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Updated LSF libraries to use Pointer instead of Structure.ByReference for struct arrays since the the latter is autoRead() and LSF doesn't always return null for empty arrays. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5417 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2011-03-10 22:58:54 +00:00
parent 2058fc12bc
commit 097a9a59e8
3 changed files with 958 additions and 1144 deletions
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1772
java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibBat.java
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327
java/src/org/broadinstitute/sting/jna/lsf/v7_0_6/LibLsf.java
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@ -31,6 +31,31 @@ import com.sun.jna.ptr.PointerByReference;
import org.broadinstitute.sting.jna.clibrary.JNAUtils; import org.broadinstitute.sting.jna.clibrary.JNAUtils;
import org.broadinstitute.sting.jna.clibrary.LibC.*; import org.broadinstitute.sting.jna.clibrary.LibC.*;
/*
NOTE: This library uses Pointer for some Struct.ByReference members going
against the JNA recommendations at http://jna.java.net/#structure_use
Instead stuct arrays are Pointers and each structure contains a
constructor that can accept the Pointer iff the size of the array is
known to be greater than zero.
This was especially problematic in jobInfoEnt->items->resName. When
jobInfo->reserveCnt was zero jobInfoItems->items was not necessarily null.
LSF will often reuse memory for structure arrays but will set the
array size / count (reserveCnt above) to zero when the array should
not be accessed. When LSF has reused memory and points to a non-null
structure pointer (items) the inner structure may contain further
garbage pointers (especially items->resName).
When JNA sees a non-null Structure.ByReference it will autoRead() the
member. When autoRead() eventually gets to the items->resName trying
to run strlen on the bad memory address causes a SIGSEGV.
By using a Pointer instead of the Structure.ByReference JNA will not
automatically autoRead(), and the API user will have to pass the
pointer to the Structure on their own.
*/
/** /**
* JNA wrappers for LSF's lsf.h and -llsf * JNA wrappers for LSF's lsf.h and -llsf
* *
@ -83,11 +108,10 @@ public class LibLsf {
} }
public static class rlimit extends Structure { public static class rlimit extends Structure {
public static class ByReference extends rlimit implements Structure.ByReference { public static class ByReference extends rlimit implements Structure.ByReference {}
} public static class ByValue extends rlimit implements Structure.ByValue {}
public rlimit() {}
public static class ByValue extends rlimit implements Structure.ByValue { public rlimit(Pointer p) { super(p); read(); }
}
public NativeLong rlim_cur; public NativeLong rlim_cur;
public NativeLong rlim_max; public NativeLong rlim_max;
@ -96,11 +120,10 @@ public class LibLsf {
public static class rusage extends Structure { public static class rusage extends Structure {
public static class ByReference extends rusage implements Structure.ByReference { public static class ByReference extends rusage implements Structure.ByReference {}
} public static class ByValue extends rusage implements Structure.ByValue {}
public rusage() {}
public static class ByValue extends rusage implements Structure.ByValue { public rusage(Pointer p) { super(p); read(); }
}
public timeval ru_utime; public timeval ru_utime;
public timeval ru_stime; public timeval ru_stime;
@ -345,11 +368,10 @@ public class LibLsf {
public static class connectEnt extends Structure { public static class connectEnt extends Structure {
public static class ByReference extends connectEnt implements Structure.ByReference { public static class ByReference extends connectEnt implements Structure.ByReference {}
} public static class ByValue extends connectEnt implements Structure.ByValue {}
public connectEnt() {}
public static class ByValue extends connectEnt implements Structure.ByValue { public connectEnt(Pointer p) { super(p); read(); }
}
public String hostname; public String hostname;
public int[] csock = new int[2]; public int[] csock = new int[2];
@ -447,11 +469,10 @@ public class LibLsf {
public static class placeInfo extends Structure { public static class placeInfo extends Structure {
