Initial import (fixes bug #105901).

(Portage version: 2.0.51.22-r2)

12 files changed, 450 insertions, 0 deletions

diff --git a/sci-chemistry/gamess/ChangeLog b/sci-chemistry/gamess/ChangeLog
new file mode 100644
index 000000000000..05deab0f24e9
--- /dev/null
+++ b/sci-chemistry/gamess/ChangeLog
@@ -0,0 +1,15 @@
+# ChangeLog for sci-chemistry/gamess
+# Copyright 1999-2005 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/ChangeLog,v 1.1 2005/09/20 02:20:37 ribosome Exp $
+
+*gamess-05272005 (20 Sep 2005)
+
+  20 Sep 2005; Olivier Fisette <ribosome@gentoo.org>
+  +files/comp-gentoo.patch, +files/compall-gentoo.patch,
+  +files/compddi-gentoo.patch, +files/ddi-use-ssh-gentoo.patch,
+  +files/lked-gentoo.patch, +files/runall-gentoo.patch,
+  +files/rungms-gentoo.patch, +metadata.xml, +gamess-05272005.ebuild:
+  Initial import (fixes bug #105901). Package masked to allow for some
+  testing. Many thanks to Markus Dittrich <markusle@gmail.com> for his ebuild
+  and patches.
+
diff --git a/sci-chemistry/gamess/Manifest b/sci-chemistry/gamess/Manifest
new file mode 100644
index 000000000000..af797af9b495
--- /dev/null
+++ b/sci-chemistry/gamess/Manifest
@@ -0,0 +1,9 @@
+MD5 febcf13175d0964e4389224b18e4c56e gamess-05272005.ebuild 6629
+MD5 bfc4049f6e2546889b161c6c9b3be72f files/runall-gentoo.patch 688
+MD5 42ad79e7a475c0246839aa8137381e43 files/digest-gamess-05272005 67
+MD5 d2f6837d02ac960e7bed4addf9632eec files/lked-gentoo.patch 783
+MD5 e980cc327bd2de746b91a395f1af3e0f files/compddi-gentoo.patch 975
+MD5 cc629344d268783ea8be555bd06249af files/comp-gentoo.patch 1276
+MD5 88aa0ef3a19289c609a5167e2176bbf6 files/compall-gentoo.patch 445
+MD5 7635651c5b13ead41c16d56094238fcb files/ddi-use-ssh-gentoo.patch 518
+MD5 5fa801207d43042213344c896962c84d files/rungms-gentoo.patch 1754
diff --git a/sci-chemistry/gamess/files/comp-gentoo.patch b/sci-chemistry/gamess/files/comp-gentoo.patch
new file mode 100644
index 000000000000..5329bc3566e7
--- /dev/null
+++ b/sci-chemistry/gamess/files/comp-gentoo.patch
@@ -0,0 +1,40 @@
+# patch to enable linux-x86 arch in GAMESS comp script
+# includes a small fix that compiles module zheev using -O1
+# since anything more agressive might break things
+
+--- gamess-orig/comp	2005-07-23 20:30:18.000000000 +0000
++++ gamess/comp	2005-09-06 16:27:07.000000000 +0000
+@@ -14,8 +14,8 @@
+ #      linux-ia64,linux-pc,mac32,macG5,necsx,sgi32,sgi64,sun32,sun64
+ #  2. Choose your GAMESS directory tree.
+ #
+-set TARGET=ibm64
+-chdir /u1/mike/gamess
++set TARGET=linux-pc
++#chdir /u1/mike/gamess
+ #
+ #    ---- and now the script begins...
+ #
+@@ -992,11 +992,12 @@
+ #   Pentium II fractionally).  None of these optimizations are used below.
+ #
+ if ($TARGET == linux-pc) then
+-   set OPT = '-O2'
++   set gentoo-OPT = '-O2'
+    if ($MODULE == ormas1) set OPT='-O2 -fno-move-all-movables' # RH9, g77 3.3
+ #
+ #   g77 does not support FORTRAN logical units above 99, or 128 bit math.
