[fink:package-submissions] #4899 gromacs/gromacs-mpi-2016.3-1

"Jack Howarth" <[email protected]>
Newsgroups gmane.os.apple.fink.tracker
Message-ID </p/fink/package-submissions/4899/985de5d8cfd389ee8103a965afe94258ed79ec80.package-submissions@fink.p.sourceforge.net> 
Regenerated patch for gromacs-libxml2.patch


Attachments:

- [gromacs-libxml2.patch](https://sourceforge.net/p/fink/package-submissions/_discuss/thread/be5ea707/c180/attachment/gromacs-libxml2.patch) (444 Bytes; application/octet-stream)


---

** [package-submissions:#4899] gromacs/gromacs-mpi-2016.3-1**

**Status:** open
**Group:** Undergoing_Validation
**Created:** Tue Mar 14, 2017 08:55 PM UTC by Jack Howarth
**Last Updated:** Tue Mar 14, 2017 08:57 PM UTC
**Owner:** nobody


Update the gromacs and gromacs-mpi packages to the current 2016.3 release and add BuildDepends: llvm-clang amd Depends: libomp-shlibs to handle the migration of upstream gromacs from using boost to using OpenMP for threaded code.

~~~
Index: gromacs.info
===================================================================
RCS file: /cvsroot/fink/dists/10.9-libcxx/stable/main/finkinfo/sci/gromacs.info,v
retrieving revision 1.6
diff -u -r1.6 gromacs.info
--- gromacs.info	7 Oct 2016 03:47:33 -0000	1.6
+++ gromacs.info	14 Mar 2017 17:56:42 -0000
@@ -1,16 +1,19 @@
 Package: gromacs
-Version: 5.1.4
-Revision: 100
+Version: 2016.3
+Revision: 1
 Depends: <<
-	gromacs1-shlibs (= %v-%r),
-	fftw3-shlibs (>= 3.3.4-2),
+	libomp-shlibs,
+	gromacs2-shlibs (= %v-%r),
+	hwloc-shlibs,
+	fftw3-shlibs (>= 3.3.5-1),
 	x11
 <<
 BuildDepends: <<
-	boost1.58-nopython,
+	llvm-clang,
 	cmake,
-	fftw3 (>= 3.3.4-2),
+	fftw3 (>= 3.3.5-1),
 	fink (>= 0.38.3),
+	hwloc,
 	x11-dev
 <<
 BuildConflicts: <<
@@ -34,10 +37,12 @@
 <<
 BuildDependsOnly: False
 UseMaxBuildJobs: True
+SetCC: llvm-clang
+SetCXX: llvm-clang++
 Source: mirror:custom:%n-%v.tar.gz
-Source-MD5: ba2e34d59b3982603b4935d650c08040
+Source-MD5: e9e3a41bd123b52fbcc6b32d09f8202b
 PatchFile: %n-libxml2.patch
-PatchFile-MD5: 463830df2e50a5df49bbbd4b0299cf76
+PatchFile-MD5: f4ae00e6b57c404fcd7d69bf677f7f28 
 CustomMirror: <<
 Primary: ftp://ftp.gromacs.org/pub/gromacs/
 <<
@@ -45,7 +50,7 @@
 InfoTest: <<
  TestSuiteSize: medium
  TestSource: http://gerrit.gromacs.org/download/regressiontests-%v.tar.gz
- TestSource-MD5: 8902358ab19343f17997d1bf85f8e69c
+ TestSource-MD5: bed92d1d9cdca66fbd2efa142b6e0dd3
  TestScript: <<
    mv ../regressiontests-%v regressiontests-%v
    # sentinel-file is flag to activate testing during InstallScript as
@@ -66,9 +71,8 @@
 InstallScript: <<
 #!/bin/bash -efv
 cd build
-CMAKE_OPTIONS="-DBOOST_ROOT=%p/opt/boost-1_58 \
+CMAKE_OPTIONS="-DGMX_FFT_LIBRARY=fftw3 \
 		-DGMX_GPU="OFF" \
-		-DGMX_FFT_LIBRARY=fftw3 \
 		-DGMX_X11="ON" \
 		-DCMAKE_INSTALL_NAME_DIR=%p/lib \
 		-DCMAKE_INSTALL_PREFIX=%p \
@@ -104,25 +108,27 @@
 make install DESTDIR=%d
 <<
 SplitOff: <<
-Package: gromacs1-shlibs
+Package: gromacs2-shlibs
 Depends: <<
-	fftw3-shlibs (>= 3.3.4-2),
+	libomp-shlibs,
+	fftw3-shlibs (>= 3.3.5-1),
+	hwloc-shlibs,
 	x11
 <<
 Files: <<
-	lib/libgromacs.1*.dylib
-	lib/libgromacs_d.1*.dylib
+	lib/libgromacs.2*.dylib
+	lib/libgromacs_d.2*.dylib
 <<
 Shlibs: <<
-	@rpath/libgromacs.1.dylib 1.0.0 %n (>= 5.1-1)
-	@rpath/libgromacs_d.1.dylib 1.0.0 %n (>= 5.1-1)
+	@rpath/libgromacs.2.dylib 2.0.0 %n (>= 2016-1)