public static class ByReference extends placeInfo implements Structure.ByReference { public static class ByReference extends placeInfo implements Structure.ByReference {}
} public static class ByValue extends placeInfo implements Structure.ByValue {}
public placeInfo() {}
public static class ByValue extends placeInfo implements Structure.ByValue { public placeInfo(Pointer p) { super(p); read(); }
}
public byte[] hostName = new byte[MAXHOSTNAMELEN]; public byte[] hostName = new byte[MAXHOSTNAMELEN];
public int numtask; public int numtask;
@ -461,11 +482,10 @@ public class LibLsf {
public static class hostLoad extends Structure { public static class hostLoad extends Structure {
public static class ByReference extends hostLoad implements Structure.ByReference { public static class ByReference extends hostLoad implements Structure.ByReference {}
} public static class ByValue extends hostLoad implements Structure.ByValue {}
public hostLoad() {}
public static class ByValue extends hostLoad implements Structure.ByValue { public hostLoad(Pointer p) { super(p); read(); }
}
public byte[] hostName = new byte[MAXHOSTNAMELEN]; public byte[] hostName = new byte[MAXHOSTNAMELEN];
public IntByReference status; public IntByReference status;
@ -503,11 +523,10 @@ public class LibLsf {
public static class resItem extends Structure { public static class resItem extends Structure {
public static class ByReference extends resItem implements Structure.ByReference { public static class ByReference extends resItem implements Structure.ByReference {}
} public static class ByValue extends resItem implements Structure.ByValue {}
public resItem() {}
public static class ByValue extends resItem implements Structure.ByValue { public resItem(Pointer p) { super(p); read(); }
}
public byte[] name = new byte[MAXLSFNAMELEN]; public byte[] name = new byte[MAXLSFNAMELEN];
public byte[] des = new byte[MAXRESDESLEN]; public byte[] des = new byte[MAXRESDESLEN];
@ -521,11 +540,10 @@ public class LibLsf {
public static class lsInfo extends Structure { public static class lsInfo extends Structure {
public static class ByReference extends lsInfo implements Structure.ByReference { public static class ByReference extends lsInfo implements Structure.ByReference {}
} public static class ByValue extends lsInfo implements Structure.ByValue {}
public lsInfo() {}
public static class ByValue extends lsInfo implements Structure.ByValue { public lsInfo(Pointer p) { super(p); read(); }
}
// The current version of JNA's Structure.getNativeAlignment passes a "null" to // The current version of JNA's Structure.getNativeAlignment passes a "null" to
// Native.getNativeSize() when accessing the contents of a 2D array. // Native.getNativeSize() when accessing the contents of a 2D array.
@ -533,7 +551,7 @@ public class LibLsf {
// comments so when we upgrade don't want to have specialized code floating around. // comments so when we upgrade don't want to have specialized code floating around.
public int nRes; public int nRes;
public resItem.ByReference resTable; public Pointer /* resItem.ByReference */ resTable;
public int nTypes; public int nTypes;
public byte[] hostTypes = new byte[MAXTYPES * MAXLSFNAMELEN]; public byte[] hostTypes = new byte[MAXTYPES * MAXLSFNAMELEN];
public int nModels; public int nModels;
@ -560,11 +578,10 @@ public class LibLsf {
public static class clusterInfo extends Structure { public static class clusterInfo extends Structure {
public static class ByReference extends clusterInfo implements Structure.ByReference { public static class ByReference extends clusterInfo implements Structure.ByReference {}
} public static class ByValue extends clusterInfo implements Structure.ByValue {}
public clusterInfo() {}
public static class ByValue extends clusterInfo implements Structure.ByValue { public clusterInfo(Pointer p) { super(p); read(); }
}
public byte[] clusterName = new byte[MAXLSFNAMELEN]; public byte[] clusterName = new byte[MAXLSFNAMELEN];
public int status; public int status;
@ -591,11 +608,10 @@ public class LibLsf {
public static class hostInfo extends Structure { public static class hostInfo extends Structure {
public static class ByReference extends hostInfo implements Structure.ByReference { public static class ByReference extends hostInfo implements Structure.ByReference {}
} public static class ByValue extends hostInfo implements Structure.ByValue {}
