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<title>[152561] trunk/dports/science/berkeleygw</title>
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<dt>Revision</dt> <dd><a href="https://trac.macports.org/changeset/152561">152561</a></dd>
<dt>Author</dt> <dd>dstrubbe@macports.org</dd>
<dt>Date</dt> <dd>2016-09-12 10:31:18 -0700 (Mon, 12 Sep 2016)</dd>
</dl>
<h3>Log Message</h3>
<pre>berkeleygw: Update to version 1.2.0. FFTW-3 is now used by default; +fftw2 uses FFTW-2. Take advantage of fixes that enable broader cpp usage. Better scalapack compatibility checking. A couple of patches to build system. Use gsed in testsuite. Enable OpenMP threads.</pre>
<h3>Modified Paths</h3>
<ul>
<li><a href="#trunkdportsscienceberkeleygwPortfile">trunk/dports/science/berkeleygw/Portfile</a></li>
</ul>
<h3>Added Paths</h3>
<ul>
<li>trunk/dports/science/berkeleygw/files/</li>
<li><a href="#trunkdportsscienceberkeleygwfilespatchCommoncommonrulesmkdiff">trunk/dports/science/berkeleygw/files/patch-Common-common-rules.mk.diff</a></li>
<li><a href="#trunkdportsscienceberkeleygwfilespatchMakefilediff">trunk/dports/science/berkeleygw/files/patch-Makefile.diff</a></li>
</ul>
</div>
<div id="patch">
<h3>Diff</h3>
<a id="trunkdportsscienceberkeleygwPortfile"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/berkeleygw/Portfile (152560 => 152561)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/berkeleygw/Portfile 2016-09-12 17:22:38 UTC (rev 152560)
+++ trunk/dports/science/berkeleygw/Portfile 2016-09-12 17:31:18 UTC (rev 152561)
</span><span class="lines">@@ -6,8 +6,7 @@
</span><span class="cx"> PortGroup linear_algebra 1.0
</span><span class="cx">
</span><span class="cx"> name berkeleygw
</span><del>-version 1.1-beta2
-revision 1
</del><ins>+version 1.2.0
</ins><span class="cx"> categories science
</span><span class="cx"> platforms darwin
</span><span class="cx"> license BSD
</span><span class="lines">@@ -21,15 +20,17 @@
</span><span class="cx"> homepage http://www.berkeleygw.org
</span><span class="cx"> master_sites ${homepage}/releases
</span><span class="cx">
</span><del>-checksums rmd160 7e1ce392da45282ef878ed1a53b34184d96c7ca2 \
- sha256 83deea17ccbd50e9e505f69fadf858595793f9b853ec012722659100d5cf8885
</del><ins>+checksums rmd160 26933a24c10ba03457c667bc5f2d3ca21df2a436 \
+ sha256 1305dc8587af666fe437bc2561a9106b2b0bcdbe91980b8f1ae7bbd491ce1e25
</ins><span class="cx">
</span><span class="cx"> distfiles BGW-${version}.tar.gz
</span><span class="cx"> # needed for case-sensitive filesystems
</span><span class="cx"> worksrcdir BerkeleyGW-${version}
</span><span class="cx">
</span><del>-depends_lib port:fftw
-# fftw port always has a Fortran variant
</del><ins>+depends_lib port:fftw-3
+if {![variant_isset fftw2]} {
+ compilers.enforce_some_fortran fftw-3
+}
</ins><span class="cx">
</span><span class="cx"> # May fail with +mpich +gcc5. Use +mpich +gfortran instead.
</span><span class="cx"> # In file included from /opt/local/include/mpich-gcc5/mpi.h:2231:0,
</span><span class="lines">@@ -38,34 +39,36 @@
</span><span class="cx"> # # error 'Please use the same version of GCC and g++ for compiling MPICH and user MPI programs'
</span><span class="cx"> # ^
</span><span class="cx">
</span><del>-# WHAT DO WE DO WHEN meaning of 'gfortran' is updated? No record... Must rename to gfortran5 etc.
