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commit: 95cf7846a9ea6fb89107b90286f560a69fd8a251 |
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Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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AuthorDate: Tue Nov 29 08:38:18 2016 +0000 |
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Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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CommitDate: Tue Nov 29 08:38:18 2016 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=95cf7846 |
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|
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sci-chemistry/gamess: Update gamess version. Clean old ones |
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|
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Package-Manager: portage-2.3.0 |
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|
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.../gamess/files/gamess-20130501.1.gentoo.patch | 206 ------------- |
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...gentoo.patch => gamess-20161808.1.gentoo.patch} | 79 +++-- |
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sci-chemistry/gamess/gamess-20130501.1.ebuild | 338 --------------------- |
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...-20141205.1.ebuild => gamess-20161808.1.ebuild} | 5 +- |
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4 files changed, 42 insertions(+), 586 deletions(-) |
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|
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diff --git a/sci-chemistry/gamess/files/gamess-20130501.1.gentoo.patch b/sci-chemistry/gamess/files/gamess-20130501.1.gentoo.patch |
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deleted file mode 100644 |
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index 54a403b..0000000 |
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--- a/sci-chemistry/gamess/files/gamess-20130501.1.gentoo.patch |
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+++ /dev/null |
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@@ -1,206 +0,0 @@ |
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-diff -urN gamess.orig/comp gamess.new/comp |
25 |
---- gamess.orig/comp 2013-05-03 23:18:53.000000000 +0300 |
26 |
-+++ gamess.new/comp 2013-09-28 18:32:46.621341822 +0300 |
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-@@ -1544,7 +1544,7 @@ |
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- # g77 does not support FORTRAN logical units above 99, or 128 bit math. |
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- # |
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- case g77: |
31 |
-- set OPT = '-O2' |
32 |
-+ set gentoo-OPT = '-O2' |
33 |
- if ($MODULE == ormas1) set OPT='-O2 -fno-move-all-movables' # RH9, g77 3.3 |
34 |
- if ($MODULE == zheev) set OPT='-O0' # defensive compiling |
35 |
- if (($MODULE == qeigen) || ($MODULE == int2c)) then |
36 |
-@@ -1574,7 +1574,7 @@ |
37 |
- # -std=legacy suppresses warnings about use of f77 constructs. |
38 |
- # |
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- case gfortran: |
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-- set OPT='-O2' |
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-+ set gentoo-OPT='-O2' |
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- if ($MODULE == zheev) set OPT='-O0' # defensive compiling |
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- if ($MODULE == pcmcv2) set OPT='-O1' # EFP+CPCM, ala Francois, v4.1.2 |
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- if ($GMS_GFORTRAN_VERNO == 4.6) then |
45 |
-@@ -1636,7 +1636,7 @@ |
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- # optimizations in 32 bit mode, as a function of the ifort version. |
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- # |
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- case ifort: |
49 |
-- set OPT = '-O3' |
50 |
-+ set gentoo-OPT = '-O2' |
51 |
- if ($MODULE == delocl) set OPT='-O0' # from Cheol |
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- if ($MODULE == prpamm) set OPT='-O0' # for exam13 |
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- if ($MODULE == zheev) set OPT='-O0' |
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-@@ -1755,7 +1755,7 @@ |
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- # -finit-real=<zero|inf|-inf|nan> could be interesting debug opt |
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- # -fno-automatic forces static storage of all local variables |
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- # -fno-whole-file suppresses argument's data type checking |
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-- set OPT='-O2' |
