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Fixed bug in JNI interface release_array 

Disabled OpenMP
This commit is contained in:
Karthik Gururaj 2014-01-20 11:07:44 -08:00
parent f614d7b0d8
commit 28891117e2
3 changed files with 3 additions and 4 deletions
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3
PairHMM_JNI/Makefile
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@ -1,5 +1,4 @@
OMPCFLAGS=-fopenmp
#OMPLDFLAGS=-lgomp
#OMPCFLAGS=-fopenmp
#CFLAGS=-O2 -std=c++11 -W -Wall -march=corei7-avx -Wa,-q -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas
#CFLAGS=-O2 -W -Wall -march=corei7 -mfpmath=sse -msse4.2 -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas

BIN
PairHMM_JNI/libJNILoglessPairHMM.so
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4
PairHMM_JNI/org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM.cc
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@ -128,7 +128,7 @@ Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPairHMM_jniInitializePrior
//Gets direct access to Java arrays
#define GET_BYTE_ARRAY_ELEMENTS env->GetPrimitiveArrayCritical
#define RELEASE_BYTE_ARRAY_ELEMENTS env->ReleasePrimitiveArrayCritical
#define JNI_RELEASE_MODE JNI_ABORT
#define JNI_RELEASE_MODE 0
#define GET_DOUBLE_ARRAY_ELEMENTS env->GetPrimitiveArrayCritical
#define RELEASE_DOUBLE_ARRAY_ELEMENTS env->ReleasePrimitiveArrayCritical
@ -384,7 +384,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_JNILoglessPai
//Release read arrays first
for(int i=readBasesArrayVector.size()-1;i>=0;--i)//note the order - reverse of GET
{
for(int j=readBasesArrayVector.size()-1;j>=0;--j)
for(int j=readBasesArrayVector[i].size()-1;j>=0;--j)
RELEASE_BYTE_ARRAY_ELEMENTS(readBasesArrayVector[i][j].first, readBasesArrayVector[i][j].second, JNI_RELEASE_MODE);
readBasesArrayVector[i].clear();
}