From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id BCDF5138010 for ; Sun, 21 Oct 2012 12:53:00 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 6037FE055C; Sun, 21 Oct 2012 12:52:52 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id C5402E055C for ; Sun, 21 Oct 2012 12:52:51 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id C7D5E33D7CE for ; Sun, 21 Oct 2012 12:52:50 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 8C0D9E5436 for ; Sun, 21 Oct 2012 12:52:48 +0000 (UTC) From: "Reinis Danne" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Reinis Danne" Message-ID: <1350820287.d97c3c6df71927687fb184e5df2fbfb39b2e921d.rei4dan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/ambertools/files/, sci-chemistry/ambertools/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/ambertools/ChangeLog sci-chemistry/ambertools/ambertools-12.ebuild sci-chemistry/ambertools/files/ambertools-12-gentoo.patch X-VCS-Directories: sci-chemistry/ambertools/files/ sci-chemistry/ambertools/ X-VCS-Committer: rei4dan X-VCS-Committer-Name: Reinis Danne X-VCS-Revision: d97c3c6df71927687fb184e5df2fbfb39b2e921d X-VCS-Branch: master Date: Sun, 21 Oct 2012 12:52:48 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: befd3d02-9af9-4c01-b3fc-6c7ede8bbbce X-Archives-Hash: 45138159be8e1d4f1e416435ca94b1f0 commit: d97c3c6df71927687fb184e5df2fbfb39b2e921d Author: Reinis Danne gmail com> AuthorDate: Sun Oct 21 11:51:27 2012 +0000 Commit: Reinis Danne gmail com> CommitDate: Sun Oct 21 11:51:27 2012 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=d97c3c6d ambertools: Fix parallel tests --- sci-chemistry/ambertools/ChangeLog | 4 + sci-chemistry/ambertools/ambertools-12.ebuild | 11 ++-- .../ambertools/files/ambertools-12-gentoo.patch | 77 ++++++++++++++++++-- 3 files changed, 78 insertions(+), 14 deletions(-) diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog index 59197eb..fb9077d 100644 --- a/sci-chemistry/ambertools/ChangeLog +++ b/sci-chemistry/ambertools/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $ + 21 Oct 2012; Reinis Danne ambertools-12.ebuild, + files/ambertools-12-gentoo.patch: + Fix parallel tests. + *ambertools-12 (20 Oct 2012) 20 Oct 2012; Reinis Danne +ambertools-12.ebuild, diff --git a/sci-chemistry/ambertools/ambertools-12.ebuild b/sci-chemistry/ambertools/ambertools-12.ebuild index 31d6f8e..5b5a3db 100644 --- a/sci-chemistry/ambertools/ambertools-12.ebuild +++ b/sci-chemistry/ambertools/ambertools-12.ebuild @@ -103,13 +103,12 @@ src_configure() { gnu } -src_compile() { - cd "${S}"/AmberTools/src - emake -} - src_test() { - cd "${S}"/AmberTools/test + # Get the number of physical cores + local ncpus=$(grep "^core id" /proc/cpuinfo | sort -u | wc -l) + # Limit number of OpenMP threads + use openmp && export OMP_NUM_THREADS=$((1+${ncpus}/2)) + emake test } diff --git a/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch index b0e7cf4..e52e39d 100644 --- a/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch +++ b/sci-chemistry/ambertools/files/ambertools-12-gentoo.patch @@ -145,10 +145,10 @@ index e5c0ded..ce8f883 100644 cuda: @echo "$(AMBERTOOLS) has no CUDA-enabled components" diff --git a/AmberTools/src/configure2 b/AmberTools/src/configure2 -index 25d3f0a..1ad86e6 100755 +index 9ce5ef0..8dfcd3e 100755 --- a/AmberTools/src/configure2 +++ b/AmberTools/src/configure2 -@@ -387,11 +387,11 @@ omp_flag= +@@ -389,11 +389,11 @@ omp_flag= mpi_flag= lex=flex flibs_mkl= @@ -164,7 +164,7 @@ index 25d3f0a..1ad86e6 100755 #----------------------------------- # skip building of xleap? -@@ -618,13 +618,14 @@ gnu) +@@ -621,13 +621,14 @@ gnu) flibs_arch="-lgfortran -w" flibsf_arch= cc=gcc @@ -182,7 +182,7 @@ index 25d3f0a..1ad86e6 100755 staticflag='-static' # If -noopt has been requested, force lack