pkgsrc-Changes archive
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Old Index]
CVS commit: pkgsrc/math
Module Name: pkgsrc
Committed By: thor
Date: Fri Jul 8 19:47:59 UTC 2022
Modified Files:
pkgsrc/math: Makefile
Added Files:
pkgsrc/math/plumed: DESCR Makefile PLIST distinfo options.mk
pkgsrc/math/plumed/patches: patch-Makefile.conf.in patch-configure
patch-configure.ac
Log Message:
math/plumed: added package for the MD algorithm library
To generate a diff of this commit:
cvs rdiff -u -r1.546 -r1.547 pkgsrc/math/Makefile
cvs rdiff -u -r0 -r1.1 pkgsrc/math/plumed/DESCR pkgsrc/math/plumed/Makefile \
pkgsrc/math/plumed/PLIST pkgsrc/math/plumed/distinfo \
pkgsrc/math/plumed/options.mk
cvs rdiff -u -r0 -r1.1 pkgsrc/math/plumed/patches/patch-Makefile.conf.in \
pkgsrc/math/plumed/patches/patch-configure \
pkgsrc/math/plumed/patches/patch-configure.ac
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
Modified files:
Index: pkgsrc/math/Makefile
diff -u pkgsrc/math/Makefile:1.546 pkgsrc/math/Makefile:1.547
--- pkgsrc/math/Makefile:1.546 Sun Jun 12 14:35:53 2022
+++ pkgsrc/math/Makefile Fri Jul 8 19:47:59 2022
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.546 2022/06/12 14:35:53 bacon Exp $
+# $NetBSD: Makefile,v 1.547 2022/07/08 19:47:59 thor Exp $
COMMENT= Mathematics
@@ -362,6 +362,7 @@ SUBDIR+= pear-Numbers_Roman
SUBDIR+= pear-Numbers_Words
SUBDIR+= php-bcmath
SUBDIR+= php-stats
+SUBDIR+= plumed
SUBDIR+= ppl
SUBDIR+= prng
SUBDIR+= pspp
Added files:
Index: pkgsrc/math/plumed/DESCR
diff -u /dev/null pkgsrc/math/plumed/DESCR:1.1
--- /dev/null Fri Jul 8 19:47:59 2022
+++ pkgsrc/math/plumed/DESCR Fri Jul 8 19:47:59 2022
@@ -0,0 +1,9 @@
+PLUMED is an open-source, community-developed library that provides a
+wide range of different methods, which include:
+
+ enhanced-sampling algorithms free-energy methods tools to analyze the
+ vast amounts of data produced by molecular dynamics (MD) simulations.
+
+These techniques can be used in combination with a large toolbox
+of collective variables that describe complex processes in physics,
+chemistry, material science, and biology.
Index: pkgsrc/math/plumed/Makefile
diff -u /dev/null pkgsrc/math/plumed/Makefile:1.1
--- /dev/null Fri Jul 8 19:47:59 2022
+++ pkgsrc/math/plumed/Makefile Fri Jul 8 19:47:59 2022
@@ -0,0 +1,42 @@
+# $NetBSD: Makefile,v 1.1 2022/07/08 19:47:59 thor Exp $
+
+DISTNAME= plumed-2.8.0
+CATEGORIES= math
+MASTER_SITES= ${MASTER_SITE_GITHUB:=plumed/plumed2/releases/download/v2.8.0/}
+EXTRACT_SUFX= .tgz
+
+MAINTAINER= thor%NetBSD.org@localhost
+HOMEPAGE= https://www.plumed.org/
+COMMENT= Molecular dynamics support library
+LICENSE= gnu-lgpl-v3
+
+GNU_CONFIGURE= yes
+USE_LANGUAGES= c c++ fortran
+USE_TOOLS+= gmake bash
+
+TEST_TARGET= check
+
+CONFIGURE_ARGS+= --enable-gsl
+CONFIGURE_ARGS+= --enable-external-blas --enable-external-lapack
+CONFIGURE_ARGS+= LIBS='${LAPACK_LIBS}'
+CONFIGURE_ARGS+= LIBRARY_PATH='${LIBRARY_PATH}:${PREFIX}/lib'
+CONFIGURE_ARGS+= --enable-rpath
+# Python module should be a separate package, I suppose.
+# it is a versioned .so file, so differing pythons might coexist.
+CONFIGURE_ARGS+= --disable-python
+
+SUBST_CLASSES+= envbash
+SUBST_STAGE.envbash= pre-configure
+SUBST_FILES.envbash= src/lib/Makefile
+SUBST_SED.envbash= -e 's,/usr/bin/env bash,${BASH},'
+
+REPLACE_BASH+= scripts/*.sh patches/*.sh
+
+.include "options.mk"
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/blas.buildlink3.mk"
+.include "../../math/fftw/buildlink3.mk"
+.include "../../math/gsl/buildlink3.mk"
+
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/math/plumed/PLIST
diff -u /dev/null pkgsrc/math/plumed/PLIST:1.1
--- /dev/null Fri Jul 8 19:47:59 2022
+++ pkgsrc/math/plumed/PLIST Fri Jul 8 19:47:59 2022
@@ -0,0 +1,530 @@
+@comment $NetBSD: PLIST,v 1.1 2022/07/08 19:47:59 thor Exp $
+bin/plumed
+bin/plumed-config
+bin/plumed-patch
+include/plumed/analysis/AnalysisBase.h
+include/plumed/analysis/AverageVessel.h
+include/plumed/analysis/DataCollectionObject.h
+include/plumed/analysis/LandmarkSelectionBase.h
+include/plumed/analysis/ReadAnalysisFrames.h
+include/plumed/asmjit/arch.h
+include/plumed/asmjit/arm.h
+include/plumed/asmjit/asmjit.h
+include/plumed/asmjit/asmjit_apibegin.h
+include/plumed/asmjit/asmjit_apiend.h
+include/plumed/asmjit/asmjit_build.h
+include/plumed/asmjit/assembler.h
+include/plumed/asmjit/base.h
+include/plumed/asmjit/codebuilder.h
+include/plumed/asmjit/codecompiler.h
+include/plumed/asmjit/codeemitter.h
+include/plumed/asmjit/codeholder.h
+include/plumed/asmjit/constpool.h
+include/plumed/asmjit/cpuinfo.h
+include/plumed/asmjit/func.h
+include/plumed/asmjit/globals.h
+include/plumed/asmjit/inst.h
+include/plumed/asmjit/logging.h
+include/plumed/asmjit/misc_p.h
+include/plumed/asmjit/moved_string.h
+include/plumed/asmjit/operand.h
+include/plumed/asmjit/osutils.h
+include/plumed/asmjit/regalloc_p.h
+include/plumed/asmjit/runtime.h
+include/plumed/asmjit/simdtypes.h
+include/plumed/asmjit/utils.h
+include/plumed/asmjit/vmem.h
+include/plumed/asmjit/x86.h
+include/plumed/asmjit/x86assembler.h
+include/plumed/asmjit/x86builder.h
+include/plumed/asmjit/x86compiler.h
+include/plumed/asmjit/x86emitter.h
+include/plumed/asmjit/x86globals.h
+include/plumed/asmjit/x86inst.h
+include/plumed/asmjit/x86instimpl_p.h
+include/plumed/asmjit/x86internal_p.h
+include/plumed/asmjit/x86logging_p.h
+include/plumed/asmjit/x86misc.h
+include/plumed/asmjit/x86operand.h
+include/plumed/asmjit/x86regalloc_p.h
+include/plumed/asmjit/zone.h
+include/plumed/bias/ActionRegister.h
+include/plumed/bias/Bias.h
+include/plumed/bias/ReweightBase.h
+include/plumed/blas/blas.h
+include/plumed/blas/def_external.h
+include/plumed/blas/def_internal.h
+include/plumed/blas/real.h
+include/plumed/cltools/CLTool.h
+include/plumed/cltools/CLToolRegister.h
+include/plumed/colvar/ActionRegister.h
+include/plumed/colvar/Colvar.h
+include/plumed/colvar/CoordinationBase.h
+include/plumed/colvar/PathMSDBase.h
+include/plumed/config/Config.h
+include/plumed/config/version.h
+include/plumed/core/Action.h
+include/plumed/core/ActionAnyorder.h
+include/plumed/core/ActionAtomistic.h
+include/plumed/core/ActionPilot.h
+include/plumed/core/ActionRegister.h
+include/plumed/core/ActionSet.h
+include/plumed/core/ActionSetup.h
+include/plumed/core/ActionShortcut.h
+include/plumed/core/ActionWithArguments.h
+include/plumed/core/ActionWithValue.h
+include/plumed/core/ActionWithVirtualAtom.h
+include/plumed/core/Atoms.h
+include/plumed/core/CLTool.h
+include/plumed/core/CLToolMain.h
+include/plumed/core/CLToolRegister.h
+include/plumed/core/Colvar.h
+include/plumed/core/DataFetchingObject.h
+include/plumed/core/ExchangePatterns.h
+include/plumed/core/FlexibleBin.h
+include/plumed/core/GREX.h
+include/plumed/core/GenericMolInfo.h
+include/plumed/core/MDAtoms.h
+include/plumed/core/PlumedMain.h
+include/plumed/core/PlumedMainInitializer.h
+include/plumed/core/TargetDist.h
+include/plumed/core/Value.h
+include/plumed/core/WithCmd.h
+include/plumed/function/ActionRegister.h
+include/plumed/function/Function.h
+include/plumed/gridtools/ActionWithGrid.h
+include/plumed/gridtools/ActionWithInputGrid.h
+include/plumed/gridtools/ActionWithIntegral.h
+include/plumed/gridtools/AverageOnGrid.h
+include/plumed/gridtools/ContourFindingBase.h
+include/plumed/gridtools/GridPrintingBase.h
+include/plumed/gridtools/GridSearch.h
+include/plumed/gridtools/GridVessel.h
+include/plumed/gridtools/HistogramOnGrid.h
+include/plumed/isdb/MetainferenceBase.h
+include/plumed/lapack/def_external.h
+include/plumed/lapack/def_internal.h
+include/plumed/lapack/lapack.h
+include/plumed/lapack/lapack_limits.h
+include/plumed/lapack/real.h
+include/plumed/lepton/CompiledExpression.h
+include/plumed/lepton/CustomFunction.h
+include/plumed/lepton/Exception.h
+include/plumed/lepton/ExpressionProgram.h
+include/plumed/lepton/ExpressionTreeNode.h
+include/plumed/lepton/Lepton.h
+include/plumed/lepton/MSVC_erfc.h
+include/plumed/lepton/Operation.h
+include/plumed/lepton/ParsedExpression.h
+include/plumed/lepton/Parser.h
+include/plumed/lepton/windowsIncludes.h
+include/plumed/mapping/Mapping.h
+include/plumed/mapping/PathBase.h
+include/plumed/mapping/PathReparameterization.h
+include/plumed/mapping/TrigonometricPathVessel.h
+include/plumed/molfile/Gromacs.h
+include/plumed/molfile/endianswap.h
+include/plumed/molfile/fastio.h
+include/plumed/molfile/largefiles.h
+include/plumed/molfile/libmolfile_plugin.h
+include/plumed/molfile/molfile_plugin.h
+include/plumed/molfile/periodic_table.h
+include/plumed/molfile/readpdb.h
+include/plumed/molfile/vmdplugin.h
+include/plumed/multicolvar/ActionVolume.h
+include/plumed/multicolvar/AtomValuePack.h
+include/plumed/multicolvar/BridgedMultiColvarFunction.h
+include/plumed/multicolvar/CatomPack.h
+include/plumed/multicolvar/MultiColvarBase.h
+include/plumed/multicolvar/MultiColvarFilter.h
+include/plumed/multicolvar/VolumeGradientBase.h
+include/plumed/reference/ArgumentOnlyDistance.h
+include/plumed/reference/DRMSD.h
+include/plumed/reference/Direction.h
+include/plumed/reference/FakeFrame.h
+include/plumed/reference/MetricRegister.h
+include/plumed/reference/MultiDomainRMSD.h
