| 1 |
alexxy 09/02/20 09:53:10 |
| 2 |
|
| 3 |
Added: gamess-20090112.1.gentoo.patch |
| 4 |
Log: |
| 5 |
GAMESS version bump |
| 6 |
(Portage version: 2.2_rc23/cvs/Linux x86_64) |
| 7 |
|
| 8 |
Revision Changes Path |
| 9 |
1.1 sci-chemistry/gamess/files/gamess-20090112.1.gentoo.patch |
| 10 |
|
| 11 |
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gamess/files/gamess-20090112.1.gentoo.patch?rev=1.1&view=markup |
| 12 |
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-chemistry/gamess/files/gamess-20090112.1.gentoo.patch?rev=1.1&content-type=text/plain |
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|
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Index: gamess-20090112.1.gentoo.patch |
| 15 |
=================================================================== |
| 16 |
diff -urN gamess.orig/comp gamess/comp |
| 17 |
--- gamess.orig/comp 2009-02-20 01:39:06.000000000 +0300 |
| 18 |
+++ gamess/comp 2009-02-20 01:39:23.000000000 +0300 |
| 19 |
@@ -12,8 +12,8 @@ |
| 20 |
# sgi32,sgi64,sun32,sun64 |
| 21 |
# 2. Choose your GAMESS directory tree. |
| 22 |
# |
| 23 |
-set TARGET=ibm64 |
| 24 |
-chdir /u1/mike/gamess |
| 25 |
+set TARGET=gentoo-target |
| 26 |
+#chdir /u1/mike/gamess |
| 27 |
# |
| 28 |
# ---- and now the script begins... |
| 29 |
# |
| 30 |
@@ -100,9 +100,7 @@ |
| 31 |
# 1st is Fedora Core's, 2nd is ASCI download from ORNL, 3rd is Atlas |
| 32 |
# the names of the latter two files on your system might well be |
| 33 |
# different from these, edit here and in 'lked' to match your paths. |
| 34 |
-if (($TARGET == linux32) && (-e /usr/lib/libblas.a)) set BLAS3=true |
| 35 |
-if (($TARGET == linux32) && (-e /usr/local/bin/libblas-asci.a)) set BLAS3=true |
| 36 |
-if (($TARGET == linux32) && (-e /usr/local/lib/libatlas.a)) set BLAS3=true |
| 37 |
+if ($TARGET == linux32) set BLAS3=true |
| 38 |
# For next two, assume that a math library will exist when |
| 39 |
# we arrive at the link step: MKL or Atlas or ACML.... |
| 40 |
if ($TARGET == linux64) set BLAS3=true |
| 41 |
@@ -1144,7 +1142,7 @@ |
| 42 |
# The only thing you need to change is the next line. |
| 43 |
# Note: you must make the analogous choice in compddi and lked, as well. |
| 44 |
# |
| 45 |
- set FORTRAN=g77 # choose from g77, gfortran, ifort, pgf77, f2c |
| 46 |
+ set FORTRAN=gentoo-g77 # choose from g77, gfortran, ifort, pgf77, f2c |
| 47 |
# |
| 48 |
switch ($FORTRAN) |
| 49 |
# |
| 50 |
@@ -1163,7 +1161,7 @@ |
| 51 |
# Pentium II fractionally). None of these optimizations are used below. |
| 52 |
# |
| 53 |
case g77: |
| 54 |
- set OPT = '-O2' |
| 55 |
+ set gentoo-OPT = '-O2' |
| 56 |
if ($MODULE == ormas1) set OPT='-O2 -fno-move-all-movables' # RH9, g77 3.3 |
| 57 |
if ($MODULE == zheev) set OPT='-O0' # defensive compiling |
| 58 |
# |
| 59 |
@@ -1199,7 +1197,7 @@ |
| 60 |
# -std=legacy suppresses warnings about use of f77 constructs. |
| 61 |
# |
| 62 |
case gfortran: |
| 63 |
- set OPT='-O2' |
| 64 |
+ set gentoo-OPT = '-O2' |
| 65 |
if ($MODULE == zheev) set OPT='-O0' # defensive compiling |
| 66 |
if ($MODULE == pcmcv2) set OPT='-O1' # EFP+CPCM, ala Francois, v4.1.2 |
| 67 |