public hostInfo() {}
public static class ByValue extends hostInfo implements Structure.ByValue { public hostInfo(Pointer p) { super(p); read(); }
}
public byte[] hostName = new byte[MAXHOSTNAMELEN]; public byte[] hostName = new byte[MAXHOSTNAMELEN];
public String hostType; public String hostType;
@ -677,11 +693,10 @@ public class LibLsf {
public static class config_param extends Structure { public static class config_param extends Structure {
public static class ByReference extends config_param implements Structure.ByReference { public static class ByReference extends config_param implements Structure.ByReference {}
} public static class ByValue extends config_param implements Structure.ByValue {}
public config_param() {}
public static class ByValue extends config_param implements Structure.ByValue { public config_param(Pointer p) { super(p); read(); }
}
public String paramName; public String paramName;
public String paramValue; public String paramValue;
@ -690,11 +705,10 @@ public class LibLsf {
public static class lsfRusage extends Structure { public static class lsfRusage extends Structure {
public static class ByReference extends lsfRusage implements Structure.ByReference { public static class ByReference extends lsfRusage implements Structure.ByReference {}
} public static class ByValue extends lsfRusage implements Structure.ByValue {}
public lsfRusage() {}
public static class ByValue extends lsfRusage implements Structure.ByValue { public lsfRusage(Pointer p) { super(p); read(); }
}
public double ru_utime; public double ru_utime;
public double ru_stime; public double ru_stime;
@ -721,11 +735,10 @@ public class LibLsf {
public static class lsfAcctRec extends Structure { public static class lsfAcctRec extends Structure {
public static class ByReference extends lsfAcctRec implements Structure.ByReference { public static class ByReference extends lsfAcctRec implements Structure.ByReference {}
} public static class ByValue extends lsfAcctRec implements Structure.ByValue {}
public lsfAcctRec() {}
public static class ByValue extends lsfAcctRec implements Structure.ByValue { public lsfAcctRec(Pointer p) { super(p); read(); }
}
public int pid; public int pid;
public String username; public String username;
@ -743,11 +756,10 @@ public class LibLsf {
public static class confNode extends Structure { public static class confNode extends Structure {
public static class ByReference extends confNode implements Structure.ByReference { public static class ByReference extends confNode implements Structure.ByReference {}
} public static class ByValue extends confNode implements Structure.ByValue {}
public confNode() {}
public static class ByValue extends confNode implements Structure.ByValue { public confNode(Pointer p) { super(p); read(); }
}
public confNode.ByReference leftPtr; public confNode.ByReference leftPtr;
public confNode.ByReference rightPtr; public confNode.ByReference rightPtr;
@ -762,11 +774,10 @@ public class LibLsf {
public static class pStack extends Structure { public static class pStack extends Structure {
public static class ByReference extends pStack implements Structure.ByReference { public static class ByReference extends pStack implements Structure.ByReference {}
} public static class ByValue extends pStack implements Structure.ByValue {}
public pStack() {}
public static class ByValue extends pStack implements Structure.ByValue { public pStack(Pointer p) { super(p); read(); }
}
public int top; public int top;
public int size; public int size;
@ -776,11 +787,10 @@ public class LibLsf {
public static class confHandle extends Structure { public static class confHandle extends Structure {
public static class ByReference extends confHandle implements Structure.ByReference { public static class ByReference extends confHandle implements Structure.ByReference {}
} public static class ByValue extends confHandle implements Structure.ByValue {}
public confHandle() {}
public static class ByValue extends confHandle implements Structure.ByValue { public confHandle(Pointer p) { super(p); read(); }
}
public confNode.ByReference rootNode; public confNode.ByReference rootNode;
public String fname; public String fname;
@ -792,11 +802,10 @@ public class LibLsf {
public static class lsConf extends Structure { public static class lsConf extends Structure {