+include/plumed/reference/RMSDBase.h
+include/plumed/reference/ReferenceArguments.h
+include/plumed/reference/ReferenceAtoms.h
+include/plumed/reference/ReferenceConfiguration.h
+include/plumed/reference/ReferenceValuePack.h
+include/plumed/reference/SingleDomainRMSD.h
+include/plumed/secondarystructure/SecondaryStructureRMSD.h
+include/plumed/setup/ActionSetup.h
+include/plumed/tools/Angle.h
+include/plumed/tools/AtomNumber.h
+include/plumed/tools/BiasRepresentation.h
+include/plumed/tools/Brent1DRootSearch.h
+include/plumed/tools/Citations.h
+include/plumed/tools/Communicator.h
+include/plumed/tools/ConjugateGradient.h
+include/plumed/tools/DLLoader.h
+include/plumed/tools/DynamicList.h
+include/plumed/tools/ERMSD.h
+include/plumed/tools/Exception.h
+include/plumed/tools/File.h
+include/plumed/tools/FileBase.h
+include/plumed/tools/ForwardDecl.h
+include/plumed/tools/Grid.h
+include/plumed/tools/HistogramBead.h
+include/plumed/tools/IFile.h
+include/plumed/tools/KernelFunctions.h
+include/plumed/tools/Keywords.h
+include/plumed/tools/LatticeReduction.h
+include/plumed/tools/LinkCells.h
+include/plumed/tools/Log.h
+include/plumed/tools/LoopUnroller.h
+include/plumed/tools/Matrix.h
+include/plumed/tools/MatrixSquareBracketsAccess.h
+include/plumed/tools/Minimise1DBrent.h
+include/plumed/tools/MinimiseBase.h
+include/plumed/tools/MolDataClass.h
+include/plumed/tools/MultiValue.h
+include/plumed/tools/NeighborList.h
+include/plumed/tools/OFile.h
+include/plumed/tools/OpenMP.h
+include/plumed/tools/PDB.h
+include/plumed/tools/Pbc.h
+include/plumed/tools/PlumedHandle.h
+include/plumed/tools/RMSD.h
+include/plumed/tools/Random.h
+include/plumed/tools/RootFindingBase.h
+include/plumed/tools/Stopwatch.h
+include/plumed/tools/Subprocess.h
+include/plumed/tools/SwitchingFunction.h
+include/plumed/tools/Tensor.h
+include/plumed/tools/Tools.h
+include/plumed/tools/Torsion.h
+include/plumed/tools/Tree.h
+include/plumed/tools/TypesafePtr.h
+include/plumed/tools/Units.h
+include/plumed/tools/Vector.h
+include/plumed/tools/h36.h
+include/plumed/vatom/ActionRegister.h
+include/plumed/vatom/ActionWithVirtualAtom.h
+include/plumed/vesselbase/ActionWithAveraging.h
+include/plumed/vesselbase/ActionWithInputVessel.h
+include/plumed/vesselbase/ActionWithVessel.h
+include/plumed/vesselbase/AveragingVessel.h
+include/plumed/vesselbase/Between.h
+include/plumed/vesselbase/BridgeVessel.h
+include/plumed/vesselbase/FunctionVessel.h
+include/plumed/vesselbase/LessThan.h
+include/plumed/vesselbase/OrderingVessel.h
+include/plumed/vesselbase/ShortcutVessel.h
+include/plumed/vesselbase/StoreDataVessel.h
+include/plumed/vesselbase/ValueVessel.h
+include/plumed/vesselbase/Vessel.h
+include/plumed/vesselbase/VesselRegister.h
+include/plumed/wrapper/Plumed.h
+include/plumed/xdrfile/xdrfile.h
+include/plumed/xdrfile/xdrfile_trr.h
+include/plumed/xdrfile/xdrfile_xtc.h
+lib/libplumed.a
+lib/libplumed.so
+lib/libplumedKernel.so
+lib/libplumedWrapper.a
+lib/pkgconfig/plumed.pc
+lib/pkgconfig/plumedInternals.pc
+lib/pkgconfig/plumedWrapper.pc
+lib/plumed/fortran/plumed.f90
+lib/plumed/fortran/plumed_f08.f90
+lib/plumed/modulefile
+lib/plumed/patches/gromacs-2019.6.config
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/CMakeLists.txt
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/CMakeLists.txt.preplumed
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdlib/force.cpp
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdlib/force.cpp.preplumed
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/legacymdrunoptions.h
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/md.cpp
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/md.cpp.preplumed
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/minimize.cpp
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/minimize.cpp.preplumed
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/replicaexchange.cpp
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/replicaexchange.h
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/runner.cpp
+lib/plumed/patches/gromacs-2019.6.diff/src/gromacs/mdrun/runner.cpp.preplumed
+lib/plumed/patches/gromacs-2020.6.config
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/CMakeLists.txt
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/CMakeLists.txt.preplumed
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdlib/expanded.cpp
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdlib/expanded.cpp.preplumed
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdlib/expanded.h
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdlib/expanded.h.preplumed
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdlib/force.cpp
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdlib/force.cpp.preplumed
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/legacymdrunoptions.h
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/md.cpp
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/md.cpp.preplumed
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/minimize.cpp
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/minimize.cpp.preplumed
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/replicaexchange.cpp
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/replicaexchange.h
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/runner.cpp
+lib/plumed/patches/gromacs-2020.6.diff/src/gromacs/mdrun/runner.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.config
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/CMakeLists.txt
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/CMakeLists.txt.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/expanded.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/expanded.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/expanded.h
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/expanded.h.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/sim_util.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdlib/sim_util.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/legacymdrunoptions.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/legacymdrunoptions.h
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/md.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/md.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/minimize.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/minimize.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/replicaexchange.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/replicaexchange.cpp.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/replicaexchange.h
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/replicaexchange.h.preplumed
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/runner.cpp
+lib/plumed/patches/gromacs-2021.4.diff/src/gromacs/mdrun/runner.cpp.preplumed
+lib/plumed/patches/gromacs-4.5.7.config
+lib/plumed/patches/gromacs-4.5.7.diff
+lib/plumed/patches/namd-2.12.config
+lib/plumed/patches/namd-2.12.diff
+lib/plumed/patches/namd-2.13.config
+lib/plumed/patches/namd-2.13.diff
+lib/plumed/patches/namd-2.14.config
+lib/plumed/patches/namd-2.14.diff
+lib/plumed/patches/patch.sh
+lib/plumed/patches/qespresso-5.0.2.config
+lib/plumed/patches/qespresso-5.0.2.diff/PW/src/forces.f90
+lib/plumed/patches/qespresso-5.0.2.diff/PW/src/forces.f90.preplumed
+lib/plumed/patches/qespresso-5.0.2.diff/PW/src/plugin_forces.f90
+lib/plumed/patches/qespresso-5.0.2.diff/PW/src/plugin_forces.f90.preplumed
+lib/plumed/patches/qespresso-5.0.2.diff/PW/src/plugin_initialization.f90
+lib/plumed/patches/qespresso-5.0.2.diff/PW/src/plugin_initialization.f90.preplumed
+lib/plumed/patches/qespresso-5.0.2.diff/PW/src/pwscf.f90
+lib/plumed/patches/qespresso-5.0.2.diff/PW/src/pwscf.f90.preplumed
+lib/plumed/patches/qespresso-6.2.config
+lib/plumed/patches/qespresso-6.2.diff/PW/src/forces.f90
+lib/plumed/patches/qespresso-6.2.diff/PW/src/forces.f90.preplumed
+lib/plumed/patches/qespresso-6.2.diff/PW/src/plugin_ext_forces.f90
+lib/plumed/patches/qespresso-6.2.diff/PW/src/plugin_ext_forces.f90.preplumed
+lib/plumed/patches/qespresso-6.2.diff/PW/src/plugin_initialization.f90
+lib/plumed/patches/qespresso-6.2.diff/PW/src/plugin_initialization.f90.preplumed
+lib/plumed/patches/qespresso-6.2.diff/PW/src/run_pwscf.f90
+lib/plumed/patches/qespresso-6.2.diff/PW/src/run_pwscf.f90.preplumed
+lib/plumed/plumed-config
+lib/plumed/plumed-mklib
+lib/plumed/plumed-newcv
+lib/plumed/plumed-partial_tempering
+lib/plumed/plumed-patch
+lib/plumed/plumed-runtime
+lib/plumed/plumed-selector
+lib/plumed/plumed-vim2html
+lib/plumed/scripts/config.sh
+lib/plumed/scripts/mklib.sh
+lib/plumed/scripts/newcv.sh
+lib/plumed/scripts/partial_tempering.sh
+lib/plumed/scripts/patch.sh
+lib/plumed/scripts/selector.sh
+lib/plumed/scripts/vim2html.sh
+lib/plumed/src/colvar/Template.cpp
+lib/plumed/src/config/compile_options.sh
+lib/plumed/src/config/config.txt
+lib/plumed/src/lib/Plumed.cmake
+lib/plumed/src/lib/Plumed.cmake.runtime
+lib/plumed/src/lib/Plumed.cmake.shared
+lib/plumed/src/lib/Plumed.cmake.static
+lib/plumed/src/lib/Plumed.inc
+lib/plumed/src/lib/Plumed.inc.runtime
+lib/plumed/src/lib/Plumed.inc.shared
+lib/plumed/src/lib/Plumed.inc.static