if (($MODULE == qeigen) || ($MODULE == int2c)) then |
| 68 |
@@ -1229,7 +1227,7 @@ |
| 69 |
# optimizations in 32 bit mode, as a function of the ifort version. |
| 70 |
# |
| 71 |
case ifort: |
| 72 |
- set OPT = '-O3' |
| 73 |
+ set gentoo-OPT = '-O2' |
| 74 |
if ($MODULE == delocl) set OPT='-O0' # from Cheol |
| 75 |
if ($MODULE == zheev) set OPT='-O0' |
| 76 |
set echo |
| 77 |
@@ -1375,12 +1373,12 @@ |
| 78 |
# Note: you must make the analogous choice in compddi and lked, as well. |
| 79 |
# If you wish to use ifort in 64 bit mode, use only target=linux-ia64. |
| 80 |
# |
| 81 |
- set FORTRAN=gfortran # choose from gfortran, pgf77, pathf90 |
| 82 |
+ set FORTRAN=gentoo-g77 # choose from gfortran, pgf77, pathf90 |
| 83 |
# |
| 84 |
switch ($FORTRAN) |
| 85 |
|
| 86 |
case gfortran: |
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- set OPT='-O2' |
| 88 |
+ set gentoo-OPT = '-O2' |
| 89 |
if ($MODULE == zheev) set OPT='-O0' # defensive compiling |
| 90 |
if (($MODULE == qeigen) || ($MODULE == int2c)) then |
| 91 |
mv -f $MODULE.f $MODULE.junk |
| 92 |
diff -urN gamess.orig/compall gamess/compall |
| 93 |
--- gamess.orig/compall 2009-02-20 01:39:06.000000000 +0300 |
| 94 |
+++ gamess/compall 2009-02-20 01:39:23.000000000 +0300 |
| 95 |
@@ -13,8 +13,8 @@ |
| 96 |
# sgi32,sgi64,sun32,sun64 |
| 97 |
# 2. Choose your GAMESS directory tree. |
| 98 |
# |
| 99 |
-set TARGET=ibm64 |
| 100 |
-chdir /u1/mike/gamess |
| 101 |
+set TARGET=gentoo-target |
| 102 |
+#chdir /u1/mike/gamess |
| 103 |
# |
| 104 |
# ----- and now the script begins... |
| 105 |
# |
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@@ -150,8 +150,8 @@ |
| 107 |
if ($TARGET == axp64) ./comp blas |
| 108 |
if ($TARGET == ibm64) ./comp blas |
| 109 |
if ($TARGET == ibm-bg) ./comp blas |
| 110 |
-if ($TARGET == linux32) ./comp blas |
| 111 |
-if ($TARGET == linux64) ./comp blas |
| 112 |
+#if ($TARGET == linux32) ./comp blas |
| 113 |
+#if ($TARGET == linux64) ./comp blas |
| 114 |
if ($TARGET == linux-ia64) ./comp blas |
| 115 |
if ($TARGET == sun32) ./comp blas |
| 116 |
if ($TARGET == sun64) ./comp blas |
| 117 |
@@ -450,7 +450,7 @@ |
| 118 |
# |
| 119 |
# optional Nuclear-Electronic Orbital method, using NEO code |
| 120 |
# |
| 121 |
-set NEO=false |
| 122 |
+set NEO=true |
| 123 |
if ($NEO == true) then |
| 124 |
./comp neo |
| 125 |
./comp neobas |
| 126 |
diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi |
| 127 |
--- gamess.orig/ddi/compddi 2009-02-20 01:39:06.000000000 +0300 |
| 128 |
+++ gamess/ddi/compddi 2009-02-20 01:39:23.000000000 +0300 |
| 129 |
@@ -15,7 +15,7 @@ |
| 130 |
# linux32,linux64,linux-ia64,mac32,mac64,macG5,necsx, |
| 131 |
# sgi32,sgi64,sun32,sun64 |
| 132 |
# |
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- set TARGET = ibm64 |
| 134 |
+ set TARGET = gentoo-target |
| 135 |
|
| 136 |
# 2. Choose DDI communication layer, the only legal values are |
| 137 |
# sockets,mixed,mpi,shmem,lapi,armci |
| 138 |
@@ -537,9 +537,9 @@ |
| 139 |
# |
| 140 |
if($TARGET == linux32) then |
| 141 |
|
| 142 |
- set FORTRAN=g77 # choose from g77, gfortran, ifort, pgf77, f2c |
