Gentoo Archives: gentoo-commits

From: "Alexey Shvetsov (alexxy)" <alexxy@g.o>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] gentoo-x86 commit in sci-chemistry/gamess/files: gamess-20100325.2.gentoo.patch
Date: Sun, 30 May 2010 07:00:05
Message-Id: 20100530070001.6095C2CAD8@corvid.gentoo.org
1 alexxy 10/05/30 07:00:01
2
3 Added: gamess-20100325.2.gentoo.patch
4 Log:
5 [sci-chemistry/gamess] make it build with new buildsystem
6 (Portage version: 2.2_rc67/cvs/Linux x86_64)
7
8 Revision Changes Path
9 1.1 sci-chemistry/gamess/files/gamess-20100325.2.gentoo.patch
10
11 file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gamess/files/gamess-20100325.2.gentoo.patch?rev=1.1&view=markup
12 plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/gamess/files/gamess-20100325.2.gentoo.patch?rev=1.1&content-type=text/plain
13
14 Index: gamess-20100325.2.gentoo.patch
15 ===================================================================
16 diff -urN gamess.orig/comp gamess/comp
17 --- gamess.orig/comp 2010-05-04 22:11:54.000000000 +0400
18 +++ gamess/comp 2010-05-30 03:46:52.000000000 +0400
19 @@ -1336,7 +1336,7 @@
20 # g77 does not support FORTRAN logical units above 99, or 128 bit math.
21 #
22 case g77:
23 - set OPT = '-O2'
24 + set gentoo-OPT = '-O2'
25 if ($MODULE == ormas1) set OPT='-O2 -fno-move-all-movables' # RH9, g77 3.3
26 if ($MODULE == zheev) set OPT='-O0' # defensive compiling
27 if (($MODULE == qeigen) || ($MODULE == int2c)) then
28 @@ -1366,7 +1366,7 @@
29 # -std=legacy suppresses warnings about use of f77 constructs.
30 #
31 case gfortran:
32 - set OPT='-O2'
33 + set gentoo-OPT = '-O2'
34 if ($MODULE == zheev) set OPT='-O0' # defensive compiling
35 if ($MODULE == pcmcv2) set OPT='-O1' # EFP+CPCM, ala Francois, v4.1.2
36 if (($MODULE == qeigen) || ($MODULE == int2c)) then
37 @@ -1392,7 +1392,7 @@
38 # optimizations in 32 bit mode, as a function of the ifort version.
39 #
40 case ifort:
41 - set OPT = '-O3'
42 + set gentoo-OPT = '-O2'
43 if ($MODULE == delocl) set OPT='-O0' # from Cheol
44 if ($MODULE == zheev) set OPT='-O0'
45 set echo
46 @@ -1504,7 +1504,7 @@
47
48 case gfortran:
49 # -finit-real=<zero|inf|-inf|nan> could be interesting debug opt
50 - set OPT='-O2'
51 + set gentoo-OPT = '-O2'
52 if ($MODULE == zheev) set OPT='-O0' # defensive compiling
53 if (($MODULE == qeigen) || ($MODULE == int2c)) then
54 mv -f $MODULE.f $MODULE.junk
55 @@ -1533,7 +1533,7 @@
56 # -WB means warn but don't fail on out-of-bounds array references
57 # -ftz flushes underflow results to zero
58 #
59 - set OPT = '-O2'
60 + set gentoo-OPT = '-O2'
61 if ($MODULE == guess) set OPT='-O0' # 10.0, exam39
62 if ($MODULE == locpol) set OPT='-O1' # 10.0, makefp/gmres
63 if ($MODULE == morokm) set OPT='-O0' # Jan Fredin
64 diff -urN gamess.orig/compall gamess/compall
65 --- gamess.orig/compall 2010-05-11 23:22:04.000000000 +0400
66 +++ gamess/compall 2010-05-30 03:46:16.000000000 +0400
67 @@ -84,15 +84,14 @@
68 endif
69 endif
70 if ($TARGET == linux32) set extraflags='-DLINUX32'
71 -if ($TARGET == linux64) then
72 +if ($TARGET == linux64) then
73 + set chip=`uname -m`
74 # Ubuntu uses the non-standard -m flag, its -p replies "unknown"
75 - set chip=`uname -p`