+lib/plumed/vim/help/ABMD.txt
+lib/plumed/vim/help/ADAPTIVE_PATH.txt
+lib/plumed/vim/help/ALPHABETA.txt
+lib/plumed/vim/help/ALPHARMSD.txt
+lib/plumed/vim/help/ANGLE.txt
+lib/plumed/vim/help/ANGLES.txt
+lib/plumed/vim/help/ANTIBETARMSD.txt
+lib/plumed/vim/help/AROUND.txt
+lib/plumed/vim/help/AVERAGE.txt
+lib/plumed/vim/help/BIASVALUE.txt
+lib/plumed/vim/help/BRIDGE.txt
+lib/plumed/vim/help/CALIBER.txt
+lib/plumed/vim/help/CAVITY.txt
+lib/plumed/vim/help/CELL.txt
+lib/plumed/vim/help/CENTER.txt
+lib/plumed/vim/help/CENTER_OF_MULTICOLVAR.txt
+lib/plumed/vim/help/COLLECT_FRAMES.txt
+lib/plumed/vim/help/COM.txt
+lib/plumed/vim/help/COMBINE.txt
+lib/plumed/vim/help/COMMITTOR.txt
+lib/plumed/vim/help/CONSTANT.txt
+lib/plumed/vim/help/CONTACTMAP.txt
+lib/plumed/vim/help/CONVERT_TO_FES.txt
+lib/plumed/vim/help/COORDINATION.txt
+lib/plumed/vim/help/COORDINATIONNUMBER.txt
+lib/plumed/vim/help/CS2BACKBONE.txt
+lib/plumed/vim/help/CUSTOM.txt
+lib/plumed/vim/help/DEBUG.txt
+lib/plumed/vim/help/DENSITY.txt
+lib/plumed/vim/help/DHENERGY.txt
+lib/plumed/vim/help/DIHCOR.txt
+lib/plumed/vim/help/DIMER.txt
+lib/plumed/vim/help/DIPOLE.txt
+lib/plumed/vim/help/DISTANCE.txt
+lib/plumed/vim/help/DISTANCES.txt
+lib/plumed/vim/help/DISTANCE_FROM_CONTOUR.txt
+lib/plumed/vim/help/DRMSD.txt
+lib/plumed/vim/help/DUMPATOMS.txt
+lib/plumed/vim/help/DUMPCUBE.txt
+lib/plumed/vim/help/DUMPDERIVATIVES.txt
+lib/plumed/vim/help/DUMPFORCES.txt
+lib/plumed/vim/help/DUMPGRID.txt
+lib/plumed/vim/help/DUMPMASSCHARGE.txt
+lib/plumed/vim/help/DUMPMULTICOLVAR.txt
+lib/plumed/vim/help/DUMPPROJECTIONS.txt
+lib/plumed/vim/help/EEFSOLV.txt
+lib/plumed/vim/help/EFFECTIVE_ENERGY_DRIFT.txt
+lib/plumed/vim/help/EMMI.txt
+lib/plumed/vim/help/ENDPLUMED.txt
+lib/plumed/vim/help/ENERGY.txt
+lib/plumed/vim/help/ENSEMBLE.txt
+lib/plumed/vim/help/ERMSD.txt
+lib/plumed/vim/help/EUCLIDEAN_DISSIMILARITIES.txt
+lib/plumed/vim/help/EXTENDED_LAGRANGIAN.txt
+lib/plumed/vim/help/EXTERNAL.txt
+lib/plumed/vim/help/EXTRACV.txt
+lib/plumed/vim/help/FAKE.txt
+lib/plumed/vim/help/FIND_CONTOUR.txt
+lib/plumed/vim/help/FIND_CONTOUR_SURFACE.txt
+lib/plumed/vim/help/FIND_SPHERICAL_CONTOUR.txt
+lib/plumed/vim/help/FIT_TO_TEMPLATE.txt
+lib/plumed/vim/help/FIXEDATOM.txt
+lib/plumed/vim/help/FLUSH.txt
+lib/plumed/vim/help/FOURIER_TRANSFORM.txt
+lib/plumed/vim/help/FRET.txt
+lib/plumed/vim/help/FUNCPATHGENERAL.txt
+lib/plumed/vim/help/FUNCPATHMSD.txt
+lib/plumed/vim/help/FUNCSUMHILLS.txt
+lib/plumed/vim/help/GHBFIX.txt
+lib/plumed/vim/help/GHOST.txt
+lib/plumed/vim/help/GPROPERTYMAP.txt
+lib/plumed/vim/help/GRID_TO_XYZ.txt
+lib/plumed/vim/help/GROUP.txt
+lib/plumed/vim/help/GYRATION.txt
+lib/plumed/vim/help/HISTOGRAM.txt
+lib/plumed/vim/help/INCLUDE.txt
+lib/plumed/vim/help/INCYLINDER.txt
+lib/plumed/vim/help/INENVELOPE.txt
+lib/plumed/vim/help/INPLANEDISTANCES.txt
+lib/plumed/vim/help/INSPHERE.txt
+lib/plumed/vim/help/INTEGRATE_GRID.txt
+lib/plumed/vim/help/INTERPOLATE_GRID.txt
+lib/plumed/vim/help/JCOUPLING.txt
+lib/plumed/vim/help/LANDMARK_SELECT_FPS.txt
+lib/plumed/vim/help/LANDMARK_SELECT_RANDOM.txt
+lib/plumed/vim/help/LANDMARK_SELECT_STAGED.txt
+lib/plumed/vim/help/LANDMARK_SELECT_STRIDE.txt
+lib/plumed/vim/help/LOAD.txt
+lib/plumed/vim/help/LOCALENSEMBLE.txt
+lib/plumed/vim/help/LOCAL_AVERAGE.txt
+lib/plumed/vim/help/LOWER_WALLS.txt
+lib/plumed/vim/help/MATHEVAL.txt
+lib/plumed/vim/help/MAXENT.txt
+lib/plumed/vim/help/MCOLV_COMBINE.txt
+lib/plumed/vim/help/MCOLV_PRODUCT.txt
+lib/plumed/vim/help/METAD.txt
+lib/plumed/vim/help/METAINFERENCE.txt
+lib/plumed/vim/help/MFILTER_BETWEEN.txt
+lib/plumed/vim/help/MFILTER_LESS.txt
+lib/plumed/vim/help/MFILTER_MORE.txt
+lib/plumed/vim/help/MOLINFO.txt
+lib/plumed/vim/help/MOVINGRESTRAINT.txt
+lib/plumed/vim/help/MTRANSFORM_BETWEEN.txt
+lib/plumed/vim/help/MTRANSFORM_LESS.txt
+lib/plumed/vim/help/MTRANSFORM_MORE.txt
+lib/plumed/vim/help/MULTICOLVARDENS.txt
+lib/plumed/vim/help/MULTI_RMSD.txt
+lib/plumed/vim/help/NLINKS.txt
+lib/plumed/vim/help/NOE.txt
+lib/plumed/vim/help/OUTPUT_ANALYSIS_DATA_TO_COLVAR.txt
+lib/plumed/vim/help/OUTPUT_ANALYSIS_DATA_TO_PDB.txt
+lib/plumed/vim/help/PARABETARMSD.txt
+lib/plumed/vim/help/PATH.txt
+lib/plumed/vim/help/PATHMSD.txt
+lib/plumed/vim/help/PBMETAD.txt
+lib/plumed/vim/help/PCARMSD.txt
+lib/plumed/vim/help/PCAVARS.txt
+lib/plumed/vim/help/PCS.txt
+lib/plumed/vim/help/PIECEWISE.txt
+lib/plumed/vim/help/PLUMED.txt
+lib/plumed/vim/help/POSITION.txt
+lib/plumed/vim/help/PRE.txt
+lib/plumed/vim/help/PRINT.txt
+lib/plumed/vim/help/PRINT_DISSIMILARITY_MATRIX.txt
+lib/plumed/vim/help/PROJECTION_ON_AXIS.txt
+lib/plumed/vim/help/PROPERTYMAP.txt
+lib/plumed/vim/help/PUCKERING.txt
+lib/plumed/vim/help/RANDOM_EXCHANGES.txt
+lib/plumed/vim/help/RDC.txt
+lib/plumed/vim/help/READ.txt
+lib/plumed/vim/help/READ_DISSIMILARITY_MATRIX.txt
+lib/plumed/vim/help/RESCALE.txt
+lib/plumed/vim/help/RESELECT_LANDMARKS.txt
+lib/plumed/vim/help/RESET_CELL.txt
+lib/plumed/vim/help/RESTART.txt
+lib/plumed/vim/help/RESTRAINT.txt
+lib/plumed/vim/help/REWEIGHT_BIAS.txt
+lib/plumed/vim/help/REWEIGHT_METAD.txt
+lib/plumed/vim/help/REWEIGHT_TEMP_PRESS.txt
+lib/plumed/vim/help/REWEIGHT_WHAM.txt
+lib/plumed/vim/help/RMSD.txt
+lib/plumed/vim/help/SAXS.txt
+lib/plumed/vim/help/SELECT.txt
+lib/plumed/vim/help/SELECTOR.txt
+lib/plumed/vim/help/SORT.txt
+lib/plumed/vim/help/STATS.txt
+lib/plumed/vim/help/TARGET.txt
+lib/plumed/vim/help/TEMPLATE.txt
+lib/plumed/vim/help/TETRAHEDRALPORE.txt
+lib/plumed/vim/help/TIME.txt
+lib/plumed/vim/help/TORSION.txt
+lib/plumed/vim/help/TORSIONS.txt
+lib/plumed/vim/help/UNITS.txt
+lib/plumed/vim/help/UPDATE_IF.txt
+lib/plumed/vim/help/UPPER_WALLS.txt
+lib/plumed/vim/help/VOLUME.txt
+lib/plumed/vim/help/WHAM_HISTOGRAM.txt
+lib/plumed/vim/help/WHAM_WEIGHTS.txt
+lib/plumed/vim/help/WHOLEMOLECULES.txt
+lib/plumed/vim/help/WRAPAROUND.txt
+lib/plumed/vim/help/XANGLES.txt
+lib/plumed/vim/help/XDISTANCES.txt
+lib/plumed/vim/help/XYDISTANCES.txt
+lib/plumed/vim/help/XYTORSIONS.txt
+lib/plumed/vim/help/XZDISTANCES.txt
+lib/plumed/vim/help/XZTORSIONS.txt
+lib/plumed/vim/help/YANGLES.txt
+lib/plumed/vim/help/YDISTANCES.txt
+lib/plumed/vim/help/YXTORSIONS.txt
+lib/plumed/vim/help/YZDISTANCES.txt
+lib/plumed/vim/help/YZTORSIONS.txt
+lib/plumed/vim/help/ZANGLES.txt
+lib/plumed/vim/help/ZDISTANCES.txt
+lib/plumed/vim/help/ZXTORSIONS.txt
+lib/plumed/vim/help/ZYTORSIONS.txt
+lib/plumed/vim/scripts.vim
+lib/plumed/vim/syntax/plumed.vim
+lib/plumed/vim/syntax/plumedf.vim
+@pkgdir lib/plumed/obj
Index: pkgsrc/math/plumed/distinfo
diff -u /dev/null pkgsrc/math/plumed/distinfo:1.1
--- /dev/null Fri Jul 8 19:47:59 2022
+++ pkgsrc/math/plumed/distinfo Fri Jul 8 19:47:59 2022
@@ -0,0 +1,8 @@
+$NetBSD: distinfo,v 1.1 2022/07/08 19:47:59 thor Exp $
+
+BLAKE2s (plumed-2.8.0.tgz) = 77d381aab5c5e227b870cc12dfb57650c1598a044d8e0343d4341152e0826da5
+SHA512 (plumed-2.8.0.tgz) = fd426893b3b6d9ccd3103f5d799a8eff1a60c1a7756d4c1788046a9496f7aaadbfea2390c1617f5645ed63255a896d2ef78c154e3e2c5092d678ef6082be0641
+Size (plumed-2.8.0.tgz) = 107630231 bytes
+SHA1 (patch-Makefile.conf.in) = db317ff45591a2aaefc95a1b93c74c8825115bef
+SHA1 (patch-configure) = 34ccd63ee2151b6a7634b477ebb38a6bfcdb88f0
+SHA1 (patch-configure.ac) = 0ec5c5a7db2057c78a99ddd329a8cbc91d05e7e3
Index: pkgsrc/math/plumed/options.mk
diff -u /dev/null pkgsrc/math/plumed/options.mk:1.1
--- /dev/null Fri Jul 8 19:47:59 2022
+++ pkgsrc/math/plumed/options.mk Fri Jul 8 19:47:59 2022
@@ -0,0 +1,17 @@
+# $NetBSD: options.mk,v 1.1 2022/07/08 19:47:59 thor Exp $
+
+PKG_OPTIONS_VAR= PKG_OPTIONS.plumed
+PKG_SUPPORTED_OPTIONS= mpi
+PKG_SUGGESTED_OPTIONS=
+
+.include "../../mk/bsd.prefs.mk"
+.include "../../mk/bsd.options.mk"
+
+.if !empty(PKG_OPTIONS:Mmpi)
+# TODO: Have mpi.bl3 provide proper compiler names and use here.
+# Needed for Intel support (mpiicpc).
+CONFIGURE_ARGS+= --enable-mpi CXX=mpicxx
+.include "../../mk/mpi.buildlink3.mk"
+.else
+CONFIGURE_ARGS+= --disable-mpi
+.endif
Index: pkgsrc/math/plumed/patches/patch-Makefile.conf.in
diff -u /dev/null pkgsrc/math/plumed/patches/patch-Makefile.conf.in:1.1
--- /dev/null Fri Jul 8 19:47:59 2022
+++ pkgsrc/math/plumed/patches/patch-Makefile.conf.in Fri Jul 8 19:47:59 2022
@@ -0,0 +1,17 @@
+$NetBSD: patch-Makefile.conf.in,v 1.1 2022/07/08 19:47:59 thor Exp $
+
+Enable rpath flags also for linking the main binary.
+
+--- Makefile.conf.in.orig 2022-07-08 18:34:07.530823035 +0000
++++ Makefile.conf.in
+@@ -11,8 +11,8 @@ DYNAMIC_LIBS=@LIBS@ @LDFLAGS@ @OPENMP_CX
+ LIBS=@STATIC_LIBS@
+ SOEXT=@SOEXT@
+ # LD is used only to link the plumed executable, so should be equivalent to the C++ compiler
+-LD=@CXX@ @CXXFLAGS@
+-LDSHARED=@LDSHARED@
++LD=@CXX@ @CXXFLAGS@ @RPATH@
++LDSHARED=@LDSHARED@ @RPATH@
+ GCCDEP=@CXX@
+ disable_dependency_tracking=@disable_dependency_tracking@
+ prefix=@prefix@
Index: pkgsrc/math/plumed/patches/patch-configure
diff -u /dev/null pkgsrc/math/plumed/patches/patch-configure:1.1
--- /dev/null Fri Jul 8 19:47:59 2022
+++ pkgsrc/math/plumed/patches/patch-configure Fri Jul 8 19:47:59 2022
@@ -0,0 +1,1016 @@
+$NetBSD: patch-configure,v 1.1 2022/07/08 19:47:59 thor Exp $
+
+Short out the rpath test that fails with pkgsrc wrappers.
