[cig-commits] r7818 - in
cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal:
. grid/job grid/security portlets
wei at geodynamics.org
wei at geodynamics.org
Tue Aug 14 17:39:45 PDT 2007
Author: wei
Date: 2007-08-14 17:39:44 -0700 (Tue, 14 Aug 2007)
New Revision: 7818
Modified:
cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/TG07.java
cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/TG07GT4.java
cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/TGHWGT4.java
cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/grid/job/SimpleRSL.java
cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/grid/security/SimpleCred.java
cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/portlets/UserPortlet.java
Log:
Updated code to run test for MAG benchmark0 case.
Modified: cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/TG07.java
===================================================================
--- cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/TG07.java 2007-08-14 23:23:10 UTC (rev 7817)
+++ cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/TG07.java 2007-08-15 00:39:44 UTC (rev 7818)
@@ -25,9 +25,9 @@
String site = (args.length==0)?"NCSA":args[0];
TG07 test = new TG07();
String testhome = System.getenv("HOME")+"/cigtg"+"/CigPortal/test2";
- String dataset = System.getenv("HOME")+"/cigtg"+"/CigPortal/cigportal/webapp/storage/samples/sample";
+ String dataset = System.getenv("HOME")+"/cigtg"+"/CigPortal/cigportal/webapp/storage/samples/par.bnch0";
System.out.println("-----------------------------------------------------");
- System.out.println("SimpleGrid java application workflow for MAG analysis");
+ System.out.println("SimpleGrid java application workflow for MAG");
System.out.println("-----------------------------------------------------");
System.out.println("Anytime, press Ctrol+C to stop the workflow\n");
// 0. load our configuration
@@ -52,11 +52,11 @@
System.out.println("\nStep 2: transfer dataset to "+site);
System.out.println("dataset: " + dataset);
SimpleTransfer ft = new SimpleTransfer(proxy, myconfig.get("grid.gridftp."+site), 2811);
- ft.local2remote(dataset, myconfig.get("grid.sites.magdir."+site)+"/datasets/sample2");
+ ft.local2remote(dataset, myconfig.get("grid.sites.magdir."+site)+"/datasets/par.sample");
// 3. submit job : GT2 method
System.out.println("\nStep 3: submit job to "+site);
- String rsl = SimpleRSL.getRSL_GT2(myconfig, site, 500, 20, "sample2", "result2");
+ String rsl = SimpleRSL.getRSL_GT2(myconfig, site, 32, 4, "par.sample", "p.sample");
System.out.println("RSL:\n"+rsl);
SimpleRunGT2 sr = new SimpleRunGT2(proxy);
String jobId = sr.execute(myconfig.get("grid.gram."+site), rsl);
@@ -70,22 +70,22 @@
// 4. transfer results back
System.out.println("\nStep 4: transfer result from "+site);
- String remotefile = myconfig.get("grid.sites.dmsdir."+site)+"/results/result2.20.dat";
+ String remotefile = myconfig.get("grid.sites.magdir."+site)+"/results/*.sample";
System.out.println("result file: " + remotefile);
- ft.remote2local(remotefile, testhome+"/result2");
+ ft.remote2local(remotefile, testhome+"/.");
- // 5. visualize results
- String s1 = System.getenv("HOME")+"/cigtg"+"/CigPortal/cigportal/webapp/storage/bnd_poly.dat";
- String s12 = System.getenv("HOME")+"/cigtg"+"/CigPortal/cigportal/webapp/storage/bnd_uspolygon.dat";