</del><ins>+# WHAT DO WE DO WHEN meaning of 'gfortran' is updated? No record... Maybe rename to gfortran5 etc. ?
</ins><span class="cx">
</span><span class="cx"> # test hangs in Epsilon with OpenMPI, for unknown reason.
</span><del>-# no appropriate way to set cpp for gcc5, gcc6, or clang
</del><span class="cx"> # dragonegg fails to link with error
</span><span class="cx"> # Undefined symbols for architecture x86_64:
</span><span class="cx"> # "_llvm.objectsize.i64", referenced from:
</span><span class="cx"> # _spg_get_international in libsymspg.a(spglib.o)
</span><span class="cx"> # _spg_get_schoenflies in libsymspg.a(spglib.o)
</span><span class="cx"> compilers.choose fc cc cxx cpp
</span><del>-mpi.setup require_fortran -dragonegg -openmpi -openmpi_devel
</del><ins>+mpi.setup require_fortran -dragonegg -openmpi -openmpi_devel -gfortran -clang -llvm
+# FIXME: +gfortran just needs smarter setting of cpp to the one from gcc;
+#clang and llvm only useful with +g95 currently (which is useless)
</ins><span class="cx">
</span><span class="cx"> # just for cpp
</span><del>-if {[variant_isset g95] || [variant_isset gcc5] || [variant_isset gcc6] || [variant_isset gfortran]} {
</del><ins>+if {[variant_isset g95]} {
</ins><span class="cx"> depends_build-append port:llvm-gcc42
</span><span class="cx"> }
</span><span class="cx">
</span><span class="cx"> # FIXME: this unnecessarily enforces scalapack also had same C compiler as we are using.
</span><span class="cx"> if {[mpi_variant_isset]} {
</span><span class="cx"> depends_lib-append port:scalapack
</span><del>- mpi.enforce_variant scalapack
</del><ins>+ if {![mpi_variant_isset]} {
+ ui_error "+scalapack requires an MPI variant. Choose +mpich, +mpich_devel, +openmpi, or +openmpi_devel."
+ return -code error "+scalapack requires an MPI variant."
+ }
</ins><span class="cx"> }
</span><span class="cx">
</span><span class="cx"> # fftw is not universal
</span><span class="cx"> universal_variant no
</span><span class="cx">
</span><del>-# FIXME: add options for threads
-
</del><span class="cx"> configure {
</span><span class="cx"> system -W ${worksrcpath} "sed 's|/opt/local|${prefix}|' < config/generic.serial.macos.mk > arch.mk"
</span><span class="cx"> reinplace -W ${worksrcpath} "s|MATHFLAG += -DHDF5||" arch.mk
</span><span class="lines">@@ -74,6 +77,9 @@
</span><span class="cx"> }
</span><span class="cx"> }
</span><span class="cx">
</span><ins>+patchfiles patch-Common-common-rules.mk.diff \
+ patch-Makefile.diff
+
</ins><span class="cx"> build.target all-flavors
</span><span class="cx"> use_parallel_build yes
</span><span class="cx">
</span><span class="lines">@@ -81,16 +87,19 @@
</span><span class="cx">
</span><span class="cx"> test.run yes
</span><span class="cx">
</span><del>-# known problems to be fixed: Graphene incorrectly has kernel_k_interpolation.
-# Si2-SAPO/sapo.inp has pointer being freed was not allocated
</del><span class="cx">
</span><ins>+#depends_build port:gsed
</ins><span class="cx"> pre-test {
</span><ins>+ reinplace -W ${worksrcpath}/testsuite "s|sed|gsed|" Graphene/Graphene.test Graphene/Graphene_3D.test \
+ Si-EPM/Si.test Si-EPM/Si_cplx_spin.test
+
</ins><span class="cx"> if {[mpi_variant_isset]} {
</span><del>- test.args-append TESTSCRIPT="MPIEXEC=${prefix}/bin/${mpi.exec} make check-parallel" PARAFLAG=-DMPI
</del><ins>+ test.args-append TESTSCRIPT="MPIEXEC=${prefix}/bin/${mpi.exec} make check-parallel"
</ins><span class="cx"> test.target check-jobscript
</span><span class="cx">
</span><ins>+ # FIXME: what about with threads? set OMP_NUM_THREADS=2 and divide ncpus by 2.
