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authorAlexey Shvetsov <alexxy@gentoo.org>2016-11-29 11:38:18 +0300
committerAlexey Shvetsov <alexxy@gentoo.org>2016-11-29 11:38:18 +0300
commit95cf7846a9ea6fb89107b90286f560a69fd8a251 (patch)
tree3b4c470a42821dfe4c7d1eb777ea01ff66e16309 /sci-chemistry
parentsci-libs/pydicom: Drop 0.9.8 (diff)
downloadsci-95cf7846a9ea6fb89107b90286f560a69fd8a251.tar.gz
sci-95cf7846a9ea6fb89107b90286f560a69fd8a251.tar.bz2
sci-95cf7846a9ea6fb89107b90286f560a69fd8a251.zip
sci-chemistry/gamess: Update gamess version. Clean old ones
Package-Manager: portage-2.3.0
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/gamess/Manifest4
-rw-r--r--sci-chemistry/gamess/files/gamess-20130501.1.gentoo.patch206
-rw-r--r--sci-chemistry/gamess/files/gamess-20161808.1.gentoo.patch (renamed from sci-chemistry/gamess/files/gamess-20141205.1.gentoo.patch)79
-rw-r--r--sci-chemistry/gamess/gamess-20130501.1.ebuild338
-rw-r--r--sci-chemistry/gamess/gamess-20161808.1.ebuild (renamed from sci-chemistry/gamess/gamess-20141205.1.ebuild)5
5 files changed, 43 insertions, 589 deletions
diff --git a/sci-chemistry/gamess/Manifest b/sci-chemistry/gamess/Manifest
index f3b616171..61a5e20d0 100644
--- a/sci-chemistry/gamess/Manifest
+++ b/sci-chemistry/gamess/Manifest
@@ -1,4 +1,2 @@
-DIST gamess-20130501.1.tar.gz 29013211 SHA256 315e6fa8f1947d8419b6f1adccf3fc7dd47b581fce107d304b7b99ef0cb15498 SHA512 56623e60762d554318111fd86c352a11393a7fa89cc0861aff7a2c68c687a953de60a4fc78f9860ec99223dd48c2cf6aa930a46a3f1c9cb019e893d871870023 WHIRLPOOL e67da7190613aeae085eea364ae3bbcc556e905e27900345cb75287eec0ea8107e0821826cb606ebb0d4f8f60ebdc264863bfa90954f846b55469c76372c1292
-DIST gamess-20141205.1.tar.gz 29993391 SHA256 6542ce730f3221d62851dc0eac573abaed19f3773567b3ffd6763b5d3ef93b4a SHA512 d48ab44957d45c2bf8d9880c63d32848807338883bb9dafaee5e47adc7eee6b12c6860a1b2e6464708fb3a850db4b09dc3a84e08b6a3f87384230c7d50b5d7f3 WHIRLPOOL 7ab71de8f888e2d70ec1abe810bcd57b11033aab6bb3dd6dae3dd8c76423ca256d2f6da38bb0d05a7560d76f45ee0454e9b9322ad3cc3eefa718e59c2e2c6e90
-DIST tinker.tar.Z 1902051 SHA256 7c52454ade7dd81d1b70a7e7722eda3672c644a3ba67ab444824a0212b4a7a8c SHA512 10f5012b6d9e32a3d6646c8d79ccc2a16f2d4322e974755e45605519bf478d36f09497457c7731c264c49ccd0c679b0fd0449d5910b4e1cfa499c7304cd28f6d WHIRLPOOL 4e81b02173f048890ec177f302818cc7664b5733c94db111c86ee6eecc830a83cc54a82797d162a2f26274be88cf786139aba096c8836e4ddd86bb0126f0908f
+DIST gamess-20161808.1.tar.gz 34208268 SHA256 4484ba6a8a2b2fc35eca3133b17ced4d59064572c122b302caaf3b5b6524b8ed SHA512 011648a403dab958a700efa08ad1bb598516178146047e61fc694076918c08816b4ad44e1bd0857400e24b54ea43f267b589de07b2249bec2cc4dd359aba1750 WHIRLPOOL e19f72b355d3590bfffb70ae509dd9f157658ccd1b7446df1778b2191a3c50dd434a21474047340b5f239347c00e31a95472b5e9e0ba072a95a61e6348fcb386