- String s2 = testhome+"/result2";
- String s3 = "";
- String s4 = testhome+"/result2.jpg";
- IDWViz viz = new IDWViz(s1, s12, s2, s3, s4);
- viz.loadBoundary();
- viz.loadUSPolygon();
- //viz.createSample(500, 500, 0, 10000, true, true);
- viz.loadDataset();
- viz.plot();
+ // 5. visualize results
+ //String s1 = System.getenv("HOME")+"/cigtg"+"/CigPortal/cigportal/webapp/storage/";
+ //String s12 = System.getenv("HOME")+"/cigtg"+"/CigPortal/cigportal/webapp/storage/";
+ //String s2 = testhome+"/";
+ //String s3 = "";
+ //String s4 = testhome+"/result2.jpg";
+ //IDWViz viz = new IDWViz(s1, s12, s2, s3, s4);
+ //viz.loadBoundary();
+ //viz.loadUSPolygon();
+ ////viz.createSample(500, 500, 0, 10000, true, true);
+ //viz.loadDataset();
+ //viz.plot();
}
}
Modified: cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/TG07GT4.java
===================================================================
--- cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/TG07GT4.java 2007-08-14 23:23:10 UTC (rev 7817)
+++ cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/TG07GT4.java 2007-08-15 00:39:44 UTC (rev 7818)
@@ -25,7 +25,7 @@
String site = (args.length==0)?"NCSA":args[0];
TG07GT4 test = new TG07GT4();
String testhome = System.getenv("HOME")+"/cigtg"+"/CigPortal/test2";
- String dataset = System.getenv("HOME")+"/cigtg"+"/CigPortal/cigportal/webapp/storage/samples/sample";
+ String dataset = System.getenv("HOME")+"/cigtg"+"/CigPortal/cigportal/webapp/storage/samples/par.bnch0";
System.out.println("-----------------------------------------------------");
System.out.println("SimpleGrid java application workflow for MAG ");
System.out.println("-----------------------------------------------------");
@@ -52,11 +52,11 @@
System.out.println("\nStep 2: transfer dataset to "+site);
System.out.println("dataset: " + dataset);
SimpleTransfer ft = new SimpleTransfer(proxy, myconfig.get("grid.gridftp."+site), 2811);
- ft.local2remote(dataset, myconfig.get("grid.sites.magdir."+site)+"/datasets/sample2");
+ ft.local2remote(dataset, myconfig.get("grid.sites.magdir."+site)+"/datasets/par.sample");
// 3. submit job : GT4 method
System.out.println("\nStep 3: submit job to "+site);
- String rsl = SimpleRSL.getRSL_GT4(myconfig, site, 500, 20, "sample2", "result2");
+ String rsl = SimpleRSL.getRSL_GT4(myconfig, site, 32, 4, "par.sample", "p.sample");
System.out.println("RSL:\n"+rsl);
SimpleRunGT4 sr = new SimpleRunGT4(proxy);
String jobId = sr.execute(myconfig.get("grid.wsgram."+site), rsl);
@@ -70,22 +70,22 @@
// 4. transfer results back
System.out.println("\nStep 4: transfer result from "+site);
- String remotefile = myconfig.get("grid.sites.dmsdir."+site)+"/results/result2.20.dat";
+ String remotefile = myconfig.get("grid.sites.magdir."+site)+"/results/*.sample";
System.out.println("result file: " + remotefile);
- ft.remote2local(remotefile, testhome+"/result2");
+ ft.remote2local(remotefile, testhome+"/.");
// 5. visualize results
- String s1 = System.getenv("HOME")+"/cigtg"+"/CigPortal/cigportal/webapp/storage/bnd_poly.dat";
- String s12 = System.getenv("HOME")+"/cigtg"+"/CigPortal/cigportal/webapp/storage/bnd_uspolygon.dat";
- String s2 = testhome+"/result2";
- String s3 = "";
- String s4 = testhome+"/result2.jpg";
- IDWViz viz = new IDWViz(s1, s12, s2, s3, s4);
- viz.loadBoundary();
- viz.loadUSPolygon();
