From c370eac5ca570d2949cfc006da0adf21f9e329a1 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Sat, 20 Mar 2010 13:33:13 +0000 Subject: Included new version of aria (Portage version: 2.2_rc67/cvs/Linux x86_64) --- sci-chemistry/cns/ChangeLog | 13 +- sci-chemistry/cns/cns-1.2.1-r3.ebuild | 211 +++++++++++++++++++++++++++ sci-chemistry/cns/files/1.2.1-aria2.3.patch | 22 +++ sci-chemistry/cns/files/1.2.1-parallel.patch | 17 +++ 4 files changed, 262 insertions(+), 1 deletion(-) create mode 100644 sci-chemistry/cns/cns-1.2.1-r3.ebuild create mode 100644 sci-chemistry/cns/files/1.2.1-aria2.3.patch create mode 100644 sci-chemistry/cns/files/1.2.1-parallel.patch (limited to 'sci-chemistry/cns') diff --git a/sci-chemistry/cns/ChangeLog b/sci-chemistry/cns/ChangeLog index 4f872ee93f4a..88656a204e5f 100644 --- a/sci-chemistry/cns/ChangeLog +++ b/sci-chemistry/cns/ChangeLog @@ -1,6 +1,17 @@ # ChangeLog for sci-chemistry/cns # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.20 2010/03/07 09:54:15 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/ChangeLog,v 1.21 2010/03/20 13:33:12 jlec Exp $ + + 20 Mar 2010; Justin Lecher (jlec) + +files/1.2.1-aria2.3.patch, +cns-1.2.1-r3.ebuild, + +files/1.2.1-parallel.patch: + Included new version of aria + +*cns-1.2.1-r3 (20 Mar 2010) + + 20 Mar 2010; Justin Lecher (jlec) + +files/1.2.1-aria2.3.patch, +cns-1.2.1-r3.ebuild: + Bump to new aria-2.3 07 Mar 2010; Justin Lecher (jlec) cns-1.2.1-r2.ebuild: Moved to EAPI=3 for PREFIX support, keyworded for *-linux, tested by me diff --git a/sci-chemistry/cns/cns-1.2.1-r3.ebuild b/sci-chemistry/cns/cns-1.2.1-r3.ebuild new file mode 100644 index 000000000000..e6cbce88bf7a --- /dev/null +++ b/sci-chemistry/cns/cns-1.2.1-r3.ebuild @@ -0,0 +1,211 @@ +# Copyright 1999-2010 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/cns/cns-1.2.1-r3.ebuild,v 1.1 2010/03/20 13:33:12 jlec Exp $ + +EAPI="3" + +inherit eutils fortran toolchain-funcs versionator flag-o-matic + +MY_PN="${PN}_solve" +MY_PV="$(delete_version_separator 2)" +MY_P="${MY_PN}_${MY_PV}" + +DESCRIPTION="Crystallography and NMR System" +HOMEPAGE="http://cns.csb.yale.edu/" +SRC_URI="${MY_P}_all-mp.tar.gz + aria? ( aria2.3.1.tar.gz )" + +SLOT="0" +LICENSE="cns" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="aria openmp" + +RDEPEND="app-shells/tcsh + !app-text/dos2unix" +DEPEND="${RDEPEND}" +PDEPEND="aria? ( ~sci-chemistry/aria-2.3.1 )" + +RESTRICT="fetch" +S="${WORKDIR}/${MY_P}" + +FORTRAN="g77 gfortran" + +pkg_nofetch() { + elog "Fill out the form at http://cns.csb.yale.edu/cns_request/" + use aria && elog "and http://aria.pasteur.fr/" + elog "and place these files:" + elog ${A} + elog "in ${DISTDIR}." +} + +pkg_setup() { + fortran_pkg_setup + + if [[ $(tc-getCC) == *gcc* ]] && + ( [[ $(gcc-major-version)$(gcc-minor-version) -lt 42 ]] || + ! built_with_use sys-devel/gcc openmp ) + then + ewarn "You are using gcc and OpenMP is only available with gcc >= 4.2 " + ewarn "Switch CC to an OpenMP capable compiler" + fi +} + +src_prepare() { + epatch "${FILESDIR}"/${PV}-gentoo.patch + epatch "${FILESDIR}"/${PV}-parallel.patch + + pushd "${WORKDIR}"/aria* >& /dev/null + if use aria; then + # Update the cns