+ #
++   if ($MODULE == zheev) set OPT='-O1' 
+    if (($MODULE == qeigen) || ($MODULE == int2c)) then
+       mv $MODULE.f $MODULE.junk
+       sed -e "s/Q-/D-/g" \
+@@ -1010,7 +1011,7 @@
+       rm -f $MODULE.junk
+    endif
+    set echo
+-   g77 -c $OPT -malign-double -fautomatic \
++   gentoo-g77 -c $OPT -malign-double -fautomatic \
+            -Wno-globals -fno-globals $MODULE.f
+    unset echo
+ endif
diff --git a/sci-chemistry/gamess/files/compall-gentoo.patch b/sci-chemistry/gamess/files/compall-gentoo.patch
new file mode 100644
index 000000000000..6ea5f77b7139
--- /dev/null
+++ b/sci-chemistry/gamess/files/compall-gentoo.patch
@@ -0,0 +1,15 @@
+# patch to enable linux-x86 arch in main GAMESS compile driver
+
+--- gamess/compall	2005-07-18 22:37:23.000000000 +0000
++++ gamess-gentoo/compall	2005-09-04 15:00:18.000000000 +0000
+@@ -12,8 +12,8 @@
+ #      linux-ia64,linux-pc,mac32,macG5,necsx,sgi32,sgi64,sun32,sun64
+ #  2. Choose your GAMESS directory tree.
+ #
+-set TARGET=ibm64
+-chdir /u1/mike/gamess
++set TARGET=linux-pc
++#chdir /u1/mike/gamess
+ #
+ #  ----- and now the script begins...
+ #
diff --git a/sci-chemistry/gamess/files/compddi-gentoo.patch b/sci-chemistry/gamess/files/compddi-gentoo.patch
new file mode 100644
index 000000000000..dcfd5d71a953
--- /dev/null
+++ b/sci-chemistry/gamess/files/compddi-gentoo.patch
@@ -0,0 +1,28 @@
+# patch to enable linux-x86 arch in GAMESS DDI socket compile
+# script
+
+--- gamess/ddi/compddi	2005-07-23 20:32:02.000000000 +0000
++++ gamess-gentoo/ddi/compddi	2005-09-05 12:20:02.000000000 +0000
+@@ -14,7 +14,7 @@
+ #      fuji-pp32,fuji-pp64,hpux32,hpux64,ibm32,ibm64,ibm64-sp,ibm-bg,
+ #      linux-ia64,linux-pc,mac32,macG5,necsx,sgi32,sgi64,sun32,sun64
+ #
+-       set TARGET = ibm64
++       set TARGET = linux-pc
+ 
+ #  2. Choose DDI communication layer, the only legal values are
+ #                   sockets,mpi,shmem,lapi
+@@ -470,11 +470,11 @@
+ #       select only one rather than two trailing underscores below.
+   if($TARGET == linux-pc) then
+ 
+-     set CC = 'gcc'
++     set gentoo-CC = 'gcc'
+      set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./include"
+      set CLIBS  = "-lpthread"
+ 
+-     set F77_OPTS = '-DINT_SIZE=int -D_UNDERSCORES=2'
++     set gentoo-F77_OPTS = '-DINT_SIZE=int -D_UNDERSCORES=2'
+ 
+      set AR_FLAGS     = 'cr'
+      set RANLIB_FLAGS = ' '
diff --git a/sci-chemistry/gamess/files/ddi-use-ssh-gentoo.patch b/sci-chemistry/gamess/files/ddi-use-ssh-gentoo.patch
new file mode 100644
index 000000000000..61c7090886a0
--- /dev/null
+++ b/sci-chemistry/gamess/files/ddi-use-ssh-gentoo.patch
@@ -0,0 +1,13 @@
+# patch to use ssh rather than rsh for TCP/IP socket communication
+# in GAMESS' DDI_SOC interface
+--- gamess/ddi/tools/ddikick/ddikick.c	2004-05-03 16:23:13.000000000 +0000
++++ gamess-gentoo/ddi/tools/ddikick/ddikick.c	2005-09-04 15:56:50.000000000 +0000
+@@ -102,7 +102,7 @@
+           remoteshell = argv[++i];
+        } else {
+           if((remoteshell = getenv("DDI_RSH")) == NULL) {
+-              remoteshell = (char *) strdup("rsh");
++              remoteshell = (char *) strdup("ssh");
+           }
+        }
+ 
diff --git a/sci-chemistry/gamess/files/digest-gamess-05272005 b/sci-chemistry/gamess/files/digest-gamess-05272005
new file mode 100644
index 000000000000..505c63894ac0
--- /dev/null
+++ b/sci-chemistry/gamess/files/digest-gamess-05272005
@@ -0,0 +1 @@
+MD5 3aa67e3db20051d372f6fc79c47c3abe gamess-current.tar.gz 5761028
diff --git a/sci-chemistry/gamess/files/lked-gentoo.patch b/sci-chemistry/gamess/files/lked-gentoo.patch
new file mode 100644
index 000000000000..defdcbfd4cf8
--- /dev/null
+++ b/sci-chemistry/gamess/files/lked-gentoo.patch
@@ -0,0 +1,26 @@
+# patch to enable linux-x86 arch in GAMESS linking script
+
+--- gamess/lked	2005-06-30 20:47:59.000000000 +0000
++++ gamess-gentoo/lked	2005-09-04 15:01:54.000000000 +0000
+@@ -14,8 +14,8 @@
+ #       linux-ia64,linux-pc,mac32,macG5,necsx,sgi32,sgi64,sun32,sun64
+ #  2. Choose your GAMESS directory tree.