- //viz.createSample(500, 500, 0, 10000, true, true);
- viz.loadDataset();
- viz.plot();
+ //String s1 = System.getenv("HOME")+"/cigtg"+"/CigPortal/cigportal/webapp/storage/";
+ //String s12 = System.getenv("HOME")+"/cigtg"+"/CigPortal/cigportal/webapp/storage/";
+ //String s2 = testhome+"/p.sample";
+ //String s3 = "";
+ //String s4 = testhome+"/";
+ //IDWViz viz = new IDWViz(s1, s12, s2, s3, s4);
+ //viz.loadBoundary();
+ //viz.loadUSPolygon();
+ ////viz.createSample(500, 500, 0, 10000, true, true);
+ //viz.loadDataset();
+ //viz.plot();
}
}
Modified: cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/TGHWGT4.java
===================================================================
--- cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/TGHWGT4.java 2007-08-14 23:23:10 UTC (rev 7817)
+++ cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/TGHWGT4.java 2007-08-15 00:39:44 UTC (rev 7818)
@@ -28,7 +28,7 @@
String testhome = cigportalhome+"/test2";
String dataset = cigportalhome+"/cigportal/webapp/storage/samples/helloworld";
System.out.println("-----------------------------------------------------");
- System.out.println("SimpleGrid java application workflow for HelloWorld analysis");
+ System.out.println("SimpleGrid java application workflow for HelloWorld");
System.out.println("-----------------------------------------------------");
System.out.println("Anytime, press Ctrol+C to stop the workflow\n");
// 0. load our configuration
@@ -53,11 +53,11 @@
System.out.println("\nStep 2: transfer dataset to "+site);
System.out.println("dataset: " + dataset);
SimpleTransfer ft = new SimpleTransfer(proxy, myconfig.get("grid.gridftp."+site), 2811);
- ft.local2remote(dataset, myconfig.get("grid.sites.dmsdir."+site)+"/datasets/sample2");
+ ft.local2remote(dataset, myconfig.get("grid.sites.dmsdir."+site)+"/datasets/helloworld.sample");
// 3. submit job : GT4 method
System.out.println("\nStep 3: submit job to "+site);
- String rsl = SimpleRSL.getRSL_GT4(myconfig, site, 500, 20, "sample2", "result2");
+ String rsl = SimpleRSL.getRSL_GT4(myconfig, site, 500, 20, "helloworld.sample", "helloworld.result");
System.out.println("RSL:\n"+rsl);
SimpleRunGT4 sr = new SimpleRunGT4(proxy);
String jobId = sr.execute(myconfig.get("grid.wsgram."+site), rsl);
@@ -71,22 +71,22 @@
// 4. transfer results back
System.out.println("\nStep 4: transfer result from "+site);
- String remotefile = myconfig.get("grid.sites.dmsdir."+site)+"/results/result2.20.dat";
+ String remotefile = myconfig.get("grid.sites.dmsdir."+site)+"/results/helloworld.result";
System.out.println("result file: " + remotefile);
- ft.remote2local(remotefile, testhome+"/result2");
+ ft.remote2local(remotefile, testhome+"/helloworld.result");
// 5. visualize results
- String s1 = cigportalhome+"/cigportal/webapp/storage/bnd_poly.dat";
- String s12 = cigportalhome+"/cigportal/webapp/storage/bnd_uspolygon.dat";
- String s2 = testhome+"/result2";
- String s3 = "";
- String s4 = testhome+"/result2.jpg";
- IDWViz viz = new IDWViz(s1, s12, s2, s3, s4);
- viz.loadBoundary();
- viz.loadUSPolygon();
- //viz.createSample(500, 500, 0, 10000, true, true);
- viz.loadDataset();
- viz.plot();
+ //String s1 = cigportalhome+"/cigportal/webapp/storage/";
+ //String s12 = cigportalhome+"/cigportal/webapp/storage/";
+ //String s2 = testhome+"/result2";
+ //String s3 = "";