sources in aria for version 1.2.1 + epatch "${FILESDIR}"/1.2.1-aria2.3.patch + + # Update the code with aria specific things + cp -rf cns/src/* "${S}"/source/ + fi + popd >& /dev/null + + use openmp && append-fflags -fopenmp + + # the code uses Intel-compiler-specific directives + epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch + + use openmp && OMPLIB="-lgomp" + + use amd64 && \ + append-cflags "-DINTEGER='long long int'" && \ + append-fflags -fdefault-integer-8 + + # Set up location for the build directory + # Uses obsolete `sort` syntax, so we set _POSIX2_VERSION + cp "${FILESDIR}"/cns_solve_env_sh "${T}"/ + sed -i \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \ + "${S}"/cns_solve_env + sed -i \ + -e "s:_CNSsolve_location_:${S}:g" \ + -e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \ + "${T}"/cns_solve_env_sh + + einfo "Fixing shebangs..." + find "${S}" -type f \ + -exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' \; || die +} + +src_compile() { + local GLOBALS + local MALIGN + if [[ ${FORTRANC} = g77 ]]; then + GLOBALS="-fno-globals" + MALIGN='\$(CNS_MALIGN_I86)' + fi + + # Set up the compiler to use + pushd instlib/machine/unsupported/g77-unix 2>/dev/null + ln -s Makefile.header Makefile.header.${FORTRANC} || die + popd 2>/dev/null + + # make install really means build, since it's expected to be used in-place + # -j1 doesn't mean we do no respect MAKEOPTS! + emake -j1 \ + CC="$(tc-getCC)" \ + F77="${FORTRANC}" \ + LD="${FORTRANC}" \ + CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \ + LDFLAGS="${LDFLAGS}" \ + F77OPT="${FFLAGS:- -O2} ${MALIGN}" \ + F77STD="${GLOBALS}" \ + OMPLIB="${OMPLIB}" \ + g77install \ + || die "emake failed" + +} + +src_test() { + # We need to force on g77 manually, because we can't get aliases working + # when we source in a -c + einfo "Running tests ..." + sh -c \ + "export CNS_G77=ON; source ${T}/cns_solve_env_sh; make run_tests" \ + || die "tests failed" + einfo "Displaying test results ..." + cat "${S}"/*_g77/test/*.diff-test +} + +src_install() { + # Install to locations resembling FHS + sed -i \ + -e "s:${S}:usr:g" \ + -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_ROOT ${EPREFIX}/usr:g" \ + -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DATA \$CNS_ROOT/share/cns:g" \ + -e "s:^\(setenv CNS_SOLVE.*\):\1\nsetenv CNS_DOC \$CNS_ROOT/share/doc/${PF}:g" \ + -e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \ + -e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \ + -e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \ + -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ + "${S}"/cns_solve_env + # I don't entirely understand why the sh version requires a leading / + # for CNS_SOLVE and CNS_ROOT, but it does + sed -i \ + -e "s:${S}:/usr:g" \ + -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_ROOT=${EPREFIX}/usr:g" \ + -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DATA=\$CNS_ROOT/share/cns:g" \ + -e "s:^\(^[[:space:]]*CNS_SOLVE=.