Date: Sat, 8 Sep 2018 18:15:37 -0600 From: Adam Weinberger <adamw@adamw.org> To: yuri@freebsd.org Cc: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: Re: svn commit: r479263 - in head/science: . namd namd/files Message-ID: <CAP7rwcgq5EpuEggex2vG369-0Cz4O9GbRPQNpbUUQ6VB15HH4Q@mail.gmail.com> In-Reply-To: <201809082328.w88NSLVF073775@repo.freebsd.org> References: <201809082328.w88NSLVF073775@repo.freebsd.org>
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Yuri, Upstream requires that people register to download the software, and the license seems to forbid any distribution on our part: "Licensee may redistribute without restriction works with up to 1/2 of their non-comment source code derived from at most 1/10 of the non-comment source code developed by Illinois and contained in the Software" "Licensee agrees to provide the Software only to any other person or entity who has registered with Illinois" "Commercial use of the Software, or derivative works based thereon, REQUIRES A COMMERCIAL LICENSE." I don't think it's a good idea for this port to remain in the tree. # Adam On Sat, Sep 8, 2018 at 5:28 PM Yuri Victorovich <yuri@freebsd.org> wrote: > > 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 simula= tion > > 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 > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D > --- 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 +=3D mpb > SUBDIR +=3D mpqc > SUBDIR +=3D multiwfn > + SUBDIR +=3D namd > SUBDIR +=3D ncs > SUBDIR +=3D netcdf > SUBDIR +=3D netcdf-cxx > > Added: head/science/namd/Makefile > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D > --- /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=3D namd > +DISTVERSION=3D 2-12-211 > +DISTVERSIONSUFFIX=3D -gfdf7ea56 > +CATEGORIES=3D science > + > +MAINTAINER=3D yuri@FreeBSD.org > +COMMENT=3D Computer software for molecular dynamics simulation > + > +LICENSE=3D NAMD_MOLECULAR_DYNAMICS_LICENSE > +LICENSE_NAME=3D NAMD Molecular Dynamics Software > +LICENSE_FILE=3D ${WRKSRC}/license.txt > +LICENSE_PERMS=3D auto-accept dist-mirror pkg-mirror > + > +ONLY_FOR_ARCHS=3D amd64 i386 > +ONLY_FOR_ARCHS_REASON=3D Not clear if it can be built on other architect= ures > +BROKEN_i386=3D need to fix the fft library handling > + > +FETCH_DEPENDS=3D git:devel/git > +BUILD_DEPENDS=3D bash:shells/bash \ > + ${LOCALBASE}/include/fftw3.h:math/fftw3 > +LIB_DEPENDS=3D libck.so:net/charm \ > + libfftw3f.so:math/fftw3-float > + > +USES=3D fortran gmake localbase:ldflags python:build shebangfix= tcl > +SHEBANG_FILES=3D config > + > +GIT_URL=3D https://charm.cs.illinois.edu/gerrit/namd.git > + > +ARCH_STR=3D Linux-${ARCH:S/amd64/x86_64/:S/i386/x86/}-g++ > +ARCH_STR_CHARM=3D linux${ARCH:S/amd64/64/:S/i386/32/} > + > +PATCH_WRKSRC=3D ${WRKSRC} > +BUILD_WRKSRC=3D ${WRKSRC}/${ARCH_STR} > + > +CFLAGS+=3D -D_NO_MALLOC_H -D_NO_ALLOCA_H > +CXXFLAGS+=3D -D_NO_MALLOC_H -D_NO_ALLOCA_H > + > +BINARY_ALIAS=3D gcc=3D${CC} g++=3D${CXX} > + > +PLIST_FILES=3D bin/flipbinpdb \ > + bin/flipdcd \ > + bin/namd2 \ > + bin/psfgen \ > + bin/sortreplicas > + > +local-makesum: # Workaround: the generic 'make makesum' is broken when c= ustom do-fetch is defined: it calls ${SCRIPTSDIR}/do-fetch.sh. > + @${MAKE} distclean fetch makesum > + > +do-fetch: > + @if [ "${FORCE_FETCH_ALL}" =3D "true" ] || ! [ -f "${DISTDIR}/${D= IST_SUBDIR}/${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 ${D= ISTVERSIONFULL} && ${RM} -r .git) && \ > + ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -and -exec ${TOUCH} -h= -d 1970-01-01T00:00:00Z {} \; && \ > + ${FIND} ${PORTNAME}-${DISTVERSIONFULL} -print0 | LC_ALL=3DC $= {SORT} -z | \ > + ${TAR} czf ${PORTNAME}-${DISTVERSIONFULL}${EXTRACT_SUFX} = --format=3Dbsdtar --uid 0 --gid 0 --options gzip:!timestamp --no-recursion = --null -T - && \ > + ${RM} -r ${PORTNAME}-${DISTVERSIONFULL}; \ > + fi > + > +do-configure: > + @cd ${WRKSRC} && ${ECHO} "CHARMBASE=3D${LOCALBASE}" > Make.config > + @cd ${WRKSRC} && ./config ${ARCH_STR} --charm-arch multicore-${AR= CH_STR_CHARM} ${ARCH:S/amd64/--with-fftw3/:S/${ARCH}//} > + @${REINPLACE_CMD} 's|CHARMBASE =3D .