+ //String s4 = testhome+"/result2.jpg";
+ //IDWViz viz = new IDWViz(s1, s12, s2, s3, s4);
+ //viz.loadBoundary();
+ //viz.loadUSPolygon();
+ ////viz.createSample(500, 500, 0, 10000, true, true);
+ //viz.loadDataset();
+ //viz.plot();
}
}
Modified: cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/grid/job/SimpleRSL.java
===================================================================
--- cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/grid/job/SimpleRSL.java 2007-08-14 23:23:10 UTC (rev 7817)
+++ cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/grid/job/SimpleRSL.java 2007-08-15 00:39:44 UTC (rev 7818)
@@ -14,7 +14,7 @@
* @author wei modified for CIG portal
*/
public class SimpleRSL {
- public static String getRSL_GT2(Config myconfig, String site, int resolution, int k, String dataset, String jobid) {
+ public static String getRSL_GT2(Config myconfig, String site, int shtruncationdegree, int k, String dataset, String jobid) {
String project = myconfig.get("grid.projectname");
String appdir = myconfig.get("grid.sites.magdir."+site);
@@ -25,20 +25,20 @@
+ " (host_count=\"1"+(site.equals("UC")?":ia64-compute":"")+"\")" + "\n"
+ (project==null?"":" (project=\""+project+"\")" + "\n")
+ " (executable=\""+appdir+"/release/runMag.sh"+"\")" + "\n"
- + " (arguments=\""+resolution+"\" \""+resolution+"\" \""+k+"\" \""
- +appdir+"/datasets/"+dataset+"\" \""
- +appdir+"/results/"+jobid+"."+k+".dat\""+")" + "\n"
- + " (directory=\""+appdir+"/release"+"\")" + "\n"
+ //+ " (arguments=\""+shtruncationdegree+"\" \""+shtruncationdegree+"\" \""+k+"\" \""
+ // +appdir+"/datasets/"+dataset+"\" \""
+ // +appdir+"/results/"+jobid+"."+k+".dat\""+")" + "\n"
+ //+ " (directory=\""+appdir+"/release"+"\")" + "\n"
+ " (stdout=\""+appdir+"/results/stdout."+jobid+"."+k+"\")" + "\n"
+ " (stderr=\""+appdir+"/results/stderr."+jobid+"."+k+"\")" + "\n"
+ "" + "\n";
}
- public static String getRSL_GT4(Config myconfig, String site, int resolution, int k, String dataset, String output) {
- return SimpleRSL.getRSL_GT4(true, myconfig, site, resolution, k, dataset, output);
+ public static String getRSL_GT4(Config myconfig, String site, int shtruncationdegree, int k, String dataset, String output) {
+ return SimpleRSL.getRSL_GT4(true, myconfig, site, shtruncationdegree, k, dataset, output);
}
- public static String getRSL_GT4(boolean header, Config myconfig, String site, int resolution, int k, String dataset, String jobid) {
+ public static String getRSL_GT4(boolean header, Config myconfig, String site, int shtruncationdegree, int k, String dataset, String jobid) {
String project = myconfig.get("grid.projectname");
- String appdir = myconfig.get("grid.sites.dmsdir."+site);
+ String appdir = myconfig.get("grid.sites.magdir."+site);
String remoteurl = myconfig.get("grid.wsgram."+site);
String remotescheduler = myconfig.get("grid.wsgram.rm."+site);
return "<job>" + "\n"
@@ -58,13 +58,13 @@
+ " <hostCount>1</hostCount>" + "\n"
*/
+ (project==null?"":" <project>"+project+"</project>" + "\n")
- + " <executable>"+appdir+"/release/process.pl"+"</executable>" + "\n"
+ + " <executable>"+appdir+"/release/runMag.sh"+"</executable>" + "\n"
+ " <directory>"+appdir+"/release"+"</directory>" + "\n"
- + " <argument>"+resolution+"</argument>" + "\n"
- + " <argument>"+resolution+"</argument>" + "\n"
- + " <argument>"+k+"</argument>" + "\n"
