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Posted to commits@airavata.apache.org by sh...@apache.org on 2016/11/01 16:12:26 UTC
[3/6] airavata git commit: Adding Autodock test job submission
Adding Autodock test job submission
Project: http://git-wip-us.apache.org/repos/asf/airavata/repo
Commit: http://git-wip-us.apache.org/repos/asf/airavata/commit/b7bebec4
Tree: http://git-wip-us.apache.org/repos/asf/airavata/tree/b7bebec4
Diff: http://git-wip-us.apache.org/repos/asf/airavata/diff/b7bebec4
Branch: refs/heads/develop
Commit: b7bebec439cbdd1e63f3b0437a4f2b9ee3995c44
Parents: b66fa88
Author: Gourav Shenoy <sh...@gmail.com>
Authored: Mon Oct 31 16:32:34 2016 -0400
Committer: Gourav Shenoy <sh...@gmail.com>
Committed: Mon Oct 31 16:32:34 2016 -0400
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.../cloud/aurora/sample/AuroraClientSample.java | 56 +++++++++++++++++---
1 file changed, 50 insertions(+), 6 deletions(-)
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http://git-wip-us.apache.org/repos/asf/airavata/blob/b7bebec4/modules/cloud/aurora-client/src/main/java/org/apache/airavata/cloud/aurora/sample/AuroraClientSample.java
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diff --git a/modules/cloud/aurora-client/src/main/java/org/apache/airavata/cloud/aurora/sample/AuroraClientSample.java b/modules/cloud/aurora-client/src/main/java/org/apache/airavata/cloud/aurora/sample/AuroraClientSample.java
index 44d0ecf..3f29969 100644
--- a/modules/cloud/aurora-client/src/main/java/org/apache/airavata/cloud/aurora/sample/AuroraClientSample.java
+++ b/modules/cloud/aurora-client/src/main/java/org/apache/airavata/cloud/aurora/sample/AuroraClientSample.java
@@ -21,8 +21,10 @@ package org.apache.airavata.cloud.aurora.sample;
import java.text.MessageFormat;
import java.util.HashSet;
+import java.util.LinkedHashSet;
import java.util.Properties;
import java.util.Set;
+import java.util.concurrent.ThreadLocalRandom;
import org.apache.airavata.cloud.aurora.client.AuroraSchedulerClientFactory;
import org.apache.airavata.cloud.aurora.client.AuroraThriftClient;
@@ -129,6 +131,43 @@ public class AuroraClientSample {
System.out.println(response);
}
+ public static void createAutoDockJob() throws Exception {
+ JobKeyBean jobKey = new JobKeyBean("devel", "centos", "test_autodock");
+ IdentityBean owner = new IdentityBean("centos");
+
+ String working_dir = "/home/centos/efs-mount-point/job_" + ThreadLocalRandom.current().nextInt(1, 101) + "/";
+ String autodock_path = "/home/centos/efs-mount-point/autodock-vina";
+ ProcessBean proc1 = new ProcessBean("process_1", "mkdir " + working_dir, false);
+ ProcessBean proc2 = new ProcessBean("process_2", "cp " + autodock_path + "/vina_screenM.sh " + working_dir, false);
+ ProcessBean proc3 = new ProcessBean("process_3", "cp " + autodock_path + "/ligand* " + working_dir, false);
+ ProcessBean proc4 = new ProcessBean("process_4", "cd " + working_dir + " && sh vina_screenM.sh", false);
+
+ Set<ProcessBean> processes = new LinkedHashSet<>();
+ processes.add(proc1);
+ processes.add(proc2);
+ processes.add(proc3);
+ processes.add(proc4);
+
+ ResourceBean resources = new ResourceBean(1.5, 125, 512);
+
+ TaskConfigBean taskConfig = new TaskConfigBean("test_autodock", processes, resources);
+ JobConfigBean jobConfig = new JobConfigBean(jobKey, owner, taskConfig, "example");
+
+ String executorConfigJson = AuroraThriftClientUtil.getExecutorConfigJson(jobConfig);
+ System.out.println(executorConfigJson);
+
+ AuroraThriftClient client = AuroraThriftClient.getAuroraThriftClient(Constants.AURORA_SCHEDULER_PROP_FILE);
+ ResponseBean response = client.createJob(jobConfig);
+ System.out.println(response);
+ }
+
+ public static void killTasks(String jobName) throws Exception {
+ JobKeyBean jobKey = new JobKeyBean("devel", "centos", jobName);
+ AuroraThriftClient client = AuroraThriftClient.getAuroraThriftClient(Constants.AURORA_SCHEDULER_PROP_FILE);
+ ResponseBean response = client.killTasks(jobKey, new HashSet<>());
+ System.out.println(response);
+ }
+
/**
* The main method.
*
@@ -141,14 +180,19 @@ public class AuroraClientSample {
String auroraPort = properties.getProperty(Constants.AURORA_SCHEDULER_PORT);
auroraSchedulerClient = AuroraSchedulerClientFactory.createReadOnlySchedulerClient(MessageFormat.format(Constants.AURORA_SCHEDULER_CONNECTION_URL, auroraHost, auroraPort));
- // get jobs summary
-// AuroraClientSample.getJobSummary(auroraSchedulerClient);
-
// create sample job
// AuroraClientSample.createJob();
- AuroraThriftClient client = AuroraThriftClient.getAuroraThriftClient(Constants.AURORA_SCHEDULER_PROP_FILE);
- ResponseBean response = client.getPendingReasonForJob(new JobKeyBean("devel", "centos", "hello_pending"));
- System.out.println(response);
+ AuroraClientSample.createAutoDockJob();
+
+ // kill pending job
+// AuroraClientSample.killTasks("test_autodock");
+
+ // get jobs summary
+ AuroraClientSample.getJobSummary(auroraSchedulerClient);
+
+// AuroraThriftClient client = AuroraThriftClient.getAuroraThriftClient(Constants.AURORA_SCHEDULER_PROP_FILE);
+// ResponseBean response = client.getPendingReasonForJob(new JobKeyBean("devel", "centos", "hello_pending"));
+// System.out.println(response);
} catch (Exception ex) {
ex.printStackTrace();
}