DIST tinker.tar.gz 1203190 SHA256 f07c98d85c7c6fb445ad81d4b19ffa5aadb8da62329996e0373ad4e4a73d1319 SHA512 db86de07ab5abc81c80db55d1576f78ecb67c8fedaf378e2f3ba2fca306aa8ab063c8c40d01dce1cdbaee541e5efeae3cc0a7b1e54d4cb2e6952aefa6df2d33b WHIRLPOOL ee366691fa6374672c82efc4ae25d9cdfa2b01198503ca9daf077dc3eeb9dd17f9732fbb555bf6f6bfcb8a1b59b0638c7a7bbe075534171d8a4f9467e8b425b1
diff --git a/sci-chemistry/gamess/files/gamess-20130501.1.gentoo.patch b/sci-chemistry/gamess/files/gamess-20130501.1.gentoo.patch
deleted file mode 100644
index 54a403b0c..000000000
--- a/sci-chemistry/gamess/files/gamess-20130501.1.gentoo.patch
+++ /dev/null
@@ -1,206 +0,0 @@
-diff -urN gamess.orig/comp gamess.new/comp
---- gamess.orig/comp 2013-05-03 23:18:53.000000000 +0300
-+++ gamess.new/comp 2013-09-28 18:32:46.621341822 +0300
-@@ -1544,7 +1544,7 @@
- # 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
-@@ -1574,7 +1574,7 @@
- # -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 ($GMS_GFORTRAN_VERNO == 4.6) then
-@@ -1636,7 +1636,7 @@
- # optimizations in 32 bit mode, as a function of the ifort version.
- #
- case ifort:
-- set OPT = '-O3'
-+ set gentoo-OPT = '-O2'
- if ($MODULE == delocl) set OPT='-O0' # from Cheol
- if ($MODULE == prpamm) set OPT='-O0' # for exam13
- if ($MODULE == zheev) set OPT='-O0'
-@@ -1755,7 +1755,7 @@
- # -finit-real=<zero|inf|-inf|nan> could be interesting debug opt
- # -fno-automatic forces static storage of all local variables
- # -fno-whole-file suppresses argument's data type checking
-- set OPT='-O2'
-+ set gentoo-OPT='-O2'
- if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS"
-
- if ($GMS_GFORTRAN_VERNO == 4.6) then
-@@ -1804,6 +1804,7 @@
- breaksw
- case 4.6:
- case 4.7:
-+ case 4.8:
- set EXTRAOPT="$EXTRAOPT -fno-whole-file"
- breaksw
- default:
-@@ -1833,7 +1834,7 @@
- # -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/ddi/compddi gamess.new/ddi/compddi
---- gamess.orig/ddi/compddi 2013-05-03 23:14:15.000000000 +0300
-+++ gamess.new/ddi/compddi 2013-09-28 18:09:10.390246354 +0300
-@@ -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"
-
-@@ -694,7 +694,7 @@
- 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.new/ddi/kickoff/ddikick.c
---- gamess.orig/ddi/kickoff/ddikick.c 2011-11-22 21:54:33.000000000 +0200
-+++ gamess.new/ddi/kickoff/ddikick.c 2013-09-28 18:10:27.380423340 +0300
-@@ -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/gms-files.csh gamess.new/gms-files.csh
---- gamess.orig/gms-files.csh 2013-05-03 22:18:03.000000000 +0300
-+++ gamess.new/gms-files.csh 2013-09-28 18:28:04.952744349 +0300
-@@ -28,7 +28,7 @@
- # to see all the file definitions (one is just below).
