From 1f68c102027c8e76ad5409a0475135b74365641f Mon Sep 17 00:00:00 2001 From: Alexey Shvetsov Date: Thu, 13 Oct 2011 12:00:38 +0000 Subject: [PATCH] [sci-chemistry/gamess] Version bump. Fixed bugs #375803 #386839 Package-Manager: portage-2.2.0_alpha67/cvs/Linux x86_64 --- sci-chemistry/gamess/ChangeLog | 10 +- sci-chemistry/gamess/Manifest | 39 ++-- ...o.patch => gamess-20110811.1.gentoo.patch} | 219 +++--------------- .../gamess/files/gamess-checktst.patch | 14 +- .../gamess/files/gamess-neo-fix.patch | 24 -- ...1.3-r1.ebuild => gamess-20110811.1.ebuild} | 22 +- sci-chemistry/gamess/metadata.xml | 1 + 7 files changed, 85 insertions(+), 244 deletions(-) rename sci-chemistry/gamess/files/{gamess-20101001.3.gentoo.patch => gamess-20110811.1.gentoo.patch} (51%) delete mode 100644 sci-chemistry/gamess/files/gamess-neo-fix.patch rename sci-chemistry/gamess/{gamess-20101001.3-r1.ebuild => gamess-20110811.1.ebuild} (94%) diff --git a/sci-chemistry/gamess/ChangeLog b/sci-chemistry/gamess/ChangeLog index a5b3458515af..d5776016713e 100644 --- a/sci-chemistry/gamess/ChangeLog +++ b/sci-chemistry/gamess/ChangeLog @@ -1,6 +1,14 @@ # ChangeLog for sci-chemistry/gamess # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/ChangeLog,v 1.55 2011/10/08 11:50:31 alexxy Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/ChangeLog,v 1.56 2011/10/13 12:00:38 alexxy Exp $ + +*gamess-20110811.1 (13 Oct 2011) + + 13 Oct 2011; Alexey Shvetsov + -gamess-20101001.3-r1.ebuild, -files/gamess-20101001.3.gentoo.patch, + +gamess-20110811.1.ebuild, +files/gamess-20110811.1.gentoo.patch, + -files/gamess-neo-fix.patch, files/gamess-checktst.patch, metadata.xml: + Version bump. Fixed bugs #375803 #386839 08 Oct 2011; Alexey Shvetsov gamess-20101001.3-r1.ebuild: Fix patch name diff --git a/sci-chemistry/gamess/Manifest b/sci-chemistry/gamess/Manifest index 2d4c3fe0355b..ac3e4f5dece0 100644 --- a/sci-chemistry/gamess/Manifest +++ b/sci-chemistry/gamess/Manifest @@ -1,29 +1,28 @@ -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 -AUX gamess-20101001.3.gentoo.patch 15443 RMD160 8878d81b1aacbfe285207cc9e09b0cc2483445ba SHA1 1deedad5156097d195adb6061c39f46b39176e1d SHA256 2da43dac3c2a720dc6340e1bf29079da84c08e9dbbd1cbe899c523ecac58ff35 -AUX gamess-checktst.patch 440 RMD160 4e874434484428b60698db8c059549f9507e456d SHA1 bf2ade75b68db62505b959368a06ec1f9c72559f SHA256 7f10da3548124203cd578dc93f4a52f318b7b17f3a9efb1847bfa4844faab6fb -AUX gamess-neo-fix.patch 824 RMD160 66e303dd6912150c262d6c00eadb6ac40e5520e6 SHA1 20feb714ec61c23b184ad2a2ddc64517b5e5cabf SHA256 2dafa7af0f6d2872f2e274d36c373735cedd0889a41ab6a175cbf22f7e850452 +AUX gamess-20110811.1.gentoo.patch 9542 RMD160 91279ec8c39826b150c1c0b171100ffe332cf8f5 SHA1 