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+ set FORTRAN=gentoo-g77 # choose from g77, gfortran, ifort, pgf77, f2c |
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|
| 145 |
- set CC = 'gcc' |
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+ set gentoo-CC = 'gcc' |
| 147 |
set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./include" |
| 148 |
|
| 149 |
switch ($FORTRAN) |
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@@ -578,12 +578,12 @@ |
| 151 |
|
| 152 |
# for generic 64 bit Linux, choose one of the following, |
| 153 |
# gfortran, pgf77, pathf90 |
| 154 |
- if ($TARGET == linux64) set FORTRAN=gfortran |
| 155 |
+ if ($TARGET == linux64) set FORTRAN=gentoo-g77 |
| 156 |
# |
| 157 |
# for linux-ia64, leave the choice set to ifort (do not change!) |
| 158 |
if ($TARGET == linux-ia64) set FORTRAN=ifort |
| 159 |
|
| 160 |
- set CC = 'gcc' |
| 161 |
+ set gentoo-CC = 'gcc' |
| 162 |
|
| 163 |
if ($TARGET == linux64) then |
| 164 |
set CFLAGS = "-DLINUX -m64 -O3 -fstrict-aliasing -I./include" |
| 165 |
diff -urN gamess.orig/ddi/tools/ddikick/ddikick.c gamess/ddi/tools/ddikick/ddikick.c |
| 166 |
--- gamess.orig/ddi/tools/ddikick/ddikick.c 2009-02-20 01:39:06.000000000 +0300 |
| 167 |
+++ gamess/ddi/tools/ddikick/ddikick.c 2009-02-20 01:39:23.000000000 +0300 |
| 168 |
@@ -105,7 +105,7 @@ |
| 169 |
remoteshell = argv[++i]; |
| 170 |
} else { |
| 171 |
if((remoteshell = getenv("DDI_RSH")) == NULL) { |
| 172 |
- remoteshell = (char *) strdup("rsh"); |
| 173 |
+ remoteshell = (char *) strdup("ssh"); |
| 174 |
} |
| 175 |
} |
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|
| 177 |
diff -urN gamess.orig/lked gamess/lked |
| 178 |
--- gamess.orig/lked 2009-02-20 01:39:06.000000000 +0300 |
| 179 |
+++ gamess/lked 2009-02-20 01:39:23.000000000 +0300 |
| 180 |
@@ -15,8 +15,8 @@ |
| 181 |
# sgi32,sgi64,sun32,sun64 |
| 182 |
# 2. Choose your GAMESS directory tree. |
| 183 |
# |
| 184 |
-set TARGET=ibm64 |
| 185 |
-chdir /u1/mike/gamess |
| 186 |
+set TARGET=linux32 |
| 187 |
+#chdir /u1/mike/gamess |
| 188 |
# |
| 189 |
# ---- and now the script begins... |
| 190 |
# |
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@@ -299,22 +299,22 @@ |
| 192 |
# |
| 193 |
if ($TARGET == linux32) then |
| 194 |
# |
| 195 |
- set FORTRAN=g77 # choose from g77, gfortran, ifort, pgf77, f2c |
| 196 |
+ set FORTRAN=gentoo-g77 # choose from g77, gfortran, ifort, pgf77, f2c |
| 197 |
# |
| 198 |
switch ($FORTRAN) |
| 199 |
case g77: |
| 200 |
set LDR='g77' |
| 201 |
- set LDOPTS=' ' # add '-Wl,-M' to see load map |
| 202 |
+ set gentoo-LDOPTS=' ' # add '-Wl,-M' to see load map |
| 203 |
set LIBRARIES=' ' |
| 204 |
breaksw |
| 205 |
case gfortran: |
| 206 |
set LDR='gfortran' |
| 207 |
- set LDOPTS=' ' |
| 208 |
+ set gentoo-LDOPTS=' ' |
| 209 |
set LIBRARIES=' ' |
| 210 |
breaksw |
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case ifort: |
| 212 |
set LDR='ifort' |
| 213 |
- set LDOPTS=' ' # add '-Wl,-M' to see load map |
| 214 |
+ set gentoo-LDOPTS=' ' # add '-Wl,-M' to see load map |
| 215 |
set LIBRARIES='-Vaxlib' |
| 216 |
breaksw |
| 217 |
case pgf77: |
| 218 |
@@ -344,22 +344,22 @@ |
| 219 |
