From c645725fc3ae392d186947cb5b3ea58f8ca5038e Mon Sep 17 00:00:00 2001 From: Karthik Gururaj Date: Wed, 26 Feb 2014 15:17:15 -0800 Subject: [PATCH] 1. Renamed directory structure from public/c++/VectorPairHMM to public/VectorPairHMM/src/main/c++ as per Khalid's suggestion 2. Use java.home in public/VectorPairHMM/pom.xml to pass environment variable JRE_HOME to the make process. This is needed because the Makefile needs to compile JNI code with the flag -I/../include (among others). Assuming that the Maven build process uses a JDK (and not just a JRE), the variable java.home points to the JRE inside maven. 3. Dropped all pretense at cross-platform compatibility. Removed Mac profile from pom.xml for VectorPairHMM --- public/{c++ => }/VectorPairHMM/pom.xml | 32 +++---------------- .../src/main/c++}/.gitignore | 0 .../src/main/c++}/JNI_README | 0 .../src/main/c++}/LoadTimeInitializer.cc | 0 .../src/main/c++}/LoadTimeInitializer.h | 0 .../src/main/c++}/Makefile | 4 +-- .../src/main/c++}/Sandbox.cc | 0 .../src/main/c++}/Sandbox.h | 0 .../src/main/c++}/Sandbox.java | 0 .../Sandbox_JNIHaplotypeDataHolderClass.h | 0 .../c++}/Sandbox_JNIReadDataHolderClass.h | 0 .../main/c++}/avx_function_instantiations.cc | 0 .../src/main/c++}/baseline.cc | 0 .../src/main/c++}/define-double.h | 0 .../src/main/c++}/define-float.h | 0 .../src/main/c++}/define-sse-double.h | 0 .../src/main/c++}/define-sse-float.h | 0 .../src/main/c++}/headers.h | 0 .../src/main/c++}/jni_common.h | 0 .../src/main/c++}/jnidebug.h | 0 ...ng_utils_pairhmm_DebugJNILoglessPairHMM.cc | 0 ...ing_utils_pairhmm_DebugJNILoglessPairHMM.h | 0 ...ting_utils_pairhmm_VectorLoglessPairHMM.cc | 0 ...sting_utils_pairhmm_VectorLoglessPairHMM.h | 0 .../src/main/c++}/pairhmm-1-base.cc | 0 .../src/main/c++}/pairhmm-template-kernel.cc | 0 .../src/main/c++}/pairhmm-template-main.cc | 0 .../src/main/c++}/run.sh | 0 .../src/main/c++}/shift_template.c | 0 .../main/c++}/sse_function_instantiations.cc | 0 .../src/main/c++}/template.h | 0 .../src/main/c++}/utils.cc | 0 .../src/main/c++}/utils.h | 0 .../src/main/c++}/vector_defs.h | 0 .../main/c++}/vector_function_prototypes.h | 0 35 files changed, 7 insertions(+), 29 deletions(-) rename public/{c++ => }/VectorPairHMM/pom.xml (80%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/.gitignore (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/JNI_README (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/LoadTimeInitializer.cc (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/LoadTimeInitializer.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/Makefile (95%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/Sandbox.cc (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/Sandbox.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/Sandbox.java (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/Sandbox_JNIHaplotypeDataHolderClass.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/Sandbox_JNIReadDataHolderClass.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/avx_function_instantiations.cc (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/baseline.cc (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/define-double.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/define-float.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/define-sse-double.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/define-sse-float.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/headers.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/jni_common.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/jnidebug.