public static class ByReference extends lsConf implements Structure.ByReference { public static class ByReference extends lsConf implements Structure.ByReference {}
} public static class ByValue extends lsConf implements Structure.ByValue {}
public lsConf() {}
public static class ByValue extends lsConf implements Structure.ByValue { public lsConf(Pointer p) { super(p); read(); }
}
public confHandle.ByReference confhandle; public confHandle.ByReference confhandle;
public int numConds; public int numConds;
@ -807,11 +816,10 @@ public class LibLsf {
public static class sharedConf extends Structure { public static class sharedConf extends Structure {
public static class ByReference extends sharedConf implements Structure.ByReference { public static class ByReference extends sharedConf implements Structure.ByReference {}
} public static class ByValue extends sharedConf implements Structure.ByValue {}
public sharedConf() {}
public static class ByValue extends sharedConf implements Structure.ByValue { public sharedConf(Pointer p) { super(p); read(); }
}
public lsInfo.ByReference lsinfo; public lsInfo.ByReference lsinfo;
public int numCls; public int numCls;
@ -823,11 +831,10 @@ public class LibLsf {
public static class lsSharedResourceInstance extends Structure { public static class lsSharedResourceInstance extends Structure {
public static class ByReference extends lsSharedResourceInstance implements Structure.ByReference { public static class ByReference extends lsSharedResourceInstance implements Structure.ByReference {}
} public static class ByValue extends lsSharedResourceInstance implements Structure.ByValue {}
public lsSharedResourceInstance() {}
public static class ByValue extends lsSharedResourceInstance implements Structure.ByValue { public lsSharedResourceInstance(Pointer p) { super(p); read(); }
}
public String value; public String value;
public int nHosts; public int nHosts;
@ -839,43 +846,40 @@ public class LibLsf {
public static class lsSharedResourceInfo extends Structure { public static class lsSharedResourceInfo extends Structure {
public static class ByReference extends lsSharedResourceInfo implements Structure.ByReference { public static class ByReference extends lsSharedResourceInfo implements Structure.ByReference {}
} public static class ByValue extends lsSharedResourceInfo implements Structure.ByValue {}
public lsSharedResourceInfo() {}
public static class ByValue extends lsSharedResourceInfo implements Structure.ByValue { public lsSharedResourceInfo(Pointer p) { super(p); read(); }
}
public String resourceName; public String resourceName;
public int nInstances; public int nInstances;
public lsSharedResourceInstance.ByReference instances; public Pointer /* lsSharedResourceInstance.ByReference */ instances;
} }
public static class clusterConf extends Structure { public static class clusterConf extends Structure {
public static class ByReference extends clusterConf implements Structure.ByReference { public static class ByReference extends clusterConf implements Structure.ByReference {}
} public static class ByValue extends clusterConf implements Structure.ByValue {}
public clusterConf() {}
public static class ByValue extends clusterConf implements Structure.ByValue { public clusterConf(Pointer p) { super(p); read(); }
}
public clusterInfo.ByReference clinfo; public clusterInfo.ByReference clinfo;
public int numHosts; public int numHosts;
public hostInfo.ByReference hosts; public Pointer /* hostInfo.ByReference */ hosts;
public int defaultFeatures; public int defaultFeatures;
public int numShareRes; public int numShareRes;
public lsSharedResourceInfo.ByReference shareRes; public Pointer /* lsSharedResourceInfo.ByReference */ shareRes;
} }
public static class pidInfo extends Structure { public static class pidInfo extends Structure {
public static class ByReference extends pidInfo implements Structure.ByReference { public static class ByReference extends pidInfo implements Structure.ByReference {}
} public static class ByValue extends pidInfo implements Structure.ByValue {}
public pidInfo() {}
public static class ByValue extends pidInfo implements Structure.ByValue { public pidInfo(Pointer p) { super(p); read(); }
}
public int pid; public int pid;
public int ppid; public int ppid;
@ -887,18 +891,17 @@ public class LibLsf {