# Additional libraries (not considered here) are 32 bit versions |
| 220 |
# of Atlas, MKL, or ACML, they are perfectly reasonable choices. |
| 221 |
# |
| 222 |
- set BLASLIBRARY=' ' |
| 223 |
- set BLAS='blas.o' # turn this off if a math library exists... |
| 224 |
+ set BLASLIBRARY=`pkg-config --libs blas` |
| 225 |
+ set BLAS='' |
| 226 |
# |
| 227 |
- if (-e /usr/lib/libblas.a) then |
| 228 |
- set BLASLIBRARY="-lblas" |
| 229 |
- set BLAS=' ' |
| 230 |
- endif |
| 231 |
- if (-e /usr/local/bin/libblas-asci.a) then |
| 232 |
- set BLASLIBRARY="/usr/local/bin/libblas-asci.a" |
| 233 |
- set BLAS=' ' |
| 234 |
- endif |
| 235 |
- if (-e /usr/local/lib/libatlas.a) then |
| 236 |
- set BLASLIBRARY="/usr/local/lib/libf77blas.a" |
| 237 |
- set BLASLIBRARY="$BLASLIBRARY /usr/local/lib/libatlas.a" |
| 238 |
- set BLAS=' ' |
| 239 |
- endif |
| 240 |
+# if (-e /usr/lib/libblas.a) then |
| 241 |
+# set BLASLIBRARY="-lblas" |
| 242 |
+# set BLAS=' ' |
| 243 |
+# endif |
| 244 |
+# if (-e /usr/local/bin/libblas-asci.a) then |
| 245 |
+# set BLASLIBRARY="/usr/local/bin/libblas-asci.a" |
| 246 |
+# set BLAS=' ' |
| 247 |
+# endif |
| 248 |
+# if (-e /usr/local/lib/libatlas.a) then |
| 249 |
+# set BLASLIBRARY="/usr/local/lib/libf77blas.a" |
| 250 |
+# set BLASLIBRARY="$BLASLIBRARY /usr/local/lib/libatlas.a" |
| 251 |
+# set BLAS=' ' |
| 252 |
+# endif |
| 253 |
# |
| 254 |
if ($BLAS == 'blas.o') then |
| 255 |
echo " " |
| 256 |
diff -urN gamess.orig/runall gamess/runall |
| 257 |
--- gamess.orig/runall 2009-02-20 01:39:07.000000000 +0300 |
| 258 |
+++ gamess/runall 2009-02-20 01:39:23.000000000 +0300 |
| 259 |
@@ -10,7 +10,7 @@ |
| 260 |
# |
| 261 |
# Only the following two lines need to be customized: |
| 262 |
# |
| 263 |
-chdir /u1/mike/gamess |
| 264 |
+#chdir /u1/mike/gamess |
| 265 |
set VERNO=00 |
| 266 |
# |
| 267 |
# Loop over all Ntest jobs supplied with GAMESS |
| 268 |
diff -urN gamess.orig/rungms gamess/rungms |
| 269 |
--- gamess.orig/rungms 2009-02-20 01:39:07.000000000 +0300 |
| 270 |
+++ gamess/rungms 2009-02-20 01:42:12.000000000 +0300 |
| 271 |
@@ -55,7 +55,7 @@ |
| 272 |
# of using LoadLeveler via a "llgms" front end in ~/gamess/misc. |
| 273 |
# |
| 274 |
set TARGET=sockets |
| 275 |
-set SCR=/scr/$USER |
| 276 |
+set SCR=`pwd` |
| 277 |
# |
| 278 |
set JOB=$1 # name of the input file xxx.inp, give only the xxx part |
| 279 |
set VERNO=$2 # revision number of the executable created by 'lked' step |
| 280 |
@@ -122,17 +122,17 @@ |
| 281 |
# |
| 282 |
set echo |
| 283 |
# ASCII input files (see explanation above) |
| 284 |
-setenv ERICFMT ~mike/gamess/ericfmt.dat |
| 285 |
-setenv MCPPATH ~mike/gamess/mcpdata |
| 286 |
+setenv ERICFMT /usr/share/gamess/ericfmt/ericfmt.dat |
| 287 |
+setenv MCPPATH /usr/share/gamess/mcpdata |
| 288 |
setenv EXTBAS /dev/null |
| 289 |
setenv NUCBAS /dev/null |
| 290 |
# |
| 291 |
-setenv MAKEFP ~$USER/scr/$JOB.efp |
| 292 |
-setenv GAMMA ~$USER/scr/$JOB.gamma |
| 293 |
-setenv TRAJECT ~$USER/scr/$JOB.trj |
| 294 |
-setenv RESTART ~$USER/scr/$JOB.rst |
| 295 |
+setenv MAKEFP $SCR/$JOB.efp |
| 296 |
+setenv GAMMA $SCR/$JOB.gamma |
| 297 |
