From owner-freebsd-ports-bugs@FreeBSD.ORG Fri Feb 13 18:50:04 2009 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 395E51065673 for ; Fri, 13 Feb 2009 18:50:04 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id 095E68FC0C for ; Fri, 13 Feb 2009 18:50:04 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.14.3/8.14.3) with ESMTP id n1DIo38J033888 for ; Fri, 13 Feb 2009 18:50:03 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.3/8.14.3/Submit) id n1DIo3Jd033887; Fri, 13 Feb 2009 18:50:03 GMT (envelope-from gnats) Resent-Date: Fri, 13 Feb 2009 18:50:03 GMT Resent-Message-Id: <200902131850.n1DIo3Jd033887@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Joerg Pulz Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 806FA106567B for ; Fri, 13 Feb 2009 18:41:34 +0000 (UTC) (envelope-from Joerg.Pulz@frm2.tum.de) Received: from mailhost.frm2.tum.de (mailhost.frm2.tum.de [129.187.179.12]) by mx1.freebsd.org (Postfix) with ESMTP id D40658FC0A for ; Fri, 13 Feb 2009 18:41:33 +0000 (UTC) (envelope-from Joerg.Pulz@frm2.tum.de) Received: from localhost (mailhost.frm2.tum.de [129.187.179.12]) by mailhost.frm2.tum.de (8.14.3/8.14.3) with ESMTP id n1DIMZ9h027877 for ; Fri, 13 Feb 2009 19:22:35 +0100 (CET) (envelope-from jpulz@frm2.tum.de) Received: from hades.admin.frm2 (hades.admin.frm2 [172.25.1.10]) by mailhost.frm2.tum.de (8.14.3/8.14.3) with ESMTP id n1DIMXpN027873 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT) for ; Fri, 13 Feb 2009 19:22:33 +0100 (CET) (envelope-from jpulz@frm2.tum.de) Received: from hades.admin.frm2 (localhost [127.0.0.1]) by hades.admin.frm2 (8.14.2/8.14.2) with ESMTP id n1DIMWWu037778 for ; Fri, 13 Feb 2009 19:22:32 +0100 (CET) (envelope-from jpulz@frm2.tum.de) Received: (from jpulz@localhost) by hades.admin.frm2 (8.14.2/8.14.2/Submit) id n1DIMW9X037769; Fri, 13 Feb 2009 19:22:32 +0100 (CET) (envelope-from jpulz) Message-Id: <200902131822.n1DIMW9X037769@hades.admin.frm2> Date: Fri, 13 Feb 2009 19:22:32 +0100 (CET) From: Joerg Pulz To: FreeBSD-gnats-submit@FreeBSD.org X-Send-Pr-Version: 3.113 Cc: Subject: ports/131655: science/gromacs: update to v4.0.3 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list Reply-To: Joerg Pulz List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 13 Feb 2009 18:50:04 -0000 >Number: 131655 >Category: ports >Synopsis: science/gromacs: update to v4.0.3 >Confidential: no >Severity: non-critical >Priority: medium >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Fri Feb 13 18:50:03 UTC 2009 >Closed-Date: >Last-Modified: >Originator: Joerg Pulz >Release: FreeBSD 7.1-RELEASE-p2 i386 >Organization: Technische Universitaet Muenchen / ZWE FRM-II >Environment: System: FreeBSD hades.admin.frm2 7.1-RELEASE-p2 FreeBSD 7.1-RELEASE-p2 #0: Mon Jan 19 12:01:54 CET 2009 root@hades.admin.frm2:/usr/obj/usr/src/sys/HADES i386 >Description: Update the science/gromacs port to version 4.0.3. Changes: Makefile - introduce OPTIONS and set reasonable defaults - update *_DEPENDS and CONFIGURE_ARGS - add manpages and sort alphabetically - allow to choose between different FFT libraries - allow to choose between MPI implementations (very useful if you want to more then one core or coputers) distinfo - regen for the new version pkg-plist - update for the new version - sort alphabetically >How-To-Repeat: >Fix: - apply the patch - remove all zero-sized patches from ${FILESDIR} - add ${FILESDIR}/patch-configure --- science_gromacs.diff begins here --- Index: Makefile =================================================================== RCS file: /home/ncvs/ports/science/gromacs/Makefile,v retrieving revision 1.12 diff -u -r1.12 Makefile --- Makefile 21 Aug 2008 06:18:12 -0000 1.12 +++ Makefile 10 Feb 2009 