+Enable rpath flags also for linking the main binary.
+Fix portability to non-bash with test = instead of test ==.
+
+--- configure.orig 2022-02-22 22:28:39.000000000 +0000
++++ configure
+@@ -635,6 +635,7 @@ dot
+ doxygen
+ make_doc
+ readelf
++RPATH
+ use_debug_glibcxx
+ OPENMP_CXXFLAGS
+ EGREP
+@@ -754,6 +755,7 @@ target_alias
+ SOEXT
+ STATIC_LIBS
+ LDSHARED
++RPATH
+ PYTHON_BIN
+ BASH_COMPLETION_DIR
+ MPIEXEC
+@@ -2433,10 +2435,10 @@ rm -f src/*.on src/*.off
+ if test "${enable_modules+set}" = set; then :
+ enableval=$enable_modules;
+ rm -f src/*.on src/*.off
+- if test "${enableval}" == yes ; then
++ if test "${enableval}" = yes ; then
+ enableval=reset
+ fi
+- if test "${enableval}" == no ; then
++ if test "${enableval}" = no ; then
+ enableval=none
+ fi
+ for modules_mod in `echo "${enableval}" | sed 's/:/ /g' | sed 's/+/ +/g' | sed 's/-/ -/g'`
+@@ -3323,7 +3325,7 @@ case `(uname)` in
+ esac
+
+ # if searching for MPI, try first mpi-like compilers
+-if test $mpi == true ; then
++if test $mpi = true ; then
+ compilers="mpic++ mpicxx mpiicpc openmpic++ openmpicxx $compilers"
+ fi
+
+@@ -4433,7 +4435,7 @@ $as_echo "$as_me: Initial LDSHARED: $
+ $as_echo "$as_me: Initial SOEXT: $SOEXT" >&6;}
+
+ # check C++ flags
+-if test $shared == true
++if test $shared = true
+ then
+
+
+@@ -4543,7 +4545,7 @@ ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+ fi
+
+-if test $basic_warnings == true
++if test $basic_warnings = true
+ then
+
+ save_CXXFLAGS="$CXXFLAGS"
+@@ -4689,7 +4691,7 @@ rm -f core conftest.err conftest.$ac_obj
+
+ fi
+
+-if test $debug == true
++if test $debug = true
+ then
+
+ save_CXXFLAGS="$CXXFLAGS"
+@@ -4739,7 +4741,7 @@ rm -f core conftest.err conftest.$ac_obj
+
+ fi
+
+-if test $gcov == true
++if test $gcov = true
+ then
+ CXX="$CXX --coverage"
+ LDSHARED="$LDSHARED --coverage"
+@@ -4773,7 +4775,7 @@ rm -f core conftest.err conftest.$ac_obj
+ STATIC_LIBS="$STATIC_LIBS --coverage"
+ fi
+
+-if test $fussy == true
++if test $fussy = true
+ then
+
+ save_CXXFLAGS="$CXXFLAGS"
+@@ -5795,7 +5797,7 @@ lapack_found=
+
+ # external lapack can only work with external blas
+ # thus, if external blas are disabled also external lapack should be disabled
+-if test "$external_blas" == false && test "$external_lapack" == true ; then
++if test "$external_blas" = false && test "$external_lapack" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: Internal blas can only be used with internal lapack" >&5
+ $as_echo "$as_me: Internal blas can only be used with internal lapack" >&6;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: Will not search for external lapack" >&5
+@@ -5804,7 +5806,7 @@ $as_echo "$as_me: Will not search for ex
+ fi
+
+ # first look for blas
+-if test "$external_blas" == true ; then
++if test "$external_blas" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether dgemv can be linked with no library" >&5
+ $as_echo_n "checking whether dgemv can be linked with no library... " >&6; }
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+@@ -5866,7 +5868,7 @@ else
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+ $as_echo "no" >&6; }
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dgemv" >&5
+ $as_echo_n "checking for library containing dgemv... " >&6; }
+ if ${ac_cv_search_dgemv+:} false; then :
+@@ -5924,7 +5926,7 @@ if test "$ac_res" != no; then :
+ else
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dgemv_" >&5
+ $as_echo_n "checking for library containing dgemv_... " >&6; }
+ if ${ac_cv_search_dgemv_+:} false; then :
+@@ -6101,7 +6103,7 @@ if test "$ac_res" != no; then :
+ else
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dgemv_" >&5
+ $as_echo_n "checking for library containing dgemv_... " >&6; }
+ if ${ac_cv_search_dgemv_+:} false; then :
+@@ -6244,14 +6246,14 @@ if test -n "$blas_found" ; then
+ $as_echo "#define __PLUMED_HAS_EXTERNAL_BLAS 1" >>confdefs.h
+
+
+-if test "$external_lapack" == true ; then
++if test "$external_lapack" = true ; then
+ # Then we look for lapack using same underscoring
+ case "$blas_found" in
+ (underscore) search_for=dsyevr_ ;;
+ (nounderscore) search_for=dsyevr ;;
+ esac
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ as_ac_Search=`$as_echo "ac_cv_search_$search_for" | $as_tr_sh`
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing $search_for" >&5
+ $as_echo_n "checking for library containing $search_for... " >&6; }
+@@ -6387,7 +6389,7 @@ fi
+ # in case external blas have been found, take note of their underscoring
+ # notice that this applies also when external blas are used with internal lapack
+ # in the latter case, also (internal) lapack names will be underscored consistently
+-if test "$blas_found" == nounderscore
++if test "$blas_found" = nounderscore
+ then
+ $as_echo "#define F77_NO_UNDERSCORE 1" >>confdefs.h
+
+@@ -6443,7 +6445,7 @@ rm -f core *.core core.conftest.* gmon.o
+ fi
+
+
+-if test "$sdot_returns_float" == no ;
++if test "$sdot_returns_float" = no ;
+ then
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether sdot returns double" >&5
+@@ -6529,7 +6531,7 @@ $as_echo "$as_me: Now we will check for
+ # GB
+ #############################################################
+
+-if test $molfile_plugins == true ; then
++if test $molfile_plugins = true ; then
+
+ # Check for molfile_plugins and use internal fallback if not found. TG
+
+@@ -6537,7 +6539,7 @@ if test $molfile_plugins == true ; then
+ $as_echo "#define __PLUMED_HAS_MOLFILE_PLUGINS 1" >>confdefs.h
+
+
+- if test "$external_molfile_plugins" == true ; then
++ if test "$external_molfile_plugins" = true ; then
+
+ found=ko
+ __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS=no
+@@ -6545,7 +6547,7 @@ $as_echo "#define __PLUMED_HAS_MOLFILE_P
+ if test "x$ac_cv_header_libmolfile_plugin_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing molfile_dcdplugin_init" >&5
+ $as_echo_n "checking for library containing molfile_dcdplugin_init... " >&6; }
+ if ${ac_cv_search_molfile_dcdplugin_init+:} false; then :
+@@ -6665,7 +6667,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS 1" >>confdefs.h
+
+ __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS=yes
+@@ -6730,7 +6732,7 @@ fi
+
+ mpi_found=ko
+ # optional libraries follow
+-if test $mpi == true ; then
++if test $mpi = true ; then
+
+ found=ko
+ __PLUMED_HAS_MPI=no
+@@ -6738,7 +6740,7 @@ if test $mpi == true ; then
+ if test "x$ac_cv_header_mpi_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing MPI_Init" >&5
+ $as_echo_n "checking for library containing MPI_Init... " >&6; }
+ if ${ac_cv_search_MPI_Init+:} false; then :
+@@ -6858,7 +6860,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_MPI 1" >>confdefs.h
+
+ __PLUMED_HAS_MPI=yes
+@@ -6943,7 +6945,7 @@ $as_echo "$ac_cv_prog_cxx_openmp" >&6; }
+
+
+
+-if test $asmjit == true ; then
++if test $asmjit = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether architecture is X86/X64" >&5
+ $as_echo_n "checking whether architecture is X86/X64... " >&6; }
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+@@ -6977,18 +6979,18 @@ fi
+ rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ fi
+
+-if test $asmjit == true && test $x86_x64 == false ; then
++if test $asmjit = true && test $x86_x64 = false ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: asmjit does not support this architecture, it will be disabled" >&5
+ $as_echo "$as_me: WARNING: asmjit does not support this architecture, it will be disabled" >&2;}
+ asmjit=false
+ fi
+
+-if test $asmjit == true ; then
++if test $asmjit = true ; then
+ found=ko
+ # asmjit calls clock_gettime and thus should be linked to rt on Linux
+ if test `(uname)` = Linux ; then
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing clock_gettime" >&5
+ $as_echo_n "checking for library containing clock_gettime... " >&6; }
+ if ${ac_cv_search_clock_gettime+:} false; then :
+@@ -7119,7 +7121,7 @@ $as_echo "$as_me: WARNING: cannot link c
+ fi
+
+
+-if test $readdir_r == true ; then
++if test $readdir_r = true ; then
+
+ found=ko
+ __PLUMED_HAS_READDIR_R=no
+@@ -7127,7 +7129,7 @@ if test $readdir_r == true ; then
+ if test "x$ac_cv_header_dirent_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing readdir_r" >&5
+ $as_echo_n "checking for library containing readdir_r... " >&6; }
+ if ${ac_cv_search_readdir_r+:} false; then :
+@@ -7247,7 +7249,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_READDIR_R 1" >>confdefs.h
+
+ __PLUMED_HAS_READDIR_R=yes
+@@ -7257,7 +7259,7 @@ $as_echo "$as_me: WARNING: cannot enable
+ fi
+
+ fi
+-if test $cregex == true ; then
++if test $cregex = true ; then
+
+ found=ko
+ __PLUMED_HAS_CREGEX=no
+@@ -7265,7 +7267,7 @@ if test $cregex == true ; then
+ if test "x$ac_cv_header_regex_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing regcomp" >&5
+ $as_echo_n "checking for library containing regcomp... " >&6; }
+ if ${ac_cv_search_regcomp+:} false; then :
+@@ -7385,7 +7387,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_CREGEX 1" >>confdefs.h
+
+ __PLUMED_HAS_CREGEX=yes
+@@ -7395,7 +7397,7 @@ $as_echo "$as_me: WARNING: cannot enable
+ fi
+
+ fi
+-if test $dlopen == true ; then
++if test $dlopen = true ; then
+
+ found=ko
+ __PLUMED_HAS_DLOPEN=no
+@@ -7403,7 +7405,7 @@ if test $dlopen == true ; then
+ if test "x$ac_cv_header_dlfcn_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dlopen" >&5
+ $as_echo_n "checking for library containing dlopen... " >&6; }
+ if ${ac_cv_search_dlopen+:} false; then :
+@@ -7523,7 +7525,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_DLOPEN 1" >>confdefs.h
+
+ __PLUMED_HAS_DLOPEN=yes
+@@ -7534,11 +7536,11 @@ $as_echo "$as_me: WARNING: cannot enable
+
+ fi
+
+-if test $rtld_default == true ; then
++if test $rtld_default = true ; then
+
+ found=ko
+ __PLUMED_HAS_RTLD_DEFAULT=no
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ testlibs=""
+ else
+ testlibs=""
+@@ -7577,12 +7579,12 @@ $as_echo "no" >&6; }
+ fi
+ rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+- if test $found == ok ; then
++ if test $found = ok ; then
+ break
+ fi
+ LIBS="$save_LIBS"
+ done
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_RTLD_DEFAULT 1" >>confdefs.h
+
+ __PLUMED_HAS_RTLD_DEFAULT=yes
+@@ -7594,7 +7596,7 @@ $as_echo "$as_me: WARNING: cannot enable
+
+ fi
+
+-if test $chdir == true ; then
++if test $chdir = true ; then
+
+ found=ko
+ __PLUMED_HAS_CHDIR=no
+@@ -7602,7 +7604,7 @@ if test $chdir == true ; then
+ if test "x$ac_cv_header_unistd_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing chdir" >&5
