Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv32393
Modified Files:
gromacs.info
Added Files:
gromacs-mpi.info gromacs.patch
Log Message:
update of gromacs package
Index: gromacs.info
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/gromacs.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- gromacs.info 9 Sep 2012 11:43:57 -0000 1.2
+++ gromacs.info 13 Feb 2013 18:57:16 -0000 1.3
@@ -1,108 +1,70 @@
Package: gromacs
-Version: 4.5.4
-Revision: 2
+Version: 4.6
+Revision: 1
Depends: %N-shlibs (= %v-%r), fftw3-shlibs, gcc47-shlibs, gsl-shlibs,
openmotif4-shlibs, x11
-BuildDepends: fftw3, gcc47-compiler, gsl, openmotif4, x11-dev
-BuildConflicts: gromacs-dev (<< %v-%r), gromacs-mpi-dev, gromacs-mpi,
gromacs-mpi-openmpi-dev, gromacs-mpi-openmpi, gromacs-mpi-lammpi-dev,
gromacs-mpi-lammpi-dev
-Conflicts: gromacs-mpi-dev, gromacs-mpi, gromacs-mpi-openmpi-dev,
gromacs-mpi-openmpi, gromacs-mpi-lammpi-dev, gromacs-mpi-lammpi-dev
-Replaces: gromacs-mpi-dev, gromacs-mpi, gromacs-mpi-openmpi-dev,
gromacs-mpi-openmpi, gromacs-mpi-lammpi-dev, gromacs-mpi-lammpi-dev
-BuildDependsOnly: false
+BuildDepends: fftw3, gcc47-compiler, gsl, openmotif4, x11-dev, cmake
+BuildConflicts: gromacs-dev, gromacs-mpi-dev
+Conflicts: gromacs-mpi, gromacs-bin (<< 4.6-1), gromacs-mpi-bin (<< 4.6-1),
gromacs-dev (<< 4.6-1), gromacs-mpi-dev (<< 4.6-1)
+Replaces: gromacs-mpi, gromacs-bin (<< 4.6-1), gromacs-mpi-bin (<< 4.6-1),
gromacs-dev (<< 4.6-1), gromacs-mpi-dev (<< 4.6-1)
+BuildDependsOnly: False
UseMaxBuildJobs: True
-SetCC: gcc
-SetCXX: g++
+Distribution: 10.7, 10.8
+SetCC: gcc-fsf-4.7
+SetCXX: g++-fsf-4.7
Source: mirror:custom:%n-%v.tar.gz
+PatchFile: %n.patch
CustomMirror: <<
Primary: ftp://ftp.gromacs.org/pub/gromacs/
<<
-Source-MD5: 5013de941017e014b92d41f82c7e86d6
-ConfigureParams: --enable-shared --prefix=%p --exec-prefix=%p
--mandir=%p/share --with-x --with-gsl --x-includes=/usr/X11/include
--x-libraries=/usr/X11/lib
+Source-MD5: d920a57884961a9fcbdcd9953ade469b
+PatchFile-MD5: 38fa52bb30693b1a9fd970b21e3e7531
DocFiles: AUTHORS COPYING README
PatchScript: <<
#!/bin/zsh -efv
+%{default_script}
perl -pi.bak -e 's|512|4096|g' src/gmxlib/futil.c
perl -pi.bak -e 's|/bin/csh|/bin/csh -f|g' share/**/* 2>/dev/null
perl -pi.bak -e 's|/lib/cpp|/usr/bin/cpp|g' share/**/* 2>/dev/null
<<
CompileScript: <<
#!/bin/bash -efv
-./configure %c --build=%m-apple-darwin`uname -r|cut -f1 -d.`
--host=%m-apple-darwin`uname -r|cut -f1 -d.`
+mkdir build
+cd build
+cmake -DGMX_GSL="ON" -DCMAKE_INSTALL_NAME_DIR=%p/lib -DCMAKE_INSTALL_PREFIX=%p
..
