New port: science/lm: Software for sampling trajectories of the reaction-diffusion equations

10 files changed, 253 insertions, 0 deletions

diff --git a/science/lm/Makefile b/science/lm/Makefile
new file mode 100644
index 000000000000..d9bbdf526c9e
--- /dev/null
+++ b/science/lm/Makefile
@@ -0,0 +1,79 @@
+# $FreeBSD$
+
+PORTNAME=	lm
+DISTVERSION=	2.3.0
+DISTVERSIONSUFFIX=	-src
+CATEGORIES=	science
+MASTER_SITES=	http://scs.illinois.edu/schulten/${PORTNAME}/download/${PORTNAME}${DISTVERSION:R:S/.//}/
+PKGNAMESUFFIX=	-uiuc
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Software for sampling trajectories of the reaction-diffusion equations
+
+LICENSE=	UIUC_OPEN_SOURCE_LICENSE
+LICENSE_NAME=	University of Illinois Open Source License
+LICENSE_FILE=	${WRKSRC}/LICENSE
+LICENSE_PERMS=	auto-accept dist-mirror dist-sell pkg-mirror pkg-sell
+
+BUILD_DEPENDS=	swig3.0:devel/swig30
+LIB_DEPENDS=	libhdf5.so:science/hdf5 \
+		libprotobuf.so:devel/protobuf \
+		libsz.so:science/szip
+
+USES=		gettext-runtime gmake localbase python
+
+WRKSRC=		${WRKDIR}/${PORTNAME}-${DISTVERSION}
+CXXFLAGS+=	-DLINUX
+MAKE_ENV=	BUILD_DIR=${WRKSRC} PROTOBUF_DIR=${LOCALBASE}
+
+OPTIONS_DEFINE=		MPI PYTHON VMD
+OPTIONS_DEFAULT=	MPI PYTHON # VMD can't be default because VMD requires manual tarball fetch
+OPTIONS_SUB=		yes
+
+MPI_USES=		fortran
+MPI_VARS=		XUSE_MPI=1
+MPI_VARS_OFF=		XUSE_MPI=0
+MPI_LIB_DEPENDS=	libmpich.so:net/mpich2
+
+PYTHON_VARS=		XUSE_PYTHON=1
+PYTHON_VARS_OFF=	XUSE_PYTHON=0
+PYTHON_CXXFLAGS=	-I${PYTHON_SITELIBDIR}/numpy/core/include
+PYTHON_BUILD_DEPENDS=	${PYTHON_SITELIBDIR}/numpy/core/include/numpy/arrayobject.h:math/py-numpy@${PY_FLAVOR}
+
+VMD_DESC=		Build the VMD plugin
+VMD_VARS=		XUSE_VMD=1
+VMD_VARS_OFF=		XUSE_VMD=0
+VMD_VARS=		VMD_ARCH=${ARCH:S/amd64/FREEBSDAMD64/:S/${ARCH}/FREEBSD/}
+VMD_BUILD_DEPENDS=	${LOCALBASE}/vmd/plugins/${VMD_ARCH}/molfile/libmolfile_plugin.h:science/vmd
+VMD_PLIST_SUB=		VMD_ARCH=${VMD_ARCH}
+
+post-patch:
+	@${CP} ${WRKSRC}/docs/config/local.mk.linux ${WRKSRC}/local.mk
+	@${REINPLACE_CMD} -i '' ' \
+		s|USE_MPI := 0|USE_MPI := ${XUSE_MPI}|; \
+		s|USE_PYTHON := 1|USE_PYTHON := ${XUSE_PYTHON}|; \
+		s|USE_VMD := 1|USE_VMD := ${XUSE_VMD}|; \
+		s|USE_CUDA := 1|USE_CUDA := 0|; \
+		s|swig|swig3.0|; \
+		s|/usr/local|${LOCALBASE}|; \
