version bump

(Portage version: 2.2.0_alpha177/cvs/Linux x86_64, signed Manifest commit with key C2000586)

3 files changed, 15 insertions, 157 deletions

diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog
index faf9b633eb6e..3b411f1bee22 100644
--- a/sci-chemistry/gromacs/ChangeLog
+++ b/sci-chemistry/gromacs/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/gromacs
 # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.125 2013/05/28 03:28:04 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/ChangeLog,v 1.126 2013/06/01 21:36:28 ottxor Exp $
+
+*gromacs-4.6.2 (01 Jun 2013)
+
+  01 Jun 2013; Christoph Junghans <ottxor@gentoo.org> +gromacs-4.6.2.ebuild,
+  -files/gromacs-4.6.1-openmm.patch, -gromacs-4.6.1.ebuild:
+  version bump
 
   28 May 2013; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.1.ebuild:
   fixed a typo, which prevented cuda build
diff --git a/sci-chemistry/gromacs/files/gromacs-4.6.1-openmm.patch b/sci-chemistry/gromacs/files/gromacs-4.6.1-openmm.patch
deleted file mode 100644
index dd4214af0513..000000000000
--- a/sci-chemistry/gromacs/files/gromacs-4.6.1-openmm.patch
+++ /dev/null
@@ -1,151 +0,0 @@
-From e96c29f92e6cd1dd05945ef80e6a78d55747cf2e Mon Sep 17 00:00:00 2001
-From: Christoph Junghans <junghans@votca.org>
-Date: Thu, 17 Jan 2013 20:30:30 -0700
-Subject: [PATCH] fix out of source build for OpenMM
-
-* introduced in e508a07b6e127fa1cf31d263bcbd33e4040066cb
-
-Change-Id: I6ad45fd2d5766d1c4a91ef2e0c442ff030fc1296
----
- CMakeLists.txt                     |  2 +-
- src/contrib/BuildMdrunOpenMM.cmake |  6 +++---
- src/contrib/CMakeLists.txt         |  3 ---
- src/contrib/mdrun_openmm.c         | 12 +++++++-----
- src/contrib/openmm_wrapper.cpp     |  1 +
- src/kernel/CMakeLists.txt          |  5 ++++-
- 6 files changed, 16 insertions(+), 13 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index df12172..4c11a29 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -153,7 +153,7 @@ mark_as_advanced(GMX_FORCE_CXX)
- option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
- mark_as_advanced(GMX_COOL_QUOTES)
- 
--if(GMX_GPU OR GMX_FORCE_CXX)
-+if(GMX_GPU OR GMX_FORCE_CXX OR GMX_OPENMM)
-     enable_language(CXX)
- endif()
- set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
-diff --git a/src/contrib/BuildMdrunOpenMM.cmake b/src/contrib/BuildMdrunOpenMM.cmake
-index bc954d6..6d04958 100644
---- a/src/contrib/BuildMdrunOpenMM.cmake
-+++ b/src/contrib/BuildMdrunOpenMM.cmake
-@@ -39,14 +39,14 @@ link_directories(${OpenMM_LIBRARY_DIR})
- # if the same OpenMM installation is used for running and building 
- add_definitions( -DOPENMM_PLUGIN_DIR="${OpenMM_PLUGIN_DIR}" ) 
- file(TO_CMAKE_PATH ${OpenMM_PLUGIN_DIR} _path)
--add_library(openmm_api_wrapper STATIC openmm_wrapper.cpp)
-+add_library(openmm_api_wrapper STATIC ${CMAKE_SOURCE_DIR}/src/contrib/openmm_wrapper.cpp)
- target_link_libraries(openmm_api_wrapper ${OpenMM_LIBRARIES})
- list(APPEND GMX_EXTRA_LIBRARIES openmm_api_wrapper ${OpenMM_LIBRARIES})   
- 
- list(REMOVE_ITEM MDRUN_SOURCES mdrun.c)
- list(APPEND MDRUN_SOURCES
--    ${CMAKE_CURRENT_SOURCE_DIR}/src/contrib/md_openmm.c
--    ${CMAKE_CURRENT_SOURCE_DIR}/src/contrib/mdrun_openmm.c)
-+    ${CMAKE_SOURCE_DIR}/src/contrib/md_openmm.c
-+    ${CMAKE_SOURCE_DIR}/src/contrib/mdrun_openmm.c)
- 
- # this is to circumvent the following MSVC error: 
- # warning LNK4098: defaultlib 'LIBCMT' conflicts with use of other libs
-diff --git a/src/contrib/CMakeLists.txt b/src/contrib/CMakeLists.txt
-index 7c5bb83..7725210 100644
---- a/src/contrib/CMakeLists.txt
-+++ b/src/contrib/CMakeLists.txt
-@@ -49,7 +49,6 @@ if(GMX_OPENMM)
-         message(FATAL_ERROR "The OpenMM build is not compatible with the native GPU build")
-     endif()
- 
--    enable_language(CXX)
-     set (GMX_BINARY_SUFFIX "-openmm")
-     set (GMX_LIBS_SUFFIX "_openmm")
- 
-@@ -99,8 +98,6 @@ if(GMX_OPENMM)
-     if(CMAKE_BUILD_TYPE STREQUAL "DEBUG")    
-         set(CUDA_VERBOSE_BUILD ON)
-     endif()
--    list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src/contrib)
--    find_package(OpenMM) 
