Hello community, here is the log from the commit of package votca-csg for openSUSE:Factory checked in at 2017-09-04 12:39:15 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Comparing /work/SRC/openSUSE:Factory/votca-csg (Old) and /work/SRC/openSUSE:Factory/.votca-csg.new (New) ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "votca-csg" Mon Sep 4 12:39:15 2017 rev:10 rq:520513 version:1.4.1 Changes: -------- --- /work/SRC/openSUSE:Factory/votca-csg/votca-csg.changes 2017-02-03 20:04:45.401324044 +0100 +++ /work/SRC/openSUSE:Factory/.votca-csg.new/votca-csg.changes 2017-09-04 12:39:18.370325429 +0200 @@ -1,0 +2,13 @@ +Sun Sep 3 13:26:48 UTC 2017 - [email protected] + +- Upgrade to 1.4.1 + * fix pkg-config files + * fix build with gmx-2017 + * added CSG_MDRUN_OPTS to run_gromacs.sh + * table_to_tab.pl: fix forces for LAMMPS + * csg_inverse: warn users of bug #179 + * run_gromacs.sh: check nstxout-compressed + * details: https://github.com/votca/csg/blob/master/CHANGELOG.md + + +------------------------------------------------------------------- Old: ---- votca-csg-1.4.tar.gz votca-csg-manual-1.4.pdf votca-csg-tutorials-1.4.tar.gz New: ---- votca-csg-1.4.1.tar.gz votca-csg-manual-1.4.1.pdf votca-csg-tutorials-1.4.1.tar.gz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Other differences: ------------------ ++++++ votca-csg.spec ++++++ --- /var/tmp/diff_new_pack.EuxP7B/_old 2017-09-04 12:39:19.634147621 +0200 +++ /var/tmp/diff_new_pack.EuxP7B/_new 2017-09-04 12:39:19.650145370 +0200 @@ -2,7 +2,7 @@ # spec file for package votca-csg # # Copyright (c) 2016 SUSE LINUX GmbH, Nuernberg, Germany. -# Copyright (c) 2013-2016 Christoph Junghans +# Copyright (c) 2013-2017 Christoph Junghans # # All modifications and additions to the file contributed by third parties # remain the property of their copyright owners, unless otherwise agreed @@ -17,8 +17,8 @@ # Name: votca-csg -Version: 1.4 -%define uversion 1.4 +Version: 1.4.1 +%define uversion 1.4.1 Release: 0 Summary: VOTCA coarse-graining engine License: Apache-2.0 ++++++ votca-csg-1.4.tar.gz -> votca-csg-1.4.1.tar.gz ++++++ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.4/.travis.yml new/csg-1.4.1/.travis.yml --- old/csg-1.4/.travis.yml 2016-10-29 18:47:47.000000000 +0200 +++ new/csg-1.4.1/.travis.yml 2017-09-03 01:45:18.000000000 +0200 @@ -33,14 +33,15 @@ - cm-super - doxygen - graphviz - - python-numpy + - ghostscript - gnuplot-nox - octave env: global: - - HDF5_VERSION=1.8.14 - - GMX_MAX_THREADS=8 + - HDF5_VERSION=1.8.18 + - GMX_MAX_THREADS=4 + - CSG_MDRUN_OPTS="-ntmpi 4" - CCACHE_CPP2=yes #for clang - GVER=4.8 matrix: #NINJA=1 is currently not support by Travis' cmake, enable when >=2.8.9 @@ -51,8 +52,8 @@ - WALL=yes GMX_DOUBLE=yes J=4 - WALL=yes GMX_VERSION=5.0 J=4 - WALL=yes GMX_VERSION=5.0 GMX_DOUBLE=yes J=4 - - WALL=yes GMX_VERSION=2016 J=4 - - WALL=yes GMX_VERSION=2016 GMX_DOUBLE=yes J=4 + - WALL=yes GMX_VERSION=5.1 J=4 + - WALL=yes GMX_VERSION=5.1 GMX_DOUBLE=yes J=4 - WALL=yes GMX_VERSION=9999 J=4 - WALL=yes GMX_VERSION=9999 GMX_DOUBLE=yes J=4 - MINIMAL=yes J=4 @@ -88,7 +89,7 @@ - wget https://raw.githubusercontent.com/votca/buildutil/master/build.sh && chmod 755 build.sh - mkdir -p "$HOME/votca/src" - if [[ ${MINIMAL} != yes ]]; then - wget -qO- https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_VERSION}/src/hdf5-${HDF5_VERSION}.tar.gz | tar -xz && + wget -qO- https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_VERSION%.