java: Fix compilation error in allToAllw using Java arrays
Java bindings in Open MPI support Java arrays and direct buffers as buffers. All non-blocking methods must use direct buffers and only blocking methods can choose between Java arrays and direct buffers. Though Comm.allToAllw() is a blocking method, Java applications using Java arrays as buffers get compilation errors. This fix enables using Java arrays in Comm.allToAllw(). Signed-off-by: Kurita, Takehiro <fj6370fp@aa.jp.fujitsu.com>
Этот коммит содержится в:
Kurita, Takehiro
родитель
0c1da0fcab
Коммит
7ece564978
@ -11,6 +11,7 @@
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* All rights reserved.
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* Copyright (c) 2015 Los Alamos National Security, LLC. All rights
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* reserved.
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* Copyright (c) 2019 FUJITSU LIMITED. All rights reserved.
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* $COPYRIGHT$
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*
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* Additional copyrights may follow
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@ -94,6 +95,15 @@ void ompi_java_getReadPtrv(
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jobject buf, jboolean db, int off, int *counts, int *displs,
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int size, int rank, MPI_Datatype type, int baseType);
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/* Gets a buffer pointer for reading, but it
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* 'size' is the number of processes.
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* if rank == -1 it copies all data from Java.
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* if rank != -1 it only copies from Java the rank data. */
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void ompi_java_getReadPtrw(
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void **ptr, ompi_java_buffer_t **item, JNIEnv *env,
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jobject buf, jboolean db, int *offs, int *counts, int *displs,
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int size, int rank, MPI_Datatype *types, int *baseTypes);
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/* Releases a buffer used for reading. */
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void ompi_java_releaseReadPtr(
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void *ptr, ompi_java_buffer_t *item, jobject buf, jboolean db);
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@ -109,6 +119,12 @@ void ompi_java_getWritePtrv(
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void **ptr, ompi_java_buffer_t **item, JNIEnv *env, jobject buf,
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jboolean db, int *counts, int *displs, int size, MPI_Datatype type);
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/* Gets a buffer pointer for writing.
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* 'size' is the number of processes. */
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void ompi_java_getWritePtrw(
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void **ptr, ompi_java_buffer_t **item, JNIEnv *env, jobject buf,
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jboolean db, int *counts, int *displs, int size, MPI_Datatype *types);
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/* Releases a buffer used for writing.
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* It copies data to Java. */
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void ompi_java_releaseWritePtr(
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@ -123,6 +139,14 @@ void ompi_java_releaseWritePtrv(
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jobject buf, jboolean db, int off, int *counts, int *displs,
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int size, MPI_Datatype type, int baseType);
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/* Releases a buffer used for writing.
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* It copies data to Java.
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* 'size' is the number of processes. */
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void ompi_java_releaseWritePtrw(
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void *ptr, ompi_java_buffer_t *item, JNIEnv *env,
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jobject buf, jboolean db, int *offs, int *counts, int *displs,
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int size, MPI_Datatype *types, int *baseTypes);
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void ompi_java_setStaticLongField(JNIEnv *env, jclass c,
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char *field, jlong value);
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@ -13,7 +13,7 @@
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* and Technology (RIST). All rights reserved.
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* Copyright (c) 2016 Los Alamos National Security, LLC. All rights
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* reserved.
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* Copyright (c) 2017 FUJITSU LIMITED. All rights reserved.
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* Copyright (c) 2017-2019 FUJITSU LIMITED. All rights reserved.