+ $as_echo_n "checking for library containing chdir... " >&6; }
+ if ${ac_cv_search_chdir+:} false; then :
+@@ -7722,7 +7724,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_CHDIR 1" >>confdefs.h
+
+ __PLUMED_HAS_CHDIR=yes
+@@ -7733,11 +7735,11 @@ $as_echo "$as_me: WARNING: cannot enable
+
+ fi
+
+-if test $subprocess == true ; then
++if test $subprocess = true ; then
+
+ found=ko
+ __PLUMED_HAS_SUBPROCESS=no
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ testlibs=""
+ else
+ testlibs=""
+@@ -7799,12 +7801,12 @@ $as_echo "no" >&6; }
+ fi
+ rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+- if test $found == ok ; then
++ if test $found = ok ; then
+ break
+ fi
+ LIBS="$save_LIBS"
+ done
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_SUBPROCESS 1" >>confdefs.h
+
+ __PLUMED_HAS_SUBPROCESS=yes
+@@ -7816,7 +7818,7 @@ $as_echo "$as_me: WARNING: cannot enable
+
+ fi
+
+-if test $getcwd == true ; then
++if test $getcwd = true ; then
+
+ found=ko
+ __PLUMED_HAS_GETCWD=no
+@@ -7824,7 +7826,7 @@ if test $getcwd == true ; then
+ if test "x$ac_cv_header_unistd_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing getcwd" >&5
+ $as_echo_n "checking for library containing getcwd... " >&6; }
+ if ${ac_cv_search_getcwd+:} false; then :
+@@ -7944,7 +7946,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_GETCWD 1" >>confdefs.h
+
+ __PLUMED_HAS_GETCWD=yes
+@@ -7955,7 +7957,7 @@ $as_echo "$as_me: WARNING: cannot enable
+
+ fi
+
+-if test $popen == true ; then
++if test $popen = true ; then
+
+ found=ko
+ __PLUMED_HAS_POPEN=no
+@@ -7963,7 +7965,7 @@ if test $popen == true ; then
+ if test "x$ac_cv_header_cstdio" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing popen" >&5
+ $as_echo_n "checking for library containing popen... " >&6; }
+ if ${ac_cv_search_popen+:} false; then :
+@@ -8083,7 +8085,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_POPEN 1" >>confdefs.h
+
+ __PLUMED_HAS_POPEN=yes
+@@ -8094,7 +8096,7 @@ $as_echo "$as_me: WARNING: cannot enable
+
+ fi
+
+-if test $execinfo == true ; then
++if test $execinfo = true ; then
+
+ found=ko
+ __PLUMED_HAS_EXECINFO=no
+@@ -8102,7 +8104,7 @@ if test $execinfo == true ; then
+ if test "x$ac_cv_header_execinfo_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing backtrace" >&5
+ $as_echo_n "checking for library containing backtrace... " >&6; }
+ if ${ac_cv_search_backtrace+:} false; then :
+@@ -8222,7 +8224,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_EXECINFO 1" >>confdefs.h
+
+ __PLUMED_HAS_EXECINFO=yes
+@@ -8232,7 +8234,7 @@ $as_echo "$as_me: WARNING: cannot enable
+ fi
+
+ fi
+-if test $zlib == true ; then
++if test $zlib = true ; then
+
+ found=ko
+ __PLUMED_HAS_ZLIB=no
+@@ -8240,7 +8242,7 @@ if test $zlib == true ; then
+ if test "x$ac_cv_header_zlib_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing gzopen" >&5
+ $as_echo_n "checking for library containing gzopen... " >&6; }
+ if ${ac_cv_search_gzopen+:} false; then :
+@@ -8360,7 +8362,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_ZLIB 1" >>confdefs.h
+
+ __PLUMED_HAS_ZLIB=yes
+@@ -8371,10 +8373,10 @@ $as_echo "$as_me: WARNING: cannot enable
+
+ fi
+
+-if test $gsl == true ; then
++if test $gsl = true ; then
+ found=ko
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing cblas_dgemv" >&5
+ $as_echo_n "checking for library containing cblas_dgemv... " >&6; }
+ if ${ac_cv_search_cblas_dgemv+:} false; then :
+@@ -8433,7 +8435,7 @@ if test "$ac_res" != no; then :
+ if test "x$ac_cv_header_gsl_gsl_vector_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing gsl_vector_alloc" >&5
+ $as_echo_n "checking for library containing gsl_vector_alloc... " >&6; }
+ if ${ac_cv_search_gsl_vector_alloc+:} false; then :
+@@ -8615,7 +8617,7 @@ if test "$ac_res" != no; then :
+ if test "x$ac_cv_header_gsl_gsl_vector_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing gsl_vector_alloc" >&5
+ $as_echo_n "checking for library containing gsl_vector_alloc... " >&6; }
+ if ${ac_cv_search_gsl_vector_alloc+:} false; then :
+@@ -8740,7 +8742,7 @@ fi
+
+ fi
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_GSL 1" >>confdefs.h
+
+ else
+@@ -8749,11 +8751,11 @@ $as_echo "$as_me: WARNING: cannot enable
+ fi
+ fi
+
+-if test $boost_graph == true ; then
++if test $boost_graph = true ; then
+
+ found=ko
+ __PLUMED_HAS_BOOST_GRAPH=no
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ testlibs=""
+ else
+ testlibs=""
+@@ -8794,12 +8796,12 @@ $as_echo "no" >&6; }
+ fi
+ rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+- if test $found == ok ; then
++ if test $found = ok ; then
+ break
+ fi
+ LIBS="$save_LIBS"
+ done
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_BOOST_GRAPH 1" >>confdefs.h
+
+ __PLUMED_HAS_BOOST_GRAPH=yes
+@@ -8811,11 +8813,11 @@ $as_echo "$as_me: WARNING: cannot enable
+
+ fi
+
+-if test $boost_serialization == true ; then
++if test $boost_serialization = true ; then
+
+ found=ko
+ __PLUMED_HAS_BOOST_SERIALIZATION=no
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ testlibs="boost_serialization boost_serialization-mt"
+ else
+ testlibs=""
+@@ -8854,12 +8856,12 @@ $as_echo "no" >&6; }
+ fi
+ rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+- if test $found == ok ; then
++ if test $found = ok ; then
+ break
+ fi
+ LIBS="$save_LIBS"
+ done
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_BOOST_SERIALIZATION 1" >>confdefs.h
+
+ __PLUMED_HAS_BOOST_SERIALIZATION=yes
+@@ -8872,7 +8874,7 @@ $as_echo "$as_me: WARNING: cannot enable
+ # notice: macports install libraries with -mt suffix
+ fi
+
+-if test $fftw == true ; then
++if test $fftw = true ; then
+
+ found=ko
+ __PLUMED_HAS_FFTW=no
+@@ -8880,7 +8882,7 @@ if test $fftw == true ; then
+ if test "x$ac_cv_header_fftw3_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing fftw_execute" >&5
+ $as_echo_n "checking for library containing fftw_execute... " >&6; }
+ if ${ac_cv_search_fftw_execute+:} false; then :
+@@ -9000,7 +9002,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_FFTW 1" >>confdefs.h
+
+ __PLUMED_HAS_FFTW=yes
+@@ -9011,7 +9013,7 @@ $as_echo "$as_me: WARNING: cannot enable
+
+ fi
+
+-if test $python == true ; then
++if test $python = true ; then
+ # if PYTHON_BIN is defined, it is expected to be the full path to python
+ # Otherwise, search from a list of names:
+ if test -z "$PYTHON_BIN" ; then
+@@ -9094,7 +9096,7 @@ $as_echo "$as_me: WARNING: cannot enable
+ fi
+ fi
+
+-if test "$af_ocl" == true ; then
++if test "$af_ocl" = true ; then
+
+ found=ko
+ __PLUMED_HAS_ARRAYFIRE=no
+@@ -9102,7 +9104,7 @@ if test "$af_ocl" == true ; then
+ if test "x$ac_cv_header_arrayfire_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing af_is_double" >&5
+ $as_echo_n "checking for library containing af_is_double... " >&6; }
+ if ${ac_cv_search_af_is_double+:} false; then :
+@@ -9222,7 +9224,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_ARRAYFIRE 1" >>confdefs.h
+
+ __PLUMED_HAS_ARRAYFIRE=yes
+@@ -9232,7 +9234,7 @@ $as_echo "$as_me: WARNING: cannot enable
+ fi
+
+ fi
+-if test "$af_cuda" == true ; then
++if test "$af_cuda" = true ; then
+
+ found=ko
+ __PLUMED_HAS_ARRAYFIRE=no
+@@ -9240,7 +9242,7 @@ if test "$af_cuda" == true ; then
+ if test "x$ac_cv_header_arrayfire_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing af_is_double" >&5
+ $as_echo_n "checking for library containing af_is_double... " >&6; }
+ if ${ac_cv_search_af_is_double+:} false; then :
+@@ -9360,7 +9362,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_ARRAYFIRE 1" >>confdefs.h
+
+ __PLUMED_HAS_ARRAYFIRE=yes
+@@ -9370,7 +9372,7 @@ $as_echo "$as_me: WARNING: cannot enable
+ fi
+
+ fi
+-if test "$af_cpu" == true ; then
++if test "$af_cpu" = true ; then
+
+ found=ko
+ __PLUMED_HAS_ARRAYFIRE=no
+@@ -9378,7 +9380,7 @@ if test "$af_cpu" == true ; then
+ if test "x$ac_cv_header_arrayfire_h" = xyes; then :
+
+
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing af_is_double" >&5
+ $as_echo_n "checking for library containing af_is_double... " >&6; }
+ if ${ac_cv_search_af_is_double+:} false; then :
+@@ -9498,7 +9500,7 @@ fi
+ fi
+
+
+- if test $found == ok ; then
++ if test $found = ok ; then
+ $as_echo "#define __PLUMED_HAS_ARRAYFIRE 1" >>confdefs.h
+
+ __PLUMED_HAS_ARRAYFIRE=yes
+@@ -9510,7 +9512,7 @@ $as_echo "$as_me: WARNING: cannot enable
+ fi
+
+ # in non-debug mode, add -DNDEBUG
+-if test "$debug" == false ; then
++if test "$debug" = false ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: Release mode, adding -DNDEBUG" >&5
+ $as_echo "$as_me: Release mode, adding -DNDEBUG" >&6;}
+ $as_echo "#define NDEBUG 1" >>confdefs.h
+@@ -9521,7 +9523,7 @@ fi
+ # in debug-glibcxx mode, add -D_GLIBCXX_DEBUG
+ # also take note that we are using this to relax `make nmcheck`
+ use_debug_glibcxx=no
+-if test "$debug_glibcxx" == true ; then
++if test "$debug_glibcxx" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: Check boundaries, adding -D_GLIBCXX_DEBUG" >&5
+ $as_echo "$as_me: Check boundaries, adding -D_GLIBCXX_DEBUG" >&6;}
+ $as_echo "#define _GLIBCXX_DEBUG 1" >>confdefs.h
+@@ -9544,7 +9546,7 @@ $as_echo "#define _REENTRANT 1" >>confde
+
+
+
+-if test "$shared" == true ; then
++if test "$shared" = true ; then
+ case `(uname)` in
+ (Darwin)
+ { $as_echo "$as_me:${as_lineno-$LINENO}: *** Special settings for dynamic libraries on OSX ***" >&5
+@@ -9596,7 +9598,7 @@ fi
+ rm -f core conftest.err conftest.$ac_objext \
+ conftest$ac_exeext conftest.$ac_ext
+
+- if test "$bsymbolic" == true ; then
++ if test "$bsymbolic" = true ; then
+
+ save_LDFLAGS="$LDFLAGS"
+ LDFLAGS="$LDFLAGS -Wl,-Bsymbolic"
+@@ -9695,19 +9697,22 @@ $as_echo "no" >&6; }
+ fi
+
+
+- if test "$readelf" == found ; then
+- test_LDSHARED="$LDSHARED -Wl,-R -Wl,/some/random/dir/"
+- $test_LDSHARED $LDFLAGS conftest.o -o conftest.$SOEXT 1>/dev/null 2>/dev/null
+- if readelf -d conftest.$SOEXT | grep RPATH | grep -q /some/random/dir ; then
+- LDSHARED="$LDSHARED -Wl,-R -Wl,\"$libdir:$LIBRARY_PATH\""
+- else
+- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: -R option seems not working, disabling rpath" >&5
+-$as_echo "$as_me: WARNING: -R option seems not working, disabling rpath" >&2;}
+- fi
+- else
+- { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: readelf not available, no way to set rpath" >&5
+-$as_echo "$as_me: WARNING: readelf not available, no way to set rpath" >&2;}
+- fi
++# Believe us that we provide a toolchain that does rpath, just not accepting
++# any random directories in pkgsrc!
