescription().getExecutablePath();
+ ProcessBean proc3 = new ProcessBean("process_3", "cd " + workingDir + " && sh " + executablePath, false);
Set<ProcessBean> processes = new LinkedHashSet<>();
// processes.add(proc1);
- processes.add(proc2);
+// processes.add(proc2);
processes.add(proc3);
ResourceBean resources = new ResourceBean(1.5, 512, 512);