*}/hdf5-${HDF5_VERSION}/src/hdf5-${HDF5_VERSION}.tar.gz | tar -xz && cd hdf5-${HDF5_VERSION} && ./configure --prefix=$HOME/hdf5 && make -j4 &> /dev/null && make install && cd ..; fi - if [[ ${GMX_VERSION} = 9999 ]]; then @@ -98,9 +99,10 @@ fi - if [[ ${MAN} ]]; then git clone --depth=1 https://github.com/votca/doxygen.git "$HOME/votca/src/devdoc"; fi - if [[ ${GVER} ]]; then export CC=gcc-${GVER}; export CXX=g++-${GVER}; fi + - pip install --user numpy script: - - PATH="$HOME/hdf5:$PATH" ./build.sh -Wu $([[ ${TRAVIS_BRANCH} = stable ]] || echo "--dev") --prefix "$HOME/votca" + - PATH="$HOME/hdf5:$PATH" ./build.sh -Wu --prefix "$HOME/votca" ${TYPE:+-DCMAKE_BUILD_TYPE=${TYPE}} ${TEST:+--runtest=$TEST} ${WERROR:+--warn-to-errors} -DWITH_H5MD=ON ${MINIMAL:+--minimal} ${MAN:+--devdoc} ${J:+-j$J} ${BDIR:+--builddir=$BDIR} ${NINJA:+--ninja} ${WALL:+--Wall} ${GMX_VERSION:+--gmx-release ${GMX_VERSION}} @@ -132,4 +134,5 @@ notifications: email: - - [email protected] + recipients: #encrypted [email protected] so that fork don't notify us (travis-ci/travis-ci#6100) + secure: 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 diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.4/CHANGELOG.md new/csg-1.4.1/CHANGELOG.md --- old/csg-1.4/CHANGELOG.md 2016-10-29 18:47:47.000000000 +0200 +++ new/csg-1.4.1/CHANGELOG.md 2017-09-03 01:45:18.000000000 +0200 @@ -1,9 +1,19 @@ For more detailed information about the changes see the history of the [repository](https://github.com/votca/csg/commits/master). +## Version 1.4.1 (released 02.09.17) +* fix pkg-config files +* fix build with gmx-2017 +* added CSG_MDRUN_OPTS to run_gromacs.sh +* table_to_tab.pl: fix forces for LAMMPS +* csg_inverse: warn users of bug #179 +* run_gromacs.sh: check nstxout-compressed +* tools: fix parallel build with mkl + ## Version 1.4 _SuperKurt_ (released 29.10.16) * added cibi tutorial and manual section * install mkl headers if mkl is enabled * updated copyright +* xmltopologyparser: tokenize on \n and \t as well (#195) * tools: added support for boost-1.62 ## Version 1.4_rc1 (released 26.09.16) diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.4/CMakeLists.txt new/csg-1.4.1/CMakeLists.txt --- old/csg-1.4/CMakeLists.txt 2016-10-29 18:47:47.000000000 +0200 +++ new/csg-1.4.1/CMakeLists.txt 2017-09-03 01:45:18.000000000 +0200 @@ -2,7 +2,7 @@ project(votca-csg) -set(PROJECT_VERSION "1.4") +set(PROJECT_VERSION "1.4.1") set(PROJECT_CONTACT "[email protected]") string(REGEX REPLACE "^[1-9]+\\.([1-9]+).*$" "\\1" SOVERSION "${PROJECT_VERSION}") if (NOT ${SOVERSION} MATCHES "[1-9]+") diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.4/share/doc/Doxyfile.in new/csg-1.4.1/share/doc/Doxyfile.in --- old/csg-1.4/share/doc/Doxyfile.in 2016-10-29 18:47:47.000000000 +0200 +++ new/csg-1.4.1/share/doc/Doxyfile.in 2017-09-03 01:45:18.000000000 +0200 @@ -31,7 +31,7 @@ # This could be handy for archiving the generated documentation or # if some version control system is used. -PROJECT_NUMBER = @VERSION@ +PROJECT_NUMBER = @PROJECT_VERSION@ # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) # base path where the generated documentation will be put. diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.4/share/scripts/inverse/functions_common.sh new/csg-1.4.1/share/scripts/inverse/functions_common.sh --- old/csg-1.4/share/scripts/inverse/functions_common.sh 2016-10-29 18:47:47.000000000 +0200 +++ new/csg-1.4.1/share/scripts/inverse/functions_common.sh 2017-09-03 01:45:18.000000000 +0200 @@ -911,6 +911,17 @@ } export -f check_for_obsolete_xml_options +check_for_bug_179() { #check if shell has bug #179 + simple_fct() { echo "Shell OK";} + export -f simple_fct + if [[ $(perl -e '$x=`bash -c "simple_fct"`; print $x' 2> /dev/null) != "Shell OK" ]]; then + die "Your shell seems to exhibit bug #179 (see https://github.com/votca/csg/issues/179)\nIn short, as a workaround you want to run 'sudo ln -fs bash /bin/sh' and re-login!" + fi + unset simple_fct +} +check_for_bug_179 +unset check_for_bug_179 + command_not_found_handle() { #print and error message if a command or a function was not found die "Command/function $1 not found (when calling from csg_call you might need to add --simprog option or set cg.inverse.program in the xml file)" } diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.4/share/scripts/inverse/run_gromacs.sh new/csg-1.4.1/share/scripts/inverse/run_gromacs.sh --- old/csg-1.4/share/scripts/inverse/run_gromacs.sh 2016-10-29 18:47:47.000000000 +0200 +++ new/csg-1.4.1/share/scripts/inverse/run_gromacs.sh 2017-09-03 01:45:18.000000000 +0200 @@ -55,7 +55,10 @@ #in a presimulation usually do care about traj and temperature check_temp || die "${0##*/}: check of tempertures failed" if [[ $traj == *.xtc ]]; then - [[ $(get_simulation_setting nstxtcout 0) -eq 0 ]] && die "${0##*/}: trajectory type (cg.inverse.gromacs.traj) is '${traj##*.}', but nstxtcout is 0 in $mdp. Please check the setting again and remove the current step." + #XXX is returned if nstxout-compressed is not in mdp file + nstxtcout=$(get_simulation_setting nstxout-compressed XXX) + [[ ${nstxtcout} = XXX ]] && nstxtcout=$(get_simulation_setting nstxtcout 0) + [[ ${nstxtcout} -eq 0 ]] && die "${0##*/}: trajectory type (cg.inverse.gromacs.traj) is '${traj##*.}', but nstxtcout is 0 in $mdp. Please check the setting again and remove the current step." elif [[ $traj == *.trr ]]; then [[ $(get_simulation_setting nstxout 0) -eq 0 ]] && die "${0##*/}: trajectory type (cg.inverse.gromacs.traj) is '${traj##*.}', but nstxout is 0 in $mdp. Please check the setting again and remove the current step." else @@ -108,6 +111,11 @@ mdrun_opts+=" -nsteps $CSG_MDRUN_STEPS" fi +if [[ ${CSG_MDRUN_OPTS} ]]; then + msg --color blue --to-stderr "Appending ${CSG_MDRUN_OPTS} to mdrun options" + mdrun_opts+=" ${CSG_MDRUN_OPTS}" +fi + #see can run grompp again as checksum of tpr does not appear in the checkpoint critical ${grompp[@]} -n "${index}" -f "${mdp}" -p "$topol_in" -o "$tpr" -c "${conf}" ${grompp_opts} 2>&1 | gromacs_log "${grompp[@]} -n "${index}" -f "${mdp}" -p "$topol_in" -o "$tpr" -c "${conf}" ${grompp_opts}" [[ -f $tpr ]] || die "${0##*/}: gromacs tpr file '$tpr' not found after runing grompp" diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.4/share/scripts/inverse/table_to_tab.pl new/csg-1.4.1/share/scripts/inverse/table_to_tab.pl --- old/csg-1.4/share/scripts/inverse/table_to_tab.pl 2016-10-29 18:47:47.000000000 +0200 +++ new/csg-1.4.1/share/scripts/inverse/table_to_tab.pl 2017-09-03 01:45:18.000000000 +0200 @@ -110,20 +110,15 @@ for(my $i=0;$i<=$#r;$i++){ printf(OUTFILE "%i %15.10e %15.10e %15.10e\n",$i+1,$r[$i], $pot[$i], -$pot_deriv[$i]); } - } elsif ( $type eq "bond" ) { + } elsif ( $type eq "bond" || $type eq "angle" || $type eq "dihedral" ) { printf(OUTFILE "VOTCA\n"); printf(OUTFILE "N %i\n\n",$#r+1); for(my $i=0;$i<=$#r;$i++){ - printf(OUTFILE "%i %12.5e %15.7e %15.7e\n",$i+1,$r[$i],$pot[$i],-$pot_deriv[$i]*$r[$i]); - } - } elsif ( $type eq "angle" || $type eq "dihedral" ) { - printf(OUTFILE "VOTCA\n"); - printf(OUTFILE "N %i\n\n",$#r+1); - my $RadToDegree=180/3.14159265359; - for(my $i=0;$i<=$#r;$i++){ - #rad -> degree: $r[$i]*$RadToDegree, and $pot_deriv[$i]/$RadToDegree - printf(OUTFILE "%i %12.5e %15.7e %15.7e\n",$i+1,$r[$i]*$RadToDegree, $pot[$i], -$pot_deriv[$i]/$RadToDegree); + printf(OUTFILE "%i %12.5e %15.7e %15.7e\n",$i+1,$r[$i], $pot[$i], -$pot_deriv[$i]); } + } else { + #should never happen + die "$progname: tabulated potentials/forces for lammps $type not implemented\n"; } } elsif ($sim_prog eq "dlpoly") { if ($type eq "non-bonded"){ diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.4/src/libcsg/libvotca_csg.pc.in new/csg-1.4.1/src/libcsg/libvotca_csg.pc.in --- old/csg-1.4/src/libcsg/libvotca_csg.pc.in 2016-10-29 18:47:47.000000000 +0200 +++ new/csg-1.4.1/src/libcsg/libvotca_csg.pc.in 2017-09-03 01:45:18.000000000 +0200 @@ -5,7 +5,7 @@ Name: libvotca_csg Description: csg functions of the votca package URL: http://www.votca.org -Version: @VERSION@ +Version: @PROJECT_VERSION@ Requires: libvotca_tools @GROMACS_PKG@ Libs: -L${libdir} -lvotca_csg @BOOST_LIBS_PKG@ @THREAD_LIBRARIES@ Libs.private: -lm diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.4/src/libcsg/modules/io/gmxtrajectorywriter.cc new/csg-1.4.1/src/libcsg/modules/io/gmxtrajectorywriter.cc --- old/csg-1.4/src/libcsg/modules/io/gmxtrajectorywriter.cc 2016-10-29 18:47:47.000000000 +0200 +++ new/csg-1.4.1/src/libcsg/modules/io/gmxtrajectorywriter.cc 2017-09-03 01:45:18.000000000 +0200 @@ -48,7 +48,9 @@ frame.bStep = true; frame.step = conf->getStep();; frame.x = x; +#if GMX < 52 frame.bTitle=false; +#endif frame.bLambda=false; frame.bAtoms=false; frame.bPrec=false; diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.4/src/libcsg/nblist.cc new/csg-1.4.1/src/libcsg/nblist.cc --- old/csg-1.4/src/libcsg/nblist.cc 2016-10-29 18:47:47.000000000 +0200 +++ new/csg-1.4.1/src/libcsg/nblist.cc 2017-09-03 01:45:18.000000000 +0200 @@ -65,9 +65,9 @@ if(top->getExclusions().IsExcluded(*iter1, *iter2)) { continue; } - if((*_match_function)(*iter1, *iter2, r, d)) - if(!FindPair(*iter1, *iter2)) - AddPair( _pair_creator(*iter1, *iter2, r)); + if((*_match_function)(*iter1, *iter2, r, d)) + if(!FindPair(*iter1, *iter2)) + AddPair( _pair_creator(*iter1, *iter2, r)); } } } diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn' '--exclude=.svnignore' old/csg-1.4/src/libcsg/nblistgrid.cc new/csg-1.4.1/src/libcsg/nblistgrid.cc --- old/csg-1.4/src/libcsg/nblistgrid.cc 2016-10-29 18:47:47.000000000 +0200 +++ new/csg-1.4.1/src/libcsg/nblistgrid.cc 2017-09-03 01:45:18.000000000 +0200 @@ -163,9 +163,9 @@ if(_top->getExclusions().IsExcluded((*iter), bead)) { continue; } - if((*_match_function)(*iter, bead, r, d)) - if(!FindPair(*iter, bead)) - AddPair(_pair_creator(*iter, bead, r)); + if((*_match_function)(*iter, bead, r, d)) + if(!FindPair(*iter, bead)) + AddPair(_pair_creator(*iter, bead, r)); } } } ++++++ votca-csg-manual-1.4.pdf -> votca-csg-manual-1.4.1.pdf ++++++ (binary differes) ++++++ votca-csg-tutorials-1.4.tar.gz -> votca-csg-tutorials-1.4.1.tar.gz ++++++ /work/SRC/openSUSE:Factory/votca-csg/votca-csg-tutorials-1.4.tar.gz /work/SRC/openSUSE:Factory/.votca-csg.new/votca-csg-tutorials-1.4.1.tar.gz differ: char 20, line 1