- + " <argument>"+appdir+"/datasets/"+dataset+"</argument>" + "\n"
- + " <argument>"+appdir+"/results/"+jobid+"."+k+".dat</argument>" + "\n"
+ //+ " <argument>"+shtruncationdegree+"</argument>" + "\n"
+ //+ " <argument>"+shtruncationdegree+"</argument>" + "\n"
+ //+ " <argument>"+k+"</argument>" + "\n"
+ //+ " <argument>"+appdir+"/datasets/"+dataset+"</argument>" + "\n"
+ //+ " <argument>"+appdir+"/results/"+jobid+"."+k+".dat</argument>" + "\n"
+ " <stdout>"+appdir+"/results/stdout."+jobid+"."+k+"</stdout>" + "\n"
+ " <stderr>"+appdir+"/results/stderr."+jobid+"."+k+"</stderr>" + "\n"
+ "</job>" + "\n";
@@ -72,9 +72,9 @@
public static void main(String[] args) throws Exception {
org.cig.portal.util.Config myconfig=new org.cig.portal.util.Config();
SimpleRSL myrsl = new SimpleRSL();
- String rsl = myrsl.getRSL_GT2(myconfig, "UC", 500, 20, "mydataset", "myoutput");
- String rsl2 = myrsl.getRSL_GT2(myconfig, "SDSC", 500, 20, "mydataset", "myoutput");
- String rsl3 = myrsl.getRSL_GT4(myconfig, "SDSC", 500, 20, "mydataset", "myoutput");
+ String rsl = myrsl.getRSL_GT2(myconfig, "UC", 32, 4, "mydataset", "myoutput");
+ String rsl2 = myrsl.getRSL_GT2(myconfig, "SDSC", 32, 4, "mydataset", "myoutput");
+ String rsl3 = myrsl.getRSL_GT4(myconfig, "SDSC", 32, 4, "mydataset", "myoutput");
}
}
Modified: cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/grid/security/SimpleCred.java
===================================================================
--- cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/grid/security/SimpleCred.java 2007-08-14 23:23:10 UTC (rev 7817)
+++ cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/grid/security/SimpleCred.java 2007-08-15 00:39:44 UTC (rev 7818)
@@ -286,11 +286,11 @@
public void setRemainingTime(int ltseconds) { this.requested_lifetime = ltseconds; }
public static void main(String[] args) {
- org.gisolve.demo.util.Config myconfig=null;
+ org.cig.portal.util.Config myconfig=null;
SimpleCred mycred=null;
try {
//String password = Util.getPrivateInput("Input password for user " + args[0]);
- myconfig = new org.gisolve.demo.util.Config();
+ myconfig = new org.cig.portal.util.Config();
mycred = new SimpleCred(myconfig.get("grid.myproxy.server"), Integer.parseInt(myconfig.get("grid.myproxy.port")), myconfig.get("grid.myproxy.username"), "", myconfig.get("grid.myproxy.proxyfile"));
GSSCredential proxy = mycred.get();
Modified: cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/portlets/UserPortlet.java
===================================================================
--- cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/portlets/UserPortlet.java 2007-08-14 23:23:10 UTC (rev 7817)
+++ cs/cigtg/trunk/cigtg-dev/CigPortal/cigportal/src/org/cig/portal/portlets/UserPortlet.java 2007-08-15 00:39:44 UTC (rev 7818)
@@ -41,10 +41,9 @@
}
/**
- * This is where we initialize in-memory storage for gisolve
+ * This is where we initialize in-memory storage for cigportal
*/
public void doView(RenderRequest req, RenderResponse res) throws PortletException, java.io.IOException {
- //if (!GISolveConfig.isSetup(request)) GISolveConfig.init(request, response);
PortletSession mysession = req.getPortletSession(true);
User user = (User) req.getAttribute(SportletProperties.PORTLET_USER);
String uid = user.getUserID();
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