+ #
+-set TARGET=ibm64
+-chdir /u1/mike/gamess
++set TARGET=linux-pc
++#chdir /u1/mike/gamess
+ #
+ #    ---- and now the script begins...
+ #
+@@ -321,8 +321,8 @@
+ #  about matching the number of trailing underscores.
+ #
+ if ($TARGET == linux-pc) then
+-   set LDR='g77'
+-   set LDOPTS=' '  # add '-Wl,-M' to see load map
++   set gentoo-LDR='g77'
++   set gentoo-LDOPTS=' '  # add '-Wl,-M' to see load map
+    if (-e /usr/lib/libblas.a) then
+       set LIBRARIES='-lblas'
+       set BLAS=' '
diff --git a/sci-chemistry/gamess/files/runall-gentoo.patch b/sci-chemistry/gamess/files/runall-gentoo.patch
new file mode 100644
index 000000000000..8ad9535cd4bb
--- /dev/null
+++ b/sci-chemistry/gamess/files/runall-gentoo.patch
@@ -0,0 +1,22 @@
+# patch to adjust paths in runall script according to our GENTOO
+# install
+
+--- gamess/runall	2005-07-05 14:08:04.000000000 +0000
++++ gamess-gentoo/runall	2005-09-05 11:05:31.000000000 +0000
+@@ -10,7 +10,7 @@
+ #  Edit this file to set the base path to GAMESS, and execute it to be
+ #  sure all the jobs TERMINATED NORMALLY, and got correct numbers too.
+ #
+-chdir /u1/mike/gamess
++#chdir /u1/mike/gamess/
+ set VERNO=00
+ #
+ foreach NUM ( 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 \
+@@ -20,6 +20,6 @@
+      gms -v $VERNO -q ti -l exam$NUM.log exam$NUM
+      sleep 5
+   else
+-     rungms exam$NUM $VERNO 1  >&  exam$NUM.log
++     ./rungms exam$NUM $VERNO 1  >&  exam$NUM.log
+   endif
+ end
diff --git a/sci-chemistry/gamess/files/rungms-gentoo.patch b/sci-chemistry/gamess/files/rungms-gentoo.patch
new file mode 100644
index 000000000000..8e6e9641145c
--- /dev/null
+++ b/sci-chemistry/gamess/files/rungms-gentoo.patch
@@ -0,0 +1,49 @@
+# patch to make rungms wrapper script for GAMESS work on our
+# gentoo install
+
+--- gamess/rungms	2005-07-23 20:33:54.000000000 +0000
++++ gamess-gentoo/rungms	2005-09-04 17:01:19.000000000 +0000
+@@ -39,7 +39,7 @@
+ #       its own list of further requirements.
+ #
+ set TARGET=sockets
+-set SCR=/scr/$USER
++set SCR=./
+ #
+ set JOB=$1      # name of the input file xxx.inp, give only the xxx part
+ set VERNO=$2    # revision number of the executable created by 'lked' step
+@@ -90,11 +90,11 @@
+ #  is therefore most suitable to be stored only once, on the file server.