+		s|INSTALL_PREFIX := /opt/lm|INSTALL_PREFIX := ${STAGEDIR}${PREFIX}|; \
+		s|BUILD_DIR := Build-linux|BUILD_DIR := Build-freebsd|; \
+		s|CCFLAGS := -m64 -O2|CCFLAGS := $$(CXXFLAGS)|; \
+		s|gcc|${CC}|; \
+		s|g++|${CXX}|; \
+		s| -lrt||' \
+		${WRKSRC}/local.mk
+
+post-patch-MPI-on:
+	@${REINPLACE_CMD} -i '' ' \
+		s|MPI_COMPILE_FLAGS = .*|MPI_COMPILE_FLAGS =|; \
+		s|MPI_LINK_FLAGS = .*|MPI_LINK_FLAGS = -lmpich ${LOCALBASE}/lib/gcc${GCC_DEFAULT}/libgcc_s.so|' \
+		${WRKSRC}/local.mk
+
+post-patch-PYTHON-on:
+	@${REINPLACE_CMD} -i '' 's|python-config|${PYTHON_CMD}-config|' ${WRKSRC}/local.mk
+
+post-patch-VMD-on:
+	@${REINPLACE_CMD} -i '' 's|LINUXAMD64|${VMD_ARCH}|' ${WRKSRC}/local.mk
+
+.include <bsd.port.mk>
diff --git a/science/lm/distinfo b/science/lm/distinfo
new file mode 100644
index 000000000000..8ce75f7be4ea
--- /dev/null
+++ b/science/lm/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1536517852
+SHA256 (lm-2.3.0-src.tar.gz) = c1a7908997e46c6590e179a4a269cbaddaab8533c7b9b3c9ff2297f5fd6dbe0c
+SIZE (lm-2.3.0-src.tar.gz) = 7657245
diff --git a/science/lm/files/patch-Makefile b/science/lm/files/patch-Makefile
new file mode 100644
index 000000000000..337fe89d34b4
--- /dev/null
+++ b/science/lm/files/patch-Makefile
@@ -0,0 +1,29 @@
+--- Makefile.orig	2016-12-06 05:23:11 UTC
++++ Makefile
+@@ -282,21 +282,23 @@ installlm:
+ 	install -d $(INSTALL_PREFIX)/bin
+ 	install -m 0755 $(MAIN) $(UTIL_BINS) $(INSTALL_PREFIX)/bin
+ 	@echo 'Installing LM libraries'
++ifeq ($(USE_PYTHON),1)
+ 	install -d $(INSTALL_PREFIX)/lib/lm
+ 	install -m 0644 $(INSTALL_LIBS) $(INSTALL_PREFIX)/lib/lm
+ 	install -d $(INSTALL_PREFIX)/lib/python/pySTDLM
+ 	install -d $(INSTALL_PREFIX)/lib/python/pyLM
+ 	install -m 0644 ./src/python/pyLM/* $(INSTALL_PREFIX)/lib/python/pyLM
+ 	install -m 0644 ./src/python/pySTDLM/* $(INSTALL_PREFIX)/lib/python/pySTDLM
++endif
+ ifeq ($(USE_MPI),1)
+-	install -m 0755 lm-mpmpd $(INSTALL_PREFIX)/bin
++	install -m 0755 ./$(BUILD_DIR)/lm-mpmpd $(INSTALL_PREFIX)/bin
+ endif
+ 
+ 
+ installvmd:
+ 	@echo 'Installing VMD plugin'
+-	install -d $(VMD_INSTALL_DIR)
+-	install -m 0644 $(VMD_PLUGIN) $(VMD_INSTALL_DIR)
++	install -d $(DESTDIR)$(VMD_INSTALL_DIR)
++	install -m 0644 $(VMD_PLUGIN) $(DESTDIR)$(VMD_INSTALL_DIR)
+ 	
+ # Build a distribution package.