- #
- #---quiet---set echo
--setenv AUXDATA $GMSPATH/auxdata
-+setenv AUXDATA /usr/share/gamess
- setenv EXTBAS /dev/null
- setenv NUCBAS /dev/null
- setenv POSBAS /dev/null
-diff -urN gamess.orig/lked gamess.new/lked
---- gamess.orig/lked 2013-05-17 19:15:06.000000000 +0300
-+++ gamess.new/lked 2013-09-28 18:20:14.922777944 +0300
-@@ -384,17 +384,17 @@
- switch ($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 pgfortran
-@@ -405,7 +405,7 @@
- breaksw
- case f2c:
- set LDR='gcc'
-- set LDOPTS=' '
-+ set gentoo-LDOPTS=' '
- set FORTLIBS='-lf2c -lm'
- breaksw
- default:
-@@ -458,12 +458,7 @@
- # 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=`${PKG_CONFIG} --libs blas`
- set BLAS=' '
- breaksw
-
-@@ -497,12 +492,12 @@
- switch ($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'
-@@ -619,13 +614,7 @@
- # 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"
-- if ($CCHEM == true) set MATHLIBS="$MATHLIBS -llapack"
-- endif
-+ set MATHLIBS=`${PKG_CONFIG} --libs blas`
- set BLAS=' '
- breaksw
-
-diff -urN gamess.orig/runall gamess.new/runall
---- gamess.orig/runall 2012-02-03 01:55:01.000000000 +0200
-+++ gamess.new/runall 2013-09-28 18:20:59.446867749 +0300
-@@ -46,7 +46,7 @@
- xgms -v $VERNO -q $QUEUE -l exam$NUM.log exam$NUM
- sleep 2
- else
-- ./rungms exam$NUM $VERNO 1 >& exam$NUM.log
-+ rungms exam$NUM $VERNO 1 >& exam$NUM.log
- endif
- @ i++
- end
-diff -urN gamess.orig/rungms gamess.new/rungms
---- gamess.orig/rungms 2013-05-17 19:15:11.000000000 +0300
-+++ gamess.new/rungms 2013-09-28 18:26:53.268594417 +0300
-@@ -60,9 +60,9 @@
- # See also a very old LoadLeveler "ll-gms" for some IBM systems.
- #
- set TARGET=sockets
--set SCR=/scr/$USER
--set USERSCR=~$USER/scr
--set GMSPATH=/u1/mike/gamess
-+set SCR=`pwd`
-+set USERSCR=`pwd`
-+set GMSPATH=/usr/bin
- #
- set JOB=$1 # name of the input file xxx.inp, give only the xxx part
- set VERNO=$2 # revision number of the executable created by 'lked' step
diff --git a/sci-chemistry/gamess/files/gamess-20141205.1.gentoo.patch b/sci-chemistry/gamess/files/gamess-20161808.1.gentoo.patch
index 742ea461b..c29200fb6 100644
--- a/sci-chemistry/gamess/files/gamess-20141205.1.gentoo.patch
+++ b/sci-chemistry/gamess/files/gamess-20161808.1.gentoo.patch
@@ -1,7 +1,7 @@
diff -urN gamess.orig/comp gamess/comp
---- gamess.orig/comp 2015-01-15 17:49:05.000000000 +0300
-+++ gamess/comp 2016-05-26 11:40:00.143511481 +0300
-@@ -1535,7 +1535,7 @@
+--- gamess.orig/comp 2016-10-08 17:15:03.000000000 +0300
++++ gamess/comp 2016-11-29 11:30:44.836507346 +0300
+@@ -1548,7 +1548,7 @@
#
case gfortran:
#
@@ -10,19 +10,18 @@ diff -urN gamess.orig/comp gamess/comp
if ($MODULE == zheev) set OPT='-O0' # defensive compiling
set EXTRAOPT=" "
-@@ -1577,6 +1577,11 @@
- breaksw
- case 4.8:
- case 4.9:
-+ case 5.0:
-+ case 5.1:
-+ case 5.2:
-+ case 5.3:
+@@ -1593,6 +1593,10 @@
+ case 5.1:
+ case 5.2:
+ case 5.3:
++ case 5.4:
+ case 6.0:
++ case 6.1:
++ case 6.2:
if ($MODULE == cosmo) set OPT='-O0'
if ($MODULE == dcscf) set OPT='-O0'
if ($MODULE == tddgrd) set OPT='-O0'
