commit: 9770d9a78d9f1fcb5c003b1b0a2ae8114f0db707
Author: Andrew Savchenko <bircoph <AT> gentoo <DOT> org>
AuthorDate: Wed Oct 24 14:52:39 2018 +0000
Commit: Andrew Savchenko <bircoph <AT> gentoo <DOT> org>
CommitDate: Wed Oct 24 14:52:39 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9770d9a7
sci-chemistry/gamess: remove old
Old version sources are no longer reachable.
Signed-off-by: Andrew Savchenko <bircoph <AT> gentoo.org>
Package-Manager: Portage-2.3.51, Repoman-2.3.11
.../gamess/files/gamess-20161808.1.gentoo.patch | 197 ------------
sci-chemistry/gamess/gamess-20161808.1.ebuild | 342 ---------------------
2 files changed, 539 deletions(-)
diff --git a/sci-chemistry/gamess/files/gamess-20161808.1.gentoo.patch
b/sci-chemistry/gamess/files/gamess-20161808.1.gentoo.patch
deleted file mode 100644
index c29200fb6..000000000
--- a/sci-chemistry/gamess/files/gamess-20161808.1.gentoo.patch
+++ /dev/null
@@ -1,197 +0,0 @@
-diff -urN gamess.orig/comp gamess/comp
---- gamess.orig/comp 2016-10-08 17:15:03.000000000 +0300
-+++ gamess/comp 2016-11-29 11:30:44.836507346 +0300
-@@ -1548,7 +1548,7 @@
- #
- case gfortran:
- #
-- set OPT='-O2'
-+ set gentoo-OPT='-O2'
- if ($MODULE == zheev) set OPT='-O0' # defensive compiling
-
- set EXTRAOPT=" "
-@@ -1593,6 +1593,10 @@
- case 5.1:
- case 5.2:
- case 5.3:
-+ case 5.4:
-+ case 6.0:
-+ case 6.1:
-+ case 6.2:
- if ($MODULE == cosmo) set OPT='-O0'
- if ($MODULE == dcscf) set OPT='-O0'
- if ($MODULE == tddgrd) set OPT='-O0'
-@@ -1621,7 +1625,7 @@
- # optimizations in 32 bit mode, as a function of the ifort version.
- #
- case ifort:
-- set OPT = '-O3'
-+ set gentoo-OPT = '-O2'
- if ($MODULE == delocl) set OPT='-O0' # from Cheol
- if ($MODULE == prpamm) set OPT='-O0' # for exam13
- if ($MODULE == zheev) set OPT='-O0'
-@@ -1766,7 +1770,7 @@
- #
- # first, initialize OPT and EXTRAOPT
- #
-- set OPT='-O2'
-+ set gentoo-OPT='-O2'
- if ($MODULE == zheev) set OPT='-O0' # defensive compiling
-
- set EXTRAOPT=" "
-@@ -1823,6 +1827,10 @@
- case 5.1:
- case 5.2:
- case 5.3:
-+ case 5.4:
-+ case 6.0:
-+ case 6.1:
-+ case 6.2:
- if ($MODULE == cosmo) set OPT='-O0' # same issue as seen in 4.6
- if ($MODULE == dcscf) set OPT='-O0' # exam44, continues from 4.7
- if ($MODULE == tddgrd) set OPT='-O0' # exam41, continues from 4.6
-@@ -1864,7 +1872,7 @@
- # -WB means warn but don't fail on out-of-bounds array references
- # -ftz flushes underflow results to zero
- #
-- set OPT = '-O2'
-+ set gentoo-OPT = '-O2'
- if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS"
- # alas, I'm so tired of hearing about so many versions failing to
- # diagonalize, that this time critical code is run w/o optimization.
-diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi
---- gamess.orig/ddi/compddi 2016-06-22 21:28:44.000000000 +0300
-+++ gamess/ddi/compddi 2016-11-29 11:28:19.067151986 +0300
-@@ -627,7 +627,7 @@
-
- set FORTRAN=$GMS_FORTRAN # might be g77, gfortran, ifort, pgf77, f2c
-
-- set CC = 'gcc'
-+ set gentoo-CC = 'gcc'
- set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./"
- set CLIBS = "-lpthread"
-
-@@ -681,7 +681,7 @@
- set ARCH='-m64'
- if (`uname -p` == ia64) set ARCH=''
-
-- set CC = 'gcc'
-+ set gentoo-CC = 'gcc'
- set CFLAGS = "-DLINUX $ARCH -O3 -fstrict-aliasing -I./"
- set CLIBS = "-lpthread"
-
-diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess/ddi/kickoff/ddikick.c
---- gamess.orig/ddi/kickoff/ddikick.c 2011-11-22 23:54:33.000000000 +0400
-+++ gamess/ddi/kickoff/ddikick.c 2016-11-29 11:28:19.068151988 +0300
-@@ -105,7 +105,7 @@
- remoteshell = argv[++i];
- } else {
- if((remoteshell = getenv("DDI_RSH")) == NULL) {
-- remoteshell = (char *) strdup("rsh");
-+ remoteshell = (char *) strdup("ssh");
- }
- }
-
-diff -urN gamess.orig/gms-files.csh gamess/gms-files.csh
---- gamess.orig/gms-files.csh 2016-09-07 22:42:51.000000000 +0300
-+++ gamess/gms-files.csh 2016-11-29 11:28:19.068151988 +0300
-@@ -28,7 +28,7 @@
- # to see all the file definitions (one is just below).