make
<<
InstallScript: <<
#!/bin/bash -efv
mkdir -p %i/include/%n
-make -j 1 install DESTDIR=%d
+cd build
+make install DESTDIR=%d
make clean
-./configure %c --build=%m-apple-darwin`uname -r|cut -f1 -d.`
--host=%m-apple-darwin`uname -r|cut -f1 -d.` --disable-float
--program-suffix="_d"
-make
-make -j 1 install DESTDIR=%d
+cmake -DGMX_DOUBLE="ON" -DGMX_GSL="ON" -DCMAKE_INSTALL_NAME_DIR=%p/lib
-DCMAKE_INSTALL_PREFIX=%p ..
+make install DESTDIR=%d
<<
SplitOff: <<
Package: %N-shlibs
Depends: fftw3-shlibs, gcc47-shlibs, gsl-shlibs, openmotif4-shlibs, x11
Files: <<
- lib/libgmx.6.dylib
- lib/libgmxana.6.0.0.dylib
- lib/libgmxana.6.dylib
- lib/libmd.6.0.0.dylib
- lib/libmd.6.dylib
- lib/libgmx_d.6.0.0.dylib
- lib/libgmx_d.6.dylib
- lib/libgmxana_d.6.0.0.dylib
- lib/libgmxana_d.6.dylib
- lib/libmd_d.6.0.0.dylib
- lib/libmd_d.6.dylib
- lib/libgmxpreprocess.6.dylib
- lib/libgmxpreprocess.6.0.0.dylib
- lib/libgmxpreprocess_d.6.dylib
- lib/libgmxpreprocess_d.6.0.0.dylib
+ lib/libgmx.6*.dylib
+ lib/libgmxana.6*.dylib
+ lib/libmd.6*.dylib
+ lib/libgmxpreprocess.6*.dylib
+ lib/libgmx_d.6*.dylib
+ lib/libgmxana_d.6*.dylib
+ lib/libmd_d.6*.dylib
+ lib/libgmxpreprocess_d.6*.dylib
<<
Shlibs: <<
-%p/lib/libgmx.6.dylib 7.0.0 %n (>= 4.5.3-1)
-%p/lib/libgmxana.6.dylib 7.0.0 %n (>= 4.5.3-1)
-%p/lib/libmd.6.dylib 7.0.0 %n (>= 4.5.3-1)
-%p/lib/libgmx_d.6.dylib 7.0.0 %n (>= 4.5.3-1)
-%p/lib/libgmxana_d.6.dylib 7.0.0 %n (>= 4.5.3-1)
-%p/lib/libmd_d.6.dylib 7.0.0 %n (>= 4.5.3-1)
-%p/lib/libgmxpreprocess.6.dylib 7.0.0 %n (>= 4.5.4-1)
-%p/lib/libgmxpreprocess_d.6.dylib 7.0.0 %n (>= 4.5.4-1)
-<<
-DocFiles: AUTHORS COPYING README
-<<
-SplitOff2: <<
-Package: %N-dev
-Depends: %N-shlibs (= %v-%r)
-Conflicts: gromacs-mpi-shlibs, gromacs-mpi-lammpi-shlibs,
gromacs-mpi-openmpi-shlibs
-Replaces: gromacs-mpi-shlibs, gromacs-mpi-lammpi-shlibs,
gromacs-mpi-openmpi-shlibs
-Files: <<
- lib/*.a
- lib/*.la
- include/gromacs
- lib/libgmx.dylib
- lib/libgmxana.dylib
- lib/libmd_d.dylib
- lib/libgmx_d.dylib
- lib/libgmxana_d.dylib
-<<
-BuildDependsOnly: True
-DocFiles: AUTHORS COPYING README
-<<
-SplitOff3: <<
-Package: %N-bin
-Conflicts: gromacs-mpi-lammpi-bin, gromacs-mpi-openmpi-bin, gromacs-mpi-bin
-Replaces: gromacs-mpi-lammpi-bin, gromacs-mpi-openmpi-bin, gromacs-mpi-bin
-Files: <<
- bin/GMXRC
- bin/GMXRC.bash
- bin/GMXRC.csh
- bin/GMXRC.zsh
