 @@ -1,14 +1,14 @@
-# $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
 SUBDIR+=	R
 SUBDIR+=	R-CGIwithR
 SUBDIR+=	R-DAAG
 SUBDIR+=	R-DBI
 SUBDIR+=	R-DEoptimR
 SUBDIR+=	R-FNN
 SUBDIR+=	R-Formula
 SUBDIR+=	R-GRASS
 SUBDIR+=	R-ISLR
 SUBDIR+=	R-ISwR
 @@ -352,26 +352,27 @@ SUBDIR+=	p5-Statistics-CaseResampling
 SUBDIR+=	p5-Statistics-Descriptive
 SUBDIR+=	p5-Statistics-Distributions
 SUBDIR+=	p5-Statistics-TTest
 SUBDIR+=	p5-Test-Number-Delta
 SUBDIR+=	pari
 SUBDIR+=	pari-galdata
 SUBDIR+=	pari23
 SUBDIR+=	pcg
 SUBDIR+=	pear-Math_BigInteger
 SUBDIR+=	pear-Numbers_Roman
 SUBDIR+=	pear-Numbers_Words
 SUBDIR+=	php-bcmath
 SUBDIR+=	php-stats
 SUBDIR+=	plumed
 SUBDIR+=	ppl
 SUBDIR+=	prng
 SUBDIR+=	pspp
 SUBDIR+=	py-Keras-Applications
 SUBDIR+=	py-Keras-Preprocessing
 SUBDIR+=	py-Theano
 SUBDIR+=	py-abcpmc
 SUBDIR+=	py-almost
 SUBDIR+=	py-arviz
 SUBDIR+=	py-asdf
 SUBDIR+=	py-asteval
 SUBDIR+=	py-astroML
 SUBDIR+=	py-astropy

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.

# $NetBSD: Makefile,v 1.1 2022/07/08 19:47:59 thor Exp $ DISTNAME= plumed-2.8.0 CATEGORIES= math MASTER_SITES= ${MASTER_SITE_GITHUB:=plumed/plumed2/releases/download/v2.8.0/} EXTRACT_SUFX= .tgz MAINTAINER= thor@NetBSD.org HOMEPAGE= https://www.plumed.org/ COMMENT= Molecular dynamics support library LICENSE= gnu-lgpl-v3 GNU_CONFIGURE= yes USE_LANGUAGES= c c++ fortran USE_TOOLS+= gmake bash TEST_TARGET= check CONFIGURE_ARGS+= --enable-gsl CONFIGURE_ARGS+= --enable-external-blas --enable-external-lapack CONFIGURE_ARGS+= LIBS='${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"

@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 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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

$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

# $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

$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@

$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

$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'])