*|CHARMBASE =3D ${LOCALBASE}|= ' ${WRKSRC}/Make.charm > + @${REINPLACE_CMD} '\ > + s|FFTDIR=3D.*|FFTDIR=3D${LOCALBASE}|; \ > + s|-lsfftw|-lfft3f|; \ > + s|-lsrfftw|-lrfft3f|; \ > + s|TCLDIR=3D.*|TCLDIR=3D${LOCALBASE}/include/tcl8.6|; \ > + s|TCLINCL=3D.*|TCLINCL=3D-I${LOCALBASE}/include/tcl8.6|; = \ > + s|TCLLIB=3D.*|TCLLIB=3D-L${LOCALBASE}/lib -ltcl86 -lpthre= ad|' \ > + ${WRKSRC}/arch/Linux* > + > +do-install: > +.for e in namd2 flipbinpdb flipdcd psfgen sortreplicas > + ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/${e} ${STAGEDIR}${PREFIX}/bin > +.endfor > + > +.include <bsd.port.mk> > > Added: head/science/namd/distinfo > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D > --- /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 =3D 1536445358 > +SHA256 (namd-2-12-211-gfdf7ea56.tar.gz) =3D 2ab3a98f7cc9fa997088502aa87a= d8cfe9218b35d4b783b7370a5d5d49f7fe15 > +SIZE (namd-2-12-211-gfdf7ea56.tar.gz) =3D 8278948 > > Added: head/science/namd/files/patch-Makefile > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D > --- /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 =3D $(CUDAOBJS) $(PLUGINLIB) $(SBLIB) > + > + # CXX is platform dependent > + CXXBASEFLAGS =3D $(COPTI)$(CHARMINC) $(COPTI)$(SRCDIR) $(COPTI)$(INCDIR= ) $(DPMTA) $(DPME) $(FMM) $(COPTI)$(PLUGININCDIR) $(COPTI)$(COLVARSINCDIR) = $(COPTD)STATIC_PLUGIN $(TCL) $(PYTHON) $(FFT) $(CUDA) $(MIC) $(MEMOPT) $(CC= S) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF) $(EXTRAINCS) $(MSA) $(CKLOOP) > +-CXXFLAGS =3D $(CXXBASEFLAGS) $(CXXOPTS) > ++CXXFLAGS +=3D $(CXXBASEFLAGS) $(CXXOPTS) > + CXXMICFLAGS =3D $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS) > + CXXTHREADFLAGS =3D $(CXXBASEFLAGS) $(CXXTHREADOPTS) > + CXXSIMPARAMFLAGS =3D $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS) > > Added: head/science/namd/files/patch-config > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D > --- /dev/null 00:00:00 1970 (empty, because file is newly added) > +++ head/science/namd/files/patch-config Sat Sep 8 23:28:21 2018 = (r479263) > @@ -0,0 +1,11 @@ > +--- config.orig 2018-09-07 20:23:43 UTC > ++++ config > +@@ -582,7 +582,7 @@ function error_exists { > + if [ -n "$CHARM_OPTS" ]; then > + echo "CHARMOPTS =3D $CHARM_OPTS" >> Make.config > + fi > +- echo 'CHARM =3D $(CHARMBASE)/$(CHARMARCH)' >> Make.config > ++ echo 'CHARM =3D $(CHARMBASE)' >> Make.config > + ARCH_SUFFIX=3D"" > + [[ "$CHARM_ARCH" =3D=3D *-scyld* ]] && ARCH_SUFFIX=3D${ARCH_SUFFIX}-S= cyld > + if [[ "$CHARM_ARCH" =3D=3D *-clustermatic* ]]; then > > Added: head/science/namd/pkg-descr > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D > --- /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 usi= ng the > +Charm++ parallel programming model. It is noted for its parallel efficie= ncy and > +is often used to simulate large systems (millions of atoms). It has been > +developed by the collaboration of the Theoretical and Computational Biop= hysics > +Group (TCB) and the Parallel Programming Laboratory (PPL) at the Univers= ity of > +Illinois at Urbana-Champaign. > + > +WWW: https://www.ks.uiuc.edu/Research/namd/ > --=20 Adam Weinberger adamw@adamw.org https://www.adamw.org
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