- 
-     # mark as advanced the unused variables
-     mark_as_advanced(FORCE GMX_CPU_ACCELERATION GMX_MPI GMX_FFT_LIBRARY 
-diff --git a/src/contrib/mdrun_openmm.c b/src/contrib/mdrun_openmm.c
-index 7771dcd..aeedeb4 100644
---- a/src/contrib/mdrun_openmm.c
-+++ b/src/contrib/mdrun_openmm.c
-@@ -153,7 +153,7 @@ int cmain(int argc,char *argv[])
-     { efXVG, "-tpi",    "tpi",      ffOPTWR },
-     { efXVG, "-tpid",   "tpidist",  ffOPTWR },
-     { efEDI, "-ei",     "sam",      ffOPTRD },
--    { efEDO, "-eo",     "sam",      ffOPTWR },
-+    { efXVG, "-eo",     "sam",      ffOPTWR },
-     { efGCT, "-j",      "wham",     ffOPTRD },
-     { efGCT, "-jo",     "bam",      ffOPTWR },
-     { efXVG, "-ffout",  "gct",      ffOPTWR },
-@@ -205,6 +205,8 @@ int cmain(int argc,char *argv[])
-     { NULL, "interleave", "pp_pme", "cartesian", NULL };
-   const char *dddlb_opt[] =
-     { NULL, "auto", "no", "yes", NULL };
-+  const char   *thread_aff_opt[threadaffNR+1] =
-+    { NULL, "auto", "no", "yes", NULL };
-   const char *nbpu_opt[] =
-     { NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
-   real rdd=0.0,rconstr=0.0,dlb_scale=0.8,pforce=-1;
-@@ -236,12 +238,12 @@ int cmain(int argc,char *argv[])
-       "Number of OpenMP threads per MPI process/thread to start (0 is guess)" },
-     { "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
-       "Number of OpenMP threads per MPI process/thread to start (0 is -ntomp)" },
--    { "-pin",     FALSE, etBOOL, {&hw_opt.bThreadPinning},
-+    { "-pin",     FALSE, etBOOL, {thread_aff_opt},
-       "Pin OpenMP threads to cores" },
--    { "-pinht",   FALSE, etBOOL, {&hw_opt.bPinHyperthreading},
--      "Always pin threads to Hyper-Threading cores" },
-     { "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
-       "Core offset for pinning (for running multiple mdrun processes on a single physical node)" },
-+    { "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
-+      "Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
-     { "-gpu_id",  FALSE, etSTR, {&hw_opt.gpu_id},
-       "List of GPU id's to use" },
-     { "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
-@@ -413,7 +415,7 @@ int cmain(int argc,char *argv[])
- 
-       if (MULTISIM(cr) && MASTER(cr))
-       {
--          check_multi_int(stdout,cr->ms,sim_part,"simulation part");
-+          check_multi_int(stdout,cr->ms,sim_part,"simulation part", TRUE);
-       }
-   } 
-   else
-diff --git a/src/contrib/openmm_wrapper.cpp b/src/contrib/openmm_wrapper.cpp
-index 07f0eca..05c3210 100644
---- a/src/contrib/openmm_wrapper.cpp
-+++ b/src/contrib/openmm_wrapper.cpp
-@@ -63,6 +63,7 @@ using namespace std;
- #include "mdrun.h"
- #include "physics.h"
- #include "string2.h"
-+#include "openmm_gpu_utils.h"
- #include "gpu_utils.h"
- #include "mtop_util.h"
- 
-diff --git a/src/kernel/CMakeLists.txt b/src/kernel/CMakeLists.txt
-index 01e290c..3f95d33 100644
---- a/src/kernel/CMakeLists.txt
-+++ b/src/kernel/CMakeLists.txt
-@@ -88,7 +88,10 @@ if(GMX_OPENMM)
-     # Even though the OpenMM build has "moved to contrib", many things
-     # have be be done from within the scope of the CMakeLists.txt that
-     # builds its mdrun, and that is here
--    include(../contrib/BuildMdrunOpenMM)
-+    list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/src/contrib)
-+    find_package(OpenMM)
-+    include_directories(${CMAKE_CURRENT_SOURCE_DIR})
-+    include(${CMAKE_SOURCE_DIR}/src/contrib/BuildMdrunOpenMM.cmake)
- endif(GMX_OPENMM)
- 
- if(GMX_GPU OR GMX_FORCE_CXX)
--- 
-1.8.1.5
-
diff --git a/sci-chemistry/gromacs/gromacs-4.6.1.ebuild b/sci-chemistry/gromacs/gromacs-4.6.2.ebuild
index a277b67824d5..be02e1d0463d 100644
--- a/sci-chemistry/gromacs/gromacs-4.6.1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-4.6.2.ebuild
@@ -1,11 +1,11 @@
 # Copyright 1999-2013 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.1.ebuild,v 1.3 2013/05/28 03:28:04 ottxor Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gromacs/gromacs-4.6.2.ebuild,v 1.1 2013/06/01 21:36:28 ottxor Exp $
 