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* $COPYRIGHT$
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*
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* Additional copyrights may follow
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@ -1612,39 +1612,67 @@ JNIEXPORT jlong JNICALL Java_mpi_Comm_iAllToAllv(
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}
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JNIEXPORT void JNICALL Java_mpi_Comm_allToAllw(
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JNIEnv *env, jobject jthis, jlong jComm,
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jobject sendBuf, jintArray sCount, jintArray sDispls, jlongArray sTypes,
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jobject recvBuf, jintArray rCount, jintArray rDispls, jlongArray rTypes)
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JNIEnv *env, jobject jthis, jlong jComm,
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jobject sBuf, jboolean sdb, jintArray sOffs, jintArray sCount,
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jintArray sDispls, jlongArray sTypes, jintArray sBtypes,
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jobject rBuf, jboolean rdb, jintArray rOffs, jintArray rCount,
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jintArray rDispls, jlongArray rTypes, jintArray rBtypes)
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{
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MPI_Comm comm = (MPI_Comm)jComm;
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MPI_Comm comm = (MPI_Comm)jComm;
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jlong* jSTypes, *jRTypes;
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MPI_Datatype *cSTypes, *cRTypes;
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int inter = isInter(env, comm),
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size = getSize(env, comm, inter);
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ompi_java_getDatatypeArray(env, sTypes, &jSTypes, &cSTypes);
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ompi_java_getDatatypeArray(env, rTypes, &jRTypes, &cRTypes);
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jlong* jSTypes, *jRTypes;
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MPI_Datatype *cSTypes, *cRTypes;
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jint *jSCount, *jRCount, *jSDispls, *jRDispls;
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int *cSCount, *cRCount, *cSDispls, *cRDispls;
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ompi_java_getIntArray(env, sCount, &jSCount, &cSCount);
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ompi_java_getIntArray(env, rCount, &jRCount, &cRCount);
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ompi_java_getIntArray(env, sDispls, &jSDispls, &cSDispls);
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ompi_java_getIntArray(env, rDispls, &jRDispls, &cRDispls);
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ompi_java_getDatatypeArray(env, sTypes, &jSTypes, &cSTypes);
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ompi_java_getDatatypeArray(env, rTypes, &jRTypes, &cRTypes);
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void *sPtr = ompi_java_getDirectBufferAddress(env, sendBuf),
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*rPtr = ompi_java_getDirectBufferAddress(env, recvBuf);
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jint *jSCount, *jRCount, *jSDispls, *jRDispls;
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int *cSCount, *cRCount, *cSDispls, *cRDispls;
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jint *jSBtypes, *jRBtypes;
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int *cSBtypes, *cRBtypes;
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jint *jSOffs, *jROffs;
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int *cSOffs, *cROffs;
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int rc = MPI_Alltoallw(
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sPtr, cSCount, cSDispls, cSTypes,
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rPtr, cRCount, cRDispls, cRTypes, comm);
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ompi_java_getIntArray(env, sCount, &jSCount, &cSCount);
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ompi_java_getIntArray(env, rCount, &jRCount, &cRCount);
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ompi_java_getIntArray(env, sDispls, &jSDispls, &cSDispls);
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ompi_java_getIntArray(env, rDispls, &jRDispls, &cRDispls);
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ompi_java_getIntArray(env, sBtypes, &jSBtypes, &cSBtypes);
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ompi_java_getIntArray(env, rBtypes, &jRBtypes, &cRBtypes);
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ompi_java_getIntArray(env, sOffs, &jSOffs, &cSOffs);
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ompi_java_getIntArray(env, rOffs, &jROffs, &cROffs);
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ompi_java_exceptionCheck(env, rc);
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ompi_java_forgetIntArray(env, sCount, jSCount, cSCount);
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ompi_java_forgetIntArray(env, rCount, jRCount, cRCount);
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ompi_java_forgetIntArray(env, sDispls, jSDispls, cSDispls);
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ompi_java_forgetIntArray(env, rDispls, jRDispls, cRDispls);
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ompi_java_forgetDatatypeArray(env, sTypes, jSTypes, cSTypes);