-@@ -1605,7 +1610,7 @@
+@@ -1621,7 +1625,7 @@
# optimizations in 32 bit mode, as a function of the ifort version.
#
case ifort:
@@ -31,7 +30,7 @@ diff -urN gamess.orig/comp gamess/comp
if ($MODULE == delocl) set OPT='-O0' # from Cheol
if ($MODULE == prpamm) set OPT='-O0' # for exam13
if ($MODULE == zheev) set OPT='-O0'
-@@ -1740,7 +1745,7 @@
+@@ -1766,7 +1770,7 @@
#
# first, initialize OPT and EXTRAOPT
#
@@ -40,19 +39,18 @@ diff -urN gamess.orig/comp gamess/comp
if ($MODULE == zheev) set OPT='-O0' # defensive compiling
set EXTRAOPT=" "
-@@ -1793,6 +1798,11 @@
- breaksw
- case 4.8:
- case 4.9:
-+ case 5.0:
-+ case 5.1:
-+ case 5.2:
-+ case 5.3:
+@@ -1823,6 +1827,10 @@
+ case 5.1:
+ case 5.2:
+ case 5.3:
++ case 5.4:
+ case 6.0:
++ case 6.1:
++ case 6.2:
if ($MODULE == cosmo) set OPT='-O0' # same issue as seen in 4.6
if ($MODULE == dcscf) set OPT='-O0' # exam44, continues from 4.7
if ($MODULE == tddgrd) set OPT='-O0' # exam41, continues from 4.6
-@@ -1829,7 +1839,7 @@
+@@ -1864,7 +1872,7 @@
# -WB means warn but don't fail on out-of-bounds array references
# -ftz flushes underflow results to zero
#
@@ -62,9 +60,9 @@ diff -urN gamess.orig/comp gamess/comp
# 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/ddi/compddi gamess/ddi/compddi
---- gamess.orig/ddi/compddi 2015-01-15 17:49:05.000000000 +0300
-+++ gamess/ddi/compddi 2016-05-26 11:30:34.601322818 +0300
-@@ -610,7 +610,7 @@
+--- gamess.orig/ddi/compddi 2016-06-22 21:28:44.000000000 +0300
++++ gamess/ddi/compddi 2016-11-29 11:28:19.067151986 +0300
+@@ -627,7 +627,7 @@
set FORTRAN=$GMS_FORTRAN # might be g77, gfortran, ifort, pgf77, f2c
@@ -73,7 +71,7 @@ diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi
set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./"
set CLIBS = "-lpthread"
-@@ -664,7 +664,7 @@
+@@ -681,7 +681,7 @@
set ARCH='-m64'
if (`uname -p` == ia64) set ARCH=''
@@ -84,7 +82,7 @@ diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi
diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess/ddi/kickoff/ddikick.c
--- gamess.orig/ddi/kickoff/ddikick.c 2011-11-22 23:54:33.000000000 +0400
-+++ gamess/ddi/kickoff/ddikick.c 2016-05-26 11:30:34.601322818 +0300
++++ gamess/ddi/kickoff/ddikick.c 2016-11-29 11:28:19.068151988 +0300
@@ -105,7 +105,7 @@
remoteshell = argv[++i];
} else {
@@ -95,8 +93,8 @@ diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess/ddi/kickoff/ddikick.c