</ins><span class="cx"> if {![catch {sysctl hw.ncpu} ncpus]} {
</span><del>- test.env-append OCT_TEST_NJOBS=$ncpus
</del><ins>+ test.env-append BGW_TEST_MPI_NPROCS=$ncpus
</ins><span class="cx"> }
</span><span class="cx"> ui_msg "Running testsuite in parallel with $ncpus MPI tasks"
</span><span class="cx"> } else {
</span><span class="lines">@@ -111,19 +120,23 @@
</span><span class="cx"> set mathflag "${mathflag} -DHDF5"
</span><span class="cx"> }
</span><span class="cx">
</span><del>- if {[variant_isset fftw3]} {
- build.args-append FFTWLIB="-L${prefix}/lib/ -lfftw3"
</del><ins>+ if {[variant_isset fftw2]} {
+ build.args-append FFTWLIB="-L${prefix}/lib/ -ldfftw"
+ } else {
+ if {[variant_isset threads]} {
+ build.args-append FFTWLIB="-L${prefix}/lib/ -lfftw3 -lfftw3_threads"
+ } else {
+ build.args-append FFTWLIB="-L${prefix}/lib/ -lfftw3"
+ }
</ins><span class="cx"> set mathflag "${mathflag} -DUSEFFTW3"
</span><del>- } else {
- build.args-append FFTWLIB="-L${prefix}/lib/ -ldfftw"
</del><span class="cx"> }
</span><span class="cx">
</span><del>- if {[variant_isset g95] || [variant_isset gcc5] || [variant_isset gcc6] || [variant_isset gfortran]} {
</del><ins>+ if {[variant_isset g95]} {
</ins><span class="cx"> set configure.cpp llvm-cpp-4.2
</span><span class="cx"> }
</span><span class="cx">
</span><span class="cx"> if {[variant_isset g95]} {
</span><del>- build.args-append COMPFLAG="-DG95" FCPP="${configure.cpp} -P -ansi" \
</del><ins>+ build.args-append COMPFLAG="-DG95" FCPP="${configure.cpp} -P -C" \
</ins><span class="cx"> F90free="${prefix}/bin/g95 -ffree-form -ffree-line-length-huge -fno-second-underscore" \
</span><span class="cx"> MOD_OPT="-fmod="
</span><span class="cx"> # test, destroot args needed just to avoid trying to build in the test/openmp directory unnecessarily
</span><span class="lines">@@ -131,19 +144,30 @@
</span><span class="cx"> destroot.args-append COMPFLAG="-DG95"
</span><span class="cx"> } else {
</span><span class="cx"> # gcc is default in arch.mk so most things do not need to be modified
</span><del>- build.args-append FCPP="${configure.cpp} -ansi" \
</del><ins>+ build.args-append FCPP="${configure.cpp} -C" \
</ins><span class="cx"> F90free="${configure.fc} -ffree-form -ffree-line-length-none -fno-second-underscore"
</span><span class="cx"> }
</span><span class="cx">
</span><ins>+ if {[variant_isset threads]} {
+ set paraflag "-DOMP"
+ } else {
+ set paraflag ""
+ }
+
</ins><span class="cx"> if {[mpi_variant_isset]} {
</span><span class="cx"> set mathflag "${mathflag} -DUSESCALAPACK"
</span><del>- build.args-append PARAFLAG="-DMPI" C_PARAFLAG="-DPARA" SCALAPACKLIB="-L${prefix}/lib/ -lscalapack"
</del><ins>+ set paraflag "${paraflag} -DMPI"
+ build.args-append C_PARAFLAG="-DPARA" SCALAPACKLIB="-L${prefix}/lib/ -lscalapack"
</ins><span class="cx"> }
</span><span class="cx">
</span><del>- build.args-append MATHFLAG="${mathflag}"
- test.args-append MATHFLAG="${mathflag}"