+ #
+ set echo
+-setenv ERICFMT ~mike/gamess/ericfmt.dat
++setenv ERICFMT /usr/share/gamess/ericfmt/ericfmt.dat
+ setenv  EXTBAS /dev/null
+-setenv IRCDATA ~/scr/$JOB.irc
++setenv IRCDATA $SCR/$JOB.irc
+ setenv   INPUT $SCR/$JOB.F05
+-setenv   PUNCH ~/scr/$JOB.dat
++setenv   PUNCH $SCR/$JOB.dat
+ setenv  AOINTS $SCR/$JOB.F08
+ setenv  MOINTS $SCR/$JOB.F09
+ setenv DICTNRY $SCR/$JOB.F10
+@@ -124,8 +124,8 @@
+ setenv  SOINTY $SCR/$JOB.F32
+ setenv  SOINTZ $SCR/$JOB.F33
+ setenv  SORESC $SCR/$JOB.F34
+-setenv   SIMEN ~/scr/$JOB.simen
+-setenv  SIMCOR ~/scr/$JOB.simcor
++setenv   SIMEN $SCR/$JOB.simen
++setenv  SIMCOR $SCR/$JOB.simcor
+ setenv GCILIST $SCR/$JOB.F37
+ setenv HESSIAN $SCR/$JOB.F38
+ setenv SOCCDAT $SCR/$JOB.F40
+@@ -266,7 +266,7 @@
+    if ($os == HP-UX)   set GMSPATH=/zr/mike/gamess
+    if ($os == IRIX)    set GMSPATH=/home/hbar4/people/schmidt/gamess
+    if ($os == IRIX64)  set GMSPATH=/home/hbar4/people/schmidt/gamess
+-   if ($os == Linux)   set GMSPATH=/cu/mike/gamess
++   if ($os == Linux)   set GMSPATH=/usr/bin
+    if ($os == OSF1)    set GMSPATH=/au/mike/gamess
+    if ($os == SunOS)   set GMSPATH=/hf/mike/gamess
+ #       special compilation for my old Sun (uname also replies SunOS)
diff --git a/sci-chemistry/gamess/gamess-05272005.ebuild b/sci-chemistry/gamess/gamess-05272005.ebuild
new file mode 100644
index 000000000000..8ac890c4cee2
--- /dev/null
+++ b/sci-chemistry/gamess/gamess-05272005.ebuild
@@ -0,0 +1,223 @@
+# Copyright 1999-2005 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/gamess-05272005.ebuild,v 1.1 2005/09/20 02:20:37 ribosome Exp $
+
+inherit eutils toolchain-funcs fortran
+
+DESCRIPTION="A powerful quantum chemistry package"
+LICENSE="gamess"
+HOMEPAGE="http://www.msg.ameslab.gov/GAMESS/GAMESS.html"
+SRC_URI="${PN}-current.tar.gz"
+
+SLOT="0"
+KEYWORDS="~x86"
+IUSE="ifc hardened blas"
+
+RESTRICT="fetch"
+
+DEPEND="app-shells/tcsh
+	ifc? ( >=dev-lang/ifc-8.1 )
+	hardened? ( sys-apps/paxctl )
+	blas? ( virtual/blas )"
+
+RDEPEND="app-shells/tcsh
+	net-misc/openssh
+	ifc? ( >=dev-lang/ifc-8.1 )"
+
+S="${WORKDIR}/${PN}"
+
+GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html"
+
+pkg_nofetch() {
+	echo
+	einfo "Please download ${PN}-current.tar.gz from"
+	einfo "${GAMESS_DOWNLOAD}"
+	einfo "after agreeing to the license and then move it to "
+	einfo "${DISTDIR}"
+	einfo "Be sure to select the version 27 JUN 2005 tarball!!"
+	echo
+}
+
+pkg_setup() {
+	# make sure we have the proper fortan compiler; 
+	# use ifc for USE="ifc" and g77 otherwise
+	if use ifc; then
+		need_fortran ifc
+	else
+		need_fortran g77
+	fi
+
+	# blas and ifc don't go together
+	if use blas && use ifc; then
+		die  "${PN} can not be compiled with USE=blas and USE=ifc"
+	fi
+}
+
+src_unpack() {
+	unpack ${A}
+
+	# apply LINUX-arch patches to gamess makesfiles
+	epatch "${FILESDIR}"/comp-gentoo.patch
+	epatch "${FILESDIR}"/compall-gentoo.patch
+	epatch "${FILESDIR}"/lked-gentoo.patch
+	epatch "${FILESDIR}"/ddi-use-ssh-gentoo.patch
+	epatch "${FILESDIR}"/compddi-gentoo.patch
+	epatch "${FILESDIR}"/rungms-gentoo.patch
+	epatch "${FILESDIR}"/runall-gentoo.patch
+
+	# for hardened-gcc let't turn off ssp, since it breakes
+	# a few routines
+	cd "${S}"
+	if use hardened && [[ $(tc-getF77) = f77 ]]; then
+		FFLAGS="${FFLAGS} -fno-stack-protector-all"
+	fi
+
+	# greate 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|$(tc-getCC) -c \$extraflags source/zunix.c|" \
+		-i compall || die "Failed setting up compall script"
+
+	# insert proper FFLAGS into GAMESS' comp makefile
+	# in case we're using ifc let's strip all the gcc
+	# specific stuff
+	if use ifc; then
+		sed -e "s/-malign-double -fautomatic /-cm -w \$MODULE.f/" \
+			-e "s/-Wno-globals -fno-globals \$MODULE.f//" \
+			-e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS} -quiet'/" \
+		    -e "s/gentoo-g77/$(tc-getF77)/" \
