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
parent
2058fc12bc
commit
097a9a59e8
File diff suppressed because it is too large
Load Diff
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@ -31,6 +31,31 @@ import com.sun.jna.ptr.PointerByReference;
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import org.broadinstitute.sting.jna.clibrary.JNAUtils;
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import org.broadinstitute.sting.jna.clibrary.LibC.*;
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/*
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NOTE: This library uses Pointer for some Struct.ByReference members going
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against the JNA recommendations at http://jna.java.net/#structure_use
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Instead stuct arrays are Pointers and each structure contains a
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constructor that can accept the Pointer iff the size of the array is
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known to be greater than zero.
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This was especially problematic in jobInfoEnt->items->resName. When
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jobInfo->reserveCnt was zero jobInfoItems->items was not necessarily null.
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LSF will often reuse memory for structure arrays but will set the
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array size / count (reserveCnt above) to zero when the array should
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not be accessed. When LSF has reused memory and points to a non-null
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structure pointer (items) the inner structure may contain further
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garbage pointers (especially items->resName).
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When JNA sees a non-null Structure.ByReference it will autoRead() the
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member. When autoRead() eventually gets to the items->resName trying
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to run strlen on the bad memory address causes a SIGSEGV.
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By using a Pointer instead of the Structure.ByReference JNA will not
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automatically autoRead(), and the API user will have to pass the
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pointer to the Structure on their own.
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*/
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/**
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* JNA wrappers for LSF's lsf.h and -llsf
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*
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@ -83,11 +108,10 @@ public class LibLsf {
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}
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public static class rlimit extends Structure {
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public static class ByReference extends rlimit implements Structure.ByReference {
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}
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public static class ByValue extends rlimit implements Structure.ByValue {
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}
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public static class ByReference extends rlimit implements Structure.ByReference {}
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public static class ByValue extends rlimit implements Structure.ByValue {}
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public rlimit() {}
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public rlimit(Pointer p) { super(p); read(); }
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public NativeLong rlim_cur;
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public NativeLong rlim_max;
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@ -96,11 +120,10 @@ public class LibLsf {
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public static class rusage extends Structure {
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public static class ByReference extends rusage implements Structure.ByReference {
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}
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public static class ByValue extends rusage implements Structure.ByValue {
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}
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public static class ByReference extends rusage implements Structure.ByReference {}
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public static class ByValue extends rusage implements Structure.ByValue {}
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public rusage() {}
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public rusage(Pointer p) { super(p); read(); }
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public timeval ru_utime;
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public timeval ru_stime;
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@ -345,11 +368,10 @@ public class LibLsf {
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public static class connectEnt extends Structure {
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public static class ByReference extends connectEnt implements Structure.ByReference {
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}
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public static class ByValue extends connectEnt implements Structure.ByValue {
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}
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public static class ByReference extends connectEnt implements Structure.ByReference {}
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public static class ByValue extends connectEnt implements Structure.ByValue {}
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public connectEnt() {}
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public connectEnt(Pointer p) { super(p); read(); }
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public String hostname;
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public int[] csock = new int[2];
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@ -447,11 +469,10 @@ public class LibLsf {
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public static class placeInfo extends Structure {
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public static class ByReference extends placeInfo implements Structure.ByReference {
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}
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public static class ByValue extends placeInfo implements Structure.ByValue {
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}
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public static class ByReference extends placeInfo implements Structure.ByReference {}
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public static class ByValue extends placeInfo implements Structure.ByValue {}
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public placeInfo() {}
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public placeInfo(Pointer p) { super(p); read(); }
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public byte[] hostName = new byte[MAXHOSTNAMELEN];
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public int numtask;
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@ -461,11 +482,10 @@ public class LibLsf {
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public static class hostLoad extends Structure {
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public static class ByReference extends hostLoad implements Structure.ByReference {
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}
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public static class ByValue extends hostLoad implements Structure.ByValue {
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}
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public static class ByReference extends hostLoad implements Structure.ByReference {}
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public static class ByValue extends hostLoad implements Structure.ByValue {}
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public hostLoad() {}
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public hostLoad(Pointer p) { super(p); read(); }
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public byte[] hostName = new byte[MAXHOSTNAMELEN];
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public IntByReference status;
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@ -503,11 +523,10 @@ public class LibLsf {
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public static class resItem extends Structure {
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public static class ByReference extends resItem implements Structure.ByReference {
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}
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public static class ByValue extends resItem implements Structure.ByValue {
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}
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public static class ByReference extends resItem implements Structure.ByReference {}
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public static class ByValue extends resItem implements Structure.ByValue {}
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public resItem() {}
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public resItem(Pointer p) { super(p); read(); }
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public byte[] name = new byte[MAXLSFNAMELEN];
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public byte[] des = new byte[MAXRESDESLEN];
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@ -521,11 +540,10 @@ public class LibLsf {
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public static class lsInfo extends Structure {
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public static class ByReference extends lsInfo implements Structure.ByReference {
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}
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public static class ByValue extends lsInfo implements Structure.ByValue {
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}
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public static class ByReference extends lsInfo implements Structure.ByReference {}
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public static class ByValue extends lsInfo implements Structure.ByValue {}
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public lsInfo() {}
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public lsInfo(Pointer p) { super(p); read(); }
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// The current version of JNA's Structure.getNativeAlignment passes a "null" to
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// Native.getNativeSize() when accessing the contents of a 2D array.
