* [gentoo-commits] gentoo-x86 commit in sci-chemistry/gamess/files: gamess-checktst.patch gamess-20110811.1.gentoo.patch gamess-neo-fix.patch gamess-20101001.3.gentoo.patch
@ 2011-10-13 12:00 Alexey Shvetsov (alexxy)
0 siblings, 0 replies; only message in thread
From: Alexey Shvetsov (alexxy) @ 2011-10-13 12:00 UTC (permalink / raw
To: gentoo-commits
alexxy 11/10/13 12:00:39
Modified: gamess-checktst.patch
Added: gamess-20110811.1.gentoo.patch
Removed: gamess-neo-fix.patch gamess-20101001.3.gentoo.patch
Log:
[sci-chemistry/gamess] Version bump. Fixed bugs #375803 #386839
(Portage version: 2.2.0_alpha67/cvs/Linux x86_64)
Revision Changes Path
1.2 sci-chemistry/gamess/files/gamess-checktst.patch
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gamess/files/gamess-checktst.patch?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gamess/files/gamess-checktst.patch?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gamess/files/gamess-checktst.patch?r1=1.1&r2=1.2
Index: gamess-checktst.patch
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/files/gamess-checktst.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- gamess-checktst.patch 6 Oct 2011 10:44:52 -0000 1.1
+++ gamess-checktst.patch 13 Oct 2011 12:00:38 -0000 1.2
@@ -1,6 +1,14 @@
---- /usr/share/gamess/tests/checktst 2011-08-19 18:08:16.000000000 +0200
-+++ ./checktst 2011-08-20 00:45:59.613091738 +0200
-@@ -61,8 +61,8 @@
+--- gamess.orig/tools/checktst/checktst 2008-12-30 16:33:09.000000000 +0100
++++ gamess/tools/checktst/checktst 2011-10-11 22:06:26.019798622 +0200
+@@ -6,7 +6,6 @@
+ #
+ # 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.
+@@ -66,8 +65,8 @@
setenv tolW 0.1
setenv tolX 0.00001
1.1 sci-chemistry/gamess/files/gamess-20110811.1.gentoo.patch
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gamess/files/gamess-20110811.1.gentoo.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gamess/files/gamess-20110811.1.gentoo.patch?rev=1.1&content-type=text/plain
Index: gamess-20110811.1.gentoo.patch
===================================================================
diff -urN gamess.orig/comp gamess/comp
--- gamess.orig/comp 2011-08-11 17:37:48.000000000 +0200
+++ gamess/comp 2011-10-11 15:17:23.349829478 +0200
@@ -1444,7 +1444,7 @@
# 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
@@ -1474,7 +1474,7 @@
# -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
@@ -1500,7 +1500,7 @@
# 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 ($MODULE == zheev) set OPT='-O0'
@@ -1617,7 +1617,7 @@
case gfortran:
# -finit-real=<zero|inf|-inf|nan> could be interesting debug opt
# -fno-automatic forces static storage of all local variables
- set OPT='-O2'
+ set gentoo-OPT = '-O2'
if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS"
if ($MODULE == zheev) set OPT='-O0' # defensive compiling
if (($MODULE == qeigen) || ($MODULE == int2c)) then
@@ -1648,7 +1648,7 @@
# -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/compall gamess/compall
--- gamess.orig/compall 2011-05-17 22:53:33.000000000 +0200
+++ gamess/compall 2011-10-11 12:13:30.041087251 +0200
@@ -84,12 +84,11 @@
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'
diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi
--- gamess.orig/ddi/compddi 2011-02-15 21:31:30.000000000 +0100
+++ gamess/ddi/compddi 2011-10-11 12:23:45.513796580 +0200
@@ -634,7 +634,7 @@
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"
@@ -687,7 +687,7 @@
set ARCH='-m64'
if (`uname -p` == ia64) set ARCH=''
- set CC = 'gcc'
+ set gentoo-CC = 'gcc'
set CFLAGS = "-DLINUX $ARCH -O3 -fstrict-aliasing -I./"
set CLIBS = "-lpthread"
diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess/ddi/kickoff/ddikick.c
--- gamess.orig/ddi/kickoff/ddikick.c 2008-05-06 12:16:12.000000000 +0200
+++ gamess/ddi/kickoff/ddikick.c 2011-10-11 12:25:11.862714681 +0200
@@ -105,7 +105,7 @@
remoteshell = argv[++i];
} else {
if((remoteshell = getenv("DDI_RSH")) == NULL) {
- remoteshell = (char *) strdup("rsh");
+ remoteshell = (char *) strdup("ssh");
}
}
diff -urN gamess.orig/lked gamess/lked
--- gamess.orig/lked 2011-08-11 17:41:02.000000000 +0200
+++ gamess/lked 2011-10-11 12:26:38.564634821 +0200
@@ -53,7 +53,7 @@
#
# 3. optional Nuclear-Electronic Orbital method, using NEO code
#
-set NEO=false
+set NEO=true
#
# 4. optional Nvidia/CUDA code, for closed shell SCF Fock construction
# see ~/gamess/libcchem/aaa.readme.1st for more information
@@ -356,17 +356,17 @@
switch ($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:
@@ -376,7 +376,7 @@
breaksw
case f2c:
set LDR='gcc'
- set LDOPTS=' '
+ set gentoo-LDOPTS=' '
set FORTLIBS='-lf2c -lm'
breaksw
default:
@@ -427,12 +427,7 @@
# 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
@@ -466,12 +461,12 @@
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'
@@ -556,12 +551,7 @@
# 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"
- endif
+ set MATHLIBS=`pkg-config --libs blas`
set BLAS=' '
breaksw
diff -urN gamess.orig/runall gamess/runall
--- gamess.orig/runall 2009-02-28 00:57:18.000000000 +0100
+++ gamess/runall 2011-10-11 12:27:32.195586568 +0200
@@ -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 2011-08-04 21:03:11.000000000 +0200
+++ gamess/rungms 2011-10-11 12:30:05.244448126 +0200
@@ -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
@@ -144,7 +144,7 @@
# used by the NEO method. See NEO's documentation for more details.
#
set echo
-setenv AUXDATA ~mike/gamess/auxdata
+setenv AUXDATA /usr/share/gamess
setenv EXTBAS /dev/null
setenv NUCBAS /dev/null
setenv POSBAS /dev/null
@@ -153,12 +153,12 @@
setenv MCPPATH $AUXDATA/MCP
setenv BASPATH $AUXDATA/BASES
setenv QUANPOL $AUXDATA/QUANPOL
-setenv MAKEFP ~$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
@@ -347,7 +347,7 @@
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
@@ -500,7 +500,7 @@
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)
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2011-10-13 12:00 [gentoo-commits] gentoo-x86 commit in sci-chemistry/gamess/files: gamess-checktst.patch gamess-20110811.1.gentoo.patch gamess-neo-fix.patch gamess-20101001.3.gentoo.patch Alexey Shvetsov (alexxy)
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