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/pairhmm-1-base.cc (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/pairhmm-template-kernel.cc (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/pairhmm-template-main.cc (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/run.sh (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/shift_template.c (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/sse_function_instantiations.cc (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/template.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/utils.cc (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/utils.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/vector_defs.h (100%) rename public/{c++/VectorPairHMM => VectorPairHMM/src/main/c++}/vector_function_prototypes.h (100%) diff --git a/public/c++/VectorPairHMM/pom.xml b/public/VectorPairHMM/pom.xml similarity index 80% rename from public/c++/VectorPairHMM/pom.xml rename to public/VectorPairHMM/pom.xml index ce0692799..b310148d6 100644 --- a/public/c++/VectorPairHMM/pom.xml +++ b/public/VectorPairHMM/pom.xml @@ -6,20 +6,20 @@ org.broadinstitute.sting sting-root 2.8-SNAPSHOT - ../../../public/sting-root + ../../public/sting-root VectorPairHMM pom Vectorized PairHMM native libraries - Builds a platform dependent version of pairhmm. During install, copies it into sting-utils. + Builds a GNU/Linux x86_64 version of VectorPairHMM. During install, copies it into sting-utils. UTF-8 ${sourceEncoding} ${sourceEncoding} - ${project.basedir}/../../.. + ${project.basedir}/../.. ${sting.basedir}/public/sting-utils ${sting-utils.basedir}/src/main/resources/org/broadinstitute/sting/utils/pairhmm @@ -33,8 +33,6 @@ --> x86_64 so - -Wall - -dynamiclib @@ -64,12 +62,10 @@ compile make - . + src/main/c++ ${pairhmm.build.architecture} - ${pairhmm.build.extension} - ${pairhmm.build.cxxflags} - ${pairhmm.build.ldflags} + ${java.home} ${project.build.directory} @@ -132,21 +128,6 @@ - - mac_x86_64 - - - mac - x86_64 - - - - mac_x86_64 - jnilib - -dynamiclib - - - linux_x86_64 @@ -157,9 +138,6 @@ linux_x86_64 - jnilib - -fPIC - -shared diff --git a/public/c++/VectorPairHMM/.gitignore b/public/VectorPairHMM/src/main/c++/.gitignore similarity index 100% rename from public/c++/VectorPairHMM/.gitignore rename to public/VectorPairHMM/src/main/c++/.gitignore diff --git a/public/c++/VectorPairHMM/JNI_README b/public/VectorPairHMM/src/main/c++/JNI_README similarity index 100% rename from public/c++/VectorPairHMM/JNI_README rename to public/VectorPairHMM/src/main/c++/JNI_README diff --git a/public/c++/VectorPairHMM/LoadTimeInitializer.cc b/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc similarity index 100% rename from public/c++/VectorPairHMM/LoadTimeInitializer.cc rename to public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc diff --git a/public/c++/VectorPairHMM/LoadTimeInitializer.h b/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h similarity index 100% rename from public/c++/VectorPairHMM/LoadTimeInitializer.h rename to public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h diff --git a/public/c++/VectorPairHMM/Makefile b/public/VectorPairHMM/src/main/c++/Makefile similarity index 95% rename from public/c++/VectorPairHMM/Makefile rename to public/VectorPairHMM/src/main/c++/Makefile index f88b38401..e1e443d2e 100644 --- a/public/c++/VectorPairHMM/Makefile +++ b/public/VectorPairHMM/src/main/c++/Makefile @@ -4,8 +4,8 @@ #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 $(OMPCFLAGS) -Wno-unknown-pragmas -JAVA_ROOT=/opt/jdk1.7.0_25/ -JNI_COMPILATION_FLAGS=-D_REENTRANT -fPIC -I${JAVA_ROOT}/include -I${JAVA_ROOT}/include/linux +JRE_HOME?