svn commit: r508832 - in head/biology/bolt-lmm: . files

Jason W. Bacon jwb at FreeBSD.org
Tue Aug 13 15:30:22 UTC 2019 

Author: jwb
Date: Tue Aug 13 15:30:21 2019
New Revision: 508832
URL: https://svnweb.freebsd.org/changeset/ports/508832

Log:
  biology/bolt-lmm: Upgrade to 2.3.4
  
  Remove previously upstreamed patches
  New Makefile patch that preserves default behavior and should be palatable
  to upstream

Deleted:
  head/biology/bolt-lmm/files/patch-src_Jackknife.cpp
  head/biology/bolt-lmm/files/patch-src_LDscoreCalibration.cpp
  head/biology/bolt-lmm/files/patch-src_SnpData.cpp
  head/biology/bolt-lmm/files/patch-src_StatsUtils.cpp
Modified:
  head/biology/bolt-lmm/Makefile
  head/biology/bolt-lmm/distinfo
  head/biology/bolt-lmm/files/patch-src_Makefile

Modified: head/biology/bolt-lmm/Makefile
==============================================================================
--- head/biology/bolt-lmm/Makefile	Tue Aug 13 14:57:22 2019	(r508831)
+++ head/biology/bolt-lmm/Makefile	Tue Aug 13 15:30:21 2019	(r508832)
@@ -1,8 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	bolt-lmm
-DISTVERSION=	2.3.2
-PORTREVISION=	2
+DISTVERSION=	2.3.4
 CATEGORIES=	biology
 MASTER_SITES=	https://data.broadinstitute.org/alkesgroup/BOLT-LMM/downloads/
 DISTNAME=	BOLT-LMM_v${PORTVERSION}
@@ -21,11 +20,19 @@ LIB_DEPENDS=	libnlopt.so:math/nlopt \
 # both merely add a GCC requirement.
 USES=		compiler:gcc-c++11-lib gmake
 
-BUILD_WRKSRC=	${WRKDIR}/${DISTNAME}/src
-INSTALL_WRKSRC=	${WRKDIR}/${DISTNAME}/src
-CXXFLAGS_i386=	-DUSE_SSE -msse -msse2
-CXXFLAGS_amd64=	-DUSE_SSE
+BUILD_WRKSRC=		${WRKDIR}/${DISTNAME}/src
+INSTALL_WRKSRC=		${WRKDIR}/${DISTNAME}/src
+CXXFLAGS_i386=		-DUSE_SSE -msse -msse2
+CXXFLAGS_amd64=		-DUSE_SSE
 CXXFLAGS_powerpc64=	-DNO_WARN_X86_INTRINSICS -mvsx
+MAKE_ARGS=		BOOST_INSTALL_DIR=${LOCALBASE} \
+			NLOPT_INSTALL_DIR=${LOCALBASE} \
+			ZLIB_STATIC_DIR=/usr/lib \
+			LIBSTDCXX_STATIC_DIR=/usr/lib \
+			GLIBC_STATIC_DIR=/usr/lib \
+			SSEFLAGS="" \
+			MEMCPY="" \
+			LLAPACK="-lopenblas -lgfortran"
 
 PORTEXAMPLES=	*
 

Modified: head/biology/bolt-lmm/distinfo
==============================================================================
--- head/biology/bolt-lmm/distinfo	Tue Aug 13 14:57:22 2019	(r508831)
+++ head/biology/bolt-lmm/distinfo	Tue Aug 13 15:30:21 2019	(r508832)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1558717810
-SHA256 (BOLT-LMM_v2.3.2.tar.gz) = ee505a04138f6c80bfefad4df4b81a2d07e72114dd8329d187c97543f5a0521f
-SIZE (BOLT-LMM_v2.3.2.tar.gz) = 335057533
+TIMESTAMP = 1565528176
+SHA256 (BOLT-LMM_v2.3.4.tar.gz) = 2477faff5028ff8fee5d8f4e6b0cab6d0752b268fd508fe64530a66807d9b0c0
+SIZE (BOLT-LMM_v2.3.4.tar.gz) = 335128004

Modified: head/biology/bolt-lmm/files/patch-src_Makefile
==============================================================================
--- head/biology/bolt-lmm/files/patch-src_Makefile	Tue Aug 13 14:57:22 2019	(r508831)
+++ head/biology/bolt-lmm/files/patch-src_Makefile	Tue Aug 13 15:30:21 2019	(r508832)
@@ -1,21 +1,27 @@
---- src/Makefile.orig	2018-03-13 02:44:52 UTC
+--- src/Makefile.orig	2019-08-11 03:05:04 UTC
 +++ src/Makefile
-@@ -1,29 +1,28 @@
+@@ -1,31 +1,35 @@
++
  ### modify these paths to local Boost and NLopt install directories
 -BOOST_INSTALL_DIR = /home/pl88/boost_1_58_0/install
 -NLOPT_INSTALL_DIR = /n/groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
-+BOOST_INSTALL_DIR ?= ${LOCALBASE}
-+# Redundant on FreeBSD NLOPT_INSTALL_DIR = /n/groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
++### by setting them in the environment or make command line args
++### which will override variables set with ?=
  
