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<title>[141098] trunk/dports/science/octopus</title>
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<dt>Revision</dt> <dd><a href="https://trac.macports.org/changeset/141098">141098</a></dd>
<dt>Author</dt> <dd>dstrubbe@macports.org</dd>
<dt>Date</dt> <dd>2015-10-10 12:54:07 -0700 (Sat, 10 Oct 2015)</dd>
</dl>
<h3>Log Message</h3>
<pre>octopus:
* Update to 5.0.0.
* New patches.
* Run testsuite with automatically determined job parallelism.
* Better MPI/ScaLAPACK error checking.</pre>
<h3>Modified Paths</h3>
<ul>
<li><a href="#trunkdportsscienceoctopusPortfile">trunk/dports/science/octopus/Portfile</a></li>
</ul>
<h3>Added Paths</h3>
<ul>
<li>trunk/dports/science/octopus/files/</li>
<li><a href="#trunkdportsscienceoctopusfilespatchm4metism4diff">trunk/dports/science/octopus/files/patch-m4-metis.m4.diff</a></li>
<li><a href="#trunkdportsscienceoctopusfilespatchtestsuitelinear_response05polarizabilitytestdiff">trunk/dports/science/octopus/files/patch-testsuite-linear_response-05-polarizability.test.diff</a></li>
</ul>
<h3>Removed Paths</h3>
<ul>
<li>trunk/dports/science/octopus/files/</li>
</ul>
</div>
<div id="patch">
<h3>Diff</h3>
<a id="trunkdportsscienceoctopusPortfile"></a>
<div class="modfile"><h4>Modified: trunk/dports/science/octopus/Portfile (141097 => 141098)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/octopus/Portfile 2015-10-10 19:45:40 UTC (rev 141097)
+++ trunk/dports/science/octopus/Portfile 2015-10-10 19:54:07 UTC (rev 141098)
</span><span class="lines">@@ -5,8 +5,7 @@
</span><span class="cx"> PortGroup mpi 1.0
</span><span class="cx">
</span><span class="cx"> name octopus
</span><del>-version 4.1.2
-revision 4
</del><ins>+version 5.0.0
</ins><span class="cx"> categories science
</span><span class="cx"> platforms darwin
</span><span class="cx"> license GPL-2+
</span><span class="lines">@@ -22,32 +21,42 @@
</span><span class="cx"> homepage http://www.tddft.org/programs/octopus
</span><span class="cx"> master_sites ${homepage}/download/${version}
</span><span class="cx">
</span><del>-checksums rmd160 0ce62e38bed99e436b83489375fe55e53e64a538 \
- sha256 c43ac301ff035caee667292841c5d9f166da986634cf2623e3f5a8aa86fe7a69
</del><ins>+checksums rmd160 2015e1adeab2ee00f87c0ee9a7eac21ee81b8666 \
+ sha256 47ed2a61022d20107bd9d8b05b65483fa280519833e93f2c79bbb51b8e3bea8b
</ins><span class="cx">
</span><del>-# dragonegg freezes when building; no acceptable way to set FCCPP for gcc5 or gcc6;
-# clang versions are unnecessary and may cause FCCPP trouble too
-mpi.setup require_fortran -dragonegg -gcc5 -gcc6 -clang
</del><ins>+# clang38: errors on operate.o
+compiler.blacklist macports-clang-3.8
+
+# dragonegg freezes when building; no acceptable way to set FCCPP for gcc5 or gcc6 though gfortran is ok;
+# clang versions are unnecessary
+# dragonegg34-gcc46 segfaults on varia.c
+mpi.setup require_fortran -dragonegg34 -gcc5 -gcc6 -clang
+# dragonegg
</ins><span class="cx"> compilers.enforce_fortran libxc
</span><span class="cx">
</span><span class="cx"> depends_lib port:atlas port:libxc port:fftw-3 port:gsl
</span><ins>+# openblas or accelerate/veclibfort instead of atlas?
</ins><span class="cx">
</span><span class="cx"> configure.args --with-libxc-prefix=${prefix} --with-blas=-lsatlas \
</span><span class="cx"> --disable-gdlib --without-sparskit --with-netcdf-prefix=no \
</span><span class="cx"> --with-etsf-io-prefix=no --with-berkeleygw-prefix=no \
</span><del>- --with-arpack=no --with-libfm=no --with-pfft-prefix=no \
</del><ins>+ --with-arpack=no --with-parpack=no --with-feast=no \
+ --with-isf-prefix=no --with-pnfft-prefix=no --with-metis-prefix=no \
+ --with-parmetis-prefix=no --with-libfm=no --with-pfft-prefix=no \
</ins><span class="cx"> --with-pspio-prefix=no --with-nfft=no --with-blacs=no \
</span><del>- --with-scalapack=no --enable-utils
</del><ins>+ --with-scalapack=no
</ins><span class="cx"> # configure will find and use these other libraries unless they are explicitly disabled
</span><span class="cx"> configure.optflags -O3
</span><span class="cx">
</span><span class="cx"> default_variants +newuoa
</span><span class="cx"> # FIXME: does fortran default variant not happen in time to make fftw-3 get
</span><span class="cx"> # installed +gcc48?
