--- /dev/null
+diff -urN gamess.orig/comp gamess/comp
+--- gamess.orig/comp 2010-05-04 22:11:54.000000000 +0400
++++ gamess/comp 2010-05-30 03:46:52.000000000 +0400
+@@ -1336,7 +1336,7 @@
+ # g77 does not support FORTRAN logical units above 99, or 128 bit math.
+ #
+ case g77:
+- set OPT = '-O2'
++ set gentoo-OPT = '-O2'
+ if ($MODULE == ormas1) set OPT='-O2 -fno-move-all-movables' # RH9, g77 3.3
+ if ($MODULE == zheev) set OPT='-O0' # defensive compiling
+ if (($MODULE == qeigen) || ($MODULE == int2c)) then
+@@ -1366,7 +1366,7 @@
+ # -std=legacy suppresses warnings about use of f77 constructs.
+ #
+ case gfortran:
+- set OPT='-O2'
++ set gentoo-OPT = '-O2'
+ if ($MODULE == zheev) set OPT='-O0' # defensive compiling
+ if ($MODULE == pcmcv2) set OPT='-O1' # EFP+CPCM, ala Francois, v4.1.2
+ if (($MODULE == qeigen) || ($MODULE == int2c)) then
+@@ -1392,7 +1392,7 @@
+ # 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 == zheev) set OPT='-O0'
+ set echo
+@@ -1504,7 +1504,7 @@
+
+ case gfortran:
+ # -finit-real=<zero|inf|-inf|nan> could be interesting debug opt
+- set OPT='-O2'
++ set gentoo-OPT = '-O2'
+ if ($MODULE == zheev) set OPT='-O0' # defensive compiling
+ if (($MODULE == qeigen) || ($MODULE == int2c)) then
+ mv -f $MODULE.f $MODULE.junk
+@@ -1533,7 +1533,7 @@
+ # -WB means warn but don't fail on out-of-bounds array references
+ # -ftz flushes underflow results to zero
+ #
+- set OPT = '-O2'
++ set gentoo-OPT = '-O2'
+ if ($MODULE == guess) set OPT='-O0' # 10.0, exam39
+ if ($MODULE == locpol) set OPT='-O1' # 10.0, makefp/gmres
+ if ($MODULE == morokm) set OPT='-O0' # Jan Fredin
+diff -urN gamess.orig/compall gamess/compall
+--- gamess.orig/compall 2010-05-11 23:22:04.000000000 +0400
++++ gamess/compall 2010-05-30 03:46:16.000000000 +0400
+@@ -84,15 +84,14 @@
+ endif
+ endif
+ if ($TARGET == linux32) set extraflags='-DLINUX32'
+-if ($TARGET == linux64) then
++if ($TARGET == linux64) then
++ set chip=`uname -m`
+ # Ubuntu uses the non-standard -m flag, its -p replies "unknown"
+- set chip=`uname -p`
+- if ($chip == unknown) set chip=`uname -m`
+- if ($chip == x86_64) set extraflags='-DLINUX64 -m64'
+- if ($chip == ia64) set extraflags='-DLINUX64' # this always 64 bits
++ if ($chip == x86_64) set extraflags='-DLINUX64 -m64'
++ if ($chip == ia64) set extraflags='-DLINUX64' # this always 64 bits
+ endif
+ if ($TARGET == mac32) set extraflags='-DLINUX32'
+-if ($TARGET == mac64) set extraflags='-DLINUX64 -m64 -I/usr/include/malloc'
++if ($TARGET == mac64) set extraflags='-DLINUX64 -m64 -I/usr/include/malloc'
+ if ($TARGET == necsx) set extraflags='-DNECSX -size_t64'
+ if ($TARGET == sgi32) set extraflags='-DSGI32 -n32'
+ if ($TARGET == sgi64) set extraflags='-DSGI64 -64'
+diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi
+--- gamess.orig/ddi/compddi 2010-05-10 17:34:25.000000000 +0400
++++ gamess/ddi/compddi 2010-05-30 03:46:16.000000000 +0400
+@@ -640,7 +640,7 @@
+
+ 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"
+
+@@ -693,7 +693,7 @@
+ set ARCH='-m64'
+ if (`uname -p` == ia64) set ARCH=''
+
+- set CC = 'gcc'
++ set gentoo-CC = 'gcc'
+ set CFLAGS = "-DLINUX $ARCH -O3 -fstrict-aliasing -I./"
+ set CLIBS = "-lpthread"
+
+diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess/ddi/kickoff/ddikick.c
+--- gamess.orig/ddi/kickoff/ddikick.c 2008-05-06 14:16:12.000000000 +0400
++++ gamess/ddi/kickoff/ddikick.c 2010-05-30 03:46:16.000000000 +0400
+@@ -105,7 +105,7 @@
+ remoteshell = argv[++i];
+ } else {
+ if((remoteshell = getenv("DDI_RSH")) == NULL) {
+- remoteshell = (char *) strdup("rsh");
++ remoteshell = (char *) strdup("ssh");
+ }
+ }
+
+diff -urN gamess.orig/lked gamess/lked
+--- gamess.orig/lked 2010-05-06 22:00:32.000000000 +0400
++++ gamess/lked 2010-05-30 03:46:16.000000000 +0400
+@@ -61,7 +61,7 @@
+ #
+ # optional Nuclear-Electronic Orbital method, using NEO code
+ # neostb.o is dummy substitute from the standard GAMESS distribution.