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ompi_java_forgetDatatypeArray(env, rTypes, jRTypes, cRTypes);
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void *sPtr, *rPtr;
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ompi_java_buffer_t *sItem, *rItem;
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ompi_java_getReadPtrw(&sPtr, &sItem, env, sBuf, sdb, cSOffs,
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cSCount, cSDispls, size, -1, cSTypes, cSBtypes);
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ompi_java_getWritePtrw(&rPtr, &rItem, env, rBuf, rdb,
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cRCount, cRDispls, size, cRTypes);
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int rc = MPI_Alltoallw(sPtr, cSCount, cSDispls, cSTypes,
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rPtr, cRCount, cRDispls, cRTypes, comm);
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ompi_java_exceptionCheck(env, rc);
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ompi_java_releaseReadPtr(sPtr, sItem, sBuf, sdb);
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ompi_java_releaseWritePtrw(rPtr, rItem, env, rBuf, rdb, cROffs,
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cRCount, cRDispls, size, cRTypes, cRBtypes);
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ompi_java_exceptionCheck(env, rc);
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ompi_java_forgetIntArray(env, sCount, jSCount, cSCount);
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ompi_java_forgetIntArray(env, rCount, jRCount, cRCount);
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ompi_java_forgetIntArray(env, sDispls, jSDispls, cSDispls);
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ompi_java_forgetIntArray(env, rDispls, jRDispls, cRDispls);
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ompi_java_forgetIntArray(env, sBtypes, jSBtypes, cSBtypes);
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ompi_java_forgetIntArray(env, rBtypes, jRBtypes, cRBtypes);
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ompi_java_forgetIntArray(env, sOffs, jSOffs, cSOffs);
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ompi_java_forgetIntArray(env, rOffs, jROffs, cROffs);
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ompi_java_forgetDatatypeArray(env, sTypes, jSTypes, cSTypes);
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ompi_java_forgetDatatypeArray(env, rTypes, jRTypes, cRTypes);
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}
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JNIEXPORT jlong JNICALL Java_mpi_Comm_iAllToAllw(
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@ -17,6 +17,7 @@
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* Copyright (c) 2015 Research Organization for Information Science
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* and Technology (RIST). All rights reserved.
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||||
* Copyright (c) 2016-2017 IBM Corporation. All rights reserved.
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* Copyright (c) 2019 FUJITSU LIMITED. All rights reserved.
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* $COPYRIGHT$
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*
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* Additional copyrights may follow
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@ -672,6 +673,39 @@ static void* getReadPtrvRank(
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return ptr;
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}
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static void* getReadPtrwRank(
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ompi_java_buffer_t **item, JNIEnv *env, jobject buf,
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int *offsets, int *counts, int *displs, int size,
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int rank, MPI_Datatype *types, int *baseTypes)
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{
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int extent = getTypeExtent(env, types[rank]),
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length = getCountv(counts, displs, size);
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void *ptr = getBuffer(env, item, length);
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int rootOff = offsets[rank] + displs[rank];
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if(opal_datatype_is_contiguous_memory_layout(&types[rank]->super, counts[rank]))
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{
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int rootLength = extent * counts[rank];
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void *rootPtr = (char*)ptr + displs[rank];
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getArrayRegion(env, buf, baseTypes[rank], rootOff, rootLength, rootPtr);
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}
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else
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{
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void *inBuf, *inBase;
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inBuf = ompi_java_getArrayCritical(&inBase, env, buf, rootOff);
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int rc = opal_datatype_copy_content_same_ddt(
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&types[rank]->super, counts[rank], ptr, inBuf);
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ompi_java_exceptionCheck(env,
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rc==OPAL_SUCCESS ? OMPI_SUCCESS : OMPI_ERROR);