+ dist:
diff --git a/science/lm/files/patch-src_c_lm_main_Main.cpp b/science/lm/files/patch-src_c_lm_main_Main.cpp
new file mode 100644
index 000000000000..912ba029e793
--- /dev/null
+++ b/science/lm/files/patch-src_c_lm_main_Main.cpp
@@ -0,0 +1,24 @@
+--- src/c/lm/main/Main.cpp.orig	2018-09-09 19:24:07 UTC
++++ src/c/lm/main/Main.cpp
+@@ -49,6 +49,9 @@
+ #include <sys/stat.h>
+ #if defined(MACOSX)
+ #include <sys/sysctl.h>
++#elif defined(__FreeBSD__)
++#include <sys/types.h>
++#include <sys/sysctl.h>
+ #elif defined(LINUX)
+ #include <sys/sysinfo.h>
+ #endif
+@@ -110,6 +113,11 @@ int getPhysicalCpuCores()
+     size_t  physicalCpuCoresSize=sizeof(physicalCpuCores);
+     sysctlbyname("hw.activecpu",&physicalCpuCores,&physicalCpuCoresSize,NULL,0);
+     return physicalCpuCores;
++    #elif defined(__FreeBSD__)
++    int	np = 0;
++    size_t	len = sizeof(np);
++    sysctlbyname("hw.ncpu",&np,&len,NULL,0);
++    return np;
+     #elif defined(LINUX)
+ 	#ifdef ARM
+ 	return get_nprocs_conf();
diff --git a/science/lm/files/patch-src_c_lm_main_runSimulation.cpp b/science/lm/files/patch-src_c_lm_main_runSimulation.cpp
new file mode 100644
index 000000000000..0774fcaac549
--- /dev/null
+++ b/science/lm/files/patch-src_c_lm_main_runSimulation.cpp
@@ -0,0 +1,22 @@
+--- src/c/lm/main/runSimulation.cpp.orig	2018-09-09 19:31:22 UTC
++++ src/c/lm/main/runSimulation.cpp
+@@ -45,6 +45,9 @@
+  */
+ #if defined(MACOSX)
+ #include <sys/sysctl.h>
++#elif defined(__FreeBSD__)
++#include <sys/types.h>
++#include <sys/sysctl.h>
+ #elif defined(LINUX)
+ #include <sys/sysinfo.h>
+ #endif
+@@ -149,6 +152,9 @@ void runSolver(char *simulationFilename,
+     size_t  physicalCpuCoresSize=sizeof(physicalCpuCores);
+     sysctlbyname("hw.activecpu",&physicalCpuCores,&physicalCpuCoresSize,NULL,0);
+     numberCpuCores = physicalCpuCores;
++#elif defined(__FreeBSD__)
++    size_t	len = sizeof(numberCpuCores);
++    sysctlbyname("hw.ncpu",&numberCpuCores,&len,NULL,0);
+ #elif defined(LINUX)
+     #ifdef ARM
+         numberCpuCores = get_nprocs_conf();
diff --git a/science/lm/files/patch-src_c_lm_rng_XORShift.cpp b/science/lm/files/patch-src_c_lm_rng_XORShift.cpp
new file mode 100644
index 000000000000..fd468235ae52
--- /dev/null
+++ b/science/lm/files/patch-src_c_lm_rng_XORShift.cpp
@@ -0,0 +1,14 @@
+--- src/c/lm/rng/XORShift.cpp.orig	2018-09-09 20:03:05 UTC
++++ src/c/lm/rng/XORShift.cpp
+@@ -42,6 +42,11 @@
+ #include "lm/rng/RandomGenerator.h"
+ #include "lm/rng/XORShift.h"
+ 
++// sincos doesn't exist on all current (2018-08) FreeBSD versions
++#if defined(__FreeBSD__)
++#  define sincos(x,s,c) *s = sin(x); *c = cos(x);
++#endif
++
+ namespace lm {
+ namespace rng {
+ 
diff --git a/science/lm/files/patch-src_c_lm_thread_Thread.cpp b/science/lm/files/patch-src_c_lm_thread_Thread.cpp
new file mode 100644
index 000000000000..edcbfccaa110
--- /dev/null
+++ b/science/lm/files/patch-src_c_lm_thread_Thread.cpp
@@ -0,0 +1,36 @@
+--- src/c/lm/thread/Thread.cpp.orig	2018-09-09 19:28:35 UTC
++++ src/c/lm/thread/Thread.cpp
+@@ -40,6 +40,7 @@
+ #include <pthread.h>
+ #include "lm/Print.h"
+ #include "lm/thread/Thread.h"
++#include <pthread_np.h>
+ 
+ namespace lm {
+ namespace thread {
+@@ -72,10 +73,10 @@ void Thread::setAffinity(int cpuNumber) 
+     if (running)
+     {