19:53:51 -0000 @@ -6,153 +6,187 @@ # PORTNAME= gromacs -PORTVERSION= 3.2.1 -PORTREVISION= 4 +PORTVERSION= 4.0.3 +#PORTREVISION= 4 CATEGORIES= science MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/ MAINTAINER= stephen@math.missouri.edu COMMENT= Compute molecular dynamics -.ifndef WITHOUT_FFTW -LIB_DEPENDS= fftw:${PORTSDIR}/math/fftw:install -.endif -.ifdef WITH_MPI -BUILD_DEPENDS= ${LOCALBASE}/mpich/bin/mpicc:${PORTSDIR}/net/mpich -RUN_DEPENDS= ${LOCALBASE}/mpich/bin/mpicc:${PORTSDIR}/net/mpich -.endif - +USE_GNOME= libxml2 USE_GMAKE= yes USE_AUTOTOOLS= libtool:15 USE_LDCONFIG= yes CONFIGURE_ENV= CPPFLAGS=-I${LOCALBASE}/include LDFLAGS=-L${LOCALBASE}/lib -CONFIGURE_ARGS= --exec-prefix=${PREFIX} +CONFIGURE_ARGS= --exec-prefix=${PREFIX} --program-suffix="" --enable-shared PLIST_SUB= BUILD=${MACHINE_ARCH}-portbld-freebsd${OSREL} -.ifndef WITHOUT_FFTW -.ifdef WITH_FLOAT -IGNORE= Cannot currently build with fftw and single precision floating point -.elifdef WITH_MPI -IGNORE= Cannot currently build with fftw and mpi support +OPTIONS= FFTW3 "Use FFT routines from math/fftw3" on \ + FFTW2 "Use FFT routines from math/fftw" off \ + GSL "Enable extra analysis using math/gsl" on \ + FLOAT "Use single instead of double precision" off \ + X11 "Build and install X11 programs" on \ + MPICH "Enable MPI support using net/mpich" off \ + OMPI "Enable MPI support using net/openmpi" off + +.include + +.if !defined(WITHOUT_FFTW3) && defined(WITH_FFTW2) +IGNORE= Cannot build with FFTW3 and FFTW2. Run 'make config' again and choose only one of them. .endif + +.if defined(WITH_MPICH) && defined(WITH_OMPI) +IGNORE= Cannot build with MPICH and OpenMPI support. Run 'make config' again and choose only one of them. .endif -.ifdef WITHOUT_X -PLIST_SUB+= WITHOUT_X="@comment " -CONFIGURE_ARGS+= --without-x +.if !defined(WITHOUT_FFTW3) +CONFIGURE_ARGS+= --with-fft=fftw3 +. if defined(WITH_FLOAT) +LIB_DEPENDS+= fftw3f.4:${PORTSDIR}/math/fftw3-float +. else +LIB_DEPENDS+= fftw3.4:${PORTSDIR}/math/fftw3 +. endif .else -PLIST_SUB+= WITHOUT_X= -CONFIGURE_ARGS+= --with-x -USE_XORG= x11 +. if defined(WITH_FFTW2) +CONFIGURE_ARGS+= --with-fft=fftw2 +. if defined(WITH_FLOAT) +LIB_DEPENDS+= sfftw.2:${PORTSDIR}/math/fftw-float +. else +LIB_DEPENDS+= fftw.2:${PORTSDIR}/math/fftw +. endif +. else +CONFIGURE_ARGS+= --with-fft=fftpack +. endif .endif -.ifndef WITH_FLOAT -CONFIGURE_ARGS+= --disable-float --program-suffix= -PLIST_SUB+= SUFFIX_D=_d SUFFIX_DOUBLE=_double +.if !defined(WITHOUT_GSL) +CONFIGURE_ARGS+= --with-gsl +LIB_DEPENDS+= gsl.13:${PORTSDIR}/math/gsl .else -PLIST_SUB+= SUFFIX_D= SUFFIX_DOUBLE= +CONFIGURE_ARGS+= --without-gsl .endif -.ifdef WITHOUT_FFTW -CONFIGURE_ARGS+= --without-fftw +.if !defined(WITHOUT_X11) +PLIST_SUB+= X11="" +CONFIGURE_ARGS+= --with-x +USE_XORG= x11 +.else +PLIST_SUB+= X11="@comment " +CONFIGURE_ARGS+= --without-x .endif -.ifdef WITH_MPI +.if defined(WITH_FLOAT) +PLIST_SUB+= SUFFIX_D="" SUFFIX_DOUBLE="" +.else +CONFIGURE_ARGS+= --disable-float +PLIST_SUB+= SUFFIX_D=_d SUFFIX_DOUBLE=_double +.endif + +.if defined(WITH_MPICH) || defined(WITH_OMPI) CONFIGURE_ARGS+= --enable-mpi +. if defined(WITH_MPICH) CONFIGURE_ENV+= MPICC=${PREFIX}/mpich/bin/mpicc -PLIST_SUB+= WITH_MPI= SUFFIX_MPI=_mpi WITHOUT_MPI="@comment " +BUILD_DEPENDS+= ${PREFIX}/mpich/bin/mpicc:${PORTSDIR}/net/mpich +RUN_DEPENDS+= ${PREFIX}/mpich/bin/mpicc:${PORTSDIR}/net/mpich +. else +CONFIGURE_ENV+= MPICC=${PREFIX}/mpi/openmpi/bin/mpicc +BUILD_DEPENDS+= ${PREFIX}/mpi/openmpi/bin/mpicc:${PORTSDIR}/net/openmpi +RUN_DEPENDS+= ${PREFIX}/mpi/openmpi/bin/mpicc:${PORTSDIR}/net/openmpi +. endif +PLIST_SUB+= SUFFIX_MPI="_mpi" MPI="" .else -PLIST_SUB+= WITH_MPI="@comment " SUFFIX_MPI= WITHOUT_MPI= +PLIST_SUB+= SUFFIX_MPI="" MPI="@comment " .endif MAN1= anadock.1 \ + do_dssp.1 \ + editconf.1 \ + eneconv.1 \ + g_anaeig.1 \ + g_analyze.1 \ + g_angle.1 \ + g_bond.1 \ + g_bundle.1 \ + g_chi.1 \ g_cluster.1 \ - g_filter.1 \ - g_potential.1 \ - g_velacc.1 \ - ngmx.1 \ - cdist.1 \ g_clustsize.1 \ - g_gyrate.1 \ - g_rama.1 \ - g_wham.1 \ - pdb2gmx.1 \ - disco.1 \ g_confrms.1 \ - g_h2order.1 \ - g_rdf.1 \ - genbox.1 \ - protonate.1 \ - do_dssp.1 \ g_covar.1 \ - g_hbond.1 \ - g_rms.1 \ - genconf.1 \ - tpbconv.1 \ - editconf.1 \ + g_current.1 \ g_density.1 \ - g_helix.1 \ - g_rmsdist.1 \ - genion.1 \ - trjcat.1 \ - eneconv.1 \ + g_densmap.1 \ g_dielectric.1 \ - g_lie.1 \ - g_rmsf.1 \ - genpr.1 \ - trjconv.1 \ - ffscan.1 \ g_dih.1 \ - g_mdmat.1 \ - g_rotacf.1 \ - gmxcheck.1 \ - trjorder.1 \ - g_anaeig.1 \ g_dipoles.1 \ - g_mindist.1 \ - g_saltbr.1 \ - gmxdump.1 \ - wheel.1 \ - g_analyze.1 \ g_disre.1 \ - g_morph.1 \ - g_sas.1 \ - grompp.1 \ - x2top.1 \ - g_angle.1 \ g_dist.1 \ - g_msd.1 \ - g_sgangle.1 \ - highway.1 \ - xpm2ps.1 \ - g_bond.1 \ g_dyndom.1 \ - g_nmeig.1 \ - g_sorient.1 \ - make_ndx.1 \ - xrama.1 \ - g_bundle.1 \ g_enemat.1 \ - g_nmens.1 \ - g_tcaf.1 \ - mdrun.1 \ - g_chi.1 \ g_energy.1 \ + g_filter.1 \ + g_gyrate.1 \ + g_h2order.1 \ + g_hbond.1 \ + g_helix.1 \ + g_helixorient.1 \ + g_kinetics.1 \ + g_lie.1 \ + g_mdmat.1 \ + g_mindist.1 \ + g_morph.1 \ + g_msd.1 \ + g_nmeig.1 \ + g_nmens.1 \ + g_nmtraj.1 \ g_order.1 \ + g_polystat.1 \ + g_potential.1 \ + g_principal.1 \ + g_rama.1 \ + g_rdf.1 \ + g_rms.1 \ + g_rmsdist.1 \ + g_rmsf.1 \ + g_rotacf.1 \ + g_saltbr.1 \ + g_sas.1 \ + g_sdf.1 \ + g_sgangle.1 \ + g_sham.1 \ + g_sorient.1 \ + g_spatial.1 \ + g_spol.1 \ + g_tcaf.1 \ g_traj.1 \ - mk_angndx.1 - -.include - -pre-fetch: - @${ECHO} - @${ECHO} "OPTIONS:" - @${ECHO} - @${ECHO} "To compile without X11: define WITHOUT_X" - @${ECHO} "To compile using single precision floating point: define WITH_FLOAT" - @${ECHO} "To compile without fftw: define WITHOUT_FFTW" - @${ECHO} "To compile with mpi: define WITH_MPI" - @${ECHO} + g_vanhove.1 \ + g_velacc.1 \ + g_wham.1 \ + gen_table.1 \ + genbox.1 \ + genconf.1 \ + genion.1 \ + genrestr.1 \ + gmxcheck.1 \ + gmxdump.1 \ + grompp.1 \ + highway.1 \ + make_edi.1 \ + make_ndx.1 \ + mdrun.1 \ + mk_angndx.1 \ + ngmx.1 \ + pdb2gmx.1 \ + protonate.1 \ + sigeps.1 \ + tpbconv.1 \ + trjcat.1 \ + trjconv.1 \ + trjorder.1 \ + wheel.1 \ + x2top.1 \ + xpm2ps.1 \ + xrama.1 .include Index: distinfo =================================================================== RCS file: /home/ncvs/ports/science/gromacs/distinfo,v retrieving revision 1.2 diff -u -r1.2 distinfo --- distinfo 24 Jan 2006 01:01:33 -0000 1.2 +++ distinfo 10 Feb 2009 19:53:51 -0000 @@ -1,3 +1,3 @@ -MD5 (gromacs-3.2.1.tar.gz) = d298386495f6ee39b3155ce951984485 -SHA256 (gromacs-3.2.1.tar.gz) = de85710553202e17a3ac67049d2cf51117939d3d8944a34aa0909aa3771bef53 -SIZE (gromacs-3.2.1.tar.gz) = 3302723 +MD5 (gromacs-4.0.3.tar.gz) = 2902403671a0f9b0934ddf3ca586b7ec +SHA256 (gromacs-4.0.3.tar.gz) = 6fc33ac9e1e9b208e2e8c73cb9e95940ed86969207fedc02bf30119f2ed58572 +SIZE (gromacs-4.0.3.tar.gz) = 8420556 Index: pkg-plist =================================================================== RCS file: /home/ncvs/ports/science/gromacs/pkg-plist,v retrieving revision 1.3 diff -u -r1.3 pkg-plist --- pkg-plist 23 Feb 2006 10:38:50 -0000 1.3 +++ pkg-plist 10 Feb 2009 19:53:51 -0000 @@ -3,16 +3,13 @@ bin/GMXRC.csh bin/GMXRC.zsh bin/anadock -bin/average -bin/cdist bin/completion.bash bin/completion.csh bin/completion.zsh -bin/disco +bin/demux.pl bin/do_dssp bin/editconf bin/eneconv -bin/ffscan bin/g_anaeig bin/g_analyze bin/g_angle @@ -23,7 +20,9 @@ bin/g_clustsize bin/g_confrms bin/g_covar +bin/g_current