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(*env)->ReleasePrimitiveArrayCritical(env, buf, inBase, JNI_ABORT);
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}
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return ptr;
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}
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static void* getReadPtrvAll(
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ompi_java_buffer_t **item, JNIEnv *env, jobject buf,
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int offset, int *counts, int *displs, int size,
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@ -716,6 +750,49 @@ static void* getReadPtrvAll(
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return ptr;
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}
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static void* getReadPtrwAll(
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ompi_java_buffer_t **item, JNIEnv *env, jobject buf,
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int *offsets, int *counts, int *displs, int size,
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MPI_Datatype *types, int *baseTypes)
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{
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int length = getCountv(counts, displs, size);
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void *ptr = getBuffer(env, item, length);
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for(int i = 0; i < size; i++)
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{
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int extent = getTypeExtent(env, types[i]);
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if(opal_datatype_is_contiguous_memory_layout(&types[i]->super, 2))
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{
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int iOff = offsets[i] + displs[i],
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iLen = extent * counts[i];
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void *iPtr = (char*)ptr + displs[i];
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getArrayRegion(env, buf, baseTypes[i], iOff, iLen, iPtr);
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}
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else
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{
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void *bufPtr, *bufBase;
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bufPtr = ompi_java_getArrayCritical(&bufBase, env, buf, offsets[i]);
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int iOff = displs[i];
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char *iBuf = iOff + (char*)bufPtr,
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*iPtr = iOff + (char*)ptr;
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int rc = opal_datatype_copy_content_same_ddt(
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&types[i]->super, counts[i], iPtr, iBuf);
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ompi_java_exceptionCheck(env,
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rc==OPAL_SUCCESS ? OMPI_SUCCESS : OMPI_ERROR);
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(*env)->ReleasePrimitiveArrayCritical(env, buf, bufBase, JNI_ABORT);
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}
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}
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return ptr;
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}
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static void* getWritePtr(ompi_java_buffer_t **item, JNIEnv *env,
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int count, MPI_Datatype type)
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{
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@ -735,6 +812,14 @@ static void* getWritePtrv(ompi_java_buffer_t **item, JNIEnv *env,
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return getBuffer(env, item, length);
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}
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static void* getWritePtrw(ompi_java_buffer_t **item, JNIEnv *env,
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int *counts, int *displs, int size, MPI_Datatype *types)
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{
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int length = getCountv(counts, displs, size);
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return getBuffer(env, item, length);
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}
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void ompi_java_getReadPtr(
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void **ptr, ompi_java_buffer_t **item, JNIEnv *env, jobject buf,
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jboolean db, int offset, int count, MPI_Datatype type, int baseType)
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@ -810,6 +895,39 @@ void ompi_java_getReadPtrv(
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}
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}
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void ompi_java_getReadPtrw(
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void **ptr, ompi_java_buffer_t **item, JNIEnv *env,
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jobject buf, jboolean db, int *offsets, int *counts, int *displs,
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int size, int rank, MPI_Datatype *types, int *baseTypes)
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{