- bin/completion.bash
- bin/completion.csh
- bin/completion.zsh
- bin/xplor2gmx.pl
- bin/demux.pl
+%p/lib/libgmx.6.dylib 6.0.0 %n (>= 4.5.3-1)
+%p/lib/libgmxana.6.dylib 6.0.0 %n (>= 4.5.3-1)
+%p/lib/libmd.6.dylib 6.0.0 %n (>= 4.5.3-1)
+%p/lib/libgmxpreprocess.6.dylib 6.0.0 %n (>= 4.5.4-1)
+%p/lib/libgmx_d.6.dylib 6.0.0 %n (>= 4.5.3-1)
+%p/lib/libgmxana_d.6.dylib 6.0.0 %n (>= 4.5.3-1)
+%p/lib/libmd_d.6.dylib 6.0.0 %n (>= 4.5.3-1)
+%p/lib/libgmxpreprocess_d.6.dylib 6.0.0 %n (>= 4.5.4-1)
<<
-BuildDependsOnly: True
DocFiles: AUTHORS COPYING README
<<
Description: Molecular dynamics package
@@ -118,6 +80,10 @@
/sw/share/gromacs Copy the tutor directory to your home
directory to use the tutorial.
<<
+DescPackaging: <<
+Shared libraries created by cmake set the compatibility version explicitly to
+major.minor.patch which is equally correct as libtool's use of major+1.
+<<
Homepage: http://www.gromacs.org
License: GPL
-Maintainer: W. G. Scott <wgsc...@users.sourceforge.net>
+Maintainer: Jack Howarth <howa...@bromo.med.uc.edu>
--- NEW FILE: gromacs-mpi.info ---
Package: gromacs-mpi
Version: 4.6
Revision: 1
Depends: %N-shlibs (= %v-%r), gsl-shlibs, fftw3-shlibs, gcc47-shlibs,
openmotif4-shlibs, openmpi-shlibs, x11
BuildDepends: gsl, fftw3, gcc47-compiler, openmpi, x11-dev, cmake
BuildConflicts: gromacs-mpi-dev, gromacs-dev
Conflicts: gromacs, gromacs-bin (<< 4.6-1), gromacs-mpi-bin (<< 4.6-1),
gromacs-dev (<< 4.6-1), gromacs-mpi-dev (<< 4.6-1)
Replaces: gromacs, gromacs-bin (<< 4.6-1), gromacs-mpi-bin (<< 4.6-1),
gromacs-dev (<< 4.6-1), gromacs-mpi-dev (<< 4.6-1)
Distribution: 10.7, 10.8
BuildDependsOnly: False
UseMaxBuildJobs: True
SetCC: gcc-fsf-4.7
SetCXX: g++-fsf-4.7
Source: mirror:custom:gromacs-%v.tar.gz
PatchFile: gromacs.patch
CustomMirror: <<
Primary: ftp://ftp.gromacs.org/pub/gromacs/
<<
Source-MD5: d920a57884961a9fcbdcd9953ade469b
PatchFile-MD5: 38fa52bb30693b1a9fd970b21e3e7531
DocFiles: AUTHORS COPYING README
PatchScript: <<
#!/bin/zsh -efv
%{default_script}
perl -pi.bak -e 's|512|4096|g' src/gmxlib/futil.c
perl -pi.bak -e 's|/bin/csh|/bin/csh -f|g' share/**/* 2>/dev/null
perl -pi.bak -e 's|/lib/cpp|/usr/bin/cpp|g' share/**/* 2>/dev/null
<<
CompileScript: <<
#!/bin/bash -efv
mkdir build
cd build
cmake -DGMX_MPI="ON" -DGMX_GSL="ON" -DCMAKE_INSTALL_NAME_DIR=%p/lib
-DCMAKE_INSTALL_PREFIX=%p ..