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-+ set gentoo-OPT='-O2' |
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- if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS" |
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- |
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- if ($GMS_GFORTRAN_VERNO == 4.6) then |
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-@@ -1804,6 +1804,7 @@ |
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- breaksw |
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- case 4.6: |
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- case 4.7: |
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-+ case 4.8: |
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- set EXTRAOPT="$EXTRAOPT -fno-whole-file" |
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- breaksw |
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- default: |
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-@@ -1833,7 +1834,7 @@ |
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- # -WB means warn but don't fail on out-of-bounds array references |
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- # -ftz flushes underflow results to zero |
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- # |
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-- set OPT = '-O2' |
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-+ set gentoo-OPT = '-O2' |
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- if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS" |
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- # alas, I'm so tired of hearing about so many versions failing to |
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- # diagonalize, that this time critical code is run w/o optimization. |
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-diff -urN gamess.orig/ddi/compddi gamess.new/ddi/compddi |
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---- gamess.orig/ddi/compddi 2013-05-03 23:14:15.000000000 +0300 |
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-+++ gamess.new/ddi/compddi 2013-09-28 18:09:10.390246354 +0300 |
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-@@ -640,7 +640,7 @@ |
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- |
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- set FORTRAN=$GMS_FORTRAN # might be g77, gfortran, ifort, pgf77, f2c |
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- |
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-- set CC = 'gcc' |
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-+ set gentoo-CC = 'gcc' |
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- set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./" |
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- set CLIBS = "-lpthread" |
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- |
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-@@ -694,7 +694,7 @@ |
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- set ARCH='-m64' |
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- if (`uname -p` == ia64) set ARCH='' |
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- |
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-- set CC = 'gcc' |
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-+ set gentoo-CC = 'gcc' |
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- set CFLAGS = "-DLINUX $ARCH -O3 -fstrict-aliasing -I./" |
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- set CLIBS = "-lpthread" |
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- |
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-diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess.new/ddi/kickoff/ddikick.c |
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---- gamess.orig/ddi/kickoff/ddikick.c 2011-11-22 21:54:33.000000000 +0200 |
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-+++ gamess.new/ddi/kickoff/ddikick.c 2013-09-28 18:10:27.380423340 +0300 |
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-@@ -105,7 +105,7 @@ |
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- remoteshell = argv[++i]; |
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- } else { |
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- if((remoteshell = getenv("DDI_RSH")) == NULL) { |
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-- remoteshell = (char *) strdup("rsh"); |
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-+ remoteshell = (char *) strdup("ssh"); |
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- } |
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- } |
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- |
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-diff -urN gamess.orig/gms-files.csh gamess.new/gms-files.csh |