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@ -533,7 +551,7 @@ public class LibLsf {
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// comments so when we upgrade don't want to have specialized code floating around.
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public int nRes;
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public resItem.ByReference resTable;
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public Pointer /* resItem.ByReference */ resTable;
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public int nTypes;
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public byte[] hostTypes = new byte[MAXTYPES * MAXLSFNAMELEN];
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public int nModels;
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@ -560,11 +578,10 @@ public class LibLsf {
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public static class clusterInfo extends Structure {
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public static class ByReference extends clusterInfo implements Structure.ByReference {
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}
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public static class ByValue extends clusterInfo implements Structure.ByValue {
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}
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public static class ByReference extends clusterInfo implements Structure.ByReference {}
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public static class ByValue extends clusterInfo implements Structure.ByValue {}
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public clusterInfo() {}
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public clusterInfo(Pointer p) { super(p); read(); }
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public byte[] clusterName = new byte[MAXLSFNAMELEN];
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public int status;
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@ -591,11 +608,10 @@ public class LibLsf {
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public static class hostInfo extends Structure {
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public static class ByReference extends hostInfo implements Structure.ByReference {
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}
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public static class ByValue extends hostInfo implements Structure.ByValue {
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}
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public static class ByReference extends hostInfo implements Structure.ByReference {}
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public static class ByValue extends hostInfo implements Structure.ByValue {}
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public hostInfo() {}
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public hostInfo(Pointer p) { super(p); read(); }
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public byte[] hostName = new byte[MAXHOSTNAMELEN];
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public String hostType;
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@ -677,11 +693,10 @@ public class LibLsf {
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public static class config_param extends Structure {
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public static class ByReference extends config_param implements Structure.ByReference {
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}
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public static class ByValue extends config_param implements Structure.ByValue {
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}
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public static class ByReference extends config_param implements Structure.ByReference {}
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public static class ByValue extends config_param implements Structure.ByValue {}
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public config_param() {}
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public config_param(Pointer p) { super(p); read(); }
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public String paramName;
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public String paramValue;
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@ -690,11 +705,10 @@ public class LibLsf {
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public static class lsfRusage extends Structure {
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public static class ByReference extends lsfRusage implements Structure.ByReference {
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}
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public static class ByValue extends lsfRusage implements Structure.ByValue {
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}
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public static class ByReference extends lsfRusage implements Structure.ByReference {}
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public static class ByValue extends lsfRusage implements Structure.ByValue {}
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public lsfRusage() {}
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public lsfRusage(Pointer p) { super(p); read(); }
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public double ru_utime;
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public double ru_stime;
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@ -721,11 +735,10 @@ public class LibLsf {
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public static class lsfAcctRec extends Structure {
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public static class ByReference extends lsfAcctRec implements Structure.ByReference {
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}
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public static class ByValue extends lsfAcctRec implements Structure.ByValue {
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}
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public static class ByReference extends lsfAcctRec implements Structure.ByReference {}
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public static class ByValue extends lsfAcctRec implements Structure.ByValue {}
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public lsfAcctRec() {}
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public lsfAcctRec(Pointer p) { super(p); read(); }
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public int pid;
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public String username;
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@ -743,11 +756,10 @@ public class LibLsf {
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public static class confNode extends Structure {
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public static class ByReference extends confNode implements Structure.ByReference {
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}
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public static class ByValue extends confNode implements Structure.ByValue {
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}
