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 <[email protected]> Authored: Wed Nov 2 19:07:14 2016 -0400 Committer: Shameera Rathnayaka <[email protected]> Committed: Wed Nov 2 19:07:14 2016 -0400 ---------------------------------------------------------------------- .../apache/airavata/gfac/impl/task/AuroraJobSubmission.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) ---------------------------------------------------------------------- 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 ---------------------------------------------------------------------- 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);