</span><ins>+# gfortran -> gfortran5?
</ins><span class="cx">
</span><del>-# Update test results for libxc 2.1.0 (distribution has results for libxc 2.0.0)
-patchfiles patch-testsuite-periodic_systems-07-tb09.test.diff \
- patch-testsuite-functionals-03-xc.test.diff
</del><ins>+# patches: (1) needed to make "--with-metis-prefix=no" work
+# (2) widen a tolerance so all tests pass
+patchfiles patch-configure.diff \
+ patch-testsuite-linear_response-05-polarizability.test.diff
</ins><span class="cx">
</span><span class="cx"> pre-fetch {
</span><span class="cx"> if {[fortran_active_variant_name fftw-3] eq ""} {
</span><span class="lines">@@ -56,42 +65,41 @@
</span><span class="cx"> }
</span><span class="cx"> }
</span><span class="cx">
</span><del>-pre-configure {
- # note: from version 5.0 the configure script will handle this
- if {[variant_isset llvm]} {
- configure.args-append FCCPP="${configure.cc} -x c -E -ansi"
- } elseif {[string match *cpp-mp-* ${configure.cpp}]} {
- # gcc's cpp will not accept the -E flag
- configure.args-append FCCPP="${configure.cpp} -ansi"
- } else {
- # clang
- configure.args-append FCCPP="${configure.cc} -E -ansi"
- }
-}
-
</del><span class="cx"> if {[mpi_variant_isset]} {
</span><span class="cx"> configure.args-delete --disable-mpi
</span><del>- configure.args-append --enable-mpi --without-external_zoltan
</del><ins>+ configure.args-append --enable-mpi
</ins><span class="cx"> }
</span><span class="cx">
</span><span class="cx"> # More options that could be added:
</span><del>-# variants: berkeleygw, openmp, threads (for fftw, atlas?), arpack
-# no way to turn off PAPI.
</del><ins>+# variants: berkeleygw, openmp, threads (for fftw, atlas?), (p)arpack, maxdim4, metis, parmetis
+# no way to turn off PAPI, but there is no port for this anyway.
</ins><span class="cx">
</span><span class="cx"> # libxc does not have universal variant, so octopus cannot either
</span><span class="cx"> universal_variant no
</span><span class="cx">
</span><span class="cx"> test.run yes
</span><del>-test.target check-full
</del><ins>+test.target check
</ins><span class="cx">
</span><span class="cx"> pre-test {
</span><ins>+ # emulate some behavior from octopus development version
+ if {![catch {sysctl hw.ncpu} result]} {
+ if {[mpi_variant_isset]} {
+ set njobs [expr {$result/4}]
+ } else {
+ set njobs $result
+ }
+ } else {
+ set njobs 1
+ }
+ test.env-append OCT_TEST_NJOBS=$njobs
+ ui_msg "Running testsuite with $njobs jobs in parallel"
+
</ins><span class="cx"> if {[mpi_variant_isset]} {
</span><span class="cx"> test.env-append MPIEXEC=${prefix}/bin/${mpi.exec}
</span><span class="cx"> }
</span><del>- if {[variant_isset openmpi] || [variant_isset openmpi-devel]} {
- ui_msg "Note: Test with OpenMPI may hang after periodic_systems/03-sodium_chain.02-ground_state_disp.inp."
- ui_msg "This does not seem necessarily to indicate a problem with the build."
- }
</del><ins>+
+ # test infrastructure uses /bin/ps for job parallelism which is forbidden by sandboxing
+ append portsandbox_profile " (allow process-exec (literal \"/bin/ps\") (with no-profile))"
</ins><span class="cx"> }
</span><span class="cx">
</span><span class="cx"> variant newuoa description {Build with internal newuoa library for optimal control} {
</span><span class="lines">@@ -129,13 +137,24 @@
</span><span class="cx"> configure.args-append --with-blacs=-lscalapack
</span><span class="cx"> depends_lib-append port:scalapack
</span><span class="cx">
</span><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"> mpi.setup require
</span><span class="cx"> # FIXME: this unnecessarily enforces scalapack had same C compiler as we are using.