</del><ins>+ build.args-append MATHFLAG="${mathflag}" PARAFLAG="${paraflag}"
+ test.args-append MATHFLAG="${mathflag}" PARAFLAG="${paraflag}"
</ins><span class="cx"> }
</span><span class="cx">
</span><ins>+variant threads description {Build with OpenMP support} conflicts g95 {
+ set configure.fc "${configure.fc} -fopenmp"
+}
+
</ins><span class="cx"> variant debug description {Add debug flags for more checking and output, but slower runs.} {
</span><span class="cx"> build.args-append DEBUGFLAG="-DDEBUG -DVERBOSE"
</span><span class="cx"> }
</span><span class="lines">@@ -154,9 +178,9 @@
</span><span class="cx"> compilers.enforce_fortran hdf5
</span><span class="cx"> }
</span><span class="cx">
</span><del>-variant fftw3 description {Build with FFTW-3 rather than FFTW-2 for better performance} {
- depends_lib-replace port:fftw port:fftw-3
- compilers.enforce_some_fortran fftw-3
</del><ins>+variant fftw2 description {Build with FFTW-2} {
+ depends_lib-replace port:fftw-3 port:fftw
+ # fftw port always has a Fortran variant
</ins><span class="cx"> }
</span><span class="cx">
</span><span class="cx"> livecheck.type none
</span></span></pre></div>
<a id="trunkdportsscienceberkeleygwfilespatchCommoncommonrulesmkdiff"></a>
<div class="addfile"><h4>Added: trunk/dports/science/berkeleygw/files/patch-Common-common-rules.mk.diff (0 => 152561)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/berkeleygw/files/patch-Common-common-rules.mk.diff (rev 0)
+++ trunk/dports/science/berkeleygw/files/patch-Common-common-rules.mk.diff 2016-09-12 17:31:18 UTC (rev 152561)
</span><span class="lines">@@ -0,0 +1,9 @@
</span><ins>+--- Common/common-rules.mk.orig 2016-09-09 10:35:06.000000000 -0700
++++ Common/common-rules.mk 2016-09-09 10:35:16.000000000 -0700
+@@ -333,4 +333,5 @@
+ clean-keepmod clean-keepmod-common \
+ clean-keepmod-utilities clean-cpp clean-wfnutils \
+ qhull clean-qhull cleanall-qhull clean-keepmod-qhull \
+-abi2bgw clean-abi2bgw cleanall-abi2bgw clean-keepmod-abi2bgw
++abi2bgw clean-abi2bgw cleanall-abi2bgw clean-keepmod-abi2bgw \
++sapo epm icm utilities
</ins></span></pre></div>
<a id="trunkdportsscienceberkeleygwfilespatchMakefilediff"></a>
<div class="addfile"><h4>Added: trunk/dports/science/berkeleygw/files/patch-Makefile.diff (0 => 152561)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/berkeleygw/files/patch-Makefile.diff (rev 0)
+++ trunk/dports/science/berkeleygw/files/patch-Makefile.diff 2016-09-12 17:31:18 UTC (rev 152561)
</span><span class="lines">@@ -0,0 +1,11 @@
</span><ins>+--- Makefile.orig 2016-09-09 18:09:20.000000000 -0400
++++ Makefile 2016-09-09 18:09:31.000000000 -0400
+@@ -106,7 +106,7 @@
+ manual: printsvninfo
+ bin/assemble_manual.sh > manual.html
+
+-install: all-flavors
++install: all
+ ifdef INSTDIR
+ mkdir -p $(INSTDIR)/bin
+ install bin/*.x $(INSTDIR)/bin/
</ins></span></pre>
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