- INTELROOT = /n/groups/price/poru/external_software/intel_mkl_2018
- MKLROOT = ${INTELROOT}/mkl
+-INTELROOT = /n/groups/price/poru/external_software/intel_mkl_2019u4
+-MKLROOT = ${INTELROOT}/mkl
 -ZLIB_STATIC_DIR = /n/groups/price/poru/external_software/zlib/zlib-1.2.11 # probably unnecessary on most systems
 -LIBSTDCXX_STATIC_DIR = /n/groups/price/poru/external_software/libstdc++/usr/lib/gcc/x86_64-redhat-linux/4.8.5/
 -GLIBC_STATIC_DIR = /home/pl88/glibc-static/usr/lib64
-+ZLIB_STATIC_DIR ?= /usr/lib
-+LIBSTDCXX_STATIC_DIR ?= /usr/lib
-+GLIBC_STATIC_DIR ?= /usr/lib
++BOOST_INSTALL_DIR ?= /home/pl88/boost_1_58_0/install
++NLOPT_INSTALL_DIR ?= /n/groups/price/poru/HSPH_SVN/src/BOLT-LMM/nlopt-2.4.2
  
++INTELROOT ?= /n/groups/price/poru/external_software/intel_mkl_2019u4
++MKLROOT ?= ${INTELROOT}/mkl
++ZLIB_STATIC_DIR ?= /n/groups/price/poru/external_software/zlib/zlib-1.2.11 # probably unnecessary on most systems
++LIBSTDCXX_STATIC_DIR ?= /n/groups/price/poru/external_software/libstdc++/usr/lib/gcc/x86_64-redhat-linux/4.8.5/
++GLIBC_STATIC_DIR ?= /home/pl88/glibc-static/usr/lib64
++
  ifeq ($(strip ${linking}),)
  	linking = dynamic
  endif
@@ -36,33 +42,25 @@
 -CFLAGS += -msse -msse2
 -CFLAGS += -DUSE_SSE -DMEASURE_DGEMM -DVERBOSE
 -CFLAGS += -Wall
-+CXXFLAGS += -DMEASURE_DGEMM -DVERBOSE
-+CXXFLAGS += -Wall
++# Set SSEFLAGS to empty string in the env or make command line if building on
++# systems with no SSE such as PowerPC
++SSEFLAGS ?= -msse -msse2 -DUSE_SSE
++CXXFLAGS += ${SSEFLAGS} -DMEASURE_DGEMM -DVERBOSE -Wall
  
- 
+-
  # add Boost include and lib paths
-@@ -38,9 +37,9 @@ endif
- # add NLopt include and lib paths
- ifneq ($(strip ${NLOPT_INSTALL_DIR}),)
- 	CPATHS += -I${NLOPT_INSTALL_DIR}/api
--	LPATHS += -L${NLOPT_INSTALL_DIR}/.libs
-+	LPATHS += -L${NLOPT_INSTALL_DIR}/libs
- 	ifeq (${linking},dynamic)
--		LPATHS += -Wl,-rpath,${NLOPT_INSTALL_DIR}/.libs
-+		LPATHS += -Wl,-rpath,${NLOPT_INSTALL_DIR}/libs
- 	endif
+ ifneq ($(strip ${BOOST_INSTALL_DIR}),)
+ 	CPATHS += -I${BOOST_INSTALL_DIR}/include
+@@ -52,7 +56,7 @@ ifneq ($(strip ${ZLIB_STATIC_DIR}),)
  endif
  
-@@ -52,7 +51,7 @@ ifneq ($(strip ${ZLIB_STATIC_DIR}),)
- endif
- 
  # add MKL paths (if not compiling with g++, i.e., compiling with icpc)
 -ifneq (${CC},g++)
-+ifneq (${CXX},${CXX})
++ifeq (${CXX},icpc)
  	CPATHS += -I${MKLROOT}/include
- 	ifeq (${linking},dynamic)
- 		LPATHS += -L${MKLROOT}/lib/intel64 -Wl,-rpath,${MKLROOT}/lib/intel64 # for libmkl*
-@@ -61,28 +60,28 @@ ifneq (${CC},g++)
+ 	ifeq (${linking},static)
+ 		LPATHS += -L${INTELROOT}/lib/intel64 '-Wl,-rpath,$$ORIGIN/lib' # for libiomp5.so (now packaged with binary)
+@@ -65,34 +69,34 @@ ifneq (${CC},g++)
  endif
  
