From owner-svn-ports-all@freebsd.org Sat Sep 8 23:28:23 2018 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 1F350106BD89; Sat, 8 Sep 2018 23:28:23 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id B6F5C7C5F3; Sat, 8 Sep 2018 23:28:22 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id AC3C111B94; Sat, 8 Sep 2018 23:28:22 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id w88NSMaY073781; Sat, 8 Sep 2018 23:28:22 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id w88NSLVF073775; Sat, 8 Sep 2018 23:28:21 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201809082328.w88NSLVF073775@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Sat, 8 Sep 2018 23:28:21 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r479263 - in head/science: . namd namd/files X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: in head/science: . namd namd/files X-SVN-Commit-Revision: 479263 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.27 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 08 Sep 2018 23:28:23 -0000 Author: yuri Date: Sat Sep 8 23:28:21 2018 New Revision: 479263 URL: https://svnweb.freebsd.org/changeset/ports/479263 Log: New port: science/namd: Computer software for molecular dynamics simulation Added: head/science/namd/ head/science/namd/Makefile (contents, props changed) head/science/namd/distinfo (contents, props changed) head/science/namd/files/ head/science/namd/files/patch-Makefile (contents, props changed) head/science/namd/files/patch-config (contents, props changed) head/science/namd/pkg-descr (contents, props changed) Modified: head/science/Makefile Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Sat Sep 8 23:26:03 2018 (r479262) +++ head/science/Makefile Sat Sep 8 23:28:21 2018 (r479263) @@ -137,6 +137,7 @@ SUBDIR += mpb SUBDIR += mpqc SUBDIR += multiwfn + SUBDIR += namd SUBDIR += ncs SUBDIR += netcdf SUBDIR += netcdf-cxx Added: head/science/namd/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/namd/Makefile Sat Sep 8 23:28:21 2018 (r479263) @@ -0,0 +1,81 @@ +# $FreeBSD$ + +PORTNAME= namd +DISTVERSION= 2-12-211 +DISTVERSIONSUFFIX= -gfdf7ea56 +CATEGORIES= science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Computer software for molecular dynamics simulation + +LICENSE= NAMD_MOLECULAR_DYNAMICS_LICENSE +LICENSE_NAME= NAMD Molecular Dynamics Software +LICENSE_FILE= ${WRKSRC}/license.txt +LICENSE_PERMS= auto-accept dist-mirror pkg-mirror + +ONLY_FOR_ARCHS= amd64 i386 +ONLY_FOR_ARCHS_REASON= Not clear if it can be built on other architectures +BROKEN_i386= need to fix the fft library handling + +FETCH_DEPENDS= git:devel/git +BUILD_DEPENDS= bash:shells/bash \ + ${LOCALBASE}/include/fftw3.h:math/fftw3 +LIB_DEPENDS= libck.so:net/charm \ + libfftw3f.so:math/fftw3-float + +USES= fortran gmake localbase:ldflags python:build shebangfix tcl +SHEBANG_FILES= config + +GIT_URL= https://charm.cs.illinois.edu/gerrit/namd.git + +ARCH_STR= Linux-${ARCH:S/amd64/x86_64/:S/i386/x86/}-g++ +ARCH_STR_CHARM= linux${ARCH:S/amd64/64/:S/i386/32/} + +PATCH_WRKSRC= ${WRKSRC} +BUILD_WRKSRC= ${WRKSRC}/${ARCH_STR} + +CFLAGS+= -D_NO_MALLOC_H -D_NO_ALLOCA_H +CXXFLAGS+= -D_NO_MALLOC_H -D_NO_ALLOCA_H + +BINARY_ALIAS= gcc=${CC} g++=${CXX} + +PLIST_FILES= bin/flipbinpdb \ + bin/flipdcd \ + bin/namd2 \ + bin/psfgen \ + bin/sortreplicas + +local-makesum: # Workaround: the generic 'make makesum' is broken when custom do-fetch is defined: it calls ${SCRIPTSDIR}/do-fetch.sh. + @${MAKE} distclean fetch makesum + +do-fetch: + @if [ "${FORCE_FETCH_ALL}" = "true" ] || ! [ -f "${DISTDIR}/${DIST_SUBDIR}/${DISTNAME}${EXTRACT_SUFX}" ]; then \ + ${MKDIR} ${DISTDIR}/${DIST_SUBDIR} && \ + cd ${DISTDIR}/${DIST_SUBDIR} && \ + git clone -q ${GIT_URL} ${PORTNAME}-${DISTVERSIONFULL} && \ + (cd ${PORTNAME}-${DISTVERSIONFULL} && git reset -q --hard ${DISTVERSIONFULL} && ${RM} -r .git) && \ + ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -and -exec ${TOUCH} -h -d 1970-01-01T00:00:00Z {} \; && \ + ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -print0 | LC_ALL=C ${SORT} -z | \ + ${TAR} czf ${PORTNAME}-${DISTVERSIONFULL}${EXTRACT_SUFX} --format=bsdtar --uid 0 --gid 0 --options gzip:!timestamp --no-recursion --null -T - && \ + ${RM} -r ${PORTNAME}-${DISTVERSIONFULL}; \ + fi + +do-configure: + @cd ${WRKSRC} && ${ECHO} "CHARMBASE=${LOCALBASE}" > Make.config + @cd ${WRKSRC} && ./config ${ARCH_STR} --charm-arch multicore-${ARCH_STR_CHARM} ${ARCH:S/amd64/--with-fftw3/:S/${ARCH}//} + @${REINPLACE_CMD} 's|CHARMBASE = .*|CHARMBASE = ${LOCALBASE}|' ${WRKSRC}/Make.charm + @${REINPLACE_CMD} '\ + s|FFTDIR=.*|FFTDIR=${LOCALBASE}|; \ + s|-lsfftw|-lfft3f|; \ + s|-lsrfftw|-lrfft3f|; \ + s|TCLDIR=.*|TCLDIR=${LOCALBASE}/include/tcl8.6|; \ + s|TCLINCL=.*|TCLINCL=-I${LOCALBASE}/include/tcl8.6|; \ + s|TCLLIB=.*|TCLLIB=-L${LOCALBASE}/lib -ltcl86 -lpthread|' \ + ${WRKSRC}/arch/Linux* + +do-install: +.for e in namd2 flipbinpdb flipdcd psfgen sortreplicas + ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/${e} ${STAGEDIR}${PREFIX}/bin +.endfor + +.include Added: head/science/namd/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/namd/distinfo Sat Sep 8 23:28:21 2018 (r479263) @@ -0,0 +1,3 @@ +TIMESTAMP = 1536445358 +SHA256 (namd-2-12-211-gfdf7ea56.tar.gz) = 2ab3a98f7cc9fa997088502aa87ad8cfe9218b35d4b783b7370a5d5d49f7fe15 +SIZE (namd-2-12-211-gfdf7ea56.tar.gz) = 8278948 Added: head/science/namd/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/namd/files/patch-Makefile Sat Sep 8 23:28:21 2018 (r479263) @@ -0,0 +1,11 @@ +--- Makefile.orig 1970-01-01 00:00:00 UTC ++++ Makefile +@@ -435,7 +435,7 @@ LIBS = $(CUDAOBJS) $(PLUGINLIB) $(SBLIB) + + # CXX is platform dependent + CXXBASEFLAGS = $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR) $(DPMTA) $(DPME) $(FMM) $(COPTI)$(PLUGININCDIR) $(COPTI)$(COLVARSINCDIR) $(COPTD)STATIC_PLUGIN $(TCL) $(PYTHON) $(FFT) $(CUDA) $(MIC) $(MEMOPT) $(CCS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA) $(CKLOOP) +-CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) ++CXXFLAGS += $(CXXBASEFLAGS) $(CXXOPTS) + CXXMICFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS) + CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS) + CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS) Added: head/science/namd/files/patch-config ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/namd/files/patch-config Sat Sep 8 23:28:21 2018 (r479263) @@ -0,0 +1,11 @@ +--- config.orig 2018-09-07 20:23:43 UTC ++++ config +@@ -582,7 +582,7 @@ function error_exists { + if [ -n "$CHARM_OPTS" ]; then + echo "CHARMOPTS = $CHARM_OPTS" >> Make.config + fi +- echo 'CHARM = $(CHARMBASE)/$(CHARMARCH)' >> Make.config ++ echo 'CHARM = $(CHARMBASE)' >> Make.config + ARCH_SUFFIX="" + [[ "$CHARM_ARCH" == *-scyld* ]] && ARCH_SUFFIX=${ARCH_SUFFIX}-Scyld + if [[ "$CHARM_ARCH" == *-clustermatic* ]]; then Added: head/science/namd/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/science/namd/pkg-descr Sat Sep 8 23:28:21 2018 (r479263) @@ -0,0 +1,8 @@ +NAMD is computer software for molecular dynamics simulation, written using the +Charm++ parallel programming model. It is noted for its parallel efficiency and +is often used to simulate large systems (millions of atoms). It has been +developed by the collaboration of the Theoretical and Computational Biophysics +Group (TCB) and the Parallel Programming Laboratory (PPL) at the University of +Illinois at Urbana-Champaign. + +WWW: https://www.ks.uiuc.edu/Research/namd/