+-set NEO=false
++set NEO=true
+ if ($NEO == true) then
+ set NEOOBJ="neo.o neobas.o neocas.o neoden.o neofci.o"
+ set NEOOBJ="$NEOOBJ neog2a.o neog2b.o neog2c.o neogrd.o"
+@@ -372,17 +372,17 @@
+ switch ($GMS_FORTRAN)
+ case g77:
+ set LDR='g77'
+- set LDOPTS=' ' # add '-Wl,-M' to see load map
++ set gentoo-LDOPTS=' ' # add '-Wl,-M' to see load map
+ set FORTLIBS=' '
+ breaksw
+ 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 pgf77:
+@@ -392,7 +392,7 @@
+ breaksw
+ case f2c:
+ set LDR='gcc'
+- set LDOPTS=' '
++ set gentoo-LDOPTS=' '
+ set FORTLIBS='-lf2c -lm'
+ breaksw
+ default:
+@@ -441,12 +441,7 @@
+ # If the ATLAS comes with static libraries, link to them
+ # so that only the compile node has to have the libraries.
+ # Otherwise, attempt a link against shared object libs.
+- 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
+
+@@ -480,12 +475,12 @@
+ 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'
+@@ -551,12 +546,7 @@
+ # If the ATLAS comes with static libraries, link to them
+ # so that only the compile node has to have the libraries.
+ # Otherwise, attempt a link against shared object libs.
+- 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
+
+diff -urN gamess.orig/runall gamess/runall
+--- gamess.orig/runall 2009-02-28 02:57:18.000000000 +0300
++++ gamess/runall 2010-05-30 03:46:16.000000000 +0400
+@@ -10,7 +10,6 @@
+ #
+ # Only the following two lines need to be customized:
+ #
+-chdir /u1/mike/gamess
+ set VERNO=00
+ #
+ # Loop over all Ntest jobs supplied with GAMESS
+@@ -27,7 +26,7 @@
+ 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
+ @ i++
+ end
+diff -urN gamess.orig/rungms gamess/rungms
+--- gamess.orig/rungms 2010-05-06 23:08:56.000000000 +0400
++++ gamess/rungms 2010-05-30 03:46:16.000000000 +0400
+@@ -55,7 +55,7 @@
+ # one for LoadLeveler "ll-gms" on the IBM SP line.
+ #
+ set TARGET=sockets
+-set SCR=/scr/$USER
++set SCR=`pwd`
+ #
+ set JOB=$1 # name of the input file xxx.inp, give only the xxx part
+ set VERNO=$2 # revision number of the executable created by 'lked' step
+@@ -122,17 +122,17 @@
+ #
+ set echo
+ # ASCII input files (see explanation above)
+-setenv ERICFMT ~mike/gamess/ericfmt.dat
+-setenv MCPPATH ~mike/gamess/mcpdata
++setenv ERICFMT /usr/share/gamess/ericfmt/ericfmt.dat
++setenv MCPPATH /usr/share/gamess/mcpdata
+ setenv EXTBAS /dev/null
+ setenv NUCBAS /dev/null
+ #
+-setenv MAKEFP ~$USER/scr/$JOB.efp
+-setenv GAMMA ~$USER/scr/$JOB.gamma
+-setenv TRAJECT ~$USER/scr/$JOB.trj
+-setenv RESTART ~$USER/scr/$JOB.rst
++setenv MAKEFP $SCR/$JOB.efp
++setenv GAMMA $SCR/$JOB.gamma
++setenv TRAJECT $SCR/$JOB.trj
++setenv RESTART $SCR/$JOB.rst
+ setenv INPUT $SCR/$JOB.F05
+-setenv PUNCH ~$USER/scr/$JOB.dat
++setenv PUNCH $SCR/$JOB.dat
+ setenv AOINTS $SCR/$JOB.F08
+ setenv MOINTS $SCR/$JOB.F09
+ setenv DICTNRY $SCR/$JOB.F10
+@@ -311,7 +311,7 @@
+ if (null$4 == null) set ELGNAME=ELGFILE
+ set echo
+ setenv AOINTS $SCR/$ELGNAME.F08
+- setenv ELGDOS ~$USER/scr/$JOB.ldos
++ setenv ELGDOS $SCR/$JOB.ldos
+ setenv ELGDAT $SCR/$ELGNAME.F71
+ setenv ELGPAR $SCR/$ELGNAME.F72
+ setenv ELGCUT $SCR/$ELGNAME.F74
+@@ -439,7 +439,7 @@
+ if ($os == AIX) set GMSPATH=/u1/mike/gamess
+ if ($os == Darwin) set GMSPATH=/Users/mike/desktop/gamess
+ if ($os == HP-UX) set GMSPATH=/zr/mike/gamess
+- if ($os == Linux) set GMSPATH=/cu/mike/gamess
++ if ($os == Linux) set GMSPATH=/usr/bin
+ if ($os == OSF1) set GMSPATH=/in/mike/gamess
+ if ($os == SunOS) set GMSPATH=/hf/mike/gamess
+ # special compilation for Sun E450 uSPARC (uname also= SunOS)
+@@ -485,67 +485,6 @@
+ set NNODES=1
+ set HOSTLIST=(`hostname`)
+ endif
+-#
+-# 2. This is an example of how to run on a 4-way SMP enclosure,
+-# where all CPUs (aka COREs) are inside a -single- NODE.