+setenv TRAJECT $SCR/$JOB.trj |
| 298 |
+setenv RESTART $SCR/$JOB.rst |
| 299 |
setenv INPUT $SCR/$JOB.F05 |
| 300 |
-setenv PUNCH ~$USER/scr/$JOB.dat |
| 301 |
+setenv PUNCH $SCR/$JOB.dat |
| 302 |
setenv AOINTS $SCR/$JOB.F08 |
| 303 |
setenv MOINTS $SCR/$JOB.F09 |
| 304 |
setenv DICTNRY $SCR/$JOB.F10 |
| 305 |
@@ -308,7 +308,7 @@ |
| 306 |
if (null$4 == null) set ELGNAME=ELGFILE |
| 307 |
set echo |
| 308 |
setenv AOINTS $SCR/$ELGNAME.F08 |
| 309 |
- setenv ELGDOS ~$USER/scr/$JOB.ldos |
| 310 |
+ setenv ELGDOS $SCR/$JOB.ldos |
| 311 |
setenv ELGDAT $SCR/$ELGNAME.F71 |
| 312 |
setenv ELGPAR $SCR/$ELGNAME.F72 |
| 313 |
setenv ELGCUT $SCR/$ELGNAME.F74 |
| 314 |
@@ -426,7 +426,7 @@ |
| 315 |
if ($os == AIX) set GMSPATH=/u1/mike/gamess |
| 316 |
if ($os == Darwin) set GMSPATH=/Users/mike/desktop/gamess |
| 317 |
if ($os == HP-UX) set GMSPATH=/zr/mike/gamess |
| 318 |
- if ($os == Linux) set GMSPATH=/cu/mike/gamess |
| 319 |
+ if ($os == Linux) set GMSPATH=/usr/bin |
| 320 |
if ($os == OSF1) set GMSPATH=/in/mike/gamess |
| 321 |
if ($os == SunOS) set GMSPATH=/hf/mike/gamess |
| 322 |
# special compilation for Sun E450 uSPARC (uname also= SunOS) |
| 323 |
@@ -471,33 +471,6 @@ |
| 324 |
set HOSTLIST=(`hostname`) |
| 325 |
endif |
| 326 |
# |
| 327 |
-# 2. This is an example of how to run on a 4-way SMP enclosure, |
| 328 |
-# where all CPUs (aka COREs) are inside a -single- NODE. |
| 329 |
-# The example is repeated for some nodes we use as 2-way's. |
| 330 |
- if ($NCPUS > 1) then |
| 331 |
- switch (`hostname`) |
| 332 |
- case ti.msg.chem.iastate.edu: |
| 333 |
- case cd.msg.chem.iastate.edu: |
| 334 |
- case zn.msg.chem.iastate.edu: |
| 335 |
- case ni.msg.chem.iastate.edu: |
| 336 |
- case co.msg.chem.iastate.edu: |
| 337 |
- case sc.msg.chem.iastate.edu: |
| 338 |
- if ($NCPUS > 4) set NCPUS=4 |
| 339 |
- set NNODES=1 |
| 340 |
- set HOSTLIST=(`hostname`:cpus=$NCPUS) |
| 341 |
- breaksw |
| 342 |
- case se.msg.chem.iastate.edu: |
| 343 |
- case sb.msg.chem.iastate.edu: |
| 344 |
- case br.msg.chem.iastate.edu: |
| 345 |
- if ($NCPUS > 2) set NCPUS=2 |
| 346 |
- set NNODES=1 |
| 347 |
- set HOSTLIST=(`hostname`:cpus=$NCPUS) |
| 348 |
- breaksw |
| 349 |
- default: |
| 350 |
- echo I do not know how to run this node in parallel. |
| 351 |
- exit 20 |
| 352 |
- endsw |
| 353 |
- endif |
| 354 |
# |
| 355 |
# 3. A phony example, of six uniprocessors (arbitrary names) |
| 356 |
# Because they are uniprocessors, we just set NNODES = NCPUS. |
| 357 |
diff -urN gamess.orig/source/zunix.c gamess/source/zunix.c |
| 358 |
--- gamess.orig/source/zunix.c 2009-02-20 01:39:07.000000000 +0300 |
| 359 |
+++ gamess/source/zunix.c 2009-02-20 01:39:23.000000000 +0300 |
| 360 |
@@ -360,6 +360,7 @@ |
| 361 |
#ifdef LINUX32 |
| 362 |
|
| 363 |
#include <stdlib.h> |
| 364 |
+#include <string.h> |
| 365 |
int memget_(nwords) int *nwords; |
| 366 |
{ int nbytes; |
| 367 |
nbytes = (*nwords+2)*8; |
| 368 |
@@ -441,6 +442,7 @@ |
| 369 |
|
| 370 |
#include <stdlib.h> |
| 371 |
#include <malloc.h> |
| 372 |
+#include <string.h> |
| 373 |
|
| 374 |
#define FORTINT long |
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