+ 		#if defined(LINUX) && !defined(ARM)
+-		cpu_set_t cpuset;
++		cpuset_t cpuset;
+ 		CPU_ZERO(&cpuset);
+ 		CPU_SET(cpuNumber, &cpuset);
+-		if (pthread_setaffinity_np(threadId, sizeof(cpu_set_t), &cpuset) != 0)
++		if (pthread_setaffinity_np(threadId, sizeof(cpuset_t), &cpuset) != 0)
+ 			Print::printf(Print::WARNING, "Could not bind thread %u to CPU core %d", threadId, cpuNumber);
+ 		#endif
+     }
+@@ -100,10 +101,10 @@ void Thread::start() throw(PthreadExcept
+         if (cpuNumber >= 0)
+         {
+ 			#if defined(LINUX) && !defined(ARM)
+-			cpu_set_t cpuset;
++			cpuset_t cpuset;
+ 			CPU_ZERO(&cpuset);
+ 			CPU_SET(cpuNumber, &cpuset);
+-			if (pthread_setaffinity_np(threadId, sizeof(cpu_set_t), &cpuset) != 0)
++			if (pthread_setaffinity_np(threadId, sizeof(cpuset_t), &cpuset) != 0)
+ 				Print::printf(Print::WARNING, "Could not bind thread %u to CPU core %d", threadId, cpuNumber);
+ 			#endif
+         }
diff --git a/science/lm/files/patch-src_swig_lm.i b/science/lm/files/patch-src_swig_lm.i
new file mode 100644
index 000000000000..61ef40d8dae0
--- /dev/null
+++ b/science/lm/files/patch-src_swig_lm.i
@@ -0,0 +1,11 @@
+--- src/swig/lm.i.orig	2018-09-09 20:47:46 UTC
++++ src/swig/lm.i
+@@ -66,7 +66,7 @@ using lm::rdme::InvalidParticleException
+ %}
+ 
+ %inline %{
+-typedef long time_t;
++//typedef long time_t;
+ typedef unsigned char       uchar;
+ typedef unsigned int        uint;
+ typedef unsigned long       ulong;
diff --git a/science/lm/pkg-descr b/science/lm/pkg-descr
new file mode 100644
index 000000000000..775688ad57b8
--- /dev/null
+++ b/science/lm/pkg-descr
@@ -0,0 +1,9 @@
+Lattice Microbes is a software package for efficiently sampling trajectories
+from the chemical and reaction-diffusion master equations (CME/RDME) on high
+performance computing (HPC) infrastructure using both exact and approximate
+methods. pyLM is a problem solving environment written in Python that leverages
+the high-performance nature of the Lattice Microbes package while providing ease
+of use for common stochastic simulations and high customizability for complex
+biological applications.
+
+WWW: http://www.scs.illinois.edu/schulten/lm/
diff --git a/science/lm/pkg-plist b/science/lm/pkg-plist
new file mode 100644
index 000000000000..b1a2790f2c63
--- /dev/null
+++ b/science/lm/pkg-plist
@@ -0,0 +1,26 @@
+bin/lm
+%%MPI%%bin/lm-mpmpd
+%%PYTHON%%bin/lm_python
+bin/lm_setdm
+bin/lm_setp
+bin/lm_setrm
+%%PYTHON%%lib/lm/_lm.so
+%%PYTHON%%lib/lm/lm.py
+%%PYTHON%%lib/python/pyLM/CME.py
+%%PYTHON%%lib/python/pyLM/LMLogger.py
+%%PYTHON%%lib/python/pyLM/RDME.py
+%%PYTHON%%lib/python/pyLM/__init__.py
+%%PYTHON%%lib/python/pyLM/ipyInterface.py
+%%PYTHON%%lib/python/pyLM/units.py
+%%PYTHON%%lib/python/pySTDLM/CellArranger.py
+%%PYTHON%%lib/python/pySTDLM/Cells.py
+%%PYTHON%%lib/python/pySTDLM/Distributions.py
+%%PYTHON%%lib/python/pySTDLM/NetworkVisualization.py
+%%PYTHON%%lib/python/pySTDLM/OnTheFly.py
+%%PYTHON%%lib/python/pySTDLM/PostProcessing.py
+%%PYTHON%%lib/python/pySTDLM/SBMLReader.py
+%%PYTHON%%lib/python/pySTDLM/StandardCells.py
+%%PYTHON%%lib/python/pySTDLM/StandardReactionSystems.py
+%%PYTHON%%lib/python/pySTDLM/StandardReactions.py
+%%PYTHON%%lib/python/pySTDLM/__init__.py
+%%VMD%%lib/vmd/plugins/%%VMD_ARCH%%/molfile/lmplugin.so