+-# The example is repeated for some nodes we use as 2-way's.
+- if ($NCPUS > 1) then
+- switch (`hostname`)
+- case ti.msg.chem.iastate.edu:
+- case cd.msg.chem.iastate.edu:
+- case zn.msg.chem.iastate.edu:
+- case ni.msg.chem.iastate.edu:
+- case co.msg.chem.iastate.edu:
+- case pb.msg.chem.iastate.edu:
+- case bi.msg.chem.iastate.edu:
+- case po.msg.chem.iastate.edu:
+- case at.msg.chem.iastate.edu:
+- case sc.msg.chem.iastate.edu:
+- if ($NCPUS > 4) set NCPUS=4
+- set NNODES=1
+- set HOSTLIST=(`hostname`:cpus=$NCPUS)
+- breaksw
+- case se.msg.chem.iastate.edu:
+- case sb.msg.chem.iastate.edu:
+- case br.msg.chem.iastate.edu:
+- if ($NCPUS > 2) set NCPUS=2
+- set NNODES=1
+- set HOSTLIST=(`hostname`:cpus=$NCPUS)
+- breaksw
+- default:
+- echo I do not know how to run this node in parallel.
+- exit 20
+- endsw
+- endif
+-#
+-# 3. A phony example, of six uniprocessors (arbitrary names)
+-# Because they are uniprocessors, we just set NNODES = NCPUS.
+-# Since their names never change, we just can just specify them.
+-# Note that we can use a short name like 'bb' if and only if
+-# system name resolution can map them onto the true host names.
+- if (`hostname` == aa.msg.chem.iastate.edu) then
+- set NNODES=$NCPUS
+- set HOSTLIST=(aa bb cc dd ee ff)
+- endif
+-#
+-# 4. An example of 16 uniprocessor boxes in a Beowulf-type cluster.
+-# Because they are uniprocessors, we just set NNODES = NCPUS.
+-# Their host names fall into the pattern fly1 to fly16,
+-# which we can turn into a HOSTLIST with a small loop.
+- if (`hostname` == fly1.fi.ameslab.gov) then
+- set NNODES=$NCPUS
+- set HOSTLIST=()
+- set nmax=$NCPUS
+- if ($nmax > 16) set nmax=16
+- @ CPU=1
+- while ($CPU <= $nmax)
+- set HOSTLIST=($HOSTLIST fly$CPU)
+- @ CPU++
+- end
+- unset $CPU
+- endif
+-#
+-# 5. Scalable Computing Lab's clusters running PBS batch queues.
+ # Here the task is to manipulate the dynamically assigned host
+ # names into the HOSTLIST string for the kickoff program,
+ # and to request the host name of the fast network adapters.
+@@ -554,8 +493,6 @@
+ #
+ # The IBM cluster has two Gigabit adapters in each 4-way SMP,
+ # while the AXP cluster is based on a Myrinet network.
+- if (`uname` == AIX) set NETEXT=".gig,.gig2"
+- if (`uname` == Linux) set NETEXT=".myri"
+ #
+ # repeated host names in the PBS host file indicate being assigned
+ # CPUs in the same SMP enclosure, which we must count up correctly.