+			-i comp || die "Failed setting up comp script"
+	else
+		sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
+		   	-e "s/gentoo-g77/$(tc-getF77)/" \
+			-i comp || die "Failed setting up comp script"
+	fi
+
+	# use proper blas 
+	if ! use blas; then
+		sed -e "s|/usr/lib/libblas.a|/usr/lib/dontuselibblas.a|" \
+			-i lked || die "Failed to adjust blas in lked"
+	fi
+
+	# fix up GAMESS' linker script;
+	if use ifc; then
+		sed -e "s/gentoo-LDR='g77'/LDR='$(tc-getF77)'/" \
+		   	-e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \
+			-i lked || die "Failed setting up lked script"
+	else
+		sed -e "s/gentoo-LDR='g77'/LDR='$(tc-getF77)'/" \
+			-e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \
+			-i lked || die "Failed patching lked script"
+	fi
+
+	# fix up GAMESS' ddi TCP/IP socket build
+	sed -e "s/gentoo-CC = 'gcc'/CC = '$(tc-getCC)'/" \
+		-i ddi/compddi || die "Failed setting up compddi script"
+
+	# for ifc we have to fix the number of underscores of fortran
+	# symbols, otherwise the linker will barf
+	if use ifc; then
+		sed -e "s/gentoo-F77_OPTS = '-DINT_SIZE=int -D_UNDERSCORES=2/F77_OPTS = '-DINT_SIZE=int -D_UNDERSCORES=1/" \
+			-i ddi/compddi || die "Failed fixing underscores in compddi"
+	else
+		sed -e "s/gentoo-F77_OPTS/F77_OPTS/" \
+		    -i ddi/compddi || die "Failed fixing underscores in compddi"
+	fi
+}
+
+src_compile() {
+	# build actvte
+	cd "${S}"/tools
+	$(tc-getF77) -o actvte.x actvte.f || die "Failed to compile actvte.x"
+
+	# for hardened (PAX) users and ifc we need to turn
+	# MPROTECT off
+	if use ifc && use hardened; then
+		/sbin/paxctl -PemRxS actvte.x 2> /dev/null || \
+			die "paxctl failed on actvte.x"
+	fi
+
+	# build gamess
+	cd "${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 use ifc && use hardened; then
+		/sbin/paxctl -PemRxS ${PN}.00.x 2> /dev/null || \
+			die "paxctl failed on actvte.x"
+	fi
+}
+
+src_install() {
+	cd "${S}"
+
+	# the executables
+	dobin ${PN}.00.x || die "Failed installing gamess executable"
+	dobin ddi/ddikick.x || die "Failed installing ddikick.x"
+
+	# the docs
+	dodoc *.DOC || die "Failed installing docs"
+
+	# install ericftm
+	insinto /usr/share/${PN}/ericfmt
+	doins ericfmt.dat || die "Failed installing ericfmt.dat"
+
+	# install rungms, also supply a copy for the test	
+	# files
+	insinto /usr/share/${PN}/rungms
+	insopts -m0744
+	doins rungms || die "Failed installing rungms"
+
+	# install the tests the user should run, and
+	# fix up the runscript; also grab a copy of rungms
+	# so the user is ready to run the tests
+	insinto /usr/share/${PN}/tests
+	insopts -m0644
+	doins tests/* || die "Failed installing tests"
+	insopts -m0744
+	doins runall rungms || die "Failed installing tests"
+}
+
+pkg_postinst() {
+	echo
+	ewarn "Before you use GAMESS for any serious work you HAVE"
+	ewarn "to run the supplied test files located in"
+	ewarn "/usr/share/gamess/tests and check them thoroughly."
+	ewarn "Otherwise all scientific publications resulting from"
+	ewarn "your GAMESS runs should be immediately rejected :)"
+	ewarn "To do so copy the content of /usr/share/gamess/tests"
+	ewarn "to some temporary location and execute './runall'. "
+	ewarn "Please consult TEST.DOC and the other docs!"
+
+	if use ifc; 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 "To perform a GAMESS run copy the the rungms script from"
+	einfo "/usr/share/gamess/rungms into your local directory"
+	einfo "and type ./rungms <myinputfile> >& <myoutputfile> "
+	einfo
+	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
+}
diff --git a/sci-chemistry/gamess/metadata.xml b/sci-chemistry/gamess/metadata.xml
new file mode 100644
index 000000000000..e9391a41a838
--- /dev/null
+++ b/sci-chemistry/gamess/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer>
+		<email>ribosome@gentoo.org</email>
+		<name>Olivier Fisette</name>
+	</maintainer>
+	<herd>sci</herd>
+</pkgmetadata>