commit: e9fc59e7cc0b16c130f16ff22fc3242f1fe3333b
Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Thu May 26 09:17:53 2016 +0000
Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Thu May 26 09:17:53 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e9fc59e7
sci-chemistry/gamess: Version bump
BugID #439908
Package-Manager: portage-2.3.0_rc1
.../gamess/files/gamess-20141205.1.gentoo.patch | 198 ++++++++++++
sci-chemistry/gamess/gamess-20141205.1.ebuild | 338 +++++++++++++++++++++
2 files changed, 536 insertions(+)
diff --git a/sci-chemistry/gamess/files/gamess-20141205.1.gentoo.patch
b/sci-chemistry/gamess/files/gamess-20141205.1.gentoo.patch
new file mode 100644
index 0000000..742ea46
--- /dev/null
+++ b/sci-chemistry/gamess/files/gamess-20141205.1.gentoo.patch
@@ -0,0 +1,198 @@
+diff -urN gamess.orig/comp gamess/comp
+--- gamess.orig/comp 2015-01-15 17:49:05.000000000 +0300
++++ gamess/comp 2016-05-26 11:40:00.143511481 +0300
+@@ -1535,7 +1535,7 @@
+ #
+ case gfortran:
+ #
+- set OPT='-O2'
++ set gentoo-OPT='-O2'
+ if ($MODULE == zheev) set OPT='-O0' # defensive compiling
+
+ set EXTRAOPT=" "
+@@ -1577,6 +1577,11 @@
+ breaksw
+ case 4.8:
+ case 4.9:
++ case 5.0:
++ case 5.1:
++ case 5.2:
++ case 5.3:
++ case 6.0:
+ if ($MODULE == cosmo) set OPT='-O0'
+ if ($MODULE == dcscf) set OPT='-O0'
+ if ($MODULE == tddgrd) set OPT='-O0'
+@@ -1605,7 +1610,7 @@
+ # 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 ($MODULE == zheev) set OPT='-O0'
+@@ -1740,7 +1745,7 @@
+ #
+ # first, initialize OPT and EXTRAOPT
+ #
+- set OPT='-O2'
++ set gentoo-OPT='-O2'
+ if ($MODULE == zheev) set OPT='-O0' # defensive compiling
+
+ set EXTRAOPT=" "
+@@ -1793,6 +1798,11 @@
+ breaksw
+ case 4.8:
+ case 4.9:
++ case 5.0:
++ case 5.1:
++ case 5.2:
++ case 5.3:
++ case 6.0:
+ 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 ($MODULE == tddgrd) set OPT='-O0' # exam41, continues from 4.6
+@@ -1829,7 +1839,7 @@
+ # -WB means warn but don't fail on out-of-bounds array references
+ # -ftz flushes underflow results to zero
+ #
+- set OPT = '-O2'
++ set gentoo-OPT = '-O2'
+ if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS"
+ # alas, I'm so tired of hearing about so many versions failing to
+ # diagonalize, that this time critical code is run w/o optimization.
+diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi
+--- gamess.orig/ddi/compddi 2015-01-15 17:49:05.000000000 +0300
++++ gamess/ddi/compddi 2016-05-26 11:30:34.601322818 +0300
+@@ -610,7 +610,7 @@
+
+ set FORTRAN=$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"
+
+@@ -664,7 +664,7 @@
+ 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 2016-05-26 11:30:34.601322818 +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 2014-05-16 18:14:43.000000000 +0400
++++ gamess/gms-files.csh 2016-05-26 11:30:34.601322818 +0300
+@@ -28,7 +28,7 @@
+ # to see all the file definitions (one is just below).
+ #
+ #---quiet---set echo
+-setenv AUXDATA $GMSPATH/auxdata
++setenv AUXDATA /usr/share/gamess
+ setenv EXTBAS /dev/null
+ setenv NUCBAS /dev/null
+ setenv POSBAS /dev/null
+diff -urN gamess.orig/lked gamess/lked
+--- gamess.orig/lked 2014-12-08 20:56:59.000000000 +0300
++++ gamess/lked 2016-05-26 11:41:11.124667982 +0300
+@@ -356,12 +356,12 @@
+ switch ($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:
+@@ -420,12 +420,7 @@
+ # 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=`${PKG_CONFIG} --libs blas`
+ set BLAS=' '
+ breaksw
+
+@@ -459,12 +454,12 @@
+ switch ($GMS_FORTRAN)
+ case gfortran:
+ set LDR='gfortran'
+- set LDOPTS=' '
++ set gentoo-LDOPTS=' '
+ set FORTLIBS=' '
+ 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'
+@@ -581,13 +576,7 @@
+ # 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 2016-05-26 11:30:34.603322822 +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 2014-12-10 19:01:06.000000000 +0300
++++ gamess/rungms 2016-05-26 11:42:23.316828732 +0300
+@@ -60,9 +60,9 @@
+ # 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-20141205.1.ebuild
b/sci-chemistry/gamess/gamess-20141205.1.ebuild
new file mode 100644
index 0000000..1fb80b7
--- /dev/null
+++ b/sci-chemistry/gamess/gamess-20141205.1.ebuild
@@ -0,0 +1,338 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+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="
+ ${P}.tar.gz
+ qmmm-tinker? ( tinker.tar.gz )"
+
+SLOT="0"
+LICENSE="gamess"
+# NOTE: PLEASE do not stabilize gamess. It does not make sense
+# since the tarball has fetch restrictions and upstream only
+# provides the latest version. In other words: As soon as a
+# new version comes out the stable version will be useless since
+# users can not get at the tarball any more.
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE="mpi neo pax_kernel qmmm-tinker"
+
+CDEPEND="
+ app-shells/tcsh
+ mpi? ( virtual/mpi )
+ virtual/blas"
+DEPEND="${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="5 DEC 2014 (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}/${P}.gentoo.patch"
+ # select arch
+ # NOTE: please leave lked alone; it should be good as is!!
+ cd "${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/$(get_libdir)/atlas
+ setenv GMS_DDI_COMM sockets
+ EOF
+
+}
+
+src_compile() {
+ # build actvte
+ cd "${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
+}