public static class jRusage extends Structure { public static class jRusage extends Structure {
public static class ByReference extends jRusage implements Structure.ByReference { public static class ByReference extends jRusage implements Structure.ByReference {}
} public static class ByValue extends jRusage implements Structure.ByValue {}
public jRusage() {}
public static class ByValue extends jRusage implements Structure.ByValue { public jRusage(Pointer p) { super(p); read(); }
}
public int mem; public int mem;
public int swap; public int swap;
public int utime; public int utime;
public int stime; public int stime;
public int npids; public int npids;
public pidInfo.ByReference pidInfo; public Pointer /* pidInfo.ByReference */ pidInfo;
public int npgids; public int npgids;
public IntByReference pgid; public IntByReference pgid;
@ -913,11 +916,10 @@ public class LibLsf {
public static final int NUM_CLASS_TYPE = 3; public static final int NUM_CLASS_TYPE = 3;
public static class licUsage extends Structure { public static class licUsage extends Structure {
public static class ByReference extends licUsage implements Structure.ByReference { public static class ByReference extends licUsage implements Structure.ByReference {}
} public static class ByValue extends licUsage implements Structure.ByValue {}
public licUsage() {}
public static class ByValue extends licUsage implements Structure.ByValue { public licUsage(Pointer p) { super(p); read(); }
}
public int licDisplayMask; public int licDisplayMask;
public int usingDemoLicense; public int usingDemoLicense;
@ -928,11 +930,10 @@ public class LibLsf {
public static class hostClassInfo extends Structure { public static class hostClassInfo extends Structure {
public static class ByReference extends hostClassInfo implements Structure.ByReference { public static class ByReference extends hostClassInfo implements Structure.ByReference {}
} public static class ByValue extends hostClassInfo implements Structure.ByValue {}
public hostClassInfo() {}
public static class ByValue extends hostClassInfo implements Structure.ByValue { public hostClassInfo(Pointer p) { super(p); read(); }
}
public int numHosts; public int numHosts;
public int numCpus; public int numCpus;
@ -942,11 +943,10 @@ public class LibLsf {
public static class lsfLicUsage extends Structure { public static class lsfLicUsage extends Structure {
public static class ByReference extends lsfLicUsage implements Structure.ByReference { public static class ByReference extends lsfLicUsage implements Structure.ByReference {}
} public static class ByValue extends lsfLicUsage implements Structure.ByValue {}
public lsfLicUsage() {}
public static class ByValue extends lsfLicUsage implements Structure.ByValue { public lsfLicUsage(Pointer p) { super(p); read(); }
}
public licUsage licUsage; public licUsage licUsage;
public hostClassInfo[] hostInfo = new hostClassInfo[NUM_CLASS_TYPE]; public hostClassInfo[] hostInfo = new hostClassInfo[NUM_CLASS_TYPE];
@ -960,11 +960,10 @@ public class LibLsf {
public static class param_entry extends Structure { public static class param_entry extends Structure {
public static class ByReference extends param_entry implements Structure.ByReference { public static class ByReference extends param_entry implements Structure.ByReference {}
} public static class ByValue extends param_entry implements Structure.ByValue {}
public param_entry() {}
public static class ByValue extends param_entry implements Structure.ByValue { public param_entry(Pointer p) { super(p); read(); }
}
public static int HAS_PARAM_VALUE = 0x001; public static int HAS_PARAM_VALUE = 0x001;
public static final int HAS_PARAM_DEFAULT = 0x002; public static final int HAS_PARAM_DEFAULT = 0x002;
@ -978,15 +977,14 @@ public class LibLsf {
public static class params_key_value_pair extends Structure { public static class params_key_value_pair extends Structure {
public static class ByReference extends params_key_value_pair implements Structure.ByReference { public static class ByReference extends params_key_value_pair implements Structure.ByReference {}
} public static class ByValue extends params_key_value_pair implements Structure.ByValue {}
public params_key_value_pair() {}
public static class ByValue extends params_key_value_pair implements Structure.ByValue { public params_key_value_pair(Pointer p) { super(p); read(); }
}
