svn commit: r479263 - in head/science: . namd namd/files
Adam Weinberger
adamw at adamw.org
Sun Sep 9 00:15:55 UTC 2018
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 at 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 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 at 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 <bsd.port.mk>
>
> 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/
>
--
Adam Weinberger
adamw at adamw.org
https://www.adamw.org
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