zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Avoid segfaults due to out of date and possibly abandonded LSF DRMAA implementation when use'ing LSF instead of .combined_LSF_SGE

This commit is contained in:
Khalid Shakir 2011-08-23 23:49:36 -04:00
parent 6e2552a9ef
commit 1ecbf05aae
1 changed files with 17 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

19
public/java/test/org/broadinstitute/sting/jna/drmaa/v1_0/LibDrmaaIntegrationTest.java
View File

@ -40,6 +40,7 @@ import java.util.Arrays;
import java.util.List; import java.util.List;
public class LibDrmaaIntegrationTest extends BaseTest { public class LibDrmaaIntegrationTest extends BaseTest {
private String implementation = null;
@Test @Test
public void testDrmaa() throws Exception { public void testDrmaa() throws Exception {
@ -79,10 +80,24 @@ public class LibDrmaaIntegrationTest extends BaseTest {
Assert.fail(String.format("Could not get DRMAA implementation from the DRMAA library: %s", error.getString(0))); Assert.fail(String.format("Could not get DRMAA implementation from the DRMAA library: %s", error.getString(0)));
System.out.println(String.format("DRMAA implementation(s): %s", drmaaImplementation.getString(0))); System.out.println(String.format("DRMAA implementation(s): %s", drmaaImplementation.getString(0)));
this.implementation = drmaaImplementation.getString(0);
} }
@Test @Test(dependsOnMethods = { "testDrmaa" })
public void testSubmitEcho() throws Exception { public void testSubmitEcho() throws Exception {
if (implementation.indexOf("LSF") >= 0) {
System.err.println(" *********************************************************");
System.err.println(" ***********************************************************");
System.err.println(" **** ****");
System.err.println(" **** Skipping LibDrmaaIntegrationTest.testSubmitEcho() ****");
System.err.println(" **** Are you using the dotkit .combined_LSF_SGE? ****");
System.err.println(" **** ****");
System.err.println(" ***********************************************************");
System.err.println(" *********************************************************");
return;
}
Memory error = new Memory(LibDrmaa.DRMAA_ERROR_STRING_BUFFER); Memory error = new Memory(LibDrmaa.DRMAA_ERROR_STRING_BUFFER);
int errnum; int errnum;
@ -129,7 +144,7 @@ public class LibDrmaaIntegrationTest extends BaseTest {
errnum = LibDrmaa.drmaa_set_vector_attribute(jt, LibDrmaa.DRMAA_V_ARGV, args, error, LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN); errnum = LibDrmaa.drmaa_set_vector_attribute(jt, LibDrmaa.DRMAA_V_ARGV, args, error, LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN);
if (errnum != LibDrmaa.DRMAA_ERRNO.DRMAA_ERRNO_SUCCESS) if (errnum != LibDrmaa.DRMAA_ERRNO.DRMAA_ERRNO_SUCCESS)
Assert.fail(String.format("Could not set attribute \"%s\": %s", LibDrmaa.DRMAA_REMOTE_COMMAND, error.getString(0))); Assert.fail(String.format("Could not set attribute \"%s\": %s", LibDrmaa.DRMAA_V_ARGV, error.getString(0)));
errnum = LibDrmaa.drmaa_run_job(jobIdMem, LibDrmaa.DRMAA_JOBNAME_BUFFER_LEN, jt, error, LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN); errnum = LibDrmaa.drmaa_run_job(jobIdMem, LibDrmaa.DRMAA_JOBNAME_BUFFER_LEN, jt, error, LibDrmaa.DRMAA_ERROR_STRING_BUFFER_LEN);