}
diff -urN gamess.orig/gms-files.csh gamess/gms-files.csh
---- gamess.orig/gms-files.csh 2014-05-16 18:14:43.000000000 +0400
-+++ gamess/gms-files.csh 2016-05-26 11:30:34.601322818 +0300
+--- gamess.orig/gms-files.csh 2016-09-07 22:42:51.000000000 +0300
++++ gamess/gms-files.csh 2016-11-29 11:28:19.068151988 +0300
@@ -28,7 +28,7 @@
# to see all the file definitions (one is just below).
#
@@ -107,9 +105,9 @@ diff -urN gamess.orig/gms-files.csh gamess/gms-files.csh
setenv NUCBAS /dev/null
setenv POSBAS /dev/null
diff -urN gamess.orig/lked gamess/lked
---- gamess.orig/lked 2014-12-08 20:56:59.000000000 +0300
-+++ gamess/lked 2016-05-26 11:41:11.124667982 +0300
-@@ -356,12 +356,12 @@
+--- gamess.orig/lked 2016-07-29 20:59:09.000000000 +0300
++++ gamess/lked 2016-11-29 11:32:22.885745512 +0300
+@@ -362,12 +362,12 @@
switch ($GMS_FORTRAN)
case gfortran:
set LDR='gfortran'
@@ -124,7 +122,7 @@ diff -urN gamess.orig/lked gamess/lked
set FORTLIBS='-Vaxlib'
breaksw
case pgfortran:
-@@ -420,12 +420,7 @@
+@@ -426,12 +426,7 @@
# 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.
@@ -138,13 +136,14 @@ diff -urN gamess.orig/lked gamess/lked
set BLAS=' '
breaksw
-@@ -459,12 +454,12 @@
+@@ -465,13 +460,13 @@
switch ($GMS_FORTRAN)
case gfortran:
set LDR='gfortran'
- set LDOPTS=' '
+ set gentoo-LDOPTS=' '
set FORTLIBS=' '
+ if ($GMS_OPENMP == true) set LDOPTS="$LDOPTS -fopenmp"
breaksw
case ifort:
set LDR='ifort'
@@ -152,8 +151,8 @@ diff -urN gamess.orig/lked gamess/lked
+ set gentoo-LDOPTS=' ' # -Wl,-M generates a load map
# this auxiliary library seems to have disappeared in ifort 10
set FORTLIBS=' '
- if($GMS_IFORT_VERNO < 10) set FORTLIBS='-Vaxlib'
-@@ -581,13 +576,7 @@
+ if ($GMS_IFORT_VERNO < 10) set FORTLIBS='-Vaxlib'
+@@ -616,13 +611,7 @@
# 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.
@@ -170,7 +169,7 @@ diff -urN gamess.orig/lked gamess/lked
diff -urN gamess.orig/runall gamess/runall
--- gamess.orig/runall 2012-02-03 03:55:01.000000000 +0400
-+++ gamess/runall 2016-05-26 11:30:34.603322822 +0300
++++ gamess/runall 2016-11-29 11:28:19.069151991 +0300
@@ -46,7 +46,7 @@
xgms -v $VERNO -q $QUEUE -l exam$NUM.log exam$NUM
sleep 2
@@ -181,9 +180,9 @@ diff -urN gamess.orig/runall gamess/runall
@ i++
end
diff -urN gamess.orig/rungms gamess/rungms
---- gamess.orig/rungms 2014-12-10 19:01:06.000000000 +0300
-+++ gamess/rungms 2016-05-26 11:42:23.316828732 +0300
-@@ -60,9 +60,9 @@
+--- gamess.orig/rungms 2016-10-08 17:16:14.000000000 +0300
++++ gamess/rungms 2016-11-29 11:28:19.070151993 +0300
+@@ -61,9 +61,9 @@
# See also a very old LoadLeveler "ll-gms" for some IBM systems.
#
set TARGET=sockets
diff --git a/sci-chemistry/gamess/gamess-20130501.1.ebuild b/sci-chemistry/gamess/gamess-20130501.1.ebuild
deleted file mode 100644
index 8cc04fb64..000000000
--- a/sci-chemistry/gamess/gamess-20130501.1.ebuild
+++ /dev/null
@@ -1,338 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils fortran-2 flag-o-matic pax-utils toolchain-funcs
-
-DESCRIPTION="A powerful quantum chemistry package"
-HOMEPAGE="http://www.msg.chem.iastate.edu/GAMESS/GAMESS.html"
-SRC_URI="
- ${P}.tar.gz
- qmmm-tinker? ( tinker.tar.Z )"
-
-SLOT="0"
-LICENSE="gamess"
-# NOTE: PLEASE do not stabilize gamess. It does not make sense
-# since the tarball has fetch restrictions and upstream only
-# provides the latest version. In other words: As soon as a
-# new version comes out the stable version will be useless since
-# users can not get at the tarball any more.