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int i;
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if(buf == NULL)
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{
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/* Allow NULL buffers to send/recv 0 items as control messages. */
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*ptr = NULL;
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*item = NULL;
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}
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else if(db)
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{
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for(i = 0; i < size; i++){
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assert(offsets[i] == 0);
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}
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*ptr = (*env)->GetDirectBufferAddress(env, buf);
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*item = NULL;
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}
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else if(rank == -1)
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{
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*ptr = getReadPtrwAll(item, env, buf, offsets, counts,
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displs, size, types, baseTypes);
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}
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else
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{
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*ptr = getReadPtrwRank(item, env, buf, offsets, counts,
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displs, size, rank, types, baseTypes);
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}
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}
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void ompi_java_releaseReadPtr(
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void *ptr, ompi_java_buffer_t *item, jobject buf, jboolean db)
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{
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@ -859,6 +977,27 @@ void ompi_java_getWritePtrv(
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}
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}
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void ompi_java_getWritePtrw(
|
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void **ptr, ompi_java_buffer_t **item, JNIEnv *env, jobject buf,
|
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jboolean db, int *counts, int *displs, int size, MPI_Datatype *types)
|
||||
{
|
||||
if(buf == NULL)
|
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{
|
||||
/* Allow NULL buffers to send/recv 0 items as control messages. */
|
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*ptr = NULL;
|
||||
*item = NULL;
|
||||
}
|
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else if(db)
|
||||
{
|
||||
*ptr = (*env)->GetDirectBufferAddress(env, buf);
|
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*item = NULL;
|
||||
}
|
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else
|
||||
{
|
||||
*ptr = getWritePtrw(item, env, counts, displs, size, types);
|
||||
}
|
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}
|
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|
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void ompi_java_releaseWritePtr(
|
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void *ptr, ompi_java_buffer_t *item, JNIEnv *env, jobject buf,
|
||||
jboolean db, int offset, int count, MPI_Datatype type, int baseType)
|
||||
@ -933,6 +1072,49 @@ void ompi_java_releaseWritePtrv(
|
||||
releaseBuffer(ptr, item);
|
||||
}
|
||||
|
||||
void ompi_java_releaseWritePtrw(
|
||||
void *ptr, ompi_java_buffer_t *item, JNIEnv *env,
|
||||
jobject buf, jboolean db, int *offsets, int *counts, int *displs,
|
||||
int size, MPI_Datatype *types, int *baseTypes)
|
||||
{
|
||||
if(db || !buf || !ptr)
|
||||
return;
|
||||
|
||||
int i;
|
||||
|
||||
for(i = 0; i < size; i++)
|
||||
{
|
||||
int extent = getTypeExtent(env, types[i]);
|
||||
|
||||
if(opal_datatype_is_contiguous_memory_layout(&types[i]->super, 2))
|
||||
{
|
||||
int iOff = offsets[i] + displs[i],
|
||||
iLen = extent * counts[i];
|
||||
void *iPtr = (char*)ptr + displs[i];
|
||||
setArrayRegion(env, buf, baseTypes[i], iOff, iLen, iPtr);
|
||||
}
|
||||
else
|
||||
{
|
||||
void *bufPtr, *bufBase;
|
||||
|
||||
bufPtr = ompi_java_getArrayCritical(&bufBase, env, buf, offsets[i]);
|
||||
int iOff = displs[i];
|
||||
char *iBuf = iOff + (char*)bufPtr,
|
||||
*iPtr = iOff + (char*)ptr;
|
||||
|
||||
int rc = opal_datatype_copy_content_same_ddt(
|
||||
&types[i]->super, counts[i], iBuf, iPtr);
|
||||
|
||||
ompi_java_exceptionCheck(env,
|
||||
rc==OPAL_SUCCESS ? OMPI_SUCCESS : OMPI_ERROR);
|
||||
|
||||
(*env)->ReleasePrimitiveArrayCritical(env, buf, bufBase, 0);
|
||||
}
|
||||
|
||||
}
|
||||
releaseBuffer(ptr, item);
|
||||
}
|
||||
|
||||
jobject ompi_java_Integer_valueOf(JNIEnv *env, jint i)
|
||||
{
|
||||
return (*env)->CallStaticObjectMethod(env,
|
||||
|
||||
@ -13,7 +13,7 @@
|
||||
* and Technology (RIST). All rights reserved.
|
||||
* Copyright (c) 2015 Los Alamos National Security, LLC. All rights
|
||||
* reserved.
|
||||
* Copyright (c) 2017-2018 FUJITSU LIMITED. All rights reserved.
|
||||
* Copyright (c) 2017-2019 FUJITSU LIMITED. All rights reserved.
|
||||
* $COPYRIGHT$
|
||||
*
|
||||
* Additional copyrights may follow
|
||||
@ -2400,24 +2400,51 @@ public class Comm implements Freeable, Cloneable
|
||||
* @throws MPIException Signals that an MPI exception of some sort has occurred.