- #
- #---quiet---set echo
--setenv AUXDATA $GMSPATH/auxdata
-+setenv AUXDATA /usr/share/gamess
- setenv EXTBAS /dev/null
- setenv NUCBAS /dev/null
- setenv POSBAS /dev/null
-diff -urN gamess.orig/lked gamess/lked
---- gamess.orig/lked 2016-07-29 20:59:09.000000000 +0300
-+++ gamess/lked 2016-11-29 11:32:22.885745512 +0300
-@@ -362,12 +362,12 @@
- switch ($GMS_FORTRAN)
- case gfortran:
- set LDR='gfortran'
-- set LDOPTS=' '
-+ set gentoo-LDOPTS=' '
- set FORTLIBS=' '
- breaksw
- case ifort:
- set LDR='ifort'
-- set LDOPTS=' ' # add '-Wl,-M' to see load map
-+ set gentoo-LDOPTS=' ' # add '-Wl,-M' to see load map
- set FORTLIBS='-Vaxlib'
- breaksw
- case pgfortran:
-@@ -426,12 +426,7 @@
- # Otherwise, attempt a link against shared object libs.
- # See the 64 bit Atlas below for a way to fix the linker's
- # not being able to locate -lf77blas, if that happens.
-- if (-e $GMS_MATHLIB_PATH/libf77blas.a) then
-- set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a"
-- set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a"
-- else
-- set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas"
-- endif
-+ set MATHLIBS=`${PKG_CONFIG} --libs blas`
- set BLAS=' '
- breaksw
-
-@@ -465,13 +460,13 @@
- switch ($GMS_FORTRAN)
- case gfortran:
- set LDR='gfortran'
-- set LDOPTS=' '
-+ set gentoo-LDOPTS=' '
- set FORTLIBS=' '
- if ($GMS_OPENMP == true) set LDOPTS="$LDOPTS -fopenmp"
- breaksw
- case ifort:
- set LDR='ifort'
-- set LDOPTS='-i8' # -Wl,-M generates a load map
-+ set gentoo-LDOPTS=' ' # -Wl,-M generates a load map
- # this auxiliary library seems to have disappeared in ifort 10
- set FORTLIBS=' '
- if ($GMS_IFORT_VERNO < 10) set FORTLIBS='-Vaxlib'
-@@ -616,13 +611,7 @@
- # ln -s liblapack_atlas.so.3.0 liblapack.so
- # ln -s liblapack.so.3.0 liblapack.so
- # It is strange the RPM's don't do these soft links for us.
-- if (-e $GMS_MATHLIB_PATH/libf77blas.a) then
-- set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a"
-- set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a"
-- else
-- set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas"
-- if ($CCHEM == true) set MATHLIBS="$MATHLIBS -llapack"
-- endif
-+ set MATHLIBS=`${PKG_CONFIG} --libs blas`
- set BLAS=' '
- breaksw
-
-diff -urN gamess.orig/runall gamess/runall
---- gamess.orig/runall 2012-02-03 03:55:01.000000000 +0400
-+++ gamess/runall 2016-11-29 11:28:19.069151991 +0300
-@@ -46,7 +46,7 @@
- xgms -v $VERNO -q $QUEUE -l exam$NUM.log exam$NUM
- sleep 2
- else
-- ./rungms exam$NUM $VERNO 1 >& exam$NUM.log
-+ rungms exam$NUM $VERNO 1 >& exam$NUM.log
- endif
- @ i++
- end
-diff -urN gamess.orig/rungms gamess/rungms
---- gamess.orig/rungms 2016-10-08 17:16:14.000000000 +0300
-+++ gamess/rungms 2016-11-29 11:28:19.070151993 +0300
-@@ -61,9 +61,9 @@
- # See also a very old LoadLeveler "ll-gms" for some IBM systems.