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE="mpi neo pax_kernel qmmm-tinker"
-
-CDEPEND="
- app-shells/tcsh
- mpi? ( virtual/mpi )
- virtual/blas"
-DEPEND="${CDEPEND}
- virtual/pkgconfig"
-RDEPEND="${CDEPEND}
- net-misc/openssh"
-
-S="${WORKDIR}/${PN}"
-
-RESTRICT="fetch"
-
-GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html"
-GAMESS_VERSION="1 MAY 2013 (R1)"
-
-pkg_nofetch() {
- echo
- elog "Please download ${PN}-current.tar.gz from"
- elog "${GAMESS_DOWNLOAD}."
- elog "Be sure to select the version ${GAMESS_VERSION} tarball!!"
- elog "Then move the tarball to"
- elog "${DISTDIR}/${P}.tar.gz"
- if use qmmm-tinker ; then
- elog "Also download http://www.msg.ameslab.gov/GAMESS/tinker.tar.Z"
- elog "and place tinker.tar.Z to ${DISTDIR}"
- fi
- echo
-}
-
-get_fcomp() {
- case $(tc-getFC) in
- *gfortran* )
- FCOMP="gfortran" ;;
- ifort )
- FCOMP="ifc" ;;
- * )
- FCOMP=$(tc-getFC) ;;
- esac
-}
-
-pkg_setup() {
- fortran-2_pkg_setup
- get_fcomp
- # currently amd64 is only supported with gfortran
- if [[ "${ARCH}" == "amd64" ]] && [[ ${FCOMP} != *gfortran* ]];
- then die "You will need gfortran to compile gamess on amd64"
- fi
-
- # note about qmmm-tinker
- if use qmmm-tinker; then
- einfo "By default MM subsistem is restricted to 1000 atoms"
- einfo "if you want larger MM subsystems then you should set"
- einfo "QMMM_GAMESS_MAXMM variable to needed value in your make.conf"
- einfo "By default maximum number of atom classes types and size of"
- einfo "hessian are restricted to 250, 500 and 1000000 respectively"
- einfo "If you want larger sizes set:"
- einfo "QMMM_GAMESS_MAXCLASS"
- einfo "QMMM_GAMESS_MAXCTYP"
- einfo "QMMM_GAMESS_MAXHESS"
- einfo "in your make.conf"
- fi
-
- #note about mpi
- if use mpi; then
- ewarn ""
- ewarn "You should adjust rungms script for your mpi implentation"
- ewarn "because deafult one will not work"
- ewarn ""
- fi
-}
-
-src_unpack() {
- unpack ${A}
-
- if use qmmm-tinker; then
- mv tinker gamess/ || die "failed to move tinker directory"
- fi
-}
-
-src_prepare() {
- tc-export PKG_CONFIG
- # apply LINUX-arch patches to gamess makesfiles
- epatch "${FILESDIR}/${P}.gentoo.patch"
- # select arch
- # NOTE: please leave lked alone; it should be good as is!!