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---- gamess.orig/gms-files.csh 2013-05-03 22:18:03.000000000 +0300 |
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-+++ gamess.new/gms-files.csh 2013-09-28 18:28:04.952744349 +0300 |
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-@@ -28,7 +28,7 @@ |
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- # to see all the file definitions (one is just below). |
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- # |
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- #---quiet---set echo |
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--setenv AUXDATA $GMSPATH/auxdata |
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-+setenv AUXDATA /usr/share/gamess |
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- setenv EXTBAS /dev/null |
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- setenv NUCBAS /dev/null |
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- setenv POSBAS /dev/null |
125 |
-diff -urN gamess.orig/lked gamess.new/lked |
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---- gamess.orig/lked 2013-05-17 19:15:06.000000000 +0300 |
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-+++ gamess.new/lked 2013-09-28 18:20:14.922777944 +0300 |
128 |
-@@ -384,17 +384,17 @@ |
129 |
- switch ($GMS_FORTRAN) |
130 |
- case g77: |
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- set LDR='g77' |
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-- set LDOPTS=' ' # add '-Wl,-M' to see load map |
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-+ set gentoo-LDOPTS=' ' # add '-Wl,-M' to see load map |
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- set FORTLIBS=' ' |
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- breaksw |
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- case gfortran: |
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- set LDR='gfortran' |
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-- set LDOPTS=' ' |
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-+ set gentoo-LDOPTS=' ' |
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- set FORTLIBS=' ' |
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- breaksw |
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- case ifort: |
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- set LDR='ifort' |
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-- set LDOPTS=' ' # add '-Wl,-M' to see load map |
145 |
-+ set gentoo-LDOPTS=' ' # add '-Wl,-M' to see load map |
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- set FORTLIBS='-Vaxlib' |
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- breaksw |
148 |
- case pgfortran |
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-@@ -405,7 +405,7 @@ |
150 |
- breaksw |
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- case f2c: |
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- set LDR='gcc' |
153 |
-- set LDOPTS=' ' |
154 |
-+ set gentoo-LDOPTS=' ' |
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- set FORTLIBS='-lf2c -lm' |
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- breaksw |
157 |
- default: |
158 |
-@@ -458,12 +458,7 @@ |
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- # Otherwise, attempt a link against shared object libs. |
160 |
- # See the 64 bit Atlas below for a way to fix the linker's |
161 |
- # not being able to locate -lf77blas, if that happens. |
162 |
-- if (-e $GMS_MATHLIB_PATH/libf77blas.a) then |
163 |
-- set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a" |
164 |
-- set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a" |
165 |
-- else |
166 |
-- set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas" |
167 |
-- endif |
168 |
-+ set MATHLIBS=`${PKG_CONFIG} --libs blas` |
169 |
- set BLAS=' ' |
170 |
- breaksw |
171 |
- |
172 |
-@@ -497,12 +492,12 @@ |
173 |
- switch ($GMS_FORTRAN) |
174 |
- case gfortran: |
175 |
- set LDR='gfortran' |
176 |
-- set LDOPTS=' ' |
177 |
-+ set gentoo-LDOPTS=' ' |
178 |
- set FORTLIBS=' ' |
179 |
- breaksw |
180 |
- case ifort: |
181 |
- set LDR='ifort' |
182 |
-- set LDOPTS='-i8' # -Wl,-M generates a load map |
183 |
-+ set gentoo-LDOPTS=' ' # -Wl,-M generates a load map |
184 |
- # this auxiliary library seems to have disappeared in ifort 10 |
185 |
- set FORTLIBS=' ' |
186 |
- if($GMS_IFORT_VERNO < 10) set FORTLIBS='-Vaxlib' |
187 |
-@@ -619,13 +614,7 @@ |
188 |
- # ln -s liblapack_atlas.so.3.0 liblapack.so |
189 |
- # ln -s liblapack.so.3.0 liblapack.so |
190 |
- # It is strange the RPM's don't do these soft links for us. |
191 |
-- if (-e $GMS_MATHLIB_PATH/libf77blas.a) then |
192 |
-- set MATHLIBS="$GMS_MATHLIB_PATH/libf77blas.a" |
193 |
-- set MATHLIBS="$MATHLIBS $GMS_MATHLIB_PATH/libatlas.a" |
194 |
-- else |
195 |
-- set MATHLIBS="-L$GMS_MATHLIB_PATH -lf77blas -latlas" |
196 |