*\):\1\nexport CNS_DOC=\$CNS_ROOT/share/doc/${PF}:g" \ + -e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \ + -e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \ + -e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \ + -e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \ + "${T}"/cns_solve_env_sh + + # Get rid of setup stuff we don't need in the installed script + sed -i \ + -e "83,$ d" \ + -e "37,46 d" \ + "${S}"/cns_solve_env + sed -i \ + -e "84,$ d" \ + -e "39,50 d" \ + "${T}"/cns_solve_env_sh + + newbin "${S}"/*_g77/bin/cns_solve* cns_solve \ + || die "install cns_solve failed" + + # Can be run by either cns_solve or cns + dosym cns_solve /usr/bin/cns + + # Don't want to install this + rm -f "${S}"/*_g77/utils/Makefile + + dobin "${S}"/*_g77/utils/* || die "install utils failed" + + sed -i \ + -e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \ + "${S}"/bin/cns_web || die + + dobin "${S}"/bin/cns_{edit,header,transfer,web} || die "install bin failed" + + insinto /usr/share/cns + doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib || die + doins "${S}"/bin/cns_info || die + + insinto /etc/profile.d + newins "${S}"/cns_solve_env cns_solve_env.csh || die + newins "${T}"/cns_solve_env_sh cns_solve_env.sh || die + + dohtml \ + -A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \ + -f all_cns_info_template,omac,def \ + -r doc/html/* || die +} + +pkg_info() { + if use openmp; then + elog "Set OMP_NUM_THREADS to the number of threads you want." + elog "If you get segfaults on large structures, set the GOMP_STACKSIZE" + elog "variable if using gcc (16384 should be good)." + fi +} + +pkg_postinst() { + pkg_info +} diff --git a/sci-chemistry/cns/files/1.2.1-aria2.3.patch b/sci-chemistry/cns/files/1.2.1-aria2.3.patch new file mode 100644 index 000000000000..8c6939d8eb92 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-aria2.3.patch @@ -0,0 +1,22 @@ +diff --git a/cns/src/cns.f b/cns/src/cns.f +index a3c2cbe..51a34f8 100644 +--- a/cns/src/cns.f ++++ b/cns/src/cns.f +@@ -470,6 +470,7 @@ C local + INTEGER HNLEN, TMP, PTRSZ, STLEN + CHARACTER*(1) CNSPTMP + CHARACTER*(4) ST ++!$ integer omp_get_max_threads + C + C write header + WRITE(6,'(10X,A)') +@@ -526,6 +527,9 @@ C + WRITE(6,'(10X,7A)') + & ' Running on machine: ',HOSTNM(1:HNLEN), + & ' (',SYSNM(1:TMP),',',ST(1:STLEN),'-bit)' ++!$ write(6,'(31x,a,i3,a)') 'with',omp_get_max_threads(), ++!$ & ' threads' ++!$C (to change use setenv OMP_NUM_THREADS x) + C + CALL GETNAM(USERNM,12,TMP) + WRITE(6,'(10X,2A)') diff --git a/sci-chemistry/cns/files/1.2.1-parallel.patch b/sci-chemistry/cns/files/1.2.1-parallel.patch new file mode 100644 index 000000000000..dfaa40021d66 --- /dev/null +++ b/sci-chemistry/cns/files/1.2.1-parallel.patch @@ -0,0 +1,17 @@ +diff --git a/instlib/source/Makefile.proto b/instlib/source/Makefile.proto +index 0d0dd3e..ae9e422 100644 +--- a/instlib/source/Makefile.proto ++++ b/instlib/source/Makefile.proto +@@ -19,9 +19,9 @@ DEPENDS = $(OBJS) dmemory.o machine_c.o + + # the default is to make the cns executable + cns_solve: +- @ make -k printflags F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" +- @ make -k exepurge ++ @ make printflags F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make ${MAKEOPTS} ../bin/cns_solve F77BUG="$(debug)" DEBUG="$(debug)" ++ @ make exepurge + + # rule for the fortran routines + $(OBJS): -- cgit v1.2.3-65-gdbad