of optimisation; -@@ -645,11 +646,11 @@ gnu) +@@ -648,11 +649,11 @@ gnu) foptflags="" else cnooptflags= @@ -197,7 +197,7 @@ index 25d3f0a..1ad86e6 100755 fi # Debugging options -@@ -2026,26 +2027,26 @@ EOF +@@ -2044,26 +2045,26 @@ EOF if [ "$sse" = "yes" ]; then enable_sse="--enable-sse2=yes" # --enable-avx=yes" fi @@ -243,7 +243,7 @@ index 25d3f0a..1ad86e6 100755 fftw3="\$(LIBDIR)/libfftw3.a" if [ "$mpi" = 'yes' ]; then flibs_fftw3="-lfftw3_mpi $flibs_fftw3" -@@ -2282,7 +2283,7 @@ LDFLAGS=$ldflags \$(CUSTOMBUILDFLAGS) +@@ -2300,7 +2301,7 @@ LDFLAGS=$ldflags \$(CUSTOMBUILDFLAGS) AMBERLDFLAGS=\$(AMBERBUILDFLAGS) LEX= $lex @@ -252,7 +252,7 @@ index 25d3f0a..1ad86e6 100755 AR= ar rv M4= $m4 RANLIB=$ranlib -@@ -2319,7 +2320,7 @@ CP=$localcp +@@ -2337,7 +2338,7 @@ CP=$localcp # Information about Fortran compilation: FC=$fc @@ -330,7 +330,7 @@ index 524dad8..5df64c6 100644 coord tc; diff --git a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py -index b01b891..24ea20f 100644 +index 0349ba9..c700beb 100644 --- a/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py +++ b/AmberTools/src/mmpbsa_py/MMPBSA_mods/amber_outputs.py @@ -210,7 +210,7 @@ class AmberOutput(object): @@ -1198,6 +1198,27 @@ index 3b49c55..61d0dc3 100644 clean: /bin/rm -f *.o *.mod *.d sqm$(SFX) +diff --git a/AmberTools/test/Makefile b/AmberTools/test/Makefile +index 27afe24..4796250 100644 +--- a/AmberTools/test/Makefile ++++ b/AmberTools/test/Makefile +@@ -3,14 +3,14 @@ include ../src/config.h + ###### Top-level targets, for general use: ############################ + + test: +- ./test_at_serial.sh ++ +./test_at_serial.sh + + test.parallel: + ./test_at_parallel.sh + + ###### Intermediate-level targets: ############################ + +-test.serial: clean is_amberhome_defined \ ++test.serial: is_amberhome_defined \ + test.nab test.ptraj test.cpptraj test.antechamber \ + test.leap test.resp test.pbsa test.mmpbsa test.parmed \ + test.ambpdb test.elsize test.chamber test.sqm test.rism1d \ diff --git a/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save b/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save index 3595375..1a0be46 100644 --- a/AmberTools/test/mmpbsa_py/01_Generalized_Born/energies.csv.save @@ -1223,6 +1244,19 @@ index 3595375..1a0be46 100644 +1,-60.9966,-35.1045,41.6205,-8.4650,-96.1011,33.1555,-62.9456 +diff --git a/AmberTools/test/nab/Makefile b/AmberTools/test/nab/Makefile +index 1bb2505..7459a15 100644 +--- a/AmberTools/test/nab/Makefile ++++ b/AmberTools/test/nab/Makefile +@@ -12,6 +12,8 @@ testrism: \ + rism_ion-noasymp rism_ion_pse1 rism_ion_pse3 rism_mdiis0 rism_mdiis1 \ + rism_sp rism_sp2 + ++.NOTPARALLEL: ++ + duplex_test:: + @./Run.duplex + diff --git a/AmberTools/test/nab/Run.rism_sp b/AmberTools/test/nab/Run.rism_sp index bd8471d..a88bf58 100755 --- a/AmberTools/test/nab/Run.rism_sp @@ -1249,3 +1283,30 @@ index a2b9521..11da8de 100755 ../dacdif -a 1e-6 guv.2.O.1.dx.check guv.2.O.1.dx ../dacdif -a 1e-6 guv.2.H1.2.dx.check guv.2.H1.2.dx ../dacdif -a 1e-6 guv.2.O.3.dx.check guv.2.O.3.dx +diff --git a/AmberTools/test/test_at_serial.sh b/AmberTools/test/test_at_serial.sh +index 15bb590..8fa52e3 100755 +--- a/AmberTools/test/test_at_serial.sh ++++ b/AmberTools/test/test_at_serial.sh +@@ -39,3 +39,9 @@ fi + + # save summary for later reporting: + tail -5 ${logfile} > ${logdir}/at_summary ++ ++if [ "${questionable_count}" -ne 0 -o "${error_count}" -ne 0 ] ++then ++ # Tests failed ++ exit 1 ++fi +diff --git a/Makefile b/Makefile +index 54ddfcb..643ba15 100644 +--- a/Makefile ++++ b/Makefile +@@ -30,7 +30,7 @@ clean.test: + test:: test.$(INSTALLTYPE) + + test.serial: +- -(cd AmberTools/test && $(MAKE) test) ++ (cd AmberTools/test && $(MAKE) test) + -@(if [ -n "$(BUILDAMBER)" ] ; then \ + cd test && $(MAKE) test; \ + echo "" ; \