 EAPI=5
 
-TEST_PV="4.6.1"
-MANUAL_PV="4.6.1"
+TEST_PV="4.6.2"
+MANUAL_PV="4.6.2"
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
@@ -20,6 +20,7 @@ if [[ $PV = *9999* ]]; then
 	inherit git-2
 	LIVE_DEPEND="doc? (
 		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
 		media-gfx/imagemagick
 		sys-apps/coreutils
 	)"
@@ -27,7 +28,6 @@ else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${P}.tar.gz
 		doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${MANUAL_PV}.pdf -> ${PN}-manual-${MANUAL_PV}.pdf )
 		test? ( http://${PN}.googlecode.com/files/regressiontests-${TEST_PV}.tar.gz )"
-	PATCHES=( "${FILESDIR}/${P}-openmm.patch" )
 	LIVE_DEPEND=""
 fi
 
@@ -182,7 +182,7 @@ src_configure() {
 		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
 		local cuda=( "-DGMX_GPU=OFF" )
 		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( -DGMX_GPU=ON -DCUDA_HOST_COMPILER_OPTIONS="${NVCCFLAGS}" )
+			cuda=( -DGMX_GPU=ON )
 		mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF
 			$(cmake-utils_use threads GMX_THREAD_MPI) "${cuda[@]}" -DGMX_OPENMM=OFF
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
@@ -243,7 +243,10 @@ src_install() {
 			mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" )
 			BUILD_DIR="${WORKDIR}"/manual_build \
 				CMAKE_USE_DIR="${WORKDIR}/manual" cmake-utils_src_configure
+			[[ ${CHOST} = *-darwin* ]] && \
+				export DYLD_LIBRARY_PATH="${DYLD_LIBRARY_PATH}${DYLD_LIBRARY_PATH:+:}${ED}/usr/$(get_libdir)"
 			BUILD_DIR="${WORKDIR}"/manual_build cmake-utils_src_make
+			[[ ${CHOST} = *-darwin* ]] && DYLD_LIBRARY_PATH="${ED}/usr/$(get_libdir)"
 			newdoc "${WORKDIR}"/manual_build/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
 		use mpi || continue