- #
- set TARGET=sockets
--set SCR=/scr/$USER
--set USERSCR=/u1/$USER/scr
--set GMSPATH=/u1/mike/gamess
-+set SCR=`pwd`
-+set USERSCR=`pwd`
-+set GMSPATH=/usr/bin
- #
- set JOB=$1 # name of the input file xxx.inp, give only the xxx part
- set VERNO=$2 # revision number of the executable created by 'lked' step
diff --git a/sci-chemistry/gamess/gamess-20161808.1.ebuild
b/sci-chemistry/gamess/gamess-20161808.1.ebuild
deleted file mode 100644
index 2cfc5747f..000000000
--- a/sci-chemistry/gamess/gamess-20161808.1.ebuild
+++ /dev/null
@@ -1,342 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils fortran-2 flag-o-matic pax-utils toolchain-funcs
-
-DESCRIPTION="A powerful quantum chemistry package"
-HOMEPAGE="http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html";
-SRC_URI="
- ${P}.tar.gz
- qmmm-tinker? ( tinker.tar.gz )"
-
-SLOT="0"
-LICENSE="gamess"
-# NOTE: PLEASE do not stabilize gamess. It does not make sense
-# since the tarball has fetch restrictions and upstream only
-# provides the latest version. In other words: As soon as a
-# new version comes out the stable version will be useless since
-# users can not get at the tarball any more.
-KEYWORDS="~amd64 ~x86"
-IUSE="mpi neo pax_kernel qmmm-tinker"
-
-CDEPEND="
- app-shells/tcsh
- mpi? ( virtual/mpi )
- virtual/blas"
-DEPEND="${CDEPEND}
- virtual/pkgconfig"
-RDEPEND="${CDEPEND}
- net-misc/openssh"
-
-S="${WORKDIR}/${PN}"
-
-RESTRICT="fetch"
-
-GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html";
-GAMESS_VERSION="18 AUG 2016 (R1)"
-
-pkg_nofetch() {
- echo
- elog "Please download ${PN}-current.tar.gz from"
- elog "${GAMESS_DOWNLOAD}."
- elog "Be sure to select the version ${GAMESS_VERSION} tarball!!"
- elog "Then move the tarball to"
- elog "${DISTDIR}/${P}.tar.gz"
- if use qmmm-tinker ; then
- elog "Also download
http://www.msg.ameslab.gov/GAMESS/tinker.tar.Z";
- elog "and place tinker.tar.Z to ${DISTDIR}"
- fi
- echo
-}
-
-get_fcomp() {
- case $(tc-getFC) in
- *gfortran* )
- FCOMP="gfortran" ;;
- ifort )
- FCOMP="ifc" ;;
- * )
- FCOMP=$(tc-getFC) ;;
- esac
-}
-
-pkg_setup() {
- fortran-2_pkg_setup
- get_fcomp
- # currently amd64 is only supported with gfortran
- if [[ "${ARCH}" == "amd64" ]] && [[ ${FCOMP} != *gfortran* ]];
- then die "You will need gfortran to compile gamess on amd64"
- fi
-
- # note about qmmm-tinker
- if use qmmm-tinker; then
- einfo "By default MM subsistem is restricted to 1000
atoms"
- einfo "if you want larger MM subsystems then you should
set"
- einfo "QMMM_GAMESS_MAXMM variable to needed value in
your make.conf"
- einfo "By default maximum number of atom classes types
and size of"
- einfo "hessian are restricted to 250, 500 and 1000000
respectively"
- einfo "If you want larger sizes set:"
- einfo "QMMM_GAMESS_MAXCLASS"
- einfo "QMMM_GAMESS_MAXCTYP"
- einfo "QMMM_GAMESS_MAXHESS"
- einfo "in your make.conf"
- fi
-
- #note about mpi
- if use mpi; then
- ewarn ""
- ewarn "You should adjust rungms script for your mpi
implentation"
- ewarn "because deafult one will not work"
- ewarn ""
- fi
-}
-
-src_unpack() {
- unpack ${A}
-
- if use qmmm-tinker; then
- mv tinker gamess/ || die "failed to move tinker directory"
- fi
-}
-
-src_prepare() {
- tc-export PKG_CONFIG
- # apply LINUX-arch patches to gamess makesfiles
- epatch "${FILESDIR}/${P}.gentoo.patch"
- eapply_user
- # select arch
- # NOTE: please leave lked alone; it should be good as is!!