bin/g_density +bin/g_densmap bin/g_dielectric bin/g_dih bin/g_dipoles @@ -37,6 +36,8 @@ bin/g_h2order bin/g_hbond bin/g_helix +bin/g_helixorient +bin/g_kinetics bin/g_lie bin/g_mdmat bin/g_mindist @@ -44,8 +45,11 @@ bin/g_msd bin/g_nmeig bin/g_nmens +bin/g_nmtraj bin/g_order +bin/g_polystat bin/g_potential +bin/g_principal bin/g_rama bin/g_rdf bin/g_rms @@ -54,77 +58,88 @@ bin/g_rotacf bin/g_saltbr bin/g_sas +bin/g_sdf bin/g_sgangle +bin/g_sham bin/g_sorient +bin/g_spatial +bin/g_spol bin/g_tcaf bin/g_traj +bin/g_vanhove bin/g_velacc bin/g_wham bin/genbox bin/genconf bin/genion -bin/genpr +bin/genrestr bin/gmxcheck bin/gmxdump bin/grompp -%%WITHOUT_X%%bin/highway +%%X11%%bin/highway bin/luck bin/make_edi bin/make_ndx bin/mdrun bin/mk_angndx -%%WITHOUT_X%%bin/ngmx +%%X11%%bin/ngmx bin/pdb2gmx bin/protonate +bin/sigeps bin/tpbconv bin/trjcat bin/trjconv bin/trjorder bin/wheel bin/x2top +bin/xplor2gmx.pl bin/xpm2ps -%%WITHOUT_X%%bin/xrama +%%X11%%bin/xrama include/gromacs/3dview.h include/gromacs/assert.h include/gromacs/atomprop.h -include/gromacs/axp_asm.h -include/gromacs/block_tx.h include/gromacs/bondf.h include/gromacs/calcgrid.h include/gromacs/calch.h include/gromacs/calcmu.h -include/gromacs/callf77.h +include/gromacs/checkpoint.h include/gromacs/confio.h include/gromacs/constr.h include/gromacs/copyrite.h -include/gromacs/detectcpu.h +include/gromacs/coulomb.h include/gromacs/dihre.h include/gromacs/disre.h include/gromacs/do_fit.h -include/gromacs/do_md.h -include/gromacs/dummies.h +include/gromacs/domdec.h +include/gromacs/domdec_network.h include/gromacs/ebin.h include/gromacs/edsam.h include/gromacs/enxio.h -include/gromacs/ewald.h -include/gromacs/ewald_util.h -include/gromacs/fatal.h include/gromacs/ffscanf.h include/gromacs/fftgrid.h -include/gromacs/fftw_wrapper.h include/gromacs/filenm.h include/gromacs/force.h include/gromacs/futil.h include/gromacs/gbutil.h include/gromacs/gmx_ana.h +include/gromacs/gmx_arpack.h +include/gromacs/gmx_blas.h +include/gromacs/gmx_cyclecounter.h +include/gromacs/gmx_fatal.h +include/gromacs/gmx_fft.h +include/gromacs/gmx_lapack.h +include/gromacs/gmx_parallel_3dfft.h include/gromacs/gmx_random.h include/gromacs/gmx_system_xdr.h +include/gromacs/gmx_thread.h +include/gromacs/gmx_wallcycle.h include/gromacs/gmxcomplex.h include/gromacs/gmxfio.h +include/gromacs/gpp_atomtype.h +include/gromacs/gpp_nextnb.h include/gromacs/grompp.h include/gromacs/gstat.h include/gromacs/index.h -include/gromacs/init.h include/gromacs/invblock.h include/gromacs/macros.h include/gromacs/magic.h @@ -134,28 +149,31 @@ include/gromacs/mdatoms.h include/gromacs/mdebin.h include/gromacs/mdrun.h -include/gromacs/metacode.h +include/gromacs/mpelogging.h include/gromacs/mshift.h +include/gromacs/mtop_util.h +include/gromacs/mtxio.h include/gromacs/mvdata.h include/gromacs/names.h include/gromacs/network.h -include/gromacs/nr.h +include/gromacs/nonbonded.h include/gromacs/nrama.h include/gromacs/nrjac.h include/gromacs/nrnb.h include/gromacs/ns.h -include/gromacs/nsb.h include/gromacs/nsgrid.h include/gromacs/orires.h +include/gromacs/partdec.h include/gromacs/pbc.h include/gromacs/pdbio.h include/gromacs/pdebug.h +include/gromacs/perf_est.h include/gromacs/physics.h include/gromacs/pme.h -include/gromacs/ppc_altivec.h include/gromacs/pppm.h include/gromacs/princ.h include/gromacs/pull.h +include/gromacs/qmmm.h include/gromacs/random.h include/gromacs/rbin.h include/gromacs/rdgroup.h @@ -163,12 +181,13 @@ include/gromacs/readinp.h include/gromacs/reorder.h include/gromacs/rmpbc.h -include/gromacs/sheader.h +include/gromacs/shellfc.h include/gromacs/shift.h -include/gromacs/shift_util.h include/gromacs/smalloc.h include/gromacs/sortwater.h +include/gromacs/sparsematrix.h include/gromacs/split.h +include/gromacs/splitter.h include/gromacs/statusio.h include/gromacs/statutil.h include/gromacs/strdb.h @@ -178,6 +197,7 @@ include/gromacs/sysstuff.h include/gromacs/tags.h include/gromacs/tgroup.h +include/gromacs/topsort.h include/gromacs/tpxio.h include/gromacs/transfer.h include/gromacs/trnio.h @@ -186,7 +206,7 @@ include/gromacs/types/atoms.h include/gromacs/types/block.h include/gromacs/types/commrec.h -include/gromacs/types/edsams.h +include/gromacs/types/constr.h include/gromacs/types/energy.h include/gromacs/types/enums.h include/gromacs/types/fcdata.h @@ -203,9 +223,11 @@ include/gromacs/types/nblist.h include/gromacs/types/nbslist.h include/gromacs/types/nrnb.h -include/gromacs/types/nsborder.h +include/gromacs/types/ns.h include/gromacs/types/nsgrid.h -include/gromacs/types/parm.h +include/gromacs/types/pbc.h +include/gromacs/types/qmmmrec.h +include/gromacs/types/shellfc.h include/gromacs/types/simple.h include/gromacs/types/state.h include/gromacs/types/symtab.h @@ -216,34 +238,27 @@ include/gromacs/vcm.h include/gromacs/vec.h include/gromacs/viewit.h +include/gromacs/vsite.h include/gromacs/wgms.h include/gromacs/wman.h include/gromacs/writeps.h -include/gromacs/x86_3dnow.h -include/gromacs/x86_sse.h -include/gromacs/x86_sse2.h include/gromacs/xdrf.h include/gromacs/xtcio.h include/gromacs/xvgr.h lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.a lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.la lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so -lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so.3 -lib/libgmxana%%SUFFIX_D%%.a -lib/libgmxana%%SUFFIX_D%%.la -lib/libgmxana%%SUFFIX_D%%.so -%%WITHOUT_MPI%%lib/libgmxana%%SUFFIX_D%%.a -%%WITHOUT_MPI%%lib/libgmxana%%SUFFIX_D%%.la -%%WITHOUT_MPI%%lib/libgmxana%%SUFFIX_D%%.so -%%WITHOUT_MPI%%lib/libgmxana%%SUFFIX_D%%.so.3 -%%WITH_MPI%%lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.a -%%WITH_MPI%%lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.la -%%WITH_MPI%%lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so -%%WITH_MPI%%lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so.3 +lib/libgmx%%SUFFIX_MPI%%%%SUFFIX_D%%.so.5 +%%MPI%%lib/libgmxana%%SUFFIX_D%%.a +%%MPI%%lib/libgmxana%%SUFFIX_D%%.so +lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.a +lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.la +lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so +lib/libgmxana%%SUFFIX_MPI%%%%SUFFIX_D%%.so.5 lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.a lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.la lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so -lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so.3 +lib/libmd%%SUFFIX_MPI%%%%SUFFIX_D%%.so.5 %%DATADIR%%/html/gmxfaq.html %%DATADIR%%/html/images/1ctf-0.2.jpg %%DATADIR%%/html/images/1ctf-0.5.jpg @@ -280,6 +295,7 @@ %%DATADIR%%/html/images/topologies.gif %%DATADIR%%/html/images/xvgr.gif %%DATADIR%%/html/online.html +%%DATADIR%%/html/online/cpt.html %%DATADIR%%/html/online/dat.html %%DATADIR%%/html/online/dlg.html %%DATADIR%%/html/online/do_dssp.html @@ -304,6 +320,7 @@ %%DATADIR%%/html/online/g_confrms.html %%DATADIR%%/html/online/g_covar.html %%DATADIR%%/html/online/g_density.html +%%DATADIR%%/html/online/g_densmap.html %%DATADIR%%/html/online/g_dielectric.html %%DATADIR%%/html/online/g_dih.html %%DATADIR%%/html/online/g_dipoles.html @@ -334,6 +351,7 @@ %%DATADIR%%/html/online/g_saltbr.html %%DATADIR%%/html/online/g_sas.html %%DATADIR%%/html/online/g_sgangle.html +%%DATADIR%%/html/online/g_sham.html %%DATADIR%%/html/online/g_sorient.html %%DATADIR%%/html/online/g_tcaf.html %%DATADIR%%/html/online/g_traj.html @@ -355,6 +373,7 @@ %%DATADIR%%/html/online/itp.html %%DATADIR%%/html/online/log.html %%DATADIR%%/html/online/m2p.html +%%DATADIR%%/html/online/make_edi.html %%DATADIR%%/html/online/make_ndx.html %%DATADIR%%/html/online/map.html %%DATADIR%%/html/online/mdp.html @@ -419,7 +438,10 @@ %%DATADIR%%/top/dmso.gro %%DATADIR%%/top/dmso.itp %%DATADIR%%/top/edissoc.dat +%%DATADIR%%/top/electroneg.dat +%%DATADIR%%/top/elements.dat %%DATADIR%%/top/export.dlg +%%DATADIR%%/top/f3c.itp %%DATADIR%%/top/fa.itp %%DATADIR%%/top/ffG43a1-c.tdb %%DATADIR%%/top/ffG43a1-n.tdb @@ -439,23 +461,57 @@ %%DATADIR%%/top/ffG43a2.rtp %%DATADIR%%/top/ffG43a2bon.itp %%DATADIR%%/top/ffG43a2nb.itp -%%DATADIR%%/top/ffG43b1-c.tdb -%%DATADIR%%/top/ffG43b1-n.tdb -%%DATADIR%%/top/ffG43b1.atp -%%DATADIR%%/top/ffG43b1.ddb -%%DATADIR%%/top/ffG43b1.hdb -%%DATADIR%%/top/ffG43b1.itp -%%DATADIR%%/top/ffG43b1.rtp -%%DATADIR%%/top/ffG43b1bon.itp -%%DATADIR%%/top/ffG43b1nb.itp +%%DATADIR%%/top/ffG45a3-c.tdb +%%DATADIR%%/top/ffG45a3-n.tdb +%%DATADIR%%/top/ffG45a3.atp +%%DATADIR%%/top/ffG45a3.ddb +%%DATADIR%%/top/ffG45a3.hdb +%%DATADIR%%/top/ffG45a3.itp +%%DATADIR%%/top/ffG45a3.rtp +%%DATADIR%%/top/ffG45a3bon.itp +%%DATADIR%%/top/ffG45a3nb.itp +%%DATADIR%%/top/ffG53a5-c.tdb +%%DATADIR%%/top/ffG53a5-n.tdb +%%DATADIR%%/top/ffG53a5.atp +%%DATADIR%%/top/ffG53a5.ddb +%%DATADIR%%/top/ffG53a5.hdb +%%DATADIR%%/top/ffG53a5.itp +%%DATADIR%%/top/ffG53a5.n2t +%%DATADIR%%/top/ffG53a5.rtp +%%DATADIR%%/top/ffG53a5bon.itp +%%DATADIR%%/top/ffG53a5nb.itp +%%DATADIR%%/top/ffG53a6-c.tdb +%%DATADIR%%/top/ffG53a6-n.tdb +%%DATADIR%%/top/ffG53a6.atp +%%DATADIR%%/top/ffG53a6.ddb +%%DATADIR%%/top/ffG53a6.hdb +%%DATADIR%%/top/ffG53a6.itp +%%DATADIR%%/top/ffG53a6.rtp +%%DATADIR%%/top/ffG53a6bon.itp +%%DATADIR%%/top/ffG53a6nb.itp %%DATADIR%%/top/ff_dum.itp +%%DATADIR%%/top/ffencads-c.tdb +%%DATADIR%%/top/ffencads-n.tdb +%%DATADIR%%/top/ffencads.atp +%%DATADIR%%/top/ffencads.hdb +%%DATADIR%%/top/ffencads.itp +%%DATADIR%%/top/ffencads.rtp +%%DATADIR%%/top/ffencadsbon.itp +%%DATADIR%%/top/ffencadsnb.itp +%%DATADIR%%/top/ffencadv-c.tdb +%%DATADIR%%/top/ffencadv-n.tdb +%%DATADIR%%/top/ffencadv.atp +%%DATADIR%%/top/ffencadv.hdb +%%DATADIR%%/top/ffencadv.itp +%%DATADIR%%/top/ffencadv.rtp +%%DATADIR%%/top/ffencadvbon.itp +%%DATADIR%%/top/ffencadvnb.itp %%DATADIR%%/top/ffgmx-c.tdb %%DATADIR%%/top/ffgmx-n.tdb %%DATADIR%%/top/ffgmx.atp %%DATADIR%%/top/ffgmx.ddb %%DATADIR%%/top/ffgmx.hdb %%DATADIR%%/top/ffgmx.itp -%%DATADIR%%/top/ffgmx.n2t %%DATADIR%%/top/ffgmx.rtp %%DATADIR%%/top/ffgmx2-c.tdb %%DATADIR%%/top/ffgmx2-n.tdb @@ -474,6 +530,7 @@ %%DATADIR%%/top/ffoplsaa.ddb %%DATADIR%%/top/ffoplsaa.hdb %%DATADIR%%/top/ffoplsaa.itp +%%DATADIR%%/top/ffoplsaa.n2t %%DATADIR%%/top/ffoplsaa.rtp %%DATADIR%%/top/ffoplsaabon.itp %%DATADIR%%/top/ffoplsaanb.itp @@ -486,6 +543,7 @@ %%DATADIR%%/top/h2p8o25.itp %%DATADIR%%/top/h2po4.itp %%DATADIR%%/top/ha-shift.dat +%%DATADIR%%/top/highway.dat %%DATADIR%%/top/ions.itp %%DATADIR%%/top/links.dat %%DATADIR%%/top/methanol.itp @@ -515,7 +573,6 @@ %%DATADIR%%/top/urea.itp %%DATADIR%%/top/vdwradii.dat %%DATADIR%%/top/xlateat.dat -%%DATADIR%%/tutor/cleanit %%DATADIR%%/tutor/gmxdemo/cpeptide.pdb %%DATADIR%%/tutor/gmxdemo/demo %%DATADIR%%/tutor/methanol/conf.gro Index: files/patch-configure =================================================================== RCS file: files/patch-configure diff -N files/patch-configure --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ files/patch-configure 10 Feb 2009 19:53:51 -0000 @@ -0,0 +1,11 @@ +--- configure.orig 2009-02-10 17:49:39.000000000 +0100 ++++ configure 2009-02-10 17:50:54.000000000 +0100 +@@ -29600,7 +29600,7 @@ + # if it isnt there. + if test "$with_xml" = "yes"; then + ac_save_CPPFLAGS="$CPPFLAGS" +- CPPFLAGS="$ac_save_CPPFLAGS -I/usr/include/libxml2" ++ CPPFLAGS="$ac_save_CPPFLAGS -I/usr/local/include/libxml2" + + for ac_header in libxml/parser.h + do Index: files/patch-src::contrib::Makefile.in =================================================================== RCS file: files/patch-src::contrib::Makefile.in diff -N files/patch-src::contrib::Makefile.in --- files/patch-src::contrib::Makefile.in 9 Dec 2004 22:45:33 -0000 1.1 +++ /dev/null 1 Jan 1970 00:00:00 -0000 @@ -1,15 +0,0 @@ ---- src/contrib/Makefile.in.orig Mon Mar 1 20:49:01 2004 -+++ src/contrib/Makefile.in Thu Dec 9 19:54:56 2004 -@@ -307,10 +307,10 @@ - @AMDEP_TRUE@ ./$(DEPDIR)/sigeps.Po - COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ - $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) --LTCOMPILE = $(LIBTOOL) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) \ -+LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) $(DEFAULT_INCLUDES) \ - $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) - CCLD = $(CC) --LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ -+LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ - $(AM_LDFLAGS) $(LDFLAGS) -o $@ - F77COMPILE = $(F77) $(AM_FFLAGS) $(FFLAGS) - LTF77COMPILE = $(LIBTOOL) --mode=compile $(F77) $(AM_FFLAGS) $(FFLAGS) Index: files/patch-src::gmxlib::Makefile.in =================================================================== RCS file: files/patch-src::gmxlib::Makefile.in diff -N files/patch-src::gmxlib::Makefile.in --- files/patch-src::gmxlib::Makefile.in 9 Dec 2004 22:45:33 -0000 1.1 +++ /dev/null 1 Jan 1970 00:00:00 -0000 @@ -1,22 +0,0 @@ ---- src/gmxlib/Makefile.in.orig Mon Mar 1 20:49:02 2004 -+++ src/gmxlib/Makefile.in Thu Dec 9 00:11:00 2004 -@@ -292,16 +292,16 @@ - @AMDEP_TRUE@ ./$(DEPDIR)/xtcio.Plo ./$(DEPDIR)/xvgr.Plo - COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ - $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) --LTCOMPILE = $(LIBTOOL) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) \ -+LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) $(DEFAULT_INCLUDES) \ - $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) - CCLD = $(CC) --LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ -+LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ - $(AM_LDFLAGS) $(LDFLAGS) -o $@ - F77COMPILE = $(F77) $(AM_FFLAGS) $(FFLAGS) - LTF77COMPILE = $(LIBTOOL) --mode=compile $(F77) $(AM_FFLAGS) $(FFLAGS) - F77LD = $(F77) - CCASCOMPILE = $(CCAS) $(AM_CCASFLAGS) $(CCASFLAGS) --LTCCASCOMPILE = $(LIBTOOL) --mode=compile $(CCAS) $(AM_CCASFLAGS) \ -+LTCCASCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CCAS) $(AM_CCASFLAGS) \ - $(CCASFLAGS) - DIST_SOURCES = $(libgmx@LIBSUFFIX@_la_SOURCES) \ - $(EXTRA_libgmx@LIBSUFFIX@_la_SOURCES) Index: files/patch-src::kernel::Makefile.in =================================================================== RCS file: files/patch-src::kernel::Makefile.in diff -N files/patch-src::kernel::Makefile.in --- files/patch-src::kernel::Makefile.in 9 Dec 2004 22:45:33 -0000 1.1 +++ /dev/null 1 Jan 1970 00:00:00 -0000 @@ -1,15 +0,0 @@ ---- src/kernel/Makefile.in.orig Mon Mar 1 20:49:03 2004 -+++ src/kernel/Makefile.in Thu Dec 9 00:33:06 2004 -@@ -367,10 +367,10 @@ - @AMDEP_TRUE@ ./$(DEPDIR)/xutils.Po - COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ - $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) --LTCOMPILE = $(LIBTOOL) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) \ -+LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) $(DEFAULT_INCLUDES) \ - $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) - CCLD = $(CC) --LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ -+LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ - $(AM_LDFLAGS) $(LDFLAGS) -o $@ - DIST_SOURCES = $(ffscan_SOURCES) $(gmxcheck_SOURCES) gmxdump.c \ - $(grompp_SOURCES) luck.c $(mdrun_SOURCES) $(pdb2gmx_SOURCES) \ Index: files/patch-src::mdlib::Makefile.in =================================================================== RCS file: files/patch-src::mdlib::Makefile.in diff -N files/patch-src::mdlib::Makefile.in --- files/patch-src::mdlib::Makefile.in 9 Dec 2004 22:45:33 -0000 1.1 +++ /dev/null 1 Jan 1970 00:00:00 -0000 @@ -1,15 +0,0 @@ ---- src/mdlib/Makefile.in.orig Mon Mar 1 20:49:03 2004 -+++ src/mdlib/Makefile.in Thu Dec 9 00:22:03 2004 -@@ -233,10 +233,10 @@ - @AMDEP_TRUE@ ./$(DEPDIR)/vcm.Plo ./$(DEPDIR)/wnblist.Plo - COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ - $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) --LTCOMPILE = $(LIBTOOL) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) \ -+LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) $(DEFAULT_INCLUDES) \ - $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) - CCLD = $(CC) --LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ -+LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ - $(AM_LDFLAGS) $(LDFLAGS) -o $@ - F77COMPILE = $(F77) $(AM_FFLAGS) $(FFLAGS) - LTF77COMPILE = $(LIBTOOL) --mode=compile $(F77) $(AM_FFLAGS) $(FFLAGS) Index: files/patch-src::ngmx::Makefile.in =================================================================== RCS file: files/patch-src::ngmx::Makefile.in diff -N files/patch-src::ngmx::Makefile.in --- files/patch-src::ngmx::Makefile.in 9 Dec 2004 22:45:33 -0000 1.1 +++ /dev/null 1 Jan 1970 00:00:00 -0000 @@ -1,15 +0,0 @@ ---- src/ngmx/Makefile.in.orig Mon Mar 1 20:49:04 2004 -+++ src/ngmx/Makefile.in Thu Dec 9 19:53:57 2004 -@@ -272,10 +272,10 @@ - @AMDEP_TRUE@ ./$(DEPDIR)/xrama.Po ./$(DEPDIR)/xutil.Po - COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ - $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) --LTCOMPILE = $(LIBTOOL) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) \ -+LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) $(DEFAULT_INCLUDES) \ - $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) - CCLD = $(CC) --LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ -+LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ - $(AM_LDFLAGS) $(LDFLAGS) -o $@ - DIST_SOURCES = $(dlg_SOURCES) $(gmxlogo_SOURCES) $(highway_SOURCES) \ - $(ngmx_SOURCES) $(scrollw_SOURCES) $(showcol_SOURCES) \ Index: files/patch-src::tools::Makefile.in =================================================================== RCS file: files/patch-src::tools::Makefile.in diff -N files/patch-src::tools::Makefile.in --- files/patch-src::tools::Makefile.in 9 Dec 2004 22:45:33 -0000 1.1 +++ /dev/null 1 Jan 1970 00:00:00 -0000 @@ -1,15 +0,0 @@ ---- src/tools/Makefile.in.orig Mon Mar 1 20:49:06 2004 -+++ src/tools/Makefile.in Thu Dec 9 19:35:43 2004 -@@ -744,10 +744,10 @@ - @AMDEP_TRUE@ ./$(DEPDIR)/xpm2ps.Po - COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ - $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) --LTCOMPILE = $(LIBTOOL) --mode=compile $(CC) $(DEFS) $(DEFAULT_INCLUDES) \ -+LTCOMPILE = $(LIBTOOL) --mode=compile --tag=CC $(CC) $(DEFS) $(DEFAULT_INCLUDES) \ - $(INCLUDES) $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) - CCLD = $(CC) --LINK = $(LIBTOOL) --mode=link $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ -+LINK = $(LIBTOOL) --mode=link --tag=CC $(CCLD) $(AM_CFLAGS) $(CFLAGS) \ - $(AM_LDFLAGS) $(LDFLAGS) -o $@ - DIST_SOURCES = $(libgmxana@LIBSUFFIX@_la_SOURCES) $(anadock_SOURCES) \ - average.c $(cdist_SOURCES) $(disco_SOURCES) do_dssp.c \ --- science_gromacs.diff ends here --- >Release-Note: >Audit-Trail: >Unformatted: