diff --git a/.gitignore b/.gitignore index 486904c..58f36dd 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ +/gromacs-*.src.rpm gromacs-4.0.7.tar.gz manual-4.0.pdf /manual-4.5.pdf @@ -35,3 +36,5 @@ manual-4.0.pdf /gromacs-d44d7d6bebdb7fa52090b744854d49f34099e044.tar.gz /gromacs-2016.tar.gz /manual-2016.pdf +/gromacs-2016.1.tar.gz +/manual-2016.1.pdf diff --git a/gromacs-tng.patch b/gromacs-tng.patch index 987465a..e19029b 100644 --- a/gromacs-tng.patch +++ b/gromacs-tng.patch @@ -1,11 +1,32 @@ -diff -up gromacs-2016/src/gromacs/CMakeLists.txt.tng gromacs-2016/src/gromacs/CMakeLists.txt ---- gromacs-2016/src/gromacs/CMakeLists.txt.tng 2016-07-09 02:55:38.000000000 +0200 -+++ gromacs-2016/src/gromacs/CMakeLists.txt 2016-08-23 23:41:58.359326148 +0200 -@@ -122,7 +122,6 @@ tmpi_get_source_list(THREAD_MPI_SOURCES - list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES}) +From 02922173c8d5f35f1d3730254eccf0621e55cbe7 Mon Sep 17 00:00:00 2001 +From: Christoph Junghans +Date: Thu, 3 Nov 2016 12:12:17 -0600 +Subject: [PATCH] cmake: fix build with GMX_EXTERNAL_TNG=ON + +tng_set_source_properties is not defined in case of GMX_EXTERNAL_TNG=ON +due to the fact that BuildTNG.cmake never gets included. Also this +call isn't really needed tng doesn't get compile when external anyway. + +Change-Id: Id3c7e0da55ce9ef8cf43d2aecaa187e965bf6ad2 +--- + src/gromacs/CMakeLists.txt | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt +index b7d9bf4..8b7fe3f 100644 +--- a/src/gromacs/CMakeLists.txt ++++ b/src/gromacs/CMakeLists.txt +@@ -123,7 +123,9 @@ list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES}) - list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES}) --tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB}) + if(GMX_USE_TNG) + list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES}) +- tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB}) ++ if (NOT GMX_EXTERNAL_TNG) ++ tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB}) ++ endif() + endif() - get_lmfit_properties(LMFIT_SOURCES LMFIT_LIBRARIES LMFIT_INCLUDE_DIRECTORY LMFIT_INCLUDE_DIR_ORDER) - include_directories(${LMFIT_INCLUDE_DIR_ORDER} SYSTEM "${LMFIT_INCLUDE_DIRECTORY}") + get_lmfit_properties(LMFIT_SOURCES LMFIT_LIBRARIES_TO_LINK LMFIT_INCLUDE_DIRECTORY LMFIT_INCLUDE_DIR_ORDER) +-- +2.7.3 + diff --git a/gromacs-use-system-lmfit.patch b/gromacs-use-system-lmfit.patch deleted file mode 100644 index 1642b81..0000000 --- a/gromacs-use-system-lmfit.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -up gromacs-2016/src/gromacs/CMakeLists.txt.lmfit gromacs-2016/src/gromacs/CMakeLists.txt ---- gromacs-2016/src/gromacs/CMakeLists.txt.lmfit 2016-07-09 02:55:38.000000000 +0200 -+++ gromacs-2016/src/gromacs/CMakeLists.txt 2016-08-24 00:20:34.262790989 +0200 -@@ -124,7 +124,7 @@ list(APPEND LIBGROMACS_SOURCES ${THREAD_ - list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES}) - tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB}) - --get_lmfit_properties(LMFIT_SOURCES LMFIT_LIBRARIES_TO_LINK LMFIT_INCLUDE_DIRECTORY LMFIT_INCLUDE_DIR_ORDER) -+get_lmfit_properties(LMFIT_SOURCES LMFIT_LIBRARIES LMFIT_INCLUDE_DIRECTORY LMFIT_INCLUDE_DIR_ORDER) - include_directories(${LMFIT_INCLUDE_DIR_ORDER} SYSTEM "${LMFIT_INCLUDE_DIRECTORY}") - list(APPEND LIBGROMACS_SOURCES ${LMFIT_SOURCES}) - -@@ -183,7 +183,7 @@ target_link_libraries(libgromacs - ${TNG_IO_LIBRARIES} - ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES} - ${XML_LIBRARIES} -- ${LMFIT_LIBRARIES_TO_LINK} -+ ${LMFIT_LIBRARIES} - ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS} ${OPENCL_LIBRARIES} - ${GMX_STDLIB_LIBRARIES}) - set_target_properties(libgromacs PROPERTIES diff --git a/gromacs.spec b/gromacs.spec index ee5892d..c0ab1a3 100644 --- a/gromacs.spec +++ b/gromacs.spec @@ -32,8 +32,8 @@ %endif Name: gromacs -Version: 2016 -Release: 2%{?dist} +Version: 2016.1 +Release: 1%{?dist} Summary: Fast, Free and Flexible Molecular Dynamics License: GPLv2+ URL: http://www.gromacs.org @@ -56,8 +56,6 @@ Source6: gromacs-README.fedora # fix path to packaged dssp # https://bugzilla.redhat.com/show_bug.cgi?id=1203754 Patch0: gromacs-dssp-path.patch -# fix build with system lmfit -Patch2: gromacs-use-system-lmfit.patch # fix building documentation Patch3: gromacs-sphinx-no-man.patch # Fix build with system TNG @@ -270,11 +268,9 @@ script. install -Dpm644 %{SOURCE1} ./serial/docs/manual/gromacs.pdf %endif %patch0 -p1 -b .dssp -%patch2 -p1 -b .lmfit -rm -r src/external/lmfit %patch8 -p1 -b .tng # Delete bundled stuff so that it doesn't get used accidentally -rm -r src/external/{fftpack,tinyxml2,tng_io} +rm -r src/external/{fftpack,tinyxml2,tng_io,lmfit} mkdir -p {serial,mpich,openmpi}{,_d} @@ -497,6 +493,11 @@ done %{_bindir}/GMXRC.csh %changelog +* Thu Nov 03 2016 Christoph Junghans - 2016.1-1 +- Update to 2016.1 +- Drop gromacs-use-system-lmfit.patch, made it upstream +- Update gromacs-tng.patch, https://gerrit.gromacs.org/#/c/6319/ + * Fri Oct 21 2016 Orion Poplawski - Rebuild for openmpi 2.0 diff --git a/sources b/sources index 5fc2ab9..1b823d2 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -302a87450cd8ba3eb2c2c29cd6232bf1 gromacs-2016.tar.gz -0c804e849a4c3a07e01e4e320d348dbe manual-2016.pdf +0eba1a1fe6c5ace51a7ce2eaf6c1c7f2 gromacs-2016.1.tar.gz +9bf68bb89315874ab3b5d0e1185abe81 manual-2016.1.pdf