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Renamed the IPFL Test to IPFL PipelineTest so that it'll be picked up by the PipelineTests. 

HACK: Turned off JNA autoRead() in the jobInfoEnt LSF structure to try and dodge the SIGSEGV during strlen calls during bmods. 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5201 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-02-05 00:06:12 +00:00
parent ce51ffb56e
commit cc5d695bcf
2 changed files with 54 additions and 4 deletions
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53
java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java
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@ -5050,6 +5050,55 @@ public class LibBat {
}
/**
* HACK: A version of the submit structure without autoread, so that
* jobInfoEnt doesn't try to populate the structure on return from lsb_readjobinfo.
* There are several reports of kernel crashes in strlen after a call to lsb_readjobinfo during the autoRead().
*
* Example:
Current thread (0x0000000050efd800): JavaThread "main" [_thread_in_native, id=22268, stack(0x0000000040dbf000,0x0000000040ec0000)]
siginfo:si_signo=SIGSEGV: si_errno=0, si_code=128 (), si_addr=0x0000000000000000
Stack: [0x0000000040dbf000,0x0000000040ec0000], sp=0x0000000040ebc018, free space=3f40000000000000018k
Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
C [libc.so.6+0x797c0] strlen+0x10
j com.sun.jna.Pointer._getString(JZ)Ljava/lang/String;+0
j com.sun.jna.Pointer.getString(JZ)Ljava/lang/String;+7
j com.sun.jna.Pointer.getString(J)Ljava/lang/String;+90
j com.sun.jna.Pointer.getValue(JLjava/lang/Class;Ljava/lang/Object;)Ljava/lang/Object;+630
j com.sun.jna.Structure.readField(Lcom/sun/jna/Structure$StructField;)Ljava/lang/Object;+168
j com.sun.jna.Structure.read()V+82
j com.sun.jna.Structure.autoRead()V+8
j com.sun.jna.Structure.updateStructureByReference(Ljava/lang/Class;Lcom/sun/jna/Structure;Lcom/sun/jna/Pointer;)Lcom/sun/jna/Structure;+68
j com.sun.jna.Pointer.getValue(JLjava/lang/Class;Ljava/lang/Object;)Ljava/lang/Object;+74
j com.sun.jna.Structure.readField(Lcom/sun/jna/Structure$StructField;)Ljava/lang/Object;+168
j com.sun.jna.Structure.read()V+82
j com.sun.jna.Structure.autoRead()V+8
v ~StubRoutines::call_stub
V [libjvm.so+0x3e756d]
V [libjvm.so+0x5f6f59]
V [libjvm.so+0x3e73a5]
V [libjvm.so+0x420904]
V [libjvm.so+0x400ea5]
C [jna1670124220621463742.tmp+0x6feb] newJavaStructure+0xdb
C [jna1670124220621463742.tmp+0xb919]
C [jna1670124220621463742.tmp+0x11008] ffi_closure_unix64_inner+0x88
C [jna1670124220621463742.tmp+0x11438] ffi_closure_unix64+0x46
j org.broadinstitute.sting.queue.engine.Lsf706JobRunner.status()Lscala/Enumeration$Value;+36
j org.broadinstitute.sting.queue.engine.FunctionEdge.status()Lscala/Enumeration$Value;+72
j org.broadinstitute.sting.queue.engine.QGraph$$anonfun$getReadyJobs$1.apply(Lorg/broadinstitute/sting/queue/engine/QEdge;)Z+44
j org.broadinstitute.sting.queue.engine.QGraph$$anonfun$getReadyJobs$1.apply(Ljava/lang/Object;)Ljava/lang/Object;+5
* Because the error is in the second level call to autoRead(), and also in a structure that has a String, we are assuming
* that the error is on the submit structure even though this problem is very hard to reproduce consistently at the moment.
*/
public static class submitWithoutAutoRead extends submit {
public submitWithoutAutoRead() {
this.setAutoRead(false);
}
}
/**
@ -6096,6 +6145,7 @@ public class LibBat {
/**
* \brief job information entry.
* HACK: The submit value in this structure currently has autoRead() set to false as a possible workaround for a SIGSEGV error.
*/
public static class jobInfoEnt extends Structure {
public static class ByReference extends jobInfoEnt implements Structure.ByReference {
@ -6242,8 +6292,9 @@ public class LibBat {
/**
* < Structure for \ref lsb_submit call.
* HACK: Use a structure that has the same size, but has autoRead turned off. Hopes to work around kernel SIGSEGV.
*/
public submit submit;
public submitWithoutAutoRead submit;
/**
* < Job exit status.

5
scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryTest.scala → scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala
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@ -1,10 +1,9 @@
package org.broadinstitute.sting.queue.pipeline
import org.testng.annotations.Test
import org.broadinstitute.sting.queue.pipeline.{PipelineTest, PipelineTestSpec}
import org.broadinstitute.sting.BaseTest
class IPFLibraryTest {
class IPFLibraryPipelineTest {
@Test
def testVCFExtractSites {
@ -69,4 +68,4 @@ class IPFLibraryTest {
spec.fileMD5s += testOut -> "ee09af803bc94987d55d044c2ebbc0b8"
}
}
}