-- if ($CCHEM == true) set MATHLIBS="$MATHLIBS -llapack" |
197 |
-- endif |
198 |
-+ set MATHLIBS=`${PKG_CONFIG} --libs blas` |
199 |
- set BLAS=' ' |
200 |
- breaksw |
201 |
- |
202 |
-diff -urN gamess.orig/runall gamess.new/runall |
203 |
---- gamess.orig/runall 2012-02-03 01:55:01.000000000 +0200 |
204 |
-+++ gamess.new/runall 2013-09-28 18:20:59.446867749 +0300 |
205 |
-@@ -46,7 +46,7 @@ |
206 |
- xgms -v $VERNO -q $QUEUE -l exam$NUM.log exam$NUM |
207 |
- sleep 2 |
208 |
- else |
209 |
-- ./rungms exam$NUM $VERNO 1 >& exam$NUM.log |
210 |
-+ rungms exam$NUM $VERNO 1 >& exam$NUM.log |
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- endif |
212 |
- @ i++ |
213 |
- end |
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-diff -urN gamess.orig/rungms gamess.new/rungms |
215 |
---- gamess.orig/rungms 2013-05-17 19:15:11.000000000 +0300 |
216 |
-+++ gamess.new/rungms 2013-09-28 18:26:53.268594417 +0300 |
217 |
-@@ -60,9 +60,9 @@ |
218 |
- # See also a very old LoadLeveler "ll-gms" for some IBM systems. |
219 |
- # |
220 |
- set TARGET=sockets |
221 |
--set SCR=/scr/$USER |
222 |
--set USERSCR=~$USER/scr |
223 |
--set GMSPATH=/u1/mike/gamess |
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-+set SCR=`pwd` |
225 |
-+set USERSCR=`pwd` |
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-+set GMSPATH=/usr/bin |
227 |
- # |
228 |
- set JOB=$1 # name of the input file xxx.inp, give only the xxx part |
229 |
- set VERNO=$2 # revision number of the executable created by 'lked' step |
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|
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diff --git a/sci-chemistry/gamess/files/gamess-20141205.1.gentoo.patch b/sci-chemistry/gamess/files/gamess-20161808.1.gentoo.patch |
232 |
similarity index 80% |
233 |
rename from sci-chemistry/gamess/files/gamess-20141205.1.gentoo.patch |
234 |
rename to sci-chemistry/gamess/files/gamess-20161808.1.gentoo.patch |
235 |
index 742ea46..c29200f 100644 |
236 |
--- a/sci-chemistry/gamess/files/gamess-20141205.1.gentoo.patch |
237 |
+++ b/sci-chemistry/gamess/files/gamess-20161808.1.gentoo.patch |
238 |
@@ -1,7 +1,7 @@ |
239 |
diff -urN gamess.orig/comp gamess/comp |
240 |
---- gamess.orig/comp 2015-01-15 17:49:05.000000000 +0300 |
241 |
-+++ gamess/comp 2016-05-26 11:40:00.143511481 +0300 |
242 |
-@@ -1535,7 +1535,7 @@ |
243 |
+--- gamess.orig/comp 2016-10-08 17:15:03.000000000 +0300 |
244 |
++++ gamess/comp 2016-11-29 11:30:44.836507346 +0300 |
245 |
+@@ -1548,7 +1548,7 @@ |
246 |
# |
247 |
case gfortran: |
248 |
# |
249 |
@@ -10,19 +10,18 @@ diff -urN gamess.orig/comp gamess/comp |
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if ($MODULE == zheev) set OPT='-O0' # defensive compiling |
251 |
|
252 |
set EXTRAOPT=" " |
253 |
-@@ -1577,6 +1577,11 @@ |
254 |
- breaksw |
255 |
- case 4.8: |
256 |
- case 4.9: |
257 |
-+ case 5.0: |
258 |
-+ case 5.1: |
259 |
-+ case 5.2: |
260 |
-+ case 5.3: |
261 |
+@@ -1593,6 +1593,10 @@ |
262 |
+ case 5.1: |
263 |
+ case 5.2: |
264 |
+ case 5.3: |
265 |
++ case 5.4: |
266 |
+ case 6.0: |
267 |
++ case 6.1: |
268 |
++ case 6.2: |
269 |
if ($MODULE == cosmo) set OPT='-O0' |
270 |
if ($MODULE == dcscf) set OPT='-O0' |
271 |
if ($MODULE == tddgrd) set OPT='-O0' |
272 |
-@@ -1605,7 +1610,7 @@ |
273 |
+@@ -1621,7 +1625,7 @@ |
274 |
# optimizations in 32 bit mode, as a function of the ifort version. |
275 |
# |
276 |
case ifort: |
277 |
@@ -31,7 +30,7 @@ diff -urN gamess.orig/comp gamess/comp |
278 |
if ($MODULE == delocl) set OPT='-O0' # from Cheol |
279 |
if ($MODULE == prpamm) set OPT='-O0' # for exam13 |
280 |
if ($MODULE == zheev) set OPT='-O0' |
281 |
-@@ -1740,7 +1745,7 @@ |
282 |
+@@ -1766,7 +1770,7 @@ |
283 |
# |
284 |
# first, initialize OPT and EXTRAOPT |
285 |
# |
286 |
@@ -40,19 +39,18 @@ diff -urN gamess.orig/comp gamess/comp |
287 |
if ($MODULE == zheev) set OPT='-O0' # defensive compiling |
288 |
|
289 |
set EXTRAOPT=" " |
290 |
-@@ -1793,6 +1798,11 @@ |
291 |
- breaksw |
292 |
- case 4.8: |
293 |
- case 4.9: |
294 |
-+ case 5.0: |
295 |
-+ case 5.1: |
296 |
-+ case 5.2: |
297 |
-+ case 5.3: |
298 |
+@@ -1823,6 +1827,10 @@ |
299 |
+ case 5.1: |
300 |
+ case 5.2: |
301 |
+ case 5.3: |
302 |
++ case 5.4: |
303 |
+ case 6.0: |
304 |
++ case 6.1: |
305 |
++ case 6.2: |
306 |
if ($MODULE == cosmo) set OPT='-O0' # same issue as seen in 4.6 |
307 |
if ($MODULE == dcscf) set OPT='-O0' # exam44, continues from 4.7 |
308 |
if ($MODULE == tddgrd) set OPT='-O0' # exam41, continues from 4.6 |
309 |
-@@ -1829,7 +1839,7 @@ |
310 |
+@@ -1864,7 +1872,7 @@ |
311 |
# -WB means warn but don't fail on out-of-bounds array references |
312 |
# -ftz flushes underflow results to zero |
313 |
# |
314 |
@@ -62,9 +60,9 @@ diff -urN gamess.orig/comp gamess/comp |
315 |
# alas, I'm so tired of hearing about so many versions failing to |
316 |