- cd "${S}"
- local active_arch;
- if [[ "${ARCH}" == "amd64" ]]; then
- active_arch="linux64";
- else
- active_arch="linux32";
- fi
-
- # for hardened-gcc let't turn off ssp, since it breakes
- # a few routines
- if use pax_kernel && [[ ${FCOMP} == g77 ]]; then
- FFLAGS="${FFLAGS} -fno-stack-protector-all"
- fi
-
- # Enable mpi stuff
- if use mpi; then
- sed -e "s:set COMM = sockets:set COMM = mpi:g" \
- -i ddi/compddi || die "Enabling mpi build failed"
- sed -e "s:MPI_INCLUDE_PATH = ' ':MPI_INCLUDE_PATH =
'-I/usr/include ':g" \
- -i ddi/compddi || die "Enabling mpi build failed"
- sed -e "s:MSG_LIBRARIES='../ddi/libddi.a
-lpthread':MSG_LIBRARIES='../ddi/libddi.a -lmpi -lpthread':g" \
- -i lked || die "Enabling mpi build failed"
- fi
-
- # enable NEO
- if use neo; then
- sed -e "s:NEO=false:NEO=true:" -i compall lked || \
- die "Failed to enable NEO code"
- else
- sed -e "s:NEO=true:NEO=false:" -i compall lked || \
- die "Failed to disable NEO code"
- fi
- # enable GAMESS-qmmm
- if use qmmm-tinker; then
- epatch "${FILESDIR}/${PN}-qmmm-tinker-fix-idate.patch"
- sed -e "s:TINKER=false:TINKER=true:" -i compall lked || \
- die "Failed to enable TINKER code"
- if [ "x$QMMM_GAMESS_MAXMM" == "x" ]; then
- einfo "No QMMM_GAMESS_MAXMM set. Using default value =
1000"
- else
- einfo "Setting QMMM_GAMESS_MAXMM to $QMMM_GAMESS_MAXMM"
- sed -e "s:maxatm=1000:maxatm=$QMMM_GAMESS_MAXMM:g" \
- -i tinker/sizes.i \
- || die "Setting QMMM_GAMESS_MAXMM failed"
- sed -e "s:MAXATM=1000:MAXATM=$QMMM_GAMESS_MAXMM:g" \
- -i source/inputb.src \
- || die "Setting QMMM_GAMESS_MAXMM failed"
- fi
- if [ "x$QMMM_GAMESS_MAXCLASS" == "x" ]; then
- einfo "No QMMM_GAMESS_MAXMM set. Using default value =
250"
- else
- sed -e
"s:maxclass=250:maxclass=$QMMM_GAMESS_MAXCLASS:g" \
- -i tinker/sizes.i \
- || die "Setting QMMM_GAMESS_MAXCLASS failed"
- fi
- if [ "x$QMMM_GAMESS_MAXCTYP" == "x" ]; then
- einfo "No QMMM_GAMESS_MAXCTYP set. Using default value
= 500"
- else
- sed -e "s:maxtyp=500:maxtyp=$QMMM_GAMESS_MAXCTYP:g" \
- -i tinker/sizes.i \
- || die "Setting QMMM_GAMESS_MAXCTYP failed"
- fi
- if [ "x$QMMM_GAMESS_MAXHESS" == "x" ]; then
- einfo "No QMMM_GAMESS_MAXHESS set. Usingdefault value =
1000000"
- else
- sed -e
"s:maxhess=1000000:maxhess=$QMMM_GAMESS_MAXHESS:g" \
- -i tinker/sizes.i \
- || die "Setting QMMM_GAMESS_MAXHESS failed"
- fi
- fi
- # create proper activate sourcefile
- cp "./tools/actvte.code" "./tools/actvte.f" || \
- die "Failed to create actvte.f"
- sed -e "s/^\*UNX/ /" -i "./tools/actvte.f" || \
- die "Failed to perform UNX substitutions in actvte.f"
-
- # fix GAMESS' compall script to use proper CC
- sed -e "s|\$CCOMP -c \$extraflags source/zunix.c|$(tc-getCC) -c
\$extraflags source/zunix.c|" \
- -i compall || die "Failed setting up compall script"
-
- # insert proper FFLAGS into GAMESS' comp makefile
- # in case we're using ifc let's strip all the gcc
- # specific stuff
- if [[ ${FCOMP} == "ifort" ]]; then
- sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS} -quiet'/" \
- -i comp || die "Failed setting up comp script"
- elif ! use x86; then
- sed -e "s/-malign-double //" \
- -e "s/gentoo-OPT='-O2'/OPT='${FFLAGS}'/" \
- -i comp || die "Failed setting up comp script"
- else
- sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
- -i comp || die "Failed setting up comp script"
- fi
-
- # fix up GAMESS' linker script;
- sed -e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \
- -i lked || die "Failed setting up lked script"
- # fix up GAMESS' ddi TCP/IP socket build
- sed -e "s/gentoo-CC = 'gcc'/CC = '$(tc-getCC)'/" \
