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# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
inherit eutils fortran-2 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="
${MY_P}_all-mp.tar.gz
aria? ( aria2.3.2.tar.gz )"
SLOT="0"
LICENSE="cns"
KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
IUSE="aria openmp"
RDEPEND="app-shells/tcsh"
DEPEND="${RDEPEND}"
FORTRAN_NEED_OPENMP=1
S="${WORKDIR}/${MY_P}"
RESTRICT="fetch test"
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}."
}
get_fcomp() {
case $(tc-getFC) in
*gfortran* )
FCOMP="gfortran" ;;
ifort )
FCOMP="ifc" ;;
* )
FCOMP=$(tc-getFC) ;;
esac
}
pkg_setup() {
fortran-2_pkg_setup
get_fcomp
}
get_bitness() {
echo > "${T}"/test.c
$(tc-getCC) ${CFLAGS} -c "${T}"/test.c -o "${T}"/test.o
case $(file "${T}"/test.o) in
*64-bit*|*ppc64*|*x86_64*) export _bitness="64";;
*32-bit*|*ppc*|*i386*) export _bitness="32";;
*) die "Failed to detect whether your arch is 64bits or 32bits, disable distcc if you're using it, please";;
esac
}
src_prepare() {
epatch \
"${FILESDIR}"/${PV}-gentoo.patch \
"${FILESDIR}"/${PV}-parallel.patch
get_bitness
if use aria; then
pushd "${WORKDIR}"/aria* >& /dev/null
# Update the cns sources in aria for version 1.2.1
epatch "${FILESDIR}"/1.2.1-aria2.3.patch
# Update the code with aria specific things
cp -rf cns/src/* "${S}"/source/ || die
popd >& /dev/null
fi
# the code uses Intel-compiler-specific directives
if [[ $(tc-getFC) =~ gfortran ]]; then
epatch "${FILESDIR}"/${PV}-allow-gcc-openmp.patch
use openmp && \
append-flags -fopenmp && append-ldflags -fopenmp
COMP="gfortran"
[[ ${_bitness} == 64 ]] && \
append-fflags -fdefault-integer-8
elif [[ $(tc-getFC) == if* ]]; then
epatch "${FILESDIR}"/${PV}-ifort.patch
use openmp && \
append-flags -openmp && append-ldflags -openmp
COMP="ifort"
[[ ${_bitness} == 64 ]] && append-fflags -i8
fi
[[ ${_bitness} == 64 ]] && \
append-cflags "-DINTEGER='long long int'"
# Set up location for the build directory
# Uses obsolete `sort` syntax, so we set _POSIX2_VERSION
cp "${FILESDIR}"/cns_solve_env_sh "${T}"/ || die
sed \
-e "s:_CNSsolve_location_:${S}:g" \
-e "17 s:\(.*\):\1\nsetenv _POSIX2_VERSION 199209:g" \
-i "${S}"/cns_solve_env || die
sed \
-e "s:_CNSsolve_location_:${S}:g" \
-e "17 s:\(.*\):\1\nexport _POSIX2_VERSION; _POSIX2_VERSION=199209:g" \
-i "${T}"/cns_solve_env_sh || die
einfo "Fixing shebangs..."
find "${S}" -type f \
-exec sed "s:/bin/csh:${EPREFIX}/bin/csh:g" -i '{}' + || die
}
src_compile() {
local GLOBALS
local MALIGN
if [[ $(tc-getFC) =~ g77 ]]; then
GLOBALS="-fno-globals"
MALIGN='\$(CNS_MALIGN_I86)'
fi
# Set up the compiler to use
ln -s Makefile.header instlib/machine/unsupported/g77-unix/Makefile.header.${FCOMP} || die
# 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="$(tc-getCC)" \
F77=$(tc-getFC) \
LD=$(tc-getFC) \
CCFLAGS="${CFLAGS} -DCNS_ARCH_TYPE_\$(CNS_ARCH_TYPE) \$(EXT_CCFLAGS)" \
LDFLAGS="${LDFLAGS}" \
F77OPT="${FCFLAGS} ${MALIGN}" \
F77STD="${GLOBALS}" \
OMPLIB="${OMPLIB}" \
compiler="${COMP}" \
install
}
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 ..."
csh -c \
"export CNS_G77=ON; source ${S}/cns_solve_env; make run_tests" \
|| die "tests failed"
einfo "Displaying test results ..."
cat "${S}"/*_g77/test/*.diff-test
}
src_install() {
# Install to locations resembling FHS
sed \
-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/${PF}:g" \
-e "s:CNS_LIB \$CNS_SOLVE/libraries:CNS_LIB \$CNS_DATA/libraries:g" \
-e "s:CNS_MODULE \$CNS_SOLVE/modules:CNS_MODULE \$CNS_DATA/modules:g" \
-e "s:CNS_HELPLIB \$CNS_SOLVE/helplib:CNS_HELPLIB \$CNS_DATA/helplib:g" \
-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-e "/^g77on/d" \
-i "${S}"/cns_solve_env || die
# I don't entirely understand why the sh version requires a leading /
# for CNS_SOLVE and CNS_ROOT, but it does
sed \
-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/${PF}:g" \
-e "s:CNS_LIB=\$CNS_SOLVE/libraries:CNS_LIB=\$CNS_DATA/libraries:g" \
-e "s:CNS_MODULE=\$CNS_SOLVE/modules:CNS_MODULE=\$CNS_DATA/modules:g" \
-e "s:CNS_HELPLIB=\$CNS_SOLVE/helplib:CNS_HELPLIB=\$CNS_DATA/helplib:g" \
-e "s:\$CNS_SOLVE/bin/cns_info:\$CNS_DATA/cns_info:g" \
-e "/^g77on/d" \
-e "/^g77off/d" \
-i "${T}"/cns_solve_env_sh || die
# Get rid of setup stuff we don't need in the installed script
sed \
-e "83,$ d" \
-e "37,46 d" \
-i "${S}"/cns_solve_env || die
sed \
-e "84,$ d" \
-e "39,50 d" \
-i "${T}"/cns_solve_env_sh || die
newbin "${S}"/*linux*/bin/cns_solve* cns_solve
# Can be run by either cns_solve or cns
dosym cns_solve /usr/bin/cns
# Don't want to install this
rm -f "${S}"/*linux*/utils/Makefile || die
dobin "${S}"/*linux*/utils/*
sed \
-e "s:\$CNS_SOLVE/doc/:\$CNS_SOLVE/share/doc/${PF}/:g" \
-i "${S}"/bin/cns_web || die
dobin "${S}"/bin/cns_{edit,header,transfer,web}
insinto /usr/share/cns
doins -r "${S}"/libraries "${S}"/modules "${S}"/helplib
doins "${S}"/bin/cns_info
insinto /etc/profile.d
newins "${S}"/cns_solve_env cns_solve_env.csh
newins "${T}"/cns_solve_env_sh cns_solve_env.sh
dohtml \
-A iq,cgi,csh,cv,def,fm,gif,hkl,inp,jpeg,lib,link,list,mask,mtf,param,pdb,pdf,pl,ps,sc,sca,sdb,seq,tbl,top \
-f all_cns_info_template,omac,def \
-r doc/html/*
# Conflits with app-text/dos2unix
rm -f "${D}"/usr/bin/dos2unix || die
}
pkg_postinst() {
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
}
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