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public static class ByReference extends confNode implements Structure.ByReference {}
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public static class ByValue extends confNode implements Structure.ByValue {}
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public confNode() {}
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public confNode(Pointer p) { super(p); read(); }
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public confNode.ByReference leftPtr;
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public confNode.ByReference rightPtr;
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@ -762,11 +774,10 @@ public class LibLsf {
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public static class pStack extends Structure {
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public static class ByReference extends pStack implements Structure.ByReference {
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}
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public static class ByValue extends pStack implements Structure.ByValue {
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}
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public static class ByReference extends pStack implements Structure.ByReference {}
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public static class ByValue extends pStack implements Structure.ByValue {}
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public pStack() {}
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public pStack(Pointer p) { super(p); read(); }
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public int top;
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public int size;
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@ -776,11 +787,10 @@ public class LibLsf {
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public static class confHandle extends Structure {
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public static class ByReference extends confHandle implements Structure.ByReference {
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}
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public static class ByValue extends confHandle implements Structure.ByValue {
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}
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public static class ByReference extends confHandle implements Structure.ByReference {}
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public static class ByValue extends confHandle implements Structure.ByValue {}
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public confHandle() {}
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public confHandle(Pointer p) { super(p); read(); }
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public confNode.ByReference rootNode;
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public String fname;
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@ -792,11 +802,10 @@ public class LibLsf {
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public static class lsConf extends Structure {
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public static class ByReference extends lsConf implements Structure.ByReference {
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}
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public static class ByValue extends lsConf implements Structure.ByValue {
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}
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public static class ByReference extends lsConf implements Structure.ByReference {}
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public static class ByValue extends lsConf implements Structure.ByValue {}
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public lsConf() {}
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public lsConf(Pointer p) { super(p); read(); }
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public confHandle.ByReference confhandle;
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public int numConds;
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@ -807,11 +816,10 @@ public class LibLsf {
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public static class sharedConf extends Structure {
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public static class ByReference extends sharedConf implements Structure.ByReference {
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}
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public static class ByValue extends sharedConf implements Structure.ByValue {
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}
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public static class ByReference extends sharedConf implements Structure.ByReference {}
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public static class ByValue extends sharedConf implements Structure.ByValue {}
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public sharedConf() {}
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public sharedConf(Pointer p) { super(p); read(); }
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public lsInfo.ByReference lsinfo;
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public int numCls;
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@ -823,11 +831,10 @@ public class LibLsf {
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public static class lsSharedResourceInstance extends Structure {
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public static class ByReference extends lsSharedResourceInstance implements Structure.ByReference {
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}
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public static class ByValue extends lsSharedResourceInstance implements Structure.ByValue {
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}
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public static class ByReference extends lsSharedResourceInstance implements Structure.ByReference {}
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public static class ByValue extends lsSharedResourceInstance implements Structure.ByValue {}
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public lsSharedResourceInstance() {}
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public lsSharedResourceInstance(Pointer p) { super(p); read(); }
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public String value;
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public int nHosts;
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@ -839,43 +846,40 @@ public class LibLsf {
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public static class lsSharedResourceInfo extends Structure {
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public static class ByReference extends lsSharedResourceInfo implements Structure.ByReference {
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}
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public static class ByValue extends lsSharedResourceInfo implements Structure.ByValue {
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}
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public static class ByReference extends lsSharedResourceInfo implements Structure.ByReference {}
