#4584 gromacs/gromacs-mpi-5.1.1-100

[Jack Howarth]

The attached Info files update the gromacs and gromacs-mpi packages to the new 5.1.1 release. Tested on 10.11 with 'fink -m'. The changes are...

--- gromacs.info    2015-12-13 19:24:36.000000000 -0500
+++ gromacs.info.new    2015-12-13 17:11:53.000000000 -0500
@@ -1,6 +1,6 @@
 Package: gromacs
-Version: 5.1
-Revision: 102
+Version: 5.1.1
+Revision: 100
 Depends: <<
    gromacs1-shlibs (= %v-%r),
    fftw3-shlibs (>= 3.3.4-2),
@@ -36,7 +36,7 @@
 UseMaxBuildJobs: True
 Distribution: 10.9, 10.10, 10.11
 Source: mirror:custom:%n-%v.tar.gz
-Source-MD5: e5ba00d47c4c6dec107951a7d4605f31
+Source-MD5: 5c075141aa69dc4859cad0a55e61d35e
 PatchFile: %n-libxml2.patch
 PatchFile-MD5: 463830df2e50a5df49bbbd4b0299cf76
 CustomMirror: <<
@@ -46,7 +46,7 @@
 InfoTest: <<
  TestSuiteSize: medium
  TestSource: http://gerrit.gromacs.org/download/regressiontests-%v.tar.gz
- TestSource-MD5: 298db2fa20a6f4b02e758687ebf48ee8
+ TestSource-MD5: 614a74e9b143bda5476f87f4ce08eec0
  TestScript: <<
    #!/bin/sh -ev
    mv ../regressiontests-%v regressiontests-%v

and

--- gromacs-mpi.info    2015-12-13 19:24:36.000000000 -0500
+++ gromacs-mpi.info.new    2015-12-13 18:30:25.000000000 -0500
@@ -1,6 +1,6 @@
 Package: gromacs-mpi
-Version: 5.1
-Revision: 102
+Version: 5.1.1
+Revision: 100
 Depends: <<
    gromacs1-mpi-shlibs (= %v-%r),
    fftw3-shlibs (>= 3.3.4-2),
@@ -38,7 +38,7 @@
 UseMaxBuildJobs: True
 Distribution: 10.9, 10.10, 10.11
 Source: mirror:custom:gromacs-%v.tar.gz
-Source-MD5: e5ba00d47c4c6dec107951a7d4605f31
+Source-MD5: 5c075141aa69dc4859cad0a55e61d35e
 PatchFile: gromacs-libxml2.patch
 PatchFile-MD5: 463830df2e50a5df49bbbd4b0299cf76
 CustomMirror: <<
@@ -48,7 +48,7 @@
 InfoTest: <<
  TestSuiteSize: medium
  TestSource: http://gerrit.gromacs.org/download/regressiontests-%v.tar.gz
- TestSource-MD5: 298db2fa20a6f4b02e758687ebf48ee8
+ TestSource-MD5: 614a74e9b143bda5476f87f4ce08eec0
  TestScript: <<
    #!/bin/sh -ev
    mv ../regressiontests-%v regressiontests-%v

[Jack Howarth]

Info file for gromacs-5.1.1-100

[Jack Howarth]

Info file for gromacs-mpi-5.1.1-100

[Hanspeter Niederstrasser]

Both the base and mpi variants check and fail to find OpenMPI:

-- Try OpenMP C flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP C flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [ ]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [/openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-Qopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-openmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-xopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [+Oopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-qsmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Try OpenMP CXX flag = [-mp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Failed
-- Could NOT find OpenMP (missing:  OpenMP_C_FLAGS OpenMP_CXX_FLAGS) 
CMake Warning at cmake/gmxManageOpenMP.cmake:78 (message):
  The compiler you are using does not support OpenMP parallelism.  This might
  hurt your performance a lot, in particular with GPUs.  Try using a more
  recent version, or a different compiler.  For now, we are proceeding by
  turning off OpenMP.
Call Stack (most recent call first):
  CMakeLists.txt:276 (include)

Also, DescUsage in gromacs-mpi says to use openmpi-dev, but there's no such package (it's just openmpi).

Lastly, why is the build sequence 'build', 'test', 'install', 'make clean', 'build again', 'test again', and finally 'install again' ?

[Jack Howarth]

The openmpi-dev build dependency is a hold-over from the 10.4 branch packaging of openmpi and should be openmpi instead. The complex build sequence is required to build both the single precision and the double precision versions of gromacs in a single build. This requires configuration/build/install/clean/configuration/build/install. The double precision binaries have the _d suffix added.

[Hanspeter Niederstrasser]

Added to the 10.9 tree.