|
||||
*/
|
||||
public final void allToAllw(
|
||||
Buffer sendBuf, int[] sendCount, int[] sDispls, Datatype[] sendTypes,
|
||||
Buffer recvBuf, int[] recvCount, int[] rDispls, Datatype[] recvTypes)
|
||||
Object sendBuf, int[] sendCount, int[] sDispls, Datatype[] sendTypes,
|
||||
Object recvBuf, int[] recvCount, int[] rDispls, Datatype[] recvTypes)
|
||||
throws MPIException
|
||||
{
|
||||
MPI.check();
|
||||
assertDirectBuffer(sendBuf, recvBuf);
|
||||
|
||||
int[] sendoffs = new int[sendTypes.length];
|
||||
int[] recvoffs = new int[recvTypes.length];
|
||||
|
||||
boolean sdb = false,
|
||||
rdb = false;
|
||||
|
||||
if(sendBuf instanceof Buffer && !(sdb = ((Buffer)sendBuf).isDirect()))
|
||||
{
|
||||
|
||||
for (int i = 0; i < sendTypes.length; i++){
|
||||
sendoffs[i] = sendTypes[i].getOffset(sendBuf);
|
||||
}
|
||||
sendBuf = ((Buffer)sendBuf).array();
|
||||
}
|
||||
|
||||
if(recvBuf instanceof Buffer && !(rdb = ((Buffer)recvBuf).isDirect()))
|
||||
{
|
||||
for (int i = 0; i < recvTypes.length; i++){
|
||||
recvoffs[i] = recvTypes[i].getOffset(recvBuf);
|
||||
}
|
||||
recvBuf = ((Buffer)recvBuf).array();
|
||||
}
|
||||
|
||||
long[] sendHandles = convertTypeArray(sendTypes);
|
||||
long[] recvHandles = convertTypeArray(recvTypes);
|
||||
int[] sendHandles_btypes = convertTypeArrayBtype(sendTypes);
|
||||
int[] recvHandles_btypes = convertTypeArrayBtype(recvTypes);
|
||||
|
||||
allToAllw(handle, sendBuf, sendCount, sDispls,
|
||||
sendHandles, recvBuf, recvCount, rDispls,
|
||||
recvHandles);
|
||||
allToAllw(handle, sendBuf, sdb, sendoffs, sendCount, sDispls,
|
||||
sendHandles, sendHandles_btypes,
|
||||
recvBuf, rdb, recvoffs, recvCount, rDispls,
|
||||
recvHandles, recvHandles_btypes);
|
||||
}
|
||||
|
||||
private native void allToAllw(long comm,
|
||||
Buffer sendBuf, int[] sendCount, int[] sDispls, long[] sendTypes,
|
||||
Buffer recvBuf, int[] recvCount, int[] rDispls, long[] recvTypes)
|
||||
Object sendBuf, boolean sdb, int[] sendOffsets,
|
||||
int[] sendCount, int[] sDispls, long[] sendTypes, int[] sendBaseTypes,
|
||||
Object recvBuf, boolean rdb, int[] recvOffsets,
|
||||
int[] recvCount, int[] rDispls, long[] recvTypes, int[] recvBaseTypes)
|
||||
throws MPIException;
|
||||
|
||||
/**
|
||||
@ -3421,4 +3448,21 @@ public class Comm implements Freeable, Cloneable
|
||||
return lArray;
|
||||
}
|
||||
|
||||
/**
|
||||
* A helper method to convert an array of Datatypes to
|
||||
* an array of ints (basetypes).
|
||||
* @param dArray Array of Datatypes
|
||||
* @return converted basetypes
|
||||
*/
|
||||
private int[] convertTypeArrayBtype(Datatype[] dArray) {
|
||||
int[] lArray = new int[dArray.length];
|
||||
|
||||
for(int i = 0; i < lArray.length; i++) {
|
||||
if(dArray[i] != null) {
|
||||
lArray[i] = dArray[i].baseType;
|
||||
}
|
||||
}
|
||||
return lArray;
|
||||
}
|
||||
|
||||
} // Comm
|
||||
|
||||
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