# diagonalize, that this time critical code is run w/o optimization. |
317 |
diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi |
318 |
---- gamess.orig/ddi/compddi 2015-01-15 17:49:05.000000000 +0300 |
319 |
-+++ gamess/ddi/compddi 2016-05-26 11:30:34.601322818 +0300 |
320 |
-@@ -610,7 +610,7 @@ |
321 |
+--- gamess.orig/ddi/compddi 2016-06-22 21:28:44.000000000 +0300 |
322 |
++++ gamess/ddi/compddi 2016-11-29 11:28:19.067151986 +0300 |
323 |
+@@ -627,7 +627,7 @@ |
324 |
|
325 |
set FORTRAN=$GMS_FORTRAN # might be g77, gfortran, ifort, pgf77, f2c |
326 |
|
327 |
@@ -73,7 +71,7 @@ diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi |
328 |
set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./" |
329 |
set CLIBS = "-lpthread" |
330 |
|
331 |
-@@ -664,7 +664,7 @@ |
332 |
+@@ -681,7 +681,7 @@ |
333 |
set ARCH='-m64' |
334 |
if (`uname -p` == ia64) set ARCH='' |
335 |
|
336 |
@@ -84,7 +82,7 @@ diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi |
337 |
|
338 |
diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess/ddi/kickoff/ddikick.c |
339 |
--- gamess.orig/ddi/kickoff/ddikick.c 2011-11-22 23:54:33.000000000 +0400 |
340 |
-+++ gamess/ddi/kickoff/ddikick.c 2016-05-26 11:30:34.601322818 +0300 |
341 |
++++ gamess/ddi/kickoff/ddikick.c 2016-11-29 11:28:19.068151988 +0300 |
342 |
@@ -105,7 +105,7 @@ |
343 |
remoteshell = argv[++i]; |
344 |
} else { |
345 |
@@ -95,8 +93,8 @@ diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess/ddi/kickoff/ddikick.c |
346 |
} |
347 |
|
348 |
diff -urN gamess.orig/gms-files.csh gamess/gms-files.csh |
349 |
---- gamess.orig/gms-files.csh 2014-05-16 18:14:43.000000000 +0400 |
350 |
-+++ gamess/gms-files.csh 2016-05-26 11:30:34.601322818 +0300 |
351 |
+--- gamess.orig/gms-files.csh 2016-09-07 22:42:51.000000000 +0300 |
352 |
++++ gamess/gms-files.csh 2016-11-29 11:28:19.068151988 +0300 |
353 |
@@ -28,7 +28,7 @@ |
354 |
# to see all the file definitions (one is just below). |
355 |
# |
356 |
@@ -107,9 +105,9 @@ diff -urN gamess.orig/gms-files.csh gamess/gms-files.csh |
357 |
setenv NUCBAS /dev/null |
358 |
setenv POSBAS /dev/null |
359 |
diff -urN gamess.orig/lked gamess/lked |
360 |
---- gamess.orig/lked 2014-12-08 20:56:59.000000000 +0300 |
361 |
-+++ gamess/lked 2016-05-26 11:41:11.124667982 +0300 |
362 |
-@@ -356,12 +356,12 @@ |
363 |
+--- gamess.orig/lked 2016-07-29 20:59:09.000000000 +0300 |
364 |
++++ gamess/lked 2016-11-29 11:32:22.885745512 +0300 |
365 |
+@@ -362,12 +362,12 @@ |
366 |
switch ($GMS_FORTRAN) |
367 |
case gfortran: |
368 |
set LDR='gfortran' |
369 |
@@ -124,7 +122,7 @@ diff -urN gamess.orig/lked gamess/lked |
370 |
set FORTLIBS='-Vaxlib' |
371 |
breaksw |
372 |
case pgfortran: |
373 |
-@@ -420,12 +420,7 @@ |
374 |
+@@ -426,12 +426,7 @@ |
375 |
# Otherwise, attempt a link against shared object libs. |
376 |
# See the 64 bit Atlas below for a way to fix the linker's |
377 |
# not being able to locate -lf77blas, if that happens. |
378 |
@@ -138,13 +136,14 @@ diff -urN gamess.orig/lked gamess/lked |
379 |
set BLAS=' ' |
380 |
breaksw |
381 |
|
382 |
-@@ -459,12 +454,12 @@ |
383 |
+@@ -465,13 +460,13 @@ |
384 |
switch ($GMS_FORTRAN) |
385 |
case gfortran: |
386 |
set LDR='gfortran' |
387 |
- set LDOPTS=' ' |
388 |
+ set gentoo-LDOPTS=' ' |
389 |
set FORTLIBS=' ' |
390 |
+ if ($GMS_OPENMP == true) set LDOPTS="$LDOPTS -fopenmp" |
391 |
breaksw |
392 |
case ifort: |
393 |
set LDR='ifort' |
394 |
@@ -152,8 +151,8 @@ diff -urN gamess.orig/lked gamess/lked |
395 |
+ set gentoo-LDOPTS=' ' # -Wl,-M generates a load map |
396 |
# this auxiliary library seems to have disappeared in ifort 10 |
397 |
set FORTLIBS=' ' |
398 |
- if($GMS_IFORT_VERNO < 10) set FORTLIBS='-Vaxlib' |
399 |
-@@ -581,13 +576,7 @@ |
400 |
+ if ($GMS_IFORT_VERNO < 10) set FORTLIBS='-Vaxlib' |
401 |
+@@ -616,13 +611,7 @@ |
402 |
# ln -s liblapack_atlas.so.3.0 liblapack.so |
403 |
# ln -s liblapack.so.3.0 liblapack.so |
404 |
# It is strange the RPM's don't do these soft links for us. |
405 |
@@ -170,7 +169,7 @@ diff -urN gamess.orig/lked gamess/lked |
406 |
|
407 |
diff -urN gamess.orig/runall gamess/runall |
408 |
--- gamess.orig/runall 2012-02-03 03:55:01.000000000 +0400 |
409 |
-+++ gamess/runall 2016-05-26 11:30:34.603322822 +0300 |
410 |
++++ gamess/runall 2016-11-29 11:28:19.069151991 +0300 |
411 |
@@ -46,7 +46,7 @@ |
412 |
xgms -v $VERNO -q $QUEUE -l exam$NUM.log exam$NUM |
413 |
sleep 2 |
414 |
@@ -181,9 +180,9 @@ diff -urN gamess.orig/runall gamess/runall |
415 |
@ i++ |
416 |
end |
417 |
diff -urN gamess.orig/rungms gamess/rungms |
418 |
---- gamess.orig/rungms 2014-12-10 19:01:06.000000000 +0300 |
419 |
-+++ gamess/rungms 2016-05-26 11:42:23.316828732 +0300 |
420 |
-@@ -60,9 +60,9 @@ |
421 |
+--- gamess.orig/rungms 2016-10-08 17:16:14.000000000 +0300 |
422 |