+@@ -586,12 +523,11 @@
+ @ NNODES = 1
+ @ NSMPCPU = 1
+ set spacer1=":cpus="
+- set spacer2=":netext="
+ while($IPROC <= $nmax)
+ set MYPROC=`sed -n -e "$IPROC p" $PBS_NODEFILE`
+ set MYPROC=`echo $MYPROC | awk '{split($0,a,"."); print a[1]}'`
+ if($MYPROC != $MYNODE) then
+- set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU$spacer2$NETEXT)
++ set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU)
+ set MYNODE=$MYPROC
+ @ NSMPCPU = 0
+ @ NNODES++
+@@ -599,13 +535,13 @@
+ @ IPROC++
+ @ NSMPCPU++
+ end
+- set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU$spacer2$NETEXT)
++ set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU)
+ endif
+ #
+ # we have now finished setting up a correct HOSTLIST.
+ # uncomment the next two if you are doing script debugging.
+-#--echo "The generated host list is"
+-#--echo $HOSTLIST
++ echo "The generated host list is"
++ echo $HOSTLIST
+ #
+
+ #
+diff -urN gamess.orig/tools/checktst/checktst gamess/tools/checktst/checktst
+--- gamess.orig/tools/checktst/checktst 2008-12-30 18:33:09.000000000 +0300
++++ gamess/tools/checktst/checktst 2010-05-30 03:46:16.000000000 +0400
+@@ -3,11 +3,6 @@
+ # Compare the results of GAMESS sample jobs to pre-stored correct values.
+ # This script can be executed from any directory with write permissions.
+ # Written by D. G. Fedorov, AIST, July 20, 2004.
+-#
+-# Only the path name in the very next line needs to be customized.
+-#
+-set GMSPATH=~/gamess
+-
+ # The Ntest outputs are assumed to be named exam01.log, exam02.log, ...
+ # but the user will be allowed to specify the directory containing them.
+ #
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/gamess-20100325.2.ebuild,v 1.2 2010/05/24 12:42:17 alexxy Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/gamess-20100325.2.ebuild,v 1.3 2010/05/30 07:00:00 alexxy Exp $
EAPI="2"
src_prepare() {
# apply LINUX-arch patches to gamess makesfiles
- epatch "${FILESDIR}"/${PN}-20090112.1.gentoo.patch
+ epatch "${FILESDIR}"/${P}.gentoo.patch
# select arch
# NOTE: please leave lked alone; it should be good as is!!
cd "${S}"
else
active_arch="linux32";
fi
- sed -e "s:gentoo-target:${active_arch}:" \
- -i comp compall ddi/compddi \
- || die "Failed to select proper architecure"
# for hardened-gcc let't turn off ssp, since it breakes
# a few routines
-i source/inputb.src \
|| die "Setting QMMM_GAMESS_MAXMM failed"
fi
- sed -e "s:maxclass=250:maxclass=$QMMM_GAMESS_MAXCLASS:g" \
- -i tinker/sizes.i \
- || die "Setting QMMM_GAMESS_MAXCLASS failed"
- sed -e "s:maxtyp=500:maxtyp=$QMMM_GAMESS_MAXCTYP:g" \
- -i tinker/sizes.i \
- || die "Setting QMMM_GAMESS_MAXCTYP failed"
- sed -e "s:maxhess=1000000:maxhess=$QMMM_GAMESS_MAXHESS:g" \
- -i tinker/sizes.i \
- || die "Setting QMMM_GAMESS_MAXHESS failed"
+ if [ "x$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=$QMMM_GAMESS_MAXHESS:g" \
+ -i tinker/sizes.i \
+ || die "Setting QMMM_GAMESS_MAXHESS failed"
+ fi
fi
# greate proper activate sourcefile
cp "./tools/actvte.code" "./tools/actvte.f" || \
# specific stuff
if [[ "${FORTRANC}" == "ifc" ]]; then
sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS} -quiet'/" \
- -e "s/gentoo-g77/${FORTRANC}/" \
-i comp || die "Failed setting up comp script"
elif ! use x86; then
sed -e "s/-malign-double //" \
-e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
- -e "s/gentoo-g77/${FORTRANC}/" \
-i comp || die "Failed setting up comp script"
else
sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
- -e "s/gentoo-g77/${FORTRANC}/" \
-i comp || die "Failed setting up comp script"
fi
# fix up GAMESS' linker script;
- sed -e "s/gentoo-g77/${FORTRANC}/" \
- -e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \
+ 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)'/" \
- -e "s/gentoo-g77/${FORTRANC}/" \
-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_TARGET $active_arch
+ setenv GMS_FORTRAN $FORTRANC
+ setenv GMS_MATHLIB atlas
+ setenv GMS_MATHLIB_PATH /usr/$(get_libdir)/atlas
+ setenv GMS_DDI_COMM sockets
+ EOF
- # fix up the checker scripts for gamess tests
- sed -e "s:set GMSPATH:#set GMSPATH:g" \
- -e "s:\$GMSPATH/tools/checktst:.:g" \
- -i tools/checktst/checktst
}
src_compile() {
projects / gentoo.git / commitdiff