- cd "${S}"
- local active_arch;
- if [[ "${ARCH}" == "amd64" ]]; then
- active_arch="linux64";
- else
- active_arch="linux32";
- fi
-
- # for hardened-gcc let't turn off ssp, since it breakes
- # a few routines
- if use pax_kernel && [[ ${FCOMP} == g77 ]]; then
- FFLAGS="${FFLAGS} -fno-stack-protector-all"
- fi
-
- # Enable mpi stuff
- if use mpi; then
- sed -e "s:set COMM = sockets:set COMM = mpi:g" \
- -i ddi/compddi || die "Enabling mpi build failed"
- sed -e "s:MPI_INCLUDE_PATH = ' ':MPI_INCLUDE_PATH = '-I/usr/include ':g" \
- -i ddi/compddi || die "Enabling mpi build failed"
- sed -e "s:MSG_LIBRARIES='../ddi/libddi.a -lpthread':MSG_LIBRARIES='../ddi/libddi.a -lmpi -lpthread':g" \
- -i lked || die "Enabling mpi build failed"
- fi
-
- # enable NEO
- if use neo; then
- sed -e "s:NEO=false:NEO=true:" -i compall lked || \
- die "Failed to enable NEO code"
- else
- sed -e "s:NEO=true:NEO=false:" -i compall lked || \
- die "Failed to disable NEO code"
- fi
- # enable GAMESS-qmmm
- if use qmmm-tinker; then
- epatch "${FILESDIR}/${PN}-qmmm-tinker-fix-idate.patch"
- sed -e "s:TINKER=false:TINKER=true:" -i compall lked || \
- die "Failed to enable TINKER code"
- if [ "x$QMMM_GAMESS_MAXMM" == "x" ]; then
- einfo "No QMMM_GAMESS_MAXMM set. Using default value = 1000"
- else
- einfo "Setting QMMM_GAMESS_MAXMM to $QMMM_GAMESS_MAXMM"
- sed -e "s:maxatm=1000:maxatm=$QMMM_GAMESS_MAXMM:g" \
- -i tinker/sizes.i \
- || die "Setting QMMM_GAMESS_MAXMM failed"
- sed -e "s:MAXATM=1000:MAXATM=$QMMM_GAMESS_MAXMM:g" \
- -i source/inputb.src \
- || die "Setting QMMM_GAMESS_MAXMM failed"
- fi
- if [ "x$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=$QMMM_GAMESS_MAXHESS:g" \
- -i tinker/sizes.i \
- || die "Setting QMMM_GAMESS_MAXHESS failed"
- fi
- fi
- # create proper activate sourcefile
- cp "./tools/actvte.code" "./tools/actvte.f" || \
- die "Failed to create actvte.f"
- sed -e "s/^\*UNX/ /" -i "./tools/actvte.f" || \
- die "Failed to perform UNX substitutions in actvte.f"
-
- # fix GAMESS' compall script to use proper CC
- sed -e "s|\$CCOMP -c \$extraflags source/zunix.c|$(tc-getCC) -c \$extraflags source/zunix.c|" \
- -i compall || die "Failed setting up compall script"
-
- # insert proper FFLAGS into GAMESS' comp makefile
- # in case we're using ifc let's strip all the gcc
- # specific stuff
- if [[ ${FCOMP} == "ifort" ]]; then
- sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS} -quiet'/" \
- -i comp || die "Failed setting up comp script"
- elif ! use x86; then
- sed -e "s/-malign-double //" \
- -e "s/gentoo-OPT='-O2'/OPT='${FFLAGS}'/" \
- -i comp || die "Failed setting up comp script"
- else
- sed -e "s/gentoo-OPT = '-O2'/OPT = '${FFLAGS}'/" \
- -i comp || die "Failed setting up comp script"
- fi
-
- # fix up GAMESS' linker script;
- 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)'/" \
- -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_BUILD_DIR $WORKDIR/gamess
- setenv GMS_TARGET $active_arch
- setenv GMS_FORTRAN $FCOMP
- setenv GMS_GFORTRAN_VERNO 4.7
- setenv GMS_MATHLIB atlas
- setenv GMS_MATHLIB_PATH /usr/$(get_libdir)/atlas
- setenv GMS_DDI_COMM sockets
- EOF
-
-}
-
-src_compile() {
- # build actvte
- cd "${S}"/tools
- ${FCOMP} -o actvte.x actvte.f || \
- die "Failed to compile actvte.x"
-
- # for hardened (PAX) users and ifc we need to turn
- # MPROTECT off
- if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then
- pax-mark -PemRxS actvte.x
- fi
-
- # build gamess
- cd "${S}"
- ./compall || die "compall failed"
-