++++ gamess/rungms 2016-11-29 11:28:19.070151993 +0300 |
423 |
+@@ -61,9 +61,9 @@ |
424 |
# See also a very old LoadLeveler "ll-gms" for some IBM systems. |
425 |
# |
426 |
set TARGET=sockets |
427 |
|
428 |
diff --git a/sci-chemistry/gamess/gamess-20130501.1.ebuild b/sci-chemistry/gamess/gamess-20130501.1.ebuild |
429 |
deleted file mode 100644 |
430 |
index 8cc04fb..0000000 |
431 |
--- a/sci-chemistry/gamess/gamess-20130501.1.ebuild |
432 |
+++ /dev/null |
433 |
@@ -1,338 +0,0 @@ |
434 |
-# Copyright 1999-2015 Gentoo Foundation |
435 |
-# Distributed under the terms of the GNU General Public License v2 |
436 |
-# $Id$ |
437 |
- |
438 |
-EAPI=5 |
439 |
- |
440 |
-inherit eutils fortran-2 flag-o-matic pax-utils toolchain-funcs |
441 |
- |
442 |
-DESCRIPTION="A powerful quantum chemistry package" |
443 |
-HOMEPAGE="http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html" |
444 |
-SRC_URI=" |
445 |
- ${P}.tar.gz |
446 |
- qmmm-tinker? ( tinker.tar.Z )" |
447 |
- |
448 |
-SLOT="0" |
449 |
-LICENSE="gamess" |
450 |
-# NOTE: PLEASE do not stabilize gamess. It does not make sense |
451 |
-# since the tarball has fetch restrictions and upstream only |
452 |
-# provides the latest version. In other words: As soon as a |
453 |
-# new version comes out the stable version will be useless since |
454 |
-# users can not get at the tarball any more. |
455 |
-KEYWORDS="~amd64 ~ppc ~x86" |
456 |
-IUSE="mpi neo pax_kernel qmmm-tinker" |
457 |
- |
458 |
-CDEPEND=" |
459 |
- app-shells/tcsh |
460 |
- mpi? ( virtual/mpi ) |
461 |
- virtual/blas" |
462 |
-DEPEND="${CDEPEND} |
463 |
- virtual/pkgconfig" |
464 |
-RDEPEND="${CDEPEND} |
465 |
- net-misc/openssh" |
466 |
- |
467 |
-S="${WORKDIR}/${PN}" |
468 |
- |
469 |
-RESTRICT="fetch" |
470 |
- |
471 |
-GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html" |
472 |
-GAMESS_VERSION="1 MAY 2013 (R1)" |
473 |
- |
474 |
-pkg_nofetch() { |
475 |
- echo |
476 |
- elog "Please download ${PN}-current.tar.gz from" |
477 |
- elog "${GAMESS_DOWNLOAD}." |
478 |
- elog "Be sure to select the version ${GAMESS_VERSION} tarball!!" |
479 |
- elog "Then move the tarball to" |
480 |
- elog "${DISTDIR}/${P}.tar.gz" |
481 |
- if use qmmm-tinker ; then |
482 |
- elog "Also download http://www.msg.ameslab.gov/GAMESS/tinker.tar.Z" |
483 |
- elog "and place tinker.tar.Z to ${DISTDIR}" |
484 |
- fi |
485 |
- echo |
486 |
-} |
487 |
- |
488 |
-get_fcomp() { |
489 |
- case $(tc-getFC) in |
490 |
- *gfortran* ) |
491 |
- FCOMP="gfortran" ;; |
492 |
- ifort ) |
493 |
- FCOMP="ifc" ;; |
494 |
- * ) |
495 |
- FCOMP=$(tc-getFC) ;; |
496 |
- esac |
497 |
-} |
498 |
- |
499 |
-pkg_setup() { |
500 |
- fortran-2_pkg_setup |
501 |
- get_fcomp |
502 |
- # currently amd64 is only supported with gfortran |
503 |
- if [[ "${ARCH}" == "amd64" ]] && [[ ${FCOMP} != *gfortran* ]]; |
504 |
- then die "You will need gfortran to compile gamess on amd64" |
505 |
- fi |
506 |
- |
507 |
- # note about qmmm-tinker |
508 |
- if use qmmm-tinker; then |
509 |
- einfo "By default MM subsistem is restricted to 1000 atoms" |
510 |
- einfo "if you want larger MM subsystems then you should set" |
511 |
- einfo "QMMM_GAMESS_MAXMM variable to needed value in your make.conf" |
512 |
- einfo "By default maximum number of atom classes types and size of" |
513 |
- einfo "hessian are restricted to 250, 500 and 1000000 respectively" |
514 |
- einfo "If you want larger sizes set:" |
515 |
- einfo "QMMM_GAMESS_MAXCLASS" |
516 |
- einfo "QMMM_GAMESS_MAXCTYP" |
517 |
- einfo "QMMM_GAMESS_MAXHESS" |
518 |
- einfo "in your make.conf" |
519 |
- fi |
520 |
- |
521 |
- #note about mpi |
522 |
- if use mpi; then |
523 |
- ewarn "" |
524 |
- ewarn "You should adjust rungms script for your mpi implentation" |
525 |
- ewarn "because deafult one will not work" |
526 |
- ewarn "" |
527 |
- fi |
528 |
-} |
529 |
- |
530 |
-src_unpack() { |
531 |
- unpack ${A} |
532 |
- |
533 |
- if use qmmm-tinker; then |
534 |
- mv tinker gamess/ || die "failed to move tinker directory" |
535 |
- fi |
536 |
-} |
537 |
- |
538 |
-src_prepare() { |
539 |
- tc-export PKG_CONFIG |
540 |
- # apply LINUX-arch patches to gamess makesfiles |
541 |
- epatch "${FILESDIR}/${P}.gentoo.patch" |
542 |
- # select arch |
543 |
- # NOTE: please leave lked alone; it should be good as is!! |
544 |
- cd "${S}" |
545 |
- local active_arch; |
546 |
- if [[ "${ARCH}" == "amd64" ]]; then |
547 |
- active_arch="linux64"; |
548 |
- else |
549 |
- active_arch="linux32"; |
550 |
- fi |
551 |
- |
552 |
- # for hardened-gcc let't turn off ssp, since it breakes |
553 |
- # a few routines |
554 |
- if use pax_kernel && [[ ${FCOMP} == g77 ]]; then |
555 |
- FFLAGS="${FFLAGS} -fno-stack-protector-all" |
556 |
- fi |
557 |
- |
558 |
- # Enable mpi stuff |
559 |
- if use mpi; then |
560 |