++# Also need rpath in LDFLAGS for plumed binary!
++# if test "$readelf" = found ; then
++# test_LDSHARED="$LDSHARED -Wl,-R -Wl,/some/random/dir/"
++# $test_LDSHARED $LDFLAGS conftest.o -o conftest.$SOEXT 1>/dev/null 2>/dev/null
++# if readelf -d conftest.$SOEXT | grep RPATH | grep -q /some/random/dir ; then
++ RPATH="-Wl,-R -Wl,\"$libdir:$LIBRARY_PATH\""
++# else
++# { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: -R option seems not working, disabling rpath" >&5
++#$as_echo "$as_me: WARNING: -R option seems not working, disabling rpath" >&2;}
++# fi
++# else
++# { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: readelf not available, no way to set rpath" >&5
++#$as_echo "$as_me: WARNING: readelf not available, no way to set rpath" >&2;}
++# fi
+ fi
+ rm -f conftest.*
+ fi
+@@ -9715,7 +9720,7 @@ fi
+
+
+ make_doc=no
+-if test "$doc" == true
++if test "$doc" = true
+ then
+
+ make_doc=yes
+@@ -9758,10 +9763,10 @@ $as_echo "no" >&6; }
+ fi
+
+
+-if test "$doxygen" == found
++if test "$doxygen" = found
+ then
+ doxygen_version=`doxygen --version | awk 'BEGIN{FS="."}{if($1>1 || ($1==1 && $2>=8)) print "ok"}'`
+- if test "$doxygen_version" == ok
++ if test "$doxygen_version" = ok
+ then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: Doxygen version is fine" >&5
+ $as_echo "$as_me: Doxygen version is fine" >&6;}
+@@ -9828,7 +9833,7 @@ fi
+
+
+ make_pdfdoc=""
+-if test "$pdfdoc" == true && test "$make_doc" == yes
++if test "$pdfdoc" = true && test "$make_doc" = yes
+ then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: A PDF version of the manual will be generated" >&5
+ $as_echo "$as_me: A PDF version of the manual will be generated" >&6;}
+@@ -9880,7 +9885,7 @@ rm -f core *.core core.conftest.* gmon.o
+ fi
+
+
+-if test $mpi_found == ok ; then
++if test $mpi_found = ok ; then
+
+ program_can_run_mpi=""
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether a program compiled with mpi can be run on this machine" >&5
+@@ -9919,7 +9924,7 @@ fi
+
+ fi
+
+-if test $mpi_found == ok ; then
++if test $mpi_found = ok ; then
+ if test -n "$MPIEXEC" ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: Regtest suite will use $MPIEXEC command to run MPI tests" >&5
+ $as_echo "$as_me: Regtest suite will use $MPIEXEC command to run MPI tests" >&6;}
+@@ -9929,15 +9934,15 @@ $as_echo "$as_me: Regtest suite will use
+ fi
+ fi
+
+-if test "$SOEXT" == "dylib" ; then
++if test "$SOEXT" = "dylib" ; then
+ use_absolute_soname=yes
+ else
+ use_absolute_soname=no
+ fi
+
+
+-if test "$absolute_soname" == true ; then
+- if test "$SOEXT" == "dylib" ; then
++if test "$absolute_soname" = true ; then
++ if test "$SOEXT" = "dylib" ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: --enable-absolute-soname has no effect on OSX" >&5
+ $as_echo "$as_me: WARNING: --enable-absolute-soname has no effect on OSX" >&2;}
+ else
+@@ -9947,8 +9952,8 @@ $as_echo "$as_me: enabling absolute sona
+ fi
+ fi
+
+-if test "$absolute_install_name" == false ; then
+- if test "$SOEXT" == "so" ; then
++if test "$absolute_install_name" = false ; then
++ if test "$SOEXT" = "so" ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: --disable-absolute-install-name has no effect on Linux" >&5
+ $as_echo "$as_me: WARNING: --disable-absolute-install-name has no effect on Linux" >&2;}
+ else
+@@ -9959,8 +9964,8 @@ $as_echo "$as_me: enabling relative inst
+ fi
+
+
+-if test "$SOEXT" == "dylib" ; then
+- if test "$loader_path" == true ; then
++if test "$SOEXT" = "dylib" ; then
++ if test "$loader_path" = true ; then
+ use_loader_path=yes
+ else
+ use_loader_path=no
+@@ -9976,7 +9981,7 @@ $as_echo "$as_me: PLUMED seems to be con
+ $as_echo "$as_me: **************************" >&6;}
+
+ LD_RO=
+-if test "$ld_r" == true ; then
++if test "$ld_r" = true ; then
+ for test_LD_RO in "$($CXX --print-prog-name=ld) -r -o" "$CXX -Wl,-r -o" "ld -r -o"
+ do
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C++ objects can be grouped with $test_LD_RO" >&5
+@@ -10020,7 +10025,7 @@ fi
+
+
+ AR_CR=
+-if test "$ar_cr" == true ; then
++if test "$ar_cr" = true ; then
+ for test_AR_CR in "$($CXX --print-prog-name=ar) cr" "ar cr"
+ do
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether static libraries can be created with $test_AR_CR" >&5
+@@ -10065,7 +10070,7 @@ fi
+ make_static_archive=no
+
+
+-if test "${static_archive}" == true ; then
++if test "${static_archive}" = true ; then
+ if test -z "$LD_RO" || test -z "$AR_CR" ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: no way to create a static archive if ld -ro or ar cr do not work" >&5
+ $as_echo "$as_me: WARNING: no way to create a static archive if ld -ro or ar cr do not work" >&2;}
+@@ -10073,7 +10078,7 @@ $as_echo "$as_me: WARNING: no way to cre
+ fi
+ fi
+
+-if test "${static_archive}" == true ; then
++if test "${static_archive}" = true ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether static-object constructors can be linked from a static archive" >&5
+ $as_echo_n "checking whether static-object constructors can be linked from a static archive... " >&6; }
+
+@@ -10116,7 +10121,7 @@ $as_echo "no" >&6; }
+ fi
+ fi
+
+-if test "${static_patch}" == true ; then
++if test "${static_patch}" = true ; then
+
+ { $as_echo "$as_me:${as_lineno-$LINENO}: I will now check if C++ objects can be linked by C/Fortran compilers" >&5
+ $as_echo "$as_me: I will now check if C++ objects can be linked by C/Fortran compilers" >&6;}
+@@ -10157,7 +10162,7 @@ EOF
+ $CXX $CXXFLAGS -c conftest.cpp
+ # start search:
+ found=
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ testlibs="-lstdc++ -lc++ -lmpi_cxx"
+ else
+ testlibs=""
+@@ -10198,7 +10203,7 @@ else
+ $as_echo "$as_me: Static patching is disabled, thus tests required for static patching will be skipped" >&6;}
+ fi
+
+-if test "$prefix" == NONE
++if test "$prefix" = NONE
+ then
+ prefix=/usr/local
+ fi
+@@ -10252,7 +10257,7 @@ done
+
+
+ if test -z "$BASH_COMPLETION_DIR" && test -n "$pkgconfig_bin"; then
+- if test "$prefix" == "$(pkg-config --variable=prefix bash-completion 2>/dev/null)"
++ if test "$prefix" = "$(pkg-config --variable=prefix bash-completion 2>/dev/null)"
+ then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: bash-completion is installed on the same prefix where plumed will be installed" >&5
+ $as_echo "$as_me: bash-completion is installed on the same prefix where plumed will be installed" >&6;}
+@@ -10348,8 +10353,8 @@ $as_echo "$as_me: WARNING: **** _$progra
+ $as_echo "$as_me: WARNING: **** complete -F _$program_name -o default $program_name" >&2;}
+ fi
+
+-if test $mpi == true; then
+- if test $mpi_found == ok; then
++if test $mpi = true; then
++ if test $mpi_found = ok; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: **** PLUMED will be compiled using MPI" >&5
+ $as_echo "$as_me: **** PLUMED will be compiled using MPI" >&6;}
+ else
+@@ -10361,13 +10366,13 @@ else
+ $as_echo "$as_me: **** PLUMED will be compiled without MPI" >&6;}
+ fi
+
+-if test $program_can_run == no ; then
++if test $program_can_run = no ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: plumed executable will not run on this machine" >&5
+ $as_echo "$as_me: WARNING: plumed executable will not run on this machine" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: to patch an MD code use 'plumed-patch'" >&5
+ $as_echo "$as_me: WARNING: to patch an MD code use 'plumed-patch'" >&2;}
+-elif test $mpi_found == ok ; then
+- if test $program_can_run_mpi == no ; then
++elif test $mpi_found = ok ; then
++ if test $program_can_run_mpi = no ; then
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: plumed executable will not run on this machine" >&5
+ $as_echo "$as_me: WARNING: plumed executable will not run on this machine" >&2;}
+ { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unless you invoke it as 'plumed --no-mpi'" >&5
Index: pkgsrc/math/plumed/patches/patch-configure.ac
diff -u /dev/null pkgsrc/math/plumed/patches/patch-configure.ac:1.1
--- /dev/null Fri Jul 8 19:47:59 2022
+++ pkgsrc/math/plumed/patches/patch-configure.ac Fri Jul 8 19:47:59 2022
@@ -0,0 +1,588 @@
+$NetBSD: patch-configure.ac,v 1.1 2022/07/08 19:47:59 thor Exp $
+
+Short out the rpath test that fails with pkgsrc wrappers.
+Enable rpath flags also for linking the main binary.
+Fix portability to non-bash with test = instead of test ==.
+
+Including the .ac patch here to motivate upstreaming at least
+of the == stuff.