=/opt/jdk1.7.0_25/ +JNI_COMPILATION_FLAGS=-D_REENTRANT -fPIC -I${JRE_HOME}/../include -I${JRE_HOME}/../include/linux COMMON_COMPILATION_FLAGS=$(JNI_COMPILATION_FLAGS) -O3 -W -Wall -pedantic $(OMPCFLAGS) -Wno-unknown-pragmas CC=icc diff --git a/public/c++/VectorPairHMM/Sandbox.cc b/public/VectorPairHMM/src/main/c++/Sandbox.cc similarity index 100% rename from public/c++/VectorPairHMM/Sandbox.cc rename to public/VectorPairHMM/src/main/c++/Sandbox.cc diff --git a/public/c++/VectorPairHMM/Sandbox.h b/public/VectorPairHMM/src/main/c++/Sandbox.h similarity index 100% rename from public/c++/VectorPairHMM/Sandbox.h rename to public/VectorPairHMM/src/main/c++/Sandbox.h diff --git a/public/c++/VectorPairHMM/Sandbox.java b/public/VectorPairHMM/src/main/c++/Sandbox.java similarity index 100% rename from public/c++/VectorPairHMM/Sandbox.java rename to public/VectorPairHMM/src/main/c++/Sandbox.java diff --git a/public/c++/VectorPairHMM/Sandbox_JNIHaplotypeDataHolderClass.h b/public/VectorPairHMM/src/main/c++/Sandbox_JNIHaplotypeDataHolderClass.h similarity index 100% rename from public/c++/VectorPairHMM/Sandbox_JNIHaplotypeDataHolderClass.h rename to public/VectorPairHMM/src/main/c++/Sandbox_JNIHaplotypeDataHolderClass.h diff --git a/public/c++/VectorPairHMM/Sandbox_JNIReadDataHolderClass.h b/public/VectorPairHMM/src/main/c++/Sandbox_JNIReadDataHolderClass.h similarity index 100% rename from public/c++/VectorPairHMM/Sandbox_JNIReadDataHolderClass.h rename to public/VectorPairHMM/src/main/c++/Sandbox_JNIReadDataHolderClass.h diff --git a/public/c++/VectorPairHMM/avx_function_instantiations.cc b/public/VectorPairHMM/src/main/c++/avx_function_instantiations.cc similarity index 100% rename from public/c++/VectorPairHMM/avx_function_instantiations.cc rename to public/VectorPairHMM/src/main/c++/avx_function_instantiations.cc diff --git a/public/c++/VectorPairHMM/baseline.cc b/public/VectorPairHMM/src/main/c++/baseline.cc similarity index 100% rename from public/c++/VectorPairHMM/baseline.cc rename to public/VectorPairHMM/src/main/c++/baseline.cc diff --git a/public/c++/VectorPairHMM/define-double.h b/public/VectorPairHMM/src/main/c++/define-double.h similarity index 100% rename from public/c++/VectorPairHMM/define-double.h rename to public/VectorPairHMM/src/main/c++/define-double.h diff --git a/public/c++/VectorPairHMM/define-float.h b/public/VectorPairHMM/src/main/c++/define-float.h similarity index 100% rename from public/c++/VectorPairHMM/define-float.h rename to public/VectorPairHMM/src/main/c++/define-float.h diff --git a/public/c++/VectorPairHMM/define-sse-double.h b/public/VectorPairHMM/src/main/c++/define-sse-double.h similarity index 100% rename from public/c++/VectorPairHMM/define-sse-double.h rename to public/VectorPairHMM/src/main/c++/define-sse-double.h diff --git a/public/c++/VectorPairHMM/define-sse-float.h b/public/VectorPairHMM/src/main/c++/define-sse-float.h similarity index 100% rename from public/c++/VectorPairHMM/define-sse-float.h rename to public/VectorPairHMM/src/main/c++/define-sse-float.h diff --git a/public/c++/VectorPairHMM/headers.h b/public/VectorPairHMM/src/main/c++/headers.h similarity index 100% rename from public/c++/VectorPairHMM/headers.h rename to public/VectorPairHMM/src/main/c++/headers.h diff --git a/public/c++/VectorPairHMM/jni_common.h b/public/VectorPairHMM/src/main/c++/jni_common.h similarity index 100% rename from public/c++/VectorPairHMM/jni_common.h rename to public/VectorPairHMM/src/main/c++/jni_common.h diff --git a/public/c++/VectorPairHMM/jnidebug.h b/public/VectorPairHMM/src/main/c++/jnidebug.h similarity index 100% rename from public/c++/VectorPairHMM/jnidebug.h rename to public/VectorPairHMM/src/main/c++/jnidebug.h diff --git a/public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc b/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc similarity index 100% rename from public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc rename to public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc diff --git a/public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h b/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h similarity index 100% rename from public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h rename to public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h diff --git a/public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc b/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc similarity index 100% rename from public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc rename to public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc diff --git a/public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h b/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h similarity index 100% rename from public/c++/VectorPairHMM/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h rename to public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h diff --git a/public/c++/VectorPairHMM/pairhmm-1-base.cc b/public/VectorPairHMM/src/main/c++/pairhmm-1-base.cc similarity index 100% rename from public/c++/VectorPairHMM/pairhmm-1-base.cc rename to public/VectorPairHMM/src/main/c++/pairhmm-1-base.cc diff --git a/public/c++/VectorPairHMM/pairhmm-template-kernel.cc b/public/VectorPairHMM/src/main/c++/pairhmm-template-kernel.cc similarity index 100% rename from public/c++/VectorPairHMM/pairhmm-template-kernel.cc rename to public/VectorPairHMM/src/main/c++/pairhmm-template-kernel.cc diff --git a/public/c++/VectorPairHMM/pairhmm-template-main.cc b/public/VectorPairHMM/src/main/c++/pairhmm-template-main.cc similarity index 100% rename from public/c++/VectorPairHMM/pairhmm-template-main.cc rename to public/VectorPairHMM/src/main/c++/pairhmm-template-main.cc diff --git a/public/c++/VectorPairHMM/run.sh b/public/VectorPairHMM/src/main/c++/run.sh similarity index 100% rename from public/c++/VectorPairHMM/run.sh rename to public/VectorPairHMM/src/main/c++/run.sh diff --git a/public/c++/VectorPairHMM/shift_template.c b/public/VectorPairHMM/src/main/c++/shift_template.c similarity index 100% rename from public/c++/VectorPairHMM/shift_template.c rename to public/VectorPairHMM/src/main/c++/shift_template.c diff --git a/public/c++/VectorPairHMM/sse_function_instantiations.cc b/public/VectorPairHMM/src/main/c++/sse_function_instantiations.cc similarity index 100% rename from public/c++/VectorPairHMM/sse_function_instantiations.cc rename to public/VectorPairHMM/src/main/c++/sse_function_instantiations.cc diff --git a/public/c++/VectorPairHMM/template.h b/public/VectorPairHMM/src/main/c++/template.h similarity index 100% rename from public/c++/VectorPairHMM/template.h rename to public/VectorPairHMM/src/main/c++/template.h diff --git a/public/c++/VectorPairHMM/utils.cc b/public/VectorPairHMM/src/main/c++/utils.cc similarity index 100% rename from public/c++/VectorPairHMM/utils.cc rename to public/VectorPairHMM/src/main/c++/utils.cc diff --git a/public/c++/VectorPairHMM/utils.h b/public/VectorPairHMM/src/main/c++/utils.h similarity index 100% rename from public/c++/VectorPairHMM/utils.h rename to public/VectorPairHMM/src/main/c++/utils.h diff --git a/public/c++/VectorPairHMM/vector_defs.h b/public/VectorPairHMM/src/main/c++/vector_defs.h similarity index 100% rename from public/c++/VectorPairHMM/vector_defs.h rename to public/VectorPairHMM/src/main/c++/vector_defs.h diff --git a/public/c++/VectorPairHMM/vector_function_prototypes.h b/public/VectorPairHMM/src/main/c++/vector_function_prototypes.h similarity index 100% rename from public/c++/VectorPairHMM/vector_function_prototypes.h rename to public/VectorPairHMM/src/main/c++/vector_function_prototypes.h