- sed -e "s:set COMM = sockets:set COMM = mpi:g" \ |
561 |
- -i ddi/compddi || die "Enabling mpi build failed" |
562 |
- sed -e "s:MPI_INCLUDE_PATH = ' ':MPI_INCLUDE_PATH = '-I/usr/include ':g" \ |
563 |
- -i ddi/compddi || die "Enabling mpi build failed" |
564 |
- sed -e "s:MSG_LIBRARIES='../ddi/libddi.a -lpthread':MSG_LIBRARIES='../ddi/libddi.a -lmpi -lpthread':g" \ |
565 |
- -i lked || die "Enabling mpi build failed" |
566 |
- fi |
567 |
- |
568 |
- # enable NEO |
569 |
- if use neo; then |
570 |
- sed -e "s:NEO=false:NEO=true:" -i compall lked || \ |
571 |
- die "Failed to enable NEO code" |
572 |
- else |
573 |
- sed -e "s:NEO=true:NEO=false:" -i compall lked || \ |
574 |
- die "Failed to disable NEO code" |
575 |
- fi |
576 |
- # enable GAMESS-qmmm |
577 |
- if use qmmm-tinker; then |
578 |
- epatch "${FILESDIR}/${PN}-qmmm-tinker-fix-idate.patch" |
579 |
- sed -e "s:TINKER=false:TINKER=true:" -i compall lked || \ |
580 |
- die "Failed to enable TINKER code" |
581 |
- if [ "x$QMMM_GAMESS_MAXMM" == "x" ]; then |
582 |
- einfo "No QMMM_GAMESS_MAXMM set. Using default value = 1000" |
583 |
- else |
584 |
- einfo "Setting QMMM_GAMESS_MAXMM to $QMMM_GAMESS_MAXMM" |
585 |
- sed -e "s:maxatm=1000:maxatm=$QMMM_GAMESS_MAXMM:g" \ |
586 |
- -i tinker/sizes.i \ |
587 |
- || die "Setting QMMM_GAMESS_MAXMM failed" |
588 |
- sed -e "s:MAXATM=1000:MAXATM=$QMMM_GAMESS_MAXMM:g" \ |
589 |
- -i source/inputb.src \ |
590 |
- || die "Setting QMMM_GAMESS_MAXMM failed" |
591 |
- fi |
592 |
- if [ "x$QMMM_GAMESS_MAXCLASS" == "x" ]; then |
593 |
- einfo "No QMMM_GAMESS_MAXMM set. Using default value = 250" |
594 |
- else |
595 |
- sed -e "s:maxclass=250:maxclass=$QMMM_GAMESS_MAXCLASS:g" \ |
596 |
- -i tinker/sizes.i \ |
597 |
- || die "Setting QMMM_GAMESS_MAXCLASS failed" |
598 |
- fi |
599 |
- if [ "x$QMMM_GAMESS_MAXCTYP" == "x" ]; then |
600 |
- einfo "No QMMM_GAMESS_MAXCTYP set. Using default value = 500" |
601 |
- else |
602 |
- sed -e "s:maxtyp=500:maxtyp=$QMMM_GAMESS_MAXCTYP:g" \ |
603 |
- -i tinker/sizes.i \ |
604 |
- || die "Setting QMMM_GAMESS_MAXCTYP failed" |
605 |
- fi |
606 |
- if [ "x$QMMM_GAMESS_MAXHESS" == "x" ]; then |
607 |
- einfo "No QMMM_GAMESS_MAXHESS set. Usingdefault value = 1000000" |
608 |
- else |
609 |
- sed -e "s:maxhess=1000000:maxhess=$QMMM_GAMESS_MAXHESS:g" \ |
610 |
- -i tinker/sizes.i \ |
611 |
- || die "Setting QMMM_GAMESS_MAXHESS failed" |
612 |
- fi |
613 |
- fi |
614 |
- # create proper activate sourcefile |
615 |
- cp "./tools/actvte.code" "./tools/actvte.f" || \ |
616 |
- die "Failed to create actvte.f" |
617 |
- sed -e "s/^\*UNX/ /" -i "./tools/actvte.f" || \ |
618 |
- die "Failed to perform UNX substitutions in actvte.f" |
619 |
- |
620 |
- # fix GAMESS' compall script to use proper CC |
621 |
- sed -e "s|\$CCOMP -c \$extraflags source/zunix.c|$(tc-getCC) -c \$extraflags source/zunix.c|" \ |
622 |
- -i compall || die "Failed setting up compall script" |
623 |
- |
624 |
- # insert proper FFLAGS into GAMESS' comp makefile |
625 |
- # in case we're using ifc let's strip all the gcc |
626 |
- # specific stuff |
627 |
- if [[ ${FCOMP} == "ifort" ]]; then |
628 |
- sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS} -quiet'/" \ |
629 |
- -i comp || die "Failed setting up comp script" |
630 |
- elif ! use x86; then |
631 |
- sed -e "s/-malign-double //" \ |
632 |
- -e "s/gentoo-OPT='-O2'/OPT='${FFLAGS}'/" \ |
633 |
- -i comp || die "Failed setting up comp script" |
634 |
- else |
635 |
- sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \ |
636 |
- -i comp || die "Failed setting up comp script" |
637 |
- fi |
638 |
- |
639 |
- # fix up GAMESS' linker script; |
640 |
- sed -e "s/gentoo-LDOPTS=' '/LDOPTS='${LDFLAGS}'/" \ |
641 |
- -i lked || die "Failed setting up lked script" |
642 |
- # fix up GAMESS' ddi TCP/IP socket build |
643 |
- sed -e "s/gentoo-CC = 'gcc'/CC = '$(tc-getCC)'/" \ |
644 |
- -i ddi/compddi || die "Failed setting up compddi script" |
645 |
- # Creating install.info |
646 |
- cat > install.info <<-EOF |
647 |
- #!/bin/csh |
648 |
- setenv GMS_PATH $WORKDIR/gamess |
649 |
- setenv GMS_BUILD_DIR $WORKDIR/gamess |
650 |
- setenv GMS_TARGET $active_arch |
651 |
- setenv GMS_FORTRAN $FCOMP |
652 |
- setenv GMS_GFORTRAN_VERNO 4.7 |
653 |
- setenv GMS_MATHLIB atlas |
654 |
- setenv GMS_MATHLIB_PATH /usr/$(get_libdir)/atlas |
655 |
- setenv GMS_DDI_COMM sockets |
656 |
- EOF |
657 |
- |
658 |
-} |
659 |
- |
660 |
-src_compile() { |
661 |
- # build actvte |
662 |
- cd "${S}"/tools |
663 |
- ${FCOMP} -o actvte.x actvte.f || \ |
664 |
- die "Failed to compile actvte.x" |
665 |
- |
666 |
- # for hardened (PAX) users and ifc we need to turn |
667 |
- # MPROTECT off |
668 |
- if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then |
669 |
- pax-mark -PemRxS actvte.x |
670 |
- fi |
671 |
- |
672 |
- # build gamess |