76 - if ($chip == unknown) set chip=`uname -m`
77 - if ($chip == x86_64) set extraflags='-DLINUX64 -m64'
78 - if ($chip == ia64) set extraflags='-DLINUX64' # this always 64 bits
79 + if ($chip == x86_64) set extraflags='-DLINUX64 -m64'
80 + if ($chip == ia64) set extraflags='-DLINUX64' # this always 64 bits
81 endif
82 if ($TARGET == mac32) set extraflags='-DLINUX32'
83 -if ($TARGET == mac64) set extraflags='-DLINUX64 -m64 -I/usr/include/malloc'
84 +if ($TARGET == mac64) set extraflags='-DLINUX64 -m64 -I/usr/include/malloc'
85 if ($TARGET == necsx) set extraflags='-DNECSX -size_t64'
86 if ($TARGET == sgi32) set extraflags='-DSGI32 -n32'
87 if ($TARGET == sgi64) set extraflags='-DSGI64 -64'
88 diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi
89 --- gamess.orig/ddi/compddi 2010-05-10 17:34:25.000000000 +0400
90 +++ gamess/ddi/compddi 2010-05-30 03:46:16.000000000 +0400
91 @@ -640,7 +640,7 @@
92
93 set FORTRAN=$GMS_FORTRAN # might be g77, gfortran, ifort, pgf77, f2c
94
95 - set CC = 'gcc'
96 + set gentoo-CC = 'gcc'
97 set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./"
98 set CLIBS = "-lpthread"
99
100 @@ -693,7 +693,7 @@
101 set ARCH='-m64'
102 if (`uname -p` == ia64) set ARCH=''
103
104 - set CC = 'gcc'
105 + set gentoo-CC = 'gcc'
106 set CFLAGS = "-DLINUX $ARCH -O3 -fstrict-aliasing -I./"
107 set CLIBS = "-lpthread"
108
109 diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess/ddi/kickoff/ddikick.c
110 --- gamess.orig/ddi/kickoff/ddikick.c 2008-05-06 14:16:12.000000000 +0400
111 +++ gamess/ddi/kickoff/ddikick.c 2010-05-30 03:46:16.000000000 +0400
112 @@ -105,7 +105,7 @@
113 remoteshell = argv[++i];
114 } else {
115 if((remoteshell = getenv("DDI_RSH")) == NULL) {
116 - remoteshell = (char *) strdup("rsh");
117 + remoteshell = (char *) strdup("ssh");
118 }
119 }
120
121 diff -urN gamess.orig/lked gamess/lked
122 --- gamess.orig/lked 2010-05-06 22:00:32.000000000 +0400
123 +++ gamess/lked 2010-05-30 03:46:16.000000000 +0400
124 @@ -61,7 +61,7 @@
125 #
126 # optional Nuclear-Electronic Orbital method, using NEO code
127 # neostb.o is dummy substitute from the standard GAMESS distribution.
128 -set NEO=false
129 +set NEO=true
130 if ($NEO == true) then
131 set NEOOBJ="neo.o neobas.o neocas.o neoden.o neofci.o"
132 set NEOOBJ="$NEOOBJ neog2a.o neog2b.o neog2c.o neogrd.o"
133 @@ -372,17 +372,17 @@
134 switch ($GMS_FORTRAN)
135 case g77:
136 set LDR='g77'
137 - set LDOPTS=' ' # add '-Wl,-M' to see load map
138 + set gentoo-LDOPTS=' ' # add '-Wl,-M' to see load map
139 set FORTLIBS=' '
140 breaksw
141 case gfortran:
142 set LDR='gfortran'
143 - set LDOPTS=' '
144 + set gentoo-LDOPTS=' '
145 set FORTLIBS=' '
146 breaksw
147 case ifort:
148 set LDR='ifort'
149 - set LDOPTS=' ' # add '-Wl,-M' to see load map
150 + set gentoo-LDOPTS=' ' # add '-Wl,-M' to see load map
151 set FORTLIBS='-Vaxlib'
152 breaksw
153 case pgf77:
154 @@ -392,7 +392,7 @@
155 breaksw
156 case f2c:
157 set LDR='gcc'
158 - set LDOPTS=' '
159 + set gentoo-LDOPTS=' '
160 set FORTLIBS='-lf2c -lm'
161 breaksw
162 default:
163 @@ -441,12 +441,7 @@
164 # If the ATLAS comes with static libraries, link to them
165 # so that only the compile node has to have the libraries.