</span><span class="cx"> # also, if +scalapack but no MPI is used, an internal error from active_variants
</span><span class="cx"> # is produced rather than saying you need MPI or just adding it to variants as intended.
</span><ins>+ # Error: active_variants: Error: invalid port depspec ''
+ # Error: expecting either: port or (bin|lib|path):foo:port
</ins><span class="cx"> mpi.enforce_variant scalapack
</span><span class="cx"> }
</span><span class="cx">
</span><span class="cx"> livecheck.type regex
</span><span class="cx"> livecheck.url ${homepage}/wiki/index.php/Main_Page
</span><span class="cx"> livecheck.regex ${name} (\[0-9.\]+)
</span><ins>+
+
+# Match beta xxx :
+# Calculated value : 0.38356457E+00
</ins></span></pre></div>
<a id="trunkdportsscienceoctopusfilespatchm4metism4diff"></a>
<div class="addfile"><h4>Added: trunk/dports/science/octopus/files/patch-m4-metis.m4.diff (0 => 141098)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/octopus/files/patch-m4-metis.m4.diff (rev 0)
+++ trunk/dports/science/octopus/files/patch-m4-metis.m4.diff 2015-10-10 19:54:07 UTC (rev 141098)
</span><span class="lines">@@ -0,0 +1,39 @@
</span><ins>+--- m4/metis.m4.orig 2015-02-26 16:20:51.000000000 -0500
++++ m4/metis.m4 2015-10-09 10:46:57.000000000 -0400
+@@ -15,7 +15,7 @@
+ ## Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA
+ ## 02110-1301, USA.
+ ##
+-## $Id: metis.m4 13225 2015-02-26 21:20:25Z dstrubbe $
++## $Id: metis.m4 14659 2015-10-09 14:17:20Z dstrubbe $
+ ##
+
+ AC_DEFUN([ACX_PATH_METIS], [
+@@ -31,15 +31,15 @@
+ AC_REQUIRE([AC_PROG_CC])
+
+ AC_ARG_WITH([metis-prefix],
+- [AC_HELP_STRING([--with-metis-prefix],
++ [AS_HELP_STRING([--with-metis-prefix=DIR],
+ [Directory where external METIS library was installed (must be single-precision)])])
+
+ case $with_metis_prefix in
+- no ) acx_external_metis=disabled ;;
++ no ) acx_external_metis=no ;;
+ "") with_metis_prefix="/usr" ;;
+ esac
+
+- if test x"$acx_external_metis" != xdisabled; then
++ if test x"$acx_external_metis" != xno; then
+
+ dnl Backup CFLAGS and LIBS
+ acx_metis_save_CFLAGS="$CFLAGS"
+@@ -86,6 +86,8 @@
+
+ CFLAGS="$acx_metis_save_CFLAGS"
+ LIBS="$acx_metis_save_LIBS"
++ else
++ AC_MSG_RESULT([disabled])
+ fi
+
+ if test x"$acx_external_metis" = xno ; then
</ins></span></pre></div>
<a id="trunkdportsscienceoctopusfilespatchtestsuitelinear_response05polarizabilitytestdiff"></a>
<div class="addfile"><h4>Added: trunk/dports/science/octopus/files/patch-testsuite-linear_response-05-polarizability.test.diff (0 => 141098)</h4>
<pre class="diff"><span>
<span class="info">--- trunk/dports/science/octopus/files/patch-testsuite-linear_response-05-polarizability.test.diff (rev 0)
+++ trunk/dports/science/octopus/files/patch-testsuite-linear_response-05-polarizability.test.diff 2015-10-10 19:54:07 UTC (rev 141098)
</span><span class="lines">@@ -0,0 +1,11 @@
</span><ins>+--- testsuite/linear_response/05-polarizability.test (revision 14663)
++++ testsuite/linear_response/05-polarizability.test (working copy)
+@@ -35,7 +35,7 @@
+ match ; Born charge diff; GREPFIELD(em_resp_fd/Born_charges, "Discrepancy", 3, 4) ; 0.003975
+
+ # These values should all be zero by symmetry.
+-Precision : 0.6
++Precision : 0.75
+ match ; beta xxx ; GREPFIELD(em_resp_fd/beta, "beta xxx", 3); -0.325014735
+ Precision : 0.3
+ match ; beta zxy ; GREPFIELD(em_resp_fd/beta, "beta zxy", 3); 0.316842919
</ins></span></pre>
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