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public static class ByValue extends lsSharedResourceInfo implements Structure.ByValue {}
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public lsSharedResourceInfo() {}
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public lsSharedResourceInfo(Pointer p) { super(p); read(); }
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public String resourceName;
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public int nInstances;
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public lsSharedResourceInstance.ByReference instances;
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public Pointer /* lsSharedResourceInstance.ByReference */ instances;
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}
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public static class clusterConf extends Structure {
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public static class ByReference extends clusterConf implements Structure.ByReference {
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}
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public static class ByValue extends clusterConf implements Structure.ByValue {
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}
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public static class ByReference extends clusterConf implements Structure.ByReference {}
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public static class ByValue extends clusterConf implements Structure.ByValue {}
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public clusterConf() {}
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public clusterConf(Pointer p) { super(p); read(); }
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public clusterInfo.ByReference clinfo;
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public int numHosts;
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public hostInfo.ByReference hosts;
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public Pointer /* hostInfo.ByReference */ hosts;
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public int defaultFeatures;
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public int numShareRes;
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public lsSharedResourceInfo.ByReference shareRes;
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public Pointer /* lsSharedResourceInfo.ByReference */ shareRes;
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}
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public static class pidInfo extends Structure {
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public static class ByReference extends pidInfo implements Structure.ByReference {
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}
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public static class ByValue extends pidInfo implements Structure.ByValue {
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}
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public static class ByReference extends pidInfo implements Structure.ByReference {}
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public static class ByValue extends pidInfo implements Structure.ByValue {}
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public pidInfo() {}
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public pidInfo(Pointer p) { super(p); read(); }
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public int pid;
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public int ppid;
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@ -887,18 +891,17 @@ public class LibLsf {
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public static class jRusage extends Structure {
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public static class ByReference extends jRusage implements Structure.ByReference {
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}
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public static class ByValue extends jRusage implements Structure.ByValue {
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}
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public static class ByReference extends jRusage implements Structure.ByReference {}
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public static class ByValue extends jRusage implements Structure.ByValue {}
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public jRusage() {}
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public jRusage(Pointer p) { super(p); read(); }
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public int mem;
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public int swap;
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public int utime;
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public int stime;
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public int npids;
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public pidInfo.ByReference pidInfo;
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public Pointer /* pidInfo.ByReference */ pidInfo;
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public int npgids;
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public IntByReference pgid;
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@ -913,11 +916,10 @@ public class LibLsf {
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public static final int NUM_CLASS_TYPE = 3;
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public static class licUsage extends Structure {
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public static class ByReference extends licUsage implements Structure.ByReference {
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}
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public static class ByValue extends licUsage implements Structure.ByValue {
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}
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public static class ByReference extends licUsage implements Structure.ByReference {}
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public static class ByValue extends licUsage implements Structure.ByValue {}
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public licUsage() {}
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public licUsage(Pointer p) { super(p); read(); }
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public int licDisplayMask;
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public int usingDemoLicense;
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@ -928,11 +930,10 @@ public class LibLsf {
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public static class hostClassInfo extends Structure {
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public static class ByReference extends hostClassInfo implements Structure.ByReference {
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}
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public static class ByValue extends hostClassInfo implements Structure.ByValue {
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}
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public static class ByReference extends hostClassInfo implements Structure.ByReference {}
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public static class ByValue extends hostClassInfo implements Structure.ByValue {}
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public hostClassInfo() {}
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public hostClassInfo(Pointer p) { super(p); read(); }
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public int numHosts;
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public int numCpus;
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@ -942,11 +943,10 @@ public class LibLsf {
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public static class lsfLicUsage extends Structure {
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public static class ByReference extends lsfLicUsage implements Structure.ByReference {
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}
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public static class ByValue extends lsfLicUsage implements Structure.ByValue {
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}
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public static class ByReference extends lsfLicUsage implements Structure.ByReference {}
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public static class ByValue extends lsfLicUsage implements Structure.ByValue {}
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public lsfLicUsage() {}
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public lsfLicUsage(Pointer p) { super(p); read(); }
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public licUsage licUsage;
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public hostClassInfo[] hostInfo = new hostClassInfo[NUM_CLASS_TYPE];
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@ -960,11 +960,10 @@ public class LibLsf {
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public static class param_entry extends Structure {
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public static class ByReference extends param_entry implements Structure.ByReference {
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}
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public static class ByValue extends param_entry implements Structure.ByValue {
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}
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public static class ByReference extends param_entry implements Structure.ByReference {}
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public static class ByValue extends param_entry implements Structure.ByValue {}
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public param_entry() {}
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public param_entry(Pointer p) { super(p); read(); }
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public static int HAS_PARAM_VALUE = 0x001;
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public static final int HAS_PARAM_DEFAULT = 0x002;
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@ -978,15 +977,14 @@ public class LibLsf {
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public static class params_key_value_pair extends Structure {
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public static class ByReference extends params_key_value_pair implements Structure.ByReference {
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}
|
||||
|
||||
public static class ByValue extends params_key_value_pair implements Structure.ByValue {
|
||||
}
|
||||
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 params_key_value_pair(Pointer p) { super(p); read(); }
|
||||
|
||||
public int num_params;
|
||||
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 ByReference extends ls_timeval implements Structure.ByReference {
|
||||
}
|
||||
|
||||
public static class ByValue extends ls_timeval implements Structure.ByValue {
|
||||
}
|
||||
public static class ByReference extends ls_timeval implements Structure.ByReference {}
|
||||
public static class ByValue extends ls_timeval implements Structure.ByValue {}
|
||||
public ls_timeval() {}
|
||||
public ls_timeval(Pointer p) { super(p); read(); }
|
||||
|
||||
public float rtime;
|
||||
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 class extResInfo extends Structure {
|
||||
public static class ByReference extends extResInfo implements Structure.ByReference {
|
||||
}
|
||||
|
||||
public static class ByValue extends extResInfo implements Structure.ByValue {
|
||||
}
|
||||
public static class ByReference extends extResInfo implements Structure.ByReference {}
|
||||
public static class ByValue extends extResInfo implements Structure.ByValue {}
|
||||
public extResInfo() {}
|
||||
public extResInfo(Pointer p) { super(p); read(); }
|
||||
|
||||
public String name;
|
||||
public String type;
|
||||
|
|
@ -1578,11 +1574,10 @@ public class LibLsf {
|
|||
|
||||
|
||||
public static class nioEvent extends Structure {
|
||||
public static class ByReference extends nioEvent implements Structure.ByReference {
|
||||
}
|
||||
|
||||
public static class ByValue extends nioEvent implements Structure.ByValue {
|
||||
}
|
||||
public static class ByReference extends nioEvent implements Structure.ByReference {}
|
||||
public static class ByValue extends nioEvent implements Structure.ByValue {}
|
||||
public nioEvent() {}
|
||||
public nioEvent(Pointer p) { super(p); read(); }
|
||||
|
||||
public int tid;
|
||||
public *//*nioType*//* int type;
|
||||
|
|
@ -1592,25 +1587,23 @@ public class LibLsf {
|
|||
|
||||
|
||||
public static class nioInfo extends Structure {
|
||||
public static class ByReference extends nioInfo implements Structure.ByReference {
|
||||
}
|
||||
|
||||
public static class ByValue extends nioInfo implements Structure.ByValue {
|
||||
}
|
||||
public static class ByReference extends nioInfo implements Structure.ByReference {}
|
||||
public static class ByValue extends nioInfo implements Structure.ByValue {}
|
||||
public nioInfo() {}
|
||||
public nioInfo(Pointer p) { super(p); read(); }
|
||||
|
||||
public int num;
|
||||
public nioEvent.ByReference ioTask;
|
||||
public Pointer / * nioEvent.ByReference * / ioTask;
|
||||
}
|
||||
|
||||
|
||||
public static final int FD_SETSIZE = 64;
|
||||
|
||||
public static class fd_set extends Structure {
|
||||
public static class ByReference extends fd_set implements Structure.ByReference {
|
||||
}
|
||||
|
||||
public static class ByValue extends fd_set implements Structure.ByValue {
|
||||
}
|
||||
public static class ByReference extends fd_set implements Structure.ByReference {}
|
||||
public static class ByValue extends fd_set implements Structure.ByValue {}
|
||||
public fd_set() {}
|
||||
public fd_set(Pointer p) { super(p); read(); }
|
||||
|
||||
public int count;
|
||||
public int[] fd = new int[FD_SETSIZE];
|
||||
|
|
|
|||
|
|
@ -62,8 +62,7 @@ class Lsf706JobRunner(val function: CommandLineFunction) extends CommandLineJobR
|
|||
for (i <- 0 until LibLsf.LSF_RLIM_NLIMITS)
|
||||
request.rLimits(i) = LibLsf.DEFAULT_RLIMIT;
|
||||
|
||||
// Set the display name of the job to the first 4000 characters
|
||||
request.jobName = function.description.take(4000)
|
||||
request.jobName = function.description.take(LibBat.MAX_JOB_NAME_LEN)
|
||||
request.options |= LibBat.SUB_JOB_NAME
|
||||
|
||||
// Set the output file for stdout
|
||||
|
|
|
|||
Loading…
Reference in New Issue