- # build the ddi TCP/IP socket stuff
- cd ${S}/"ddi"
- ./compddi || die "compddi failed"
-
- # finally, link it all together
- cd "${S}"
- ./lked || die "lked failed"
-
- # for hardened (PAX) users and ifc we need to turn
- # MPROTECT off
- if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then
- pax-mark -PemRxS ${PN}.00.x
- fi
-}
-
-src_install() {
- # the executables
- dobin ${PN}.00.x rungms gms-files.csh \
- || die "Failed installing binaries"
- if use !mpi; then
- dobin ddi/ddikick.x \
- || die "Failed installing binaries"
- fi
-
- # the docs
- dodoc *.DOC qmnuc/*.DOC
-
- # install ericftm
- insinto /usr/share/${PN}
- doins auxdata/ericfmt.dat
-
- # install mcpdata
- insinto /usr/share/${PN}/MCP
- doins auxdata/MCP/*
-
- # install BASES
- insinto /usr/share/${PN}/BASES
- doins auxdata/BASES/*
-
- # install QUANPOL
- insinto /usr/share/${PN}/QUANPOL
- doins auxdata/QUANPOL/*
-
- # install tinker params in case of qmmm
- if use qmmm-tinker ; then
- dodoc tinker/simomm.doc
- insinto /usr/share/${PN}
- doins -r tinker/params51
- fi
-
- # install the tests the user should run, and
- # fix up the runscript; also grab a copy of rungms
- # so the user is ready to run the tests
- insinto /usr/share/${PN}/tests
- insopts -m0644
- doins -r tests/*
- insopts -m0744
- doins runall
- #doins tools/checktst/checktst tools/checktst/chkabs || \
- # die "Failed to install main test checker"
- #doins tools/checktst/exam* || \
- # die "Failed to install individual test files"
-
- insinto /usr/share/${PN}/neotests
- insopts -m0644
- doins -r qmnuc/neotests/*
-}
-
-pkg_postinst() {
- echo
- einfo "Before you use GAMESS for any serious work you HAVE"
- einfo "to run the supplied test files located in"
- einfo "/usr/share/gamess/tests and check them thoroughly."
- einfo "Otherwise all scientific publications resulting from"
- einfo "your GAMESS runs should be immediately rejected :)"
- einfo "To do so copy the content of /usr/share/gamess/tests"
- einfo "to some temporary location and execute './runall'. "
- einfo "Then run the checktst script in the same directory to"
- einfo "validate the tests."
- einfo "Please consult TEST.DOC and the other docs!"
-
- if [[ ${FCOMP} == "ifort" ]]; then
- echo
- ewarn "IMPORTANT NOTE: We STRONGLY recommend to stay away"
- ewarn "from ifc-9.0 for now and use the ifc-8.1 series of"
- ewarn "compilers UNLESS you can run through ALL of the "
- ewarn "test cases (see above) successfully."
- fi
-
- echo
- einfo "If you want to run on more than a single CPU"
- einfo "you will have to acquaint yourself with the way GAMESS"
- einfo "does multiprocessor runs and adjust rungms according to"
- einfo "your target network architecture."
- echo
-}
diff --git a/sci-chemistry/gamess/gamess-20141205.1.ebuild b/sci-chemistry/gamess/gamess-20161808.1.ebuild
index 1fb80b763..8f62aa664 100644
--- a/sci-chemistry/gamess/gamess-20141205.1.ebuild
+++ b/sci-chemistry/gamess/gamess-20161808.1.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
inherit eutils fortran-2 flag-o-matic pax-utils toolchain-funcs
@@ -36,7 +36,7 @@ S="${WORKDIR}/${PN}"
RESTRICT="fetch"
GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html"
-GAMESS_VERSION="5 DEC 2014 (R1)"
+GAMESS_VERSION="18 AUG 2016 (R1)"
pkg_nofetch() {
echo
@@ -106,6 +106,7 @@ src_prepare() {
tc-export PKG_CONFIG
# apply LINUX-arch patches to gamess makesfiles
epatch "${FILESDIR}/${P}.gentoo.patch"
+ eapply_user
# select arch
# NOTE: please leave lked alone; it should be good as is!!
cd "${S}"