make
<<
InstallScript: <<
#!/bin/bash -efv
mkdir -p %i/include/%n
cd build
make install DESTDIR=%d
make clean
cmake -DGMX_MPI="ON" -DGMX_DOUBLE="ON" -DGMX_GSL="ON"
-DCMAKE_INSTALL_NAME_DIR=%p/lib -DCMAKE_INSTALL_PREFIX=%p ..
make install DESTDIR=%d
<<
SplitOff: <<
Package: %N-shlibs
Depends: gsl-shlibs, fftw3-shlibs, gcc47-shlibs, openmotif4-shlibs,
openmpi-shlibs, x11
Files: <<
lib/libgmx_mpi.6*.dylib
lib/libgmxana_mpi.6*.dylib
lib/libmd_mpi.6*.dylib
lib/libgmxpreprocess_mpi.6*.dylib
lib/libgmx_mpi_d.6*.dylib
lib/libgmxana_mpi_d.6*.dylib
lib/libmd_mpi_d.6*.dylib
lib/libgmxpreprocess_mpi_d.6*.dylib
<<
Shlibs: <<
%p/lib/libgmx_mpi.6.dylib 6.0.0 %n (>= 4..54-1)
%p/lib/libgmxana_mpi.6.dylib 6.0.0 %n (>= 4.5.4-1)
%p/lib/libmd_mpi.6.dylib 6.0.0 %n (>= 4.5.4-1)
%p/lib/libgmxpreprocess_mpi.6.dylib 6.0.0 %n (>= 4.5.4-1)
%p/lib/libgmx_mpi_d.6.dylib 6.0.0 %n (>= 4.5.4-1)
%p/lib/libgmxana_mpi_d.6.dylib 6.0.0 %n (>= 4.5.4-1)
%p/lib/libmd_mpi_d.6.dylib 6.0.0 %n (>= 4.5.4-1)
%p/lib/libgmxpreprocess_mpi_d.6.dylib 6.0.0 %n (>= 4.5.4-1)
<<
DocFiles: AUTHORS COPYING README
<<
Description: Molecular dynamics package (Parallel version)
DescDetail: <<
GROMACS is a versatile and extremely well optimized package
to perform molecular dynamics computer simulations and
subsequent trajectory analysis. It is developed for
biomolecules like proteins, but the extremely high
performance means it is used also in several other field
like polymer chemistry and solid state physics. This
version has parallel processing support for the main
GROMACS package.
<<
DescUsage: <<
Any package using gromacs-mpi-openmpi-dev or gromacs-mpi-lammpi-dev
should BuildDepends either openmpi-dev or lammpi-dev as well.
<<
DescPackaging: <<
Shared libraries created by cmake set the compatibility version explicitly to
major.minor.patch which is equally correct as libtool's use of major+1.
<<
Homepage: http://www.gromacs.org
License: GPL
Maintainer: Jack Howarth <howa...@bromo.med.uc.edu>
--- NEW FILE: gromacs.patch ---
diff -uNr gromacs-4.6/CMakeLists.txt gromacs-4.6.fink/CMakeLists.txt
--- gromacs-4.6/CMakeLists.txt 2013-01-18 15:46:08.000000000 -0500
+++ gromacs-4.6.fink/CMakeLists.txt 2013-02-12 18:23:54.000000000 -0500
@@ -64,6 +64,7 @@
set(PROJECT_VERSION ${CUSTOM_VERSION_STRING})
endif (CUSTOM_VERSION_STRING)
set(SOVERSION 6)
+set(VERSION 6.0.0)