673 |
- cd "${S}" |
674 |
- ./compall || die "compall failed" |
675 |
- |
676 |
- # build the ddi TCP/IP socket stuff |
677 |
- cd ${S}/"ddi" |
678 |
- ./compddi || die "compddi failed" |
679 |
- |
680 |
- # finally, link it all together |
681 |
- cd "${S}" |
682 |
- ./lked || die "lked failed" |
683 |
- |
684 |
- # for hardened (PAX) users and ifc we need to turn |
685 |
- # MPROTECT off |
686 |
- if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then |
687 |
- pax-mark -PemRxS ${PN}.00.x |
688 |
- fi |
689 |
-} |
690 |
- |
691 |
-src_install() { |
692 |
- # the executables |
693 |
- dobin ${PN}.00.x rungms gms-files.csh \ |
694 |
- || die "Failed installing binaries" |
695 |
- if use !mpi; then |
696 |
- dobin ddi/ddikick.x \ |
697 |
- || die "Failed installing binaries" |
698 |
- fi |
699 |
- |
700 |
- # the docs |
701 |
- dodoc *.DOC qmnuc/*.DOC |
702 |
- |
703 |
- # install ericftm |
704 |
- insinto /usr/share/${PN} |
705 |
- doins auxdata/ericfmt.dat |
706 |
- |
707 |
- # install mcpdata |
708 |
- insinto /usr/share/${PN}/MCP |
709 |
- doins auxdata/MCP/* |
710 |
- |
711 |
- # install BASES |
712 |
- insinto /usr/share/${PN}/BASES |
713 |
- doins auxdata/BASES/* |
714 |
- |
715 |
- # install QUANPOL |
716 |
- insinto /usr/share/${PN}/QUANPOL |
717 |
- doins auxdata/QUANPOL/* |
718 |
- |
719 |
- # install tinker params in case of qmmm |
720 |
- if use qmmm-tinker ; then |
721 |
- dodoc tinker/simomm.doc |
722 |
- insinto /usr/share/${PN} |
723 |
- doins -r tinker/params51 |
724 |
- fi |
725 |
- |
726 |
- # install the tests the user should run, and |
727 |
- # fix up the runscript; also grab a copy of rungms |
728 |
- # so the user is ready to run the tests |
729 |
- insinto /usr/share/${PN}/tests |
730 |
- insopts -m0644 |
731 |
- doins -r tests/* |
732 |
- insopts -m0744 |
733 |
- doins runall |
734 |
- #doins tools/checktst/checktst tools/checktst/chkabs || \ |
735 |
- # die "Failed to install main test checker" |
736 |
- #doins tools/checktst/exam* || \ |
737 |
- # die "Failed to install individual test files" |
738 |
- |
739 |
- insinto /usr/share/${PN}/neotests |
740 |
- insopts -m0644 |
741 |
- doins -r qmnuc/neotests/* |
742 |
-} |
743 |
- |
744 |
-pkg_postinst() { |
745 |
- echo |
746 |
- einfo "Before you use GAMESS for any serious work you HAVE" |
747 |
- einfo "to run the supplied test files located in" |
748 |
- einfo "/usr/share/gamess/tests and check them thoroughly." |
749 |
- einfo "Otherwise all scientific publications resulting from" |
750 |
- einfo "your GAMESS runs should be immediately rejected :)" |
751 |
- einfo "To do so copy the content of /usr/share/gamess/tests" |
752 |
- einfo "to some temporary location and execute './runall'. " |
753 |
- einfo "Then run the checktst script in the same directory to" |
754 |
- einfo "validate the tests." |
755 |
- einfo "Please consult TEST.DOC and the other docs!" |
756 |
- |
757 |
- if [[ ${FCOMP} == "ifort" ]]; then |
758 |
- echo |
759 |
- ewarn "IMPORTANT NOTE: We STRONGLY recommend to stay away" |
760 |
- ewarn "from ifc-9.0 for now and use the ifc-8.1 series of" |
761 |
- ewarn "compilers UNLESS you can run through ALL of the " |
762 |
- ewarn "test cases (see above) successfully." |
763 |
- fi |
764 |
- |
765 |
- echo |
766 |
- einfo "If you want to run on more than a single CPU" |
767 |
- einfo "you will have to acquaint yourself with the way GAMESS" |
768 |
- einfo "does multiprocessor runs and adjust rungms according to" |
769 |
- einfo "your target network architecture." |
770 |
- echo |
771 |
-} |
772 |
|
773 |
diff --git a/sci-chemistry/gamess/gamess-20141205.1.ebuild b/sci-chemistry/gamess/gamess-20161808.1.ebuild |
774 |
similarity index 99% |
775 |
rename from sci-chemistry/gamess/gamess-20141205.1.ebuild |
776 |
rename to sci-chemistry/gamess/gamess-20161808.1.ebuild |
777 |
index 1fb80b7..8f62aa6 100644 |
778 |
--- a/sci-chemistry/gamess/gamess-20141205.1.ebuild |
779 |
+++ b/sci-chemistry/gamess/gamess-20161808.1.ebuild |
780 |
@@ -2,7 +2,7 @@ |
781 |
# Distributed under the terms of the GNU General Public License v2 |
782 |
# $Id$ |
783 |
|
784 |
-EAPI=5 |
785 |
+EAPI=6 |
786 |
|
787 |
inherit eutils fortran-2 flag-o-matic pax-utils toolchain-funcs |
788 |
|
789 |
@@ -36,7 +36,7 @@ S="${WORKDIR}/${PN}" |
790 |
RESTRICT="fetch" |
791 |
|
792 |
GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html" |
793 |
-GAMESS_VERSION="5 DEC 2014 (R1)" |
794 |
+GAMESS_VERSION="18 AUG 2016 (R1)" |
795 |
|
796 |
pkg_nofetch() { |
797 |
echo |
798 |
@@ -106,6 +106,7 @@ src_prepare() { |
799 |
tc-export PKG_CONFIG |
800 |
# apply LINUX-arch patches to gamess makesfiles |
801 |
epatch "${FILESDIR}/${P}.gentoo.patch" |
802 |
+ eapply_user |
803 |
# select arch |
804 |
# NOTE: please leave lked alone; it should be good as is!! |
805 |
cd "${S}" |