+
+--- configure.ac.orig 2022-02-22 22:28:39.000000000 +0000
++++ configure.ac
+@@ -89,7 +89,7 @@ AC_DEFUN([PLUMED_CHECK_LDFLAGS], [
+ # same as AC_SEARCH_LIBS, but does not try any library unless $libsearch==true
+ # Should be used instead of AC_SEARCH_LIBS in order to make --disable-libsearch work correctly
+ AC_DEFUN([PLUMED_SEARCH_LIBS], [
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ AC_SEARCH_LIBS([$1],[$2],[$3],[$4],[$5])
+ else
+ AC_SEARCH_LIBS([$1],[],[$3],[$4],[])
+@@ -106,7 +106,7 @@ AC_DEFUN([PLUMED_CHECK_PACKAGE], [
+ AC_CHECK_HEADER( [$1],[
+ PLUMED_SEARCH_LIBS([$2],[$4],[found=ok])
+ ])
+- if test $found == ok ; then
++ if test $found = ok ; then
+ AC_DEFINE([$3])
+ $3=yes
+ else
+@@ -122,7 +122,7 @@ AC_DEFUN([PLUMED_CHECK_PACKAGE], [
+ AC_DEFUN([PLUMED_CHECK_CXX_PACKAGE], [
+ found=ko
+ $3=no
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ testlibs="$4"
+ else
+ testlibs=""
+@@ -141,12 +141,12 @@ AC_DEFUN([PLUMED_CHECK_CXX_PACKAGE], [
+ [AC_MSG_RESULT([yes])],
+ [AC_MSG_RESULT([no])]
+ )
+- if test $found == ok ; then
++ if test $found = ok ; then
+ break
+ fi
+ LIBS="$save_LIBS"
+ done
+- if test $found == ok ; then
++ if test $found = ok ; then
+ AC_DEFINE([$3])
+ $3=yes
+ else
+@@ -164,10 +164,10 @@ AC_ARG_ENABLE([modules],
+ AS_HELP_STRING([--enable-modules], [all/none/reset or : separated list such as +crystallization:-bias default: reset]),
+ [
+ rm -f src/*.on src/*.off
+- if test "${enableval}" == yes ; then
++ if test "${enableval}" = yes ; then
+ enableval=reset
+ fi
+- if test "${enableval}" == no ; then
++ if test "${enableval}" = no ; then
+ enableval=none
+ fi
+ for modules_mod in `echo "${enableval}" | sed 's/:/ /g' | sed 's/+/ +/g' | sed 's/-/ -/g'`
+@@ -313,7 +313,7 @@ case `(uname)` in
+ esac
+
+ # if searching for MPI, try first mpi-like compilers
+-if test $mpi == true ; then
++if test $mpi = true ; then
+ compilers="mpic++ mpicxx mpiicpc openmpic++ openmpicxx $compilers"
+ fi
+
+@@ -346,13 +346,13 @@ AC_MSG_NOTICE([Initial LDSHARED: $LDS
+ AC_MSG_NOTICE([Initial SOEXT: $SOEXT])
+
+ # check C++ flags
+-if test $shared == true
++if test $shared = true
+ then
+ PLUMED_CHECK_CXXFLAG([-fPIC])
+ PLUMED_CHECK_CFLAG([-fPIC])
+ fi
+
+-if test $basic_warnings == true
++if test $basic_warnings = true
+ then
+ PLUMED_CHECK_CXXFLAG([-Wall])
+ PLUMED_CHECK_CXXFLAG([-pedantic])
+@@ -363,12 +363,12 @@ then
+ PLUMED_CHECK_CXXFLAG([-std=c++$cxx_level])
+ fi
+
+-if test $debug == true
++if test $debug = true
+ then
+ PLUMED_CHECK_CXXFLAG([-g])
+ fi
+
+-if test $gcov == true
++if test $gcov = true
+ then
+ CXX="$CXX --coverage"
+ LDSHARED="$LDSHARED --coverage"
+@@ -377,7 +377,7 @@ then
+ STATIC_LIBS="$STATIC_LIBS --coverage"
+ fi
+
+-if test $fussy == true
++if test $fussy = true
+ then
+ PLUMED_CHECK_CXXFLAG([-Wextra])
+ PLUMED_CHECK_CXXFLAG([-Wfloat-equal])
+@@ -499,14 +499,14 @@ lapack_found=
+
+ # external lapack can only work with external blas
+ # thus, if external blas are disabled also external lapack should be disabled
+-if test "$external_blas" == false && test "$external_lapack" == true ; then
++if test "$external_blas" = false && test "$external_lapack" = true ; then
+ AC_MSG_NOTICE([Internal blas can only be used with internal lapack])
+ AC_MSG_NOTICE([Will not search for external lapack])
+ external_lapack=false
+ fi
+
+ # first look for blas
+-if test "$external_blas" == true ; then
++if test "$external_blas" = true ; then
+ AC_MSG_CHECKING([whether dgemv can be linked with no library])
+ AC_LINK_IFELSE([AC_LANG_CALL([], [dgemv])],[
+ AC_MSG_RESULT([yes])
+@@ -536,7 +536,7 @@ if test -n "$blas_found" ; then
+
+ AC_DEFINE([__PLUMED_HAS_EXTERNAL_BLAS])
+
+-if test "$external_lapack" == true ; then
++if test "$external_lapack" = true ; then
+ # Then we look for lapack using same underscoring
+ case "$blas_found" in
+ (underscore) search_for=dsyevr_ ;;
+@@ -557,7 +557,7 @@ fi
+ # in case external blas have been found, take note of their underscoring
+ # notice that this applies also when external blas are used with internal lapack
+ # in the latter case, also (internal) lapack names will be underscored consistently
+-if test "$blas_found" == nounderscore
++if test "$blas_found" = nounderscore
+ then
+ AC_DEFINE([F77_NO_UNDERSCORE])
+ fi
+@@ -596,7 +596,7 @@ AC_RUN_IFELSE([AC_LANG_SOURCE([PLUMED_TE
+ [ AC_MSG_RESULT([not checked (cross compiling)]) ]
+ )
+
+-if test "$sdot_returns_float" == no ;
++if test "$sdot_returns_float" = no ;
+ then
+
+ AC_MSG_CHECKING([whether sdot returns double])
+@@ -638,14 +638,14 @@ AC_MSG_NOTICE([Now we will check for opt
+ # GB
+ #############################################################
+
+-if test $molfile_plugins == true ; then
++if test $molfile_plugins = true ; then
+
+ # Check for molfile_plugins and use internal fallback if not found. TG
+
+ # We always have molfile, now
+ AC_DEFINE([__PLUMED_HAS_MOLFILE_PLUGINS])
+
+- if test "$external_molfile_plugins" == true ; then
++ if test "$external_molfile_plugins" = true ; then
+ PLUMED_CHECK_PACKAGE([libmolfile_plugin.h],[molfile_dcdplugin_init],[__PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS],molfile_plugin)
+ if test "$__PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS" != yes ; then
+ AC_MSG_WARN([using internal molfile_plugins, which only support dcd/xtc/trr/trj/crd files])
+@@ -662,7 +662,7 @@ AC_CHECK_LIB([dl],dlopen, [STATIC_LIBS="
+
+ mpi_found=ko
+ # optional libraries follow
+-if test $mpi == true ; then
++if test $mpi = true ; then
+ PLUMED_CHECK_PACKAGE([mpi.h],[MPI_Init],[__PLUMED_HAS_MPI])
+ if test "$__PLUMED_HAS_MPI" = yes; then
+ mpi_found=ok
+@@ -675,7 +675,7 @@ fi
+ # when configuring with --disable-openmp
+ AC_OPENMP
+
+-if test $asmjit == true ; then
++if test $asmjit = true ; then
+ AC_MSG_CHECKING([whether architecture is X86/X64])
+ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([
+ #if !(defined(_M_IX86 ) || defined(__X86__ ) || defined(__i386 ) || \
+@@ -692,12 +692,12 @@ this_is_not_x86_x64
+ x86_x64=false])
+ fi
+
+-if test $asmjit == true && test $x86_x64 == false ; then
++if test $asmjit = true && test $x86_x64 = false ; then
+ AC_MSG_WARN([asmjit does not support this architecture, it will be disabled])
+ asmjit=false
+ fi
+
+-if test $asmjit == true ; then
++if test $asmjit = true ; then
+ found=ko
+ # asmjit calls clock_gettime and thus should be linked to rt on Linux
+ if test `(uname)` = Linux ; then
+@@ -714,17 +714,17 @@ if test $asmjit == true ; then
+ fi
+
+
+-if test $readdir_r == true ; then
++if test $readdir_r = true ; then
+ PLUMED_CHECK_PACKAGE([dirent.h],[readdir_r],[__PLUMED_HAS_READDIR_R])
+ fi
+-if test $cregex == true ; then
++if test $cregex = true ; then
+ PLUMED_CHECK_PACKAGE([regex.h],[regcomp],[__PLUMED_HAS_CREGEX])
+ fi
+-if test $dlopen == true ; then
++if test $dlopen = true ; then
+ PLUMED_CHECK_PACKAGE([dlfcn.h],[dlopen],[__PLUMED_HAS_DLOPEN])
+ fi
+
+-if test $rtld_default == true ; then
++if test $rtld_default = true ; then
+ PLUMED_CHECK_CXX_PACKAGE([RTLD_DEFAULT],[
+ #include <dlfcn.h>
+ int
+@@ -736,11 +736,11 @@ main ()
+ ], [__PLUMED_HAS_RTLD_DEFAULT])
+ fi
+
+-if test $chdir == true ; then
++if test $chdir = true ; then
+ PLUMED_CHECK_PACKAGE([unistd.h],[chdir],[__PLUMED_HAS_CHDIR])
+ fi
+
+-if test $subprocess == true ; then
++if test $subprocess = true ; then
+ PLUMED_CHECK_CXX_PACKAGE([subprocess],[
+ /* random program calling all the functions needed to manage a subprocess */
+ #include <cstdio>
+@@ -775,36 +775,36 @@ main ()
+ ], [__PLUMED_HAS_SUBPROCESS])
+ fi
+
+-if test $getcwd == true ; then
++if test $getcwd = true ; then
+ PLUMED_CHECK_PACKAGE([unistd.h],[getcwd],[__PLUMED_HAS_GETCWD])
+ fi
+
+-if test $popen == true ; then
++if test $popen = true ; then
+ PLUMED_CHECK_PACKAGE([cstdio],[popen],[__PLUMED_HAS_POPEN])
+ fi
+
+-if test $execinfo == true ; then
++if test $execinfo = true ; then
+ PLUMED_CHECK_PACKAGE([execinfo.h],[backtrace],[__PLUMED_HAS_EXECINFO])
+ fi
+-if test $zlib == true ; then
++if test $zlib = true ; then
+ PLUMED_CHECK_PACKAGE([zlib.h],[gzopen],[__PLUMED_HAS_ZLIB],[z])
+ fi
+
+-if test $gsl == true ; then
++if test $gsl = true ; then
+ found=ko
+ PLUMED_SEARCH_LIBS([cblas_dgemv],[gslcblas], [
+ AC_CHECK_HEADER( [gsl/gsl_vector.h], [
+ PLUMED_SEARCH_LIBS([gsl_vector_alloc],[gsl],[found=ok])
+ ])
+ ])
+- if test $found == ok ; then
++ if test $found = ok ; then
+ AC_DEFINE([__PLUMED_HAS_GSL])
+ else
+ AC_MSG_WARN([cannot enable __PLUMED_HAS_GSL])
+ fi
+ fi
+
+-if test $boost_graph == true ; then
++if test $boost_graph = true ; then
+ PLUMED_CHECK_CXX_PACKAGE([boost graph],[
+ #include <boost/graph/graph_utility.hpp>
+ #include <boost/graph/adjacency_matrix.hpp>
+@@ -818,7 +818,7 @@ main ()
+ ], [__PLUMED_HAS_BOOST_GRAPH])
+ fi
+
+-if test $boost_serialization == true ; then
++if test $boost_serialization = true ; then
+ PLUMED_CHECK_CXX_PACKAGE([boost serialization],[
+ #include <fstream>
+ #include <boost/archive/text_oarchive.hpp>
+@@ -831,11 +831,11 @@ int main() {
+ # notice: macports install libraries with -mt suffix
+ fi
+
+-if test $fftw == true ; then
++if test $fftw = true ; then
+ PLUMED_CHECK_PACKAGE([fftw3.h],[fftw_execute],[__PLUMED_HAS_FFTW],[fftw3])
+ fi
+
+-if test $python == true ; then
++if test $python = true ; then
+ # if PYTHON_BIN is defined, it is expected to be the full path to python
+ # Otherwise, search from a list of names:
+ if test -z "$PYTHON_BIN" ; then
+@@ -870,18 +870,18 @@ if sys.version_info < (3,):
+ fi
+ fi
+
+-if test "$af_ocl" == true ; then
++if test "$af_ocl" = true ; then
+ PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE],[afopencl])
+ fi
+-if test "$af_cuda" == true ; then
++if test "$af_cuda" = true ; then
+ PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE],[afcuda])
+ fi
+-if test "$af_cpu" == true ; then
++if test "$af_cpu" = true ; then
+ PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE],[afcpu])
+ fi
+
+ # in non-debug mode, add -DNDEBUG
+-if test "$debug" == false ; then
++if test "$debug" = false ; then
+ AC_MSG_NOTICE([Release mode, adding -DNDEBUG])
+ AC_DEFINE([NDEBUG])
+ fi
+@@ -890,7 +890,7 @@ AC_SUBST(use_debug_glibcxx)
+ # in debug-glibcxx mode, add -D_GLIBCXX_DEBUG
+ # also take note that we are using this to relax `make nmcheck`
+ use_debug_glibcxx=no
+-if test "$debug_glibcxx" == true ; then
++if test "$debug_glibcxx" = true ; then
+ AC_MSG_NOTICE([Check boundaries, adding -D_GLIBCXX_DEBUG])
+ AC_DEFINE([_GLIBCXX_DEBUG])
+ use_debug_glibcxx=yes
+@@ -903,6 +903,7 @@ AC_DEFINE([_REENTRANT])
+ #### Options for dynamic library to work properly ####
+ AC_SUBST(SOEXT)
+ AC_SUBST(LDSHARED)
++AC_SUBST(RPATH)
+ # these are libraries that should be linked also to MD engines
+ AC_SUBST(STATIC_LIBS)
+ # python executable
+@@ -910,7 +911,7 @@ AC_SUBST(PYTHON_BIN)
+
+ AC_SUBST(MPIEXEC)
+
+-if test "$shared" == true ; then
++if test "$shared" = true ; then
+ case `(uname)` in
+ (Darwin)
+ AC_MSG_NOTICE([*** Special settings for dynamic libraries on OSX ***])
+@@ -930,7 +931,7 @@ if test "$shared" == true ; then
+ SOEXT=so
+ LDSHARED="$LDSHARED -shared"
+ PLUMED_CHECK_LDFLAGS([-rdynamic])
+- if test "$bsymbolic" == true ; then
++ if test "$bsymbolic" = true ; then
+ PLUMED_CHECK_LDFLAGS([-Wl,-Bsymbolic])
+ fi
+ ;;
+@@ -961,17 +962,20 @@ then
+ rm -f conftest.$SOEXT
+ readelf=""
+ AC_CHECK_PROG([readelf],[readelf],[found])
+- if test "$readelf" == found ; then
+- test_LDSHARED="$LDSHARED -Wl,-R -Wl,/some/random/dir/"
+- $test_LDSHARED $LDFLAGS conftest.o -o conftest.$SOEXT 1>/dev/null 2>/dev/null
+- if readelf -d conftest.$SOEXT | grep RPATH | grep -q /some/random/dir ; then
+- LDSHARED="$LDSHARED -Wl,-R -Wl,\"$libdir:$LIBRARY_PATH\""
+- else
+- AC_MSG_WARN([-R option seems not working, disabling rpath])
+- fi
+- else
+- AC_MSG_WARN([readelf not available, no way to set rpath])
+- fi
++# Believe us that we provide a toolchain that does rpath, just not accepting
++# any random directories in pkgsrc!