public int num_params; public int num_params;
public String daemon_time; public String daemon_time;
public param_entry.ByReference param; public Pointer /* param_entry.ByReference */ param;
} }
@ -1149,11 +1147,10 @@ public class LibLsf {
*/ */
public static class ls_timeval extends Structure { public static class ls_timeval extends Structure {
public static class ByReference extends ls_timeval implements Structure.ByReference { public static class ByReference extends ls_timeval implements Structure.ByReference {}
} public static class ByValue extends ls_timeval implements Structure.ByValue {}
public ls_timeval() {}
public static class ByValue extends ls_timeval implements Structure.ByValue { public ls_timeval(Pointer p) { super(p); read(); }
}
public float rtime; public float rtime;
public float utime; public float utime;
@ -1489,11 +1486,10 @@ public class LibLsf {
public static native int ls_postmultievent(int int1, String string1, Pointer stringArray1, int int2, int int3); public static native int ls_postmultievent(int int1, String string1, Pointer stringArray1, int int2, int int3);
public static class extResInfo extends Structure { public static class extResInfo extends Structure {
public static class ByReference extends extResInfo implements Structure.ByReference { public static class ByReference extends extResInfo implements Structure.ByReference {}
} public static class ByValue extends extResInfo implements Structure.ByValue {}
public extResInfo() {}
public static class ByValue extends extResInfo implements Structure.ByValue { public extResInfo(Pointer p) { super(p); read(); }
}
public String name; public String name;
public String type; public String type;
@ -1578,11 +1574,10 @@ public class LibLsf {
public static class nioEvent extends Structure { public static class nioEvent extends Structure {
public static class ByReference extends nioEvent implements Structure.ByReference { public static class ByReference extends nioEvent implements Structure.ByReference {}
} public static class ByValue extends nioEvent implements Structure.ByValue {}
public nioEvent() {}
public static class ByValue extends nioEvent implements Structure.ByValue { public nioEvent(Pointer p) { super(p); read(); }
}
public int tid; public int tid;
public *//*nioType*//* int type; public *//*nioType*//* int type;
@ -1592,25 +1587,23 @@ public class LibLsf {
public static class nioInfo extends Structure { public static class nioInfo extends Structure {
public static class ByReference extends nioInfo implements Structure.ByReference { public static class ByReference extends nioInfo implements Structure.ByReference {}
} public static class ByValue extends nioInfo implements Structure.ByValue {}
public nioInfo() {}
public static class ByValue extends nioInfo implements Structure.ByValue { public nioInfo(Pointer p) { super(p); read(); }
}
public int num; public int num;
public nioEvent.ByReference ioTask; public Pointer / * nioEvent.ByReference * / ioTask;
} }
public static final int FD_SETSIZE = 64; public static final int FD_SETSIZE = 64;
public static class fd_set extends Structure { public static class fd_set extends Structure {
public static class ByReference extends fd_set implements Structure.ByReference { public static class ByReference extends fd_set implements Structure.ByReference {}
} public static class ByValue extends fd_set implements Structure.ByValue {}
public fd_set() {}
public static class ByValue extends fd_set implements Structure.ByValue { public fd_set(Pointer p) { super(p); read(); }
}
public int count; public int count;
public int[] fd = new int[FD_SETSIZE]; public int[] fd = new int[FD_SETSIZE];

3
scala/src/org/broadinstitute/sting/queue/engine/lsf/Lsf706JobRunner.scala
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@ -62,8 +62,7 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR
for (i <- 0 until LibLsf.LSF_RLIM_NLIMITS) for (i <- 0 until LibLsf.LSF_RLIM_NLIMITS)
request.rLimits(i) = LibLsf.DEFAULT_RLIMIT; request.rLimits(i) = LibLsf.DEFAULT_RLIMIT;
// Set the display name of the job to the first 4000 characters request.jobName = function.description.take(LibBat.MAX_JOB_NAME_LEN)
request.jobName = function.description.take(4000)
request.options |= LibBat.SUB_JOB_NAME request.options |= LibBat.SUB_JOB_NAME
// Set the output file for stdout // Set the output file for stdout