- -i ddi/compddi || die "Failed setting up compddi script"
- # Creating install.info
- cat > install.info <<-EOF
- #!/bin/csh
- setenv GMS_PATH $WORKDIR/gamess
- setenv GMS_BUILD_DIR $WORKDIR/gamess
- setenv GMS_TARGET $active_arch
- setenv GMS_FORTRAN $FCOMP
- setenv GMS_GFORTRAN_VERNO $(gcc-major-version).$(gcc-minor-version)
- setenv GMS_MATHLIB atlas
- setenv GMS_MATHLIB_PATH /usr/$(get_libdir)/atlas
- setenv GMS_DDI_COMM sockets
- setenv GMS_LIBCCHEM false
- setenv GMS_PHI false
- setenv GMS_SHMTYPE sysv
- setenv GMS_OPENMP false
- EOF
-
-}
-
-src_compile() {
- # build actvte
- cd "${S}"/tools
- ${FCOMP} -o actvte.x actvte.f || \
- die "Failed to compile actvte.x"
-
- # for hardened (PAX) users and ifc we need to turn
- # MPROTECT off
- if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then
- pax-mark -PemRxS actvte.x
- fi
-
- # build gamess
- cd "${S}"
- ./compall || die "compall failed"
-
- # build the ddi TCP/IP socket stuff
- cd ${S}/"ddi"
- ./compddi || die "compddi failed"
-
- # finally, link it all together
- cd "${S}"
- ./lked || die "lked failed"
-
- # for hardened (PAX) users and ifc we need to turn
- # MPROTECT off
- if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then
- pax-mark -PemRxS ${PN}.00.x
- fi
-}
-
-src_install() {
- # the executables
- dobin ${PN}.00.x rungms gms-files.csh \
- || die "Failed installing binaries"
- if use !mpi; then
- dobin ddi/ddikick.x \
- || die "Failed installing binaries"
- fi
-
- # the docs
- dodoc *.DOC qmnuc/*.DOC
-
- # install ericftm
- insinto /usr/share/${PN}
- doins auxdata/ericfmt.dat
-
- # install mcpdata
- insinto /usr/share/${PN}/MCP
- doins auxdata/MCP/*
-
- # install BASES
- insinto /usr/share/${PN}/BASES
- doins auxdata/BASES/*
-
- # install QUANPOL
- insinto /usr/share/${PN}/QUANPOL
- doins auxdata/QUANPOL/*
-
- # install tinker params in case of qmmm
- if use qmmm-tinker ; then
- dodoc tinker/simomm.doc
- insinto /usr/share/${PN}
- doins -r tinker/params51
- fi
-
- # install the tests the user should run, and
- # fix up the runscript; also grab a copy of rungms
- # so the user is ready to run the tests
- insinto /usr/share/${PN}/tests
- insopts -m0644
- doins -r tests/*
- insopts -m0744
- doins runall
- #doins tools/checktst/checktst tools/checktst/chkabs || \
- # die "Failed to install main test checker"
- #doins tools/checktst/exam* || \
- # die "Failed to install individual test files"
-
- insinto /usr/share/${PN}/neotests
- insopts -m0644
- doins -r qmnuc/neotests/*
-}
-
-pkg_postinst() {
- echo
- einfo "Before you use GAMESS for any serious work you HAVE"
- einfo "to run the supplied test files located in"
- einfo "/usr/share/gamess/tests and check them thoroughly."
- einfo "Otherwise all scientific publications resulting from"
- einfo "your GAMESS runs should be immediately rejected :)"
- einfo "To do so copy the content of /usr/share/gamess/tests"
- einfo "to some temporary location and execute './runall'. "
- einfo "Then run the checktst script in the same directory to"
- einfo "validate the tests."
- einfo "Please consult TEST.DOC and the other docs!"
-
- if [[ ${FCOMP} == "ifort" ]]; then
- echo
- ewarn "IMPORTANT NOTE: We STRONGLY recommend to stay away"
- ewarn "from ifc-9.0 for now and use the ifc-8.1 series of"
- ewarn "compilers UNLESS you can run through ALL of the "
- ewarn "test cases (see above) successfully."
- fi
-
- echo
- einfo "If you want to run on more than a single CPU"
- einfo "you will have to acquaint yourself with the way GAMESS"
- einfo "does multiprocessor runs and adjust rungms according to"
- einfo "your target network architecture."
- echo
-}