166 # Otherwise, attempt a link against shared object libs.
167 - if (-e $GMS_MATHLIB_PATH/libf77blas.a) then
168 - set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a"
169 - set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a"
170 - else
171 - set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas"
172 - endif
173 + set MATHLIBS=`pkg-config --libs blas`
174 set BLAS=' '
175 breaksw
176
177 @@ -480,12 +475,12 @@
178 switch ($GMS_FORTRAN)
179 case gfortran:
180 set LDR='gfortran'
181 - set LDOPTS=' '
182 + set gentoo-LDOPTS=' '
183 set FORTLIBS=' '
184 breaksw
185 case ifort:
186 set LDR='ifort'
187 - set LDOPTS='-i8' # -Wl,-M generates a load map
188 + set gentoo-LDOPTS=' ' # -Wl,-M generates a load map
189 # this auxiliary library seems to have disappeared in ifort 10
190 set FORTLIBS=' '
191 if($GMS_IFORT_VERNO < 10) set FORTLIBS='-Vaxlib'
192 @@ -551,12 +546,7 @@
193 # If the ATLAS comes with static libraries, link to them
194 # so that only the compile node has to have the libraries.
195 # Otherwise, attempt a link against shared object libs.
196 - if (-e $GMS_MATHLIB_PATH/libf77blas.a) then
197 - set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a"
198 - set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a"
199 - else
200 - set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas"
201 - endif
202 + set MATHLIBS=`pkg-config --libs blas`
203 set BLAS=' '
204 breaksw
205
206 diff -urN gamess.orig/runall gamess/runall
207 --- gamess.orig/runall 2009-02-28 02:57:18.000000000 +0300
208 +++ gamess/runall 2010-05-30 03:46:16.000000000 +0400
209 @@ -10,7 +10,6 @@
210 #
211 # Only the following two lines need to be customized:
212 #
213 -chdir /u1/mike/gamess
214 set VERNO=00
215 #
216 # Loop over all Ntest jobs supplied with GAMESS
217 @@ -27,7 +26,7 @@
218 gms -v $VERNO -q ti -l exam$NUM.log exam$NUM
219 sleep 5
220 else
221 - ./rungms exam$NUM $VERNO 1 >& exam$NUM.log
222 + rungms exam$NUM $VERNO 1 >& exam$NUM.log
223 endif
224 @ i++
225 end
226 diff -urN gamess.orig/rungms gamess/rungms
227 --- gamess.orig/rungms 2010-05-06 23:08:56.000000000 +0400
228 +++ gamess/rungms 2010-05-30 03:46:16.000000000 +0400
229 @@ -55,7 +55,7 @@
230 # one for LoadLeveler "ll-gms" on the IBM SP line.
