[gentoo-commits] proj/sci:master commit in: sci-chemistry/gamess/, sci-chemistry/gamess/files/

[Alexey Shvetsov]

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
+}