++# Also need rpath in LDFLAGS for plumed binary!
++# if test "$readelf" = found ; then
++# test_LDSHARED="$LDSHARED -Wl,-R -Wl,/some/random/dir/"
++# $test_LDSHARED $LDFLAGS conftest.o -o conftest.$SOEXT 1>/dev/null 2>/dev/null
++# if readelf -d conftest.$SOEXT | grep RPATH | grep -q /some/random/dir ; then
++ RPATH="-Wl,-R -Wl,\"$libdir:$LIBRARY_PATH\""
++# else
++# AC_MSG_WARN([-R option seems not working, disabling rpath])
++# fi
++# else
++# AC_MSG_WARN([readelf not available, no way to set rpath])
++# fi
+ fi
+ rm -f conftest.*
+ fi
+@@ -979,17 +983,17 @@ fi
+
+ AC_SUBST(make_doc)
+ make_doc=no
+-if test "$doc" == true
++if test "$doc" = true
+ then
+
+ make_doc=yes
+
+ ### Look for doxygen
+ AC_CHECK_PROG([doxygen],[doxygen],[found])
+-if test "$doxygen" == found
++if test "$doxygen" = found
+ then
+ doxygen_version=`doxygen --version | awk 'BEGIN{FS="."}{if($1>1 || ($1==1 && $2>=8)) print "ok"}'`
+- if test "$doxygen_version" == ok
++ if test "$doxygen_version" = ok
+ then
+ AC_MSG_NOTICE([Doxygen version is fine])
+ else
+@@ -1015,7 +1019,7 @@ fi
+
+ AC_SUBST(make_pdfdoc)
+ make_pdfdoc=""
+-if test "$pdfdoc" == true && test "$make_doc" == yes
++if test "$pdfdoc" = true && test "$make_doc" = yes
+ then
+ AC_MSG_NOTICE([A PDF version of the manual will be generated])
+ make_pdfdoc=yes
+@@ -1049,7 +1053,7 @@ int main(int argc,char*argv[[]]){
+ [ program_can_run=no ; AC_MSG_RESULT([no (cross compiling)]) ]
+ )
+
+-if test $mpi_found == ok ; then
++if test $mpi_found = ok ; then
+ AC_SUBST(program_can_run_mpi)
+ program_can_run_mpi=""
+ AC_MSG_CHECKING([whether a program compiled with mpi can be run on this machine])
+@@ -1072,7 +1076,7 @@ int main(int argc,char*argv[[]]){
+ )
+ fi
+
+-if test $mpi_found == ok ; then
++if test $mpi_found = ok ; then
+ if test -n "$MPIEXEC" ; then
+ AC_MSG_NOTICE([Regtest suite will use $MPIEXEC command to run MPI tests])
+ else
+@@ -1080,15 +1084,15 @@ if test $mpi_found == ok ; then
+ fi
+ fi
+
+-if test "$SOEXT" == "dylib" ; then
++if test "$SOEXT" = "dylib" ; then
+ use_absolute_soname=yes
+ else
+ use_absolute_soname=no
+ fi
+
+ AC_SUBST(use_absolute_soname)
+-if test "$absolute_soname" == true ; then
+- if test "$SOEXT" == "dylib" ; then
++if test "$absolute_soname" = true ; then
++ if test "$SOEXT" = "dylib" ; then
+ AC_MSG_WARN([--enable-absolute-soname has no effect on OSX])
+ else
+ AC_MSG_NOTICE([enabling absolute soname. Full path will be hardcoded in plumed library soname])
+@@ -1096,8 +1100,8 @@ if test "$absolute_soname" == true ; the
+ fi
+ fi
+
+-if test "$absolute_install_name" == false ; then
+- if test "$SOEXT" == "so" ; then
++if test "$absolute_install_name" = false ; then
++ if test "$SOEXT" = "so" ; then
+ AC_MSG_WARN([--disable-absolute-install-name has no effect on Linux])
+ else
+ AC_MSG_NOTICE([enabling relative install_name. You will have to set DYLD_LIBRARY_PATH yor plumed libraries to be found at runtime])
+@@ -1106,8 +1110,8 @@ if test "$absolute_install_name" == fals
+ fi
+
+ AC_SUBST(use_loader_path)
+-if test "$SOEXT" == "dylib" ; then
+- if test "$loader_path" == true ; then
++if test "$SOEXT" = "dylib" ; then
++ if test "$loader_path" = true ; then
+ use_loader_path=yes
+ else
+ use_loader_path=no
+@@ -1121,7 +1125,7 @@ AC_MSG_NOTICE([PLUMED seems to be config
+ AC_MSG_NOTICE([**************************])
+ AC_SUBST(LD_RO)
+ LD_RO=
+-if test "$ld_r" == true ; then
++if test "$ld_r" = true ; then
+ for test_LD_RO in "$($CXX --print-prog-name=ld) -r -o" "$CXX -Wl,-r -o" "ld -r -o"
+ do
+ AC_MSG_CHECKING([whether C++ objects can be grouped with $test_LD_RO])
+@@ -1162,7 +1166,7 @@ fi
+
+ AC_SUBST(AR_CR)
+ AR_CR=
+-if test "$ar_cr" == true ; then
++if test "$ar_cr" = true ; then
+ for test_AR_CR in "$($CXX --print-prog-name=ar) cr" "ar cr"
+ do
+ AC_MSG_CHECKING([whether static libraries can be created with $test_AR_CR])
+@@ -1204,14 +1208,14 @@ fi
+ make_static_archive=no
+ AC_SUBST(make_static_archive)
+
+-if test "${static_archive}" == true ; then
++if test "${static_archive}" = true ; then
+ if test -z "$LD_RO" || test -z "$AR_CR" ; then
+ AC_MSG_WARN([no way to create a static archive if ld -ro or ar cr do not work])
+ static_archive=false
+ fi
+ fi
+
+-if test "${static_archive}" == true ; then
++if test "${static_archive}" = true ; then
+ AC_MSG_CHECKING([whether static-object constructors can be linked from a static archive])
+
+ magic_token=c1bc476d093a3a5c67b4530e6c54c633593fe9aa
+@@ -1251,7 +1255,7 @@ EOF
+ fi
+ fi
+
+-if test "${static_patch}" == true ; then
++if test "${static_patch}" = true ; then
+
+ AC_MSG_NOTICE([I will now check if C++ objects can be linked by C/Fortran compilers])
+ AC_MSG_NOTICE([This is relevant if you want to use plumed patch --static on a non-C++ code])
+@@ -1290,7 +1294,7 @@ EOF
+ $CXX $CXXFLAGS -c conftest.cpp
+ # start search:
+ found=
+- if test "${libsearch}" == true ; then
++ if test "${libsearch}" = true ; then
+ testlibs="-lstdc++ -lc++ -lmpi_cxx"
+ else
+ testlibs=""
+@@ -1324,7 +1328,7 @@ else
+ AC_MSG_NOTICE([Static patching is disabled, thus tests required for static patching will be skipped])
+ fi
+
+-if test "$prefix" == NONE
++if test "$prefix" = NONE
+ then
+ prefix=/usr/local
+ fi
+@@ -1334,7 +1338,7 @@ pkgconfig_bin=""
+ AC_PATH_PROGS(pkgconfig_bin,pkg-config)
+
+ if test -z "$BASH_COMPLETION_DIR" && test -n "$pkgconfig_bin"; then
+- if test "$prefix" == "$(pkg-config --variable=prefix bash-completion 2>/dev/null)"
++ if test "$prefix" = "$(pkg-config --variable=prefix bash-completion 2>/dev/null)"
+ then
+ AC_MSG_NOTICE([bash-completion is installed on the same prefix where plumed will be installed])
+ if pkg-config --variable=completionsdir bash-completion 2>/dev/null >/dev/null ; then
+@@ -1401,8 +1405,8 @@ if test -z "$BASH_COMPLETION_DIR" ; then
+ AC_MSG_WARN([**** complete -F _$program_name -o default $program_name])
+ fi
+
+-if test $mpi == true; then
+- if test $mpi_found == ok; then
++if test $mpi = true; then
++ if test $mpi_found = ok; then
+ AC_MSG_NOTICE([**** PLUMED will be compiled using MPI])
+ else
+ AC_MSG_WARN([**** PLUMED will NOT be compiled using MPI because MPI have not been found!])
+@@ -1411,11 +1415,11 @@ else
+ AC_MSG_NOTICE([**** PLUMED will be compiled without MPI])
+ fi
+
+-if test $program_can_run == no ; then
++if test $program_can_run = no ; then
+ AC_MSG_WARN([plumed executable will not run on this machine])
+ AC_MSG_WARN([to patch an MD code use 'plumed-patch'])
+-elif test $mpi_found == ok ; then
+- if test $program_can_run_mpi == no ; then
++elif test $mpi_found = ok ; then
++ if test $program_can_run_mpi = no ; then
+ AC_MSG_WARN([plumed executable will not run on this machine])
+ AC_MSG_WARN([unless you invoke it as 'plumed --no-mpi'])
+ AC_MSG_WARN([all command line tools are thus available as 'plumed --no-mpi name-of-the-tool'])
Home |
Main Index |
Thread Index |
Old Index