231 #
232 set TARGET=sockets
233 -set SCR=/scr/$USER
234 +set SCR=`pwd`
235 #
236 set JOB=$1 # name of the input file xxx.inp, give only the xxx part
237 set VERNO=$2 # revision number of the executable created by 'lked' step
238 @@ -122,17 +122,17 @@
239 #
240 set echo
241 # ASCII input files (see explanation above)
242 -setenv ERICFMT ~mike/gamess/ericfmt.dat
243 -setenv MCPPATH ~mike/gamess/mcpdata
244 +setenv ERICFMT /usr/share/gamess/ericfmt/ericfmt.dat
245 +setenv MCPPATH /usr/share/gamess/mcpdata
246 setenv EXTBAS /dev/null
247 setenv NUCBAS /dev/null
248 #
249 -setenv MAKEFP ~$USER/scr/$JOB.efp
250 -setenv GAMMA ~$USER/scr/$JOB.gamma
251 -setenv TRAJECT ~$USER/scr/$JOB.trj
252 -setenv RESTART ~$USER/scr/$JOB.rst
253 +setenv MAKEFP $SCR/$JOB.efp
254 +setenv GAMMA $SCR/$JOB.gamma
255 +setenv TRAJECT $SCR/$JOB.trj
256 +setenv RESTART $SCR/$JOB.rst
257 setenv INPUT $SCR/$JOB.F05
258 -setenv PUNCH ~$USER/scr/$JOB.dat
259 +setenv PUNCH $SCR/$JOB.dat
260 setenv AOINTS $SCR/$JOB.F08
261 setenv MOINTS $SCR/$JOB.F09
262 setenv DICTNRY $SCR/$JOB.F10
263 @@ -311,7 +311,7 @@
264 if (null$4 == null) set ELGNAME=ELGFILE
265 set echo
266 setenv AOINTS $SCR/$ELGNAME.F08
267 - setenv ELGDOS ~$USER/scr/$JOB.ldos
268 + setenv ELGDOS $SCR/$JOB.ldos
269 setenv ELGDAT $SCR/$ELGNAME.F71
270 setenv ELGPAR $SCR/$ELGNAME.F72
271 setenv ELGCUT $SCR/$ELGNAME.F74
272 @@ -439,7 +439,7 @@
273 if ($os == AIX) set GMSPATH=/u1/mike/gamess
274 if ($os == Darwin) set GMSPATH=/Users/mike/desktop/gamess
275 if ($os == HP-UX) set GMSPATH=/zr/mike/gamess
276 - if ($os == Linux) set GMSPATH=/cu/mike/gamess
277 + if ($os == Linux) set GMSPATH=/usr/bin
278 if ($os == OSF1) set GMSPATH=/in/mike/gamess
279 if ($os == SunOS) set GMSPATH=/hf/mike/gamess
280 # special compilation for Sun E450 uSPARC (uname also= SunOS)
281 @@ -485,67 +485,6 @@
282 set NNODES=1
283 set HOSTLIST=(`hostname`)
284 endif
285 -#
286 -# 2. This is an example of how to run on a 4-way SMP enclosure,
287 -# where all CPUs (aka COREs) are inside a -single- NODE.
288 -# The example is repeated for some nodes we use as 2-way's.
289 - if ($NCPUS > 1) then
290 - switch (`hostname`)
291 - case ti.msg.chem.iastate.edu:
292 - case cd.msg.chem.iastate.edu:
293 - case zn.msg.chem.iastate.edu:
294 - case ni.msg.chem.iastate.edu:
295 - case co.msg.chem.iastate.edu:
296 - case pb.msg.chem.iastate.edu:
297 - case bi.msg.chem.iastate.edu:
298 - case po.msg.chem.iastate.edu:
299 - case at.msg.chem.iastate.edu:
300 - case sc.msg.chem.iastate.edu:
301 - if ($NCPUS > 4) set NCPUS=4
302 - set NNODES=1
303 - set HOSTLIST=(`hostname`:cpus=$NCPUS)
304 - breaksw
305 - case se.msg.chem.iastate.edu:
306 - case sb.msg.chem.iastate.edu:
307 - case br.msg.chem.iastate.edu:
308 - if ($NCPUS > 2) set NCPUS=2
309 - set NNODES=1
310 - set HOSTLIST=(`hostname`:cpus=$NCPUS)
311 - breaksw
312 - default:
313 - echo I do not know how to run this node in parallel.