  # add flags for static linking; build LAPACK/MKL component of link line
@@ -70,10 +68,10 @@
 -	CFLAGS += -fopenmp
 -	LFLAGS += -fopenmp
 -	LLAPACK = -llapack -lgfortran
-+ifeq (${CXX},${CXX})
++ifneq (${CXX},icpc)
 +	CXXFLAGS += -fopenmp
 +	LDFLAGS += -fopenmp
-+	LLAPACK = -lopenblas -lgfortran
++	LLAPACK ?= -llapack -lgfortran
  	ifeq (${linking},static)
 -		LFLAGS += -static
 +		LDFLAGS += -static
@@ -92,39 +90,47 @@
 +	CXXFLAGS += -qopenmp
 +	LDFLAGS += -qopenmp
 +	CXXFLAGS += -Wunused-variable -Wpointer-arith -Wuninitialized -Wreturn-type -Wcheck -Wshadow
+ 	LIOMP5 = -liomp5
+ 	LDL = -ldl
  	ifeq (${linking},static)
 -		LFLAGS += -static
 +		LDFLAGS += -static
  		LPATHS += -L${GLIBC_STATIC_DIR} -L${ZLIB_STATIC_DIR}
- 		LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a -Wl,--end-group
+ 		LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group
  	else ifeq (${linking},static-except-glibc)
 -		LFLAGS += -static-intel -static-libstdc++ -static-libgcc
 +		LDFLAGS += -static-intel -static-libstdc++ -static-libgcc
  		LPATHS += -L${ZLIB_STATIC_DIR}
- 		LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a -Wl,--end-group
+ 		LLAPACK = -Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_intel_thread.a ${MKLROOT}/lib/intel64/libmkl_core.a -Wl,--end-group
+ 	else ifeq (${linking},static-except-glibc-intel)
+-		LFLAGS += -static-libstdc++ -static-libgcc
++		LDFLAGS += -static-libstdc++ -static-libgcc
+ 		LPATHS += -L${ZLIB_STATIC_DIR}
+ 		LLAPACK = -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
  	else
-@@ -95,7 +94,8 @@ else
+@@ -105,7 +109,7 @@ else
  endif
  
  # build link line (minus flags)
 -LLIBS = -lboost_program_options -lboost_iostreams -lz -lnlopt
 +LLIBS = -lnlopt -lboost_program_options -lboost_iostreams -lz
-+# LLIBS = /usr/local/lib/libboost_program_options.a -lnlopt -lboost_iostreams -lz
  ifeq (${linking},static-except-glibc)
- 	L = -L${LIBSTDCXX_STATIC_DIR} ${LPATHS} -Wl,--wrap=memcpy -Wl,-Bstatic ${LLIBS} ${LLAPACK} -Wl,-Bdynamic -lpthread -lm
- else
-@@ -105,16 +105,18 @@ endif
+ 	L = -L${LIBSTDCXX_STATIC_DIR} ${LPATHS} -Wl,--wrap=memcpy -Wl,-Bstatic ${LLIBS} ${LLAPACK} -Wl,-Bdynamic ${LIOMP5} -lpthread -lm ${LDL}
+ else ifeq (${linking},static-except-glibc-intel)
+@@ -117,16 +121,20 @@ endif
  
  
  T = bolt
 -O = Bolt.o BoltParams.o BoltParEstCV.o BoltReml.o CovariateBasis.o DataMatrix.o FileUtils.o Jackknife.o LDscoreCalibration.o MapInterpolater.o MatrixUtils.o MemoryUtils.o NonlinearOptMulti.o NumericUtils.o PhenoBuilder.o RestrictSnpSet.o SnpData.o SnpInfo.o SpectrumTools.o StatsUtils.o StringUtils.o Timer.o memcpy.o
-+O = Bolt.o BoltParams.o BoltParEstCV.o BoltReml.o CovariateBasis.o DataMatrix.o FileUtils.o Jackknife.o LDscoreCalibration.o MapInterpolater.o MatrixUtils.o MemoryUtils.o NonlinearOptMulti.o NumericUtils.o PhenoBuilder.o RestrictSnpSet.o SnpData.o SnpInfo.o SpectrumTools.o StatsUtils.o StringUtils.o Timer.o
++# Set to empty string in env or make command line to use system memcpy
++MEMCPY ?= memcpy.o
++O = Bolt.o BoltParams.o BoltParEstCV.o BoltReml.o CovariateBasis.o DataMatrix.o FileUtils.o Jackknife.o LDscoreCalibration.o MapInterpolater.o MatrixUtils.o MemoryUtils.o NonlinearOptMulti.o NumericUtils.o PhenoBuilder.o RestrictSnpSet.o SnpData.o SnpInfo.o SpectrumTools.o StatsUtils.o StringUtils.o Timer.o ${MEMCPY}
  OMAIN = BoltMain.o $O
  
 -.PHONY: clean
 +.PHONY: clean all
  
-+all: $T
++all: ${T}
 +
  %.o: %.cpp
 -	${CC} ${CFLAGS} ${CPATHS} -o $@ -c $<

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