# It is a bit irritating, but this has to be set separately for now!
SET(CPACK_PACKAGE_VERSION_MAJOR "4")
SET(CPACK_PACKAGE_VERSION_MINOR "6")
diff -uNr gromacs-4.6/src/gmxlib/CMakeLists.txt
gromacs-4.6.fink/src/gmxlib/CMakeLists.txt
--- gromacs-4.6/src/gmxlib/CMakeLists.txt 2013-01-18 15:38:57.000000000
-0500
+++ gromacs-4.6.fink/src/gmxlib/CMakeLists.txt 2013-02-12 18:25:19.000000000
-0500
@@ -117,7 +117,7 @@
if(USE_VERSION_H)
add_dependencies(gmx gmx_version)
endif()
-set_target_properties(gmx PROPERTIES OUTPUT_NAME "gmx${GMX_LIBS_SUFFIX}"
SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
+set_target_properties(gmx PROPERTIES OUTPUT_NAME "gmx${GMX_LIBS_SUFFIX}"
SOVERSION ${SOVERSION} VERSION ${VERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
COMPILE_FLAGS "${OpenMP_C_FLAGS}" COMPILE_DEFINITIONS "TMPI_EXPORTS")
install(TARGETS gmx DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries)
diff -uNr gromacs-4.6/src/kernel/CMakeLists.txt
gromacs-4.6.fink/src/kernel/CMakeLists.txt
--- gromacs-4.6/src/kernel/CMakeLists.txt 2013-01-18 15:38:58.000000000
-0500
+++ gromacs-4.6.fink/src/kernel/CMakeLists.txt 2013-02-12 18:26:51.000000000
-0500
@@ -76,7 +76,7 @@
add_library(gmxpreprocess ${GMXPREPROCESS_SOURCES})
target_link_libraries(gmxpreprocess md)
-set_target_properties(gmxpreprocess PROPERTIES OUTPUT_NAME
"gmxpreprocess${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR
"${LIB_INSTALL_DIR}"
+set_target_properties(gmxpreprocess PROPERTIES OUTPUT_NAME
"gmxpreprocess${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} VERSION ${VERSION}
INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
COMPILE_FLAGS "${OpenMP_C_FLAGS}")
diff -uNr gromacs-4.6/src/mdlib/CMakeLists.txt
gromacs-4.6.fink/src/mdlib/CMakeLists.txt
--- gromacs-4.6/src/mdlib/CMakeLists.txt 2013-01-18 15:38:58.000000000
-0500
+++ gromacs-4.6.fink/src/mdlib/CMakeLists.txt 2013-02-12 18:25:52.000000000
-0500
@@ -73,7 +73,7 @@
else()
set(MD_PREFIX)
endif()
-set_target_properties(md PROPERTIES OUTPUT_NAME
"${MD_PREFIX}md${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR
"${LIB_INSTALL_DIR}"
+set_target_properties(md PROPERTIES OUTPUT_NAME
"${MD_PREFIX}md${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} VERSION ${VERSION}
INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
COMPILE_FLAGS "${OpenMP_C_FLAGS}")
install(TARGETS md DESTINATION ${LIB_INSTALL_DIR} COMPONENT libraries)
diff -uNr gromacs-4.6/src/tools/CMakeLists.txt
gromacs-4.6.fink/src/tools/CMakeLists.txt
--- gromacs-4.6/src/tools/CMakeLists.txt 2013-01-18 15:38:58.000000000
-0500
+++ gromacs-4.6.fink/src/tools/CMakeLists.txt 2013-02-12 18:28:59.000000000
-0500
@@ -71,7 +71,7 @@
target_link_libraries(gmxana md gmx ${GSL_LIBRARIES})
-set_target_properties(gmxana PROPERTIES OUTPUT_NAME "gmxana${GMX_LIBS_SUFFIX}"
SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
+set_target_properties(gmxana PROPERTIES OUTPUT_NAME "gmxana${GMX_LIBS_SUFFIX}"
SOVERSION ${SOVERSION} VERSION ${VERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
COMPILE_FLAGS "${OpenMP_C_FLAGS}")
# List of programs with single corresponding .c source file,
------------------------------------------------------------------------------
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