diff options
| author | Jason W. Bacon <jwb@FreeBSD.org> | 2022-03-20 15:23:35 +0000 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2022-03-20 15:29:01 +0000 |
| commit | 0297052e221a1c1e754fa6d10380a527985f4cf5 (patch) | |
| tree | 531053688495d90f10f2ca4ed9460bb956926303 | |
| parent | ffdd1f6dafd2db6be5d0b065470ed670f5ee961d (diff) | |
| -rw-r--r-- | biology/bolt-lmm/Makefile | 9 | ||||
| -rw-r--r-- | biology/bolt-lmm/distinfo | 6 | ||||
| -rw-r--r-- | biology/bolt-lmm/files/patch-src_MemoryUtils.cpp | 12 | ||||
| -rw-r--r-- | biology/bolt-lmm/files/patch-src_MemoryUtils.hpp | 12 |
4 files changed, 30 insertions, 9 deletions
diff --git a/biology/bolt-lmm/Makefile b/biology/bolt-lmm/Makefile index 7302e3ef897b..a1f1d09f21eb 100644 --- a/biology/bolt-lmm/Makefile +++ b/biology/bolt-lmm/Makefile @@ -1,6 +1,5 @@ PORTNAME= bolt-lmm -DISTVERSION= 2.3.4 -PORTREVISION= 4 +DISTVERSION= 2.3.6 CATEGORIES= biology MASTER_SITES= https://data.broadinstitute.org/alkesgroup/BOLT-LMM/downloads/ DISTNAME= BOLT-LMM_v${PORTVERSION} @@ -15,9 +14,7 @@ LIB_DEPENDS= libnlopt.so:math/nlopt \ libopenblas.so:math/openblas \ libboost_program_options.so:devel/boost-libs -# gcc-c++11-lib needed to link with boost. Also requires compiler:openmp, but -# both merely add a GCC requirement. -USES= compiler:gcc-c++11-lib gmake +USES= gmake BUILD_WRKSRC= ${WRKDIR}/${DISTNAME}/src INSTALL_WRKSRC= ${WRKDIR}/${DISTNAME}/src @@ -32,7 +29,7 @@ MAKE_ARGS= BOOST_INSTALL_DIR=${LOCALBASE} \ GLIBC_STATIC_DIR=/usr/lib \ SSEFLAGS="" \ MEMCPY="" \ - LLAPACK="-lopenblas -lgfortran" + LLAPACK="-lopenblas" CONFLICTS_INSTALL= rubygem-bolt # bin/bolt diff --git a/biology/bolt-lmm/distinfo b/biology/bolt-lmm/distinfo index 618a36d60050..4711694315b8 100644 --- a/biology/bolt-lmm/distinfo +++ b/biology/bolt-lmm/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1565528176 -SHA256 (BOLT-LMM_v2.3.4.tar.gz) = 2477faff5028ff8fee5d8f4e6b0cab6d0752b268fd508fe64530a66807d9b0c0 -SIZE (BOLT-LMM_v2.3.4.tar.gz) = 335128004 +TIMESTAMP = 1647782880 +SHA256 (BOLT-LMM_v2.3.6.tar.gz) = bc82a5166b3d2d480bcda1f4455c29e1018db733706d28c35d8bf8de7e1e85d5 +SIZE (BOLT-LMM_v2.3.6.tar.gz) = 335131602 diff --git a/biology/bolt-lmm/files/patch-src_MemoryUtils.cpp b/biology/bolt-lmm/files/patch-src_MemoryUtils.cpp new file mode 100644 index 000000000000..e6a2f20061f9 --- /dev/null +++ b/biology/bolt-lmm/files/patch-src_MemoryUtils.cpp @@ -0,0 +1,12 @@ +--- src/MemoryUtils.cpp.orig 2022-03-20 14:01:47 UTC ++++ src/MemoryUtils.cpp +@@ -26,7 +26,8 @@ void *ALIGNED_MALLOC(uint64 size) { + #ifdef USE_MKL_MALLOC + void *p = mkl_malloc(size, MEM_ALIGNMENT); + #else +- void *p = _mm_malloc(size, MEM_ALIGNMENT); ++ //void *p = _mm_malloc(size, MEM_ALIGNMENT); ++ void *p = aligned_alloc(MEM_ALIGNMENT, size); + #endif + // TODO: change to assert() or dispense with altogether and change ALIGNED_MALLOC to macro? + if (p == NULL) { diff --git a/biology/bolt-lmm/files/patch-src_MemoryUtils.hpp b/biology/bolt-lmm/files/patch-src_MemoryUtils.hpp new file mode 100644 index 000000000000..a9ccbd3d78e7 --- /dev/null +++ b/biology/bolt-lmm/files/patch-src_MemoryUtils.hpp @@ -0,0 +1,12 @@ +--- src/MemoryUtils.hpp.orig 2022-03-20 13:40:42 UTC ++++ src/MemoryUtils.hpp +@@ -31,8 +31,7 @@ void *ALIGNED_MALLOC(uint64 size); + #include <mkl.h> + #define ALIGNED_FREE mkl_free + #else +-#include <xmmintrin.h> +-#define ALIGNED_FREE _mm_free ++#define ALIGNED_FREE free + #endif + + #define ALIGNED_MALLOC_DOUBLES(numDoubles) (double *) ALIGNED_MALLOC((numDoubles)*sizeof(double)) |