314 - exit 20
315 - endsw
316 - endif
317 -#
318 -# 3. A phony example, of six uniprocessors (arbitrary names)
319 -# Because they are uniprocessors, we just set NNODES = NCPUS.
320 -# Since their names never change, we just can just specify them.
321 -# Note that we can use a short name like 'bb' if and only if
322 -# system name resolution can map them onto the true host names.
323 - if (`hostname` == aa.msg.chem.iastate.edu) then
324 - set NNODES=$NCPUS
325 - set HOSTLIST=(aa bb cc dd ee ff)
326 - endif
327 -#
328 -# 4. An example of 16 uniprocessor boxes in a Beowulf-type cluster.
329 -# Because they are uniprocessors, we just set NNODES = NCPUS.
330 -# Their host names fall into the pattern fly1 to fly16,
331 -# which we can turn into a HOSTLIST with a small loop.
332 - if (`hostname` == fly1.fi.ameslab.gov) then
333 - set NNODES=$NCPUS
334 - set HOSTLIST=()
335 - set nmax=$NCPUS
336 - if ($nmax > 16) set nmax=16
337 - @ CPU=1
338 - while ($CPU <= $nmax)
339 - set HOSTLIST=($HOSTLIST fly$CPU)
340 - @ CPU++
341 - end
342 - unset $CPU
343 - endif
344 -#
345 -# 5. Scalable Computing Lab's clusters running PBS batch queues.
346 # Here the task is to manipulate the dynamically assigned host
347 # names into the HOSTLIST string for the kickoff program,
348 # and to request the host name of the fast network adapters.
349 @@ -554,8 +493,6 @@
350 #
351 # The IBM cluster has two Gigabit adapters in each 4-way SMP,
352 # while the AXP cluster is based on a Myrinet network.
353 - if (`uname` == AIX) set NETEXT=".gig,.gig2"
354 - if (`uname` == Linux) set NETEXT=".myri"
355 #
356 # repeated host names in the PBS host file indicate being assigned
357 # CPUs in the same SMP enclosure, which we must count up correctly.
358 @@ -586,12 +523,11 @@
359 @ NNODES = 1
360 @ NSMPCPU = 1
361 set spacer1=":cpus="
362 - set spacer2=":netext="
363 while($IPROC <= $nmax)
364 set MYPROC=`sed -n -e "$IPROC p" $PBS_NODEFILE`
365 set MYPROC=`echo $MYPROC | awk '{split($0,a,"."); print a[1]}'`
366 if($MYPROC != $MYNODE) then
367 - set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU$spacer2$NETEXT)
368 + set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU)
369 set MYNODE=$MYPROC
370 @ NSMPCPU = 0
371 @ NNODES++
372 @@ -599,13 +535,13 @@
373 @ IPROC++
374 @ NSMPCPU++
375 end
376 - set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU$spacer2$NETEXT)
377 + set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU)
378 endif
379 #
380 # we have now finished setting up a correct HOSTLIST.
381 # uncomment the next two if you are doing script debugging.
382 -#--echo "The generated host list is"
383 -#--echo $HOSTLIST
384 + echo "The generated host list is"
385 + echo $HOSTLIST
386 #
387
388 #
389 diff -urN gamess.orig/tools/checktst/checktst gamess/tools/checktst/checktst
390 --- gamess.orig/tools/checktst/checktst 2008-12-30 18:33:09.000000000 +0300
391 +++ gamess/tools/checktst/checktst 2010-05-30 03:46:16.000000000 +0400
392 @@ -3,11 +3,6 @@
393 # Compare the results of GAMESS sample jobs to pre-stored correct values.
394 # This script can be executed from any directory with write permissions.
395 # Written by D. G. Fedorov, AIST, July 20, 2004.
396 -#
397 -# Only the path name in the very next line needs to be customized.
398 -#
399 -set GMSPATH=~/gamess
400 -
401 # The Ntest outputs are assumed to be named exam01.log, exam02.log, ...
402 # but the user will be allowed to specify the directory containing them.
403 #