+	@rpath/libgromacs_d.2.dylib 2.0.0 %n (>= 2016-1)
 <<
 DocFiles: AUTHORS COPYING README
 <<
 SplitOff2: <<
 Package: %N-dev
 Depends: <<
-	gromacs1-shlibs (= %v-%r)
+	gromacs2-shlibs (= %v-%r)
 <<
 Conflicts: <<
 	gromacs (<= 4.6-1),
~~~

~~~
Index: gromacs-mpi.info
===================================================================
RCS file: /cvsroot/fink/dists/10.9-libcxx/stable/main/finkinfo/sci/gromacs-mpi.info,v
retrieving revision 1.6
diff -u -r1.6 gromacs-mpi.info
--- gromacs-mpi.info	7 Oct 2016 03:47:33 -0000	1.6
+++ gromacs-mpi.info	14 Mar 2017 17:56:42 -0000
@@ -1,17 +1,20 @@
 Package: gromacs-mpi
-Version: 5.1.4
-Revision: 100
+Version: 2016.3
+Revision: 1
 Depends: <<
-	gromacs1-mpi-shlibs (= %v-%r),
-	fftw3-shlibs (>= 3.3.4-2),
+	libomp-shlibs,
+	gromacs2-mpi-shlibs (= %v-%r),
+	fftw3-shlibs (>= 3.3.5-1),
+	hwloc-shlibs,
 	openmpi (>= 1.10.0-1),
 	x11
 <<
 BuildDepends: <<
-	boost1.58-nopython,
+	llvm-clang,
 	cmake,
-	fftw3 (>= 3.3.4-2),
+	fftw3 (>= 3.3.5-1),
 	fink (>= 0.38.3),
+	hwloc,
 	openmpi (>= 1.10.0-1),
 	x11-dev
 <<
@@ -36,10 +39,12 @@
 <<
 BuildDependsOnly: False
 UseMaxBuildJobs: True
+SetCC: llvm-clang
+SetCXX: llvm-clang++
 Source: mirror:custom:gromacs-%v.tar.gz
-Source-MD5: ba2e34d59b3982603b4935d650c08040
+Source-MD5: e9e3a41bd123b52fbcc6b32d09f8202b
 PatchFile: gromacs-libxml2.patch
-PatchFile-MD5: 463830df2e50a5df49bbbd4b0299cf76
+PatchFile-MD5: f4ae00e6b57c404fcd7d69bf677f7f28
 CustomMirror: <<
 Primary: ftp://ftp.gromacs.org/pub/gromacs/
 <<
@@ -47,7 +52,7 @@
 InfoTest: <<
  TestSuiteSize: medium
  TestSource: http://gerrit.gromacs.org/download/regressiontests-%v.tar.gz
- TestSource-MD5: 8902358ab19343f17997d1bf85f8e69c
+ TestSource-MD5: bed92d1d9cdca66fbd2efa142b6e0dd3
  TestScript: <<
    mv ../regressiontests-%v regressiontests-%v
    # sentinel-file is flag to activate testing during InstallScript as
@@ -68,9 +73,8 @@
 InstallScript: <<
 #!/bin/bash -efv
 cd build
-CMAKE_OPTIONS="-DBOOST_ROOT=%p/opt/boost-1_58 \
+CMAKE_OPTIONS="-DGMX_FFT_LIBRARY=fftw3 \
 		-DGMX_GPU="OFF" \
-		-DGMX_FFT_LIBRARY=fftw3 \
 		-DGMX_X11="ON" \
 		-DGMX_MPI="ON" \
 		-DCMAKE_INSTALL_NAME_DIR=%p/lib \
@@ -108,26 +112,28 @@
 make install DESTDIR=%d
 <<
 SplitOff: <<
-Package: gromacs1-mpi-shlibs
+Package: gromacs2-mpi-shlibs
 Depends: <<
-	fftw3-shlibs (>= 3.3.4-2),
+	libomp-shlibs,
+	fftw3-shlibs (>= 3.3.5-1),
+	hwloc-shlibs,
 	openmpi-shlibs (>= 1.10.0-1),
 	x11
 <<
 Files: <<
-	lib/libgromacs_mpi.1*.dylib
-	lib/libgromacs_mpi_d.1*.dylib
+	lib/libgromacs_mpi.2*.dylib
+	lib/libgromacs_mpi_d.2*.dylib
 <<
 Shlibs: <<
-	@rpath/libgromacs_mpi.1.dylib 1.0.0 %n (>= 5.1-1)
-	@rpath/libgromacs_mpi_d.1.dylib 1.0.0 %n (>= 5.1-1)
+	@rpath/libgromacs_mpi.2.dylib 2.0.0 %n (>= 2016-1)
+	@rpath/libgromacs_mpi_d.2.dylib 2.0.0 %n (>= 2016-1)
 <<
 DocFiles: AUTHORS COPYING README
 <<
 SplitOff2: <<
 Package: %N-dev
 Depends: <<
-	gromacs1-mpi-shlibs (= %v-%r)
+	gromacs2-mpi-shlibs (= %v-%r)
 <<
 Conflicts: <<
 	gromacs (<= 4.6-1),
~~~

Tested on 10.12 with 'fink -m'. This packaging depends on the new llvm40 packaging which introduces the new common llvm-clang, libomp-shlibs and libomp-dev split-offs.

https://sourceforge.net/p/fink/package-submissions/4896/

Supplants https://sourceforge.net/p/fink/package-submissions/4840/


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