ada492d7cc5048ee245d5dfa00df6a530484a952 SHA256 72f5da6ad4cfd260d1061e337ce60da2f0924153d599196f56b6291e00dc7042 +AUX gamess-checktst.patch 724 RMD160 33757849fb863fc2a85bd728b107c92ccc507be8 SHA1 5a37731a5e11aca9d426604b6404899d776294ab SHA256 48b00306f39158a8ba4d9a6bcbaee3bf8d8abe4367b30d91e3c5f5d21f64e018 AUX gamess-qmmm-tinker-fix-idate.patch 611 RMD160 cdcf164d80f36db3a631659d85b7e099118c971d SHA1 3e29aed5b0933ebe598f8d2c9d7315c4f48da0be SHA256 db62d639b96f64493754baa5565322ff21b295e8abee40fca270d9c95dfaa435 -DIST gamess-20101001.3.tar.gz 21075234 RMD160 f1b46bb51a74de8a6c60d2caa9b0840573b9b372 SHA1 1840046e1fb50cea41b13e925130f450b5075cd9 SHA256 e34285fb20df26c78744a09dbeba34554b85b92f8138a022e2a156a1776e6e3b +DIST gamess-20110811.1.tar.gz 21105973 RMD160 29ca747d3a3a78b593add370f5bcc33ab691fe2e SHA1 6edbc6c4cb5c1864870f2275df4b3eb1e14adac5 SHA256 b7b7af0eb141c140da31bcd9ef29fbafd82fbe45c087cadd7948d4c0a3cefe57 DIST tinker.tar.Z 1902051 RMD160 b467fe3231d469309c1d48d29ee15975a3f305c0 SHA1 e1e9fde440de1854a8b49b6ae2259df27e871651 SHA256 7c52454ade7dd81d1b70a7e7722eda3672c644a3ba67ab444824a0212b4a7a8c -EBUILD gamess-20101001.3-r1.ebuild 10356 RMD160 4a98ae51ff75a1554ca1c197dfd7ea71e69acb2c SHA1 56ef68e8e6f61b398b1d0626a74e1d807dc47c07 SHA256 4d3c63fe23f4e986b9f03c7bc73735aa19dd29f96efc60d2878b6e75d9cfa7f7 -MISC ChangeLog 11445 RMD160 8cddc21b8ac77ee29229c883095b32a956175e18 SHA1 f6353e78047dfb215895a06717c78f7211c82d11 SHA256 7a991c7b7d7c7b6addad39cd5569639b7e190158dc33605a290a5795eb60c87d -MISC metadata.xml 398 RMD160 f441866b09b98748e6380af772f89c892b8d316c SHA1 5a160b87bd8197bb7983873169ee3d12540dd2b0 SHA256 b70b10d57db92e0c8058ea30dd6c078241fae2590d19242f42286210e47a4165 +EBUILD gamess-20110811.1.ebuild 10183 RMD160 8fa8b9fd7314092fd406b7381b9cb54333db5557 SHA1 94e9a489ad145ae2c360c1ed283b8bb40d212de2 SHA256 f6fcbb0e701d3dc825d2b46e788d3a8560d801d5dc8ce4bdd6ec445942ebd8d4 +MISC ChangeLog 11787 RMD160 b09ba772d0c82143451acee2f6d695b7de17a7b6 SHA1 61f04646f2161e2a7e56b8586c7f7751827ee6bd SHA256 0cf30db648eb199fda39353fe81da5b329f9e642d11d25af9beb3cecc3272237 +MISC metadata.xml 469 RMD160 9cc783399378e569bfb8cdeeff543bcae39b470f SHA1 3f07222bf4249de8d4be93bb1c9e902189ad66f3 SHA256 0d6e4ec21b044006f67afde991de455be6e1a5d642b6fd5da804c3bd4f0d8e24 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.18 (GNU/Linux) -iQIcBAEBCAAGBQJOkDkhAAoJEOf+E+/4L5LmVn8P/jpFYzh7rGOS5sZSLpZw3ZeV -q2AnxQp83HMcU4anY+1pzidyJUB3Zbi9LaBkAwk5NW8JHjGl44nSrB09eHlK7WxZ -HjDyekgWWADq7ifrtDzO/l0TaeOmJYBYc7wR22FMMdlhTlgINKWKbxxOZz2pC3MM -RtbDu5tZNE2aP9k4QiGsMdv9dIqun8ekD/ms+VSLgGn59p8CpoLiCOH6PJhBaWOe -odEcWIxVSEY9tpADENg+tZjWeWyMRS84MRRGJUBArGauOCr+zgnkcNtf/m819aPO -ULwppKU+w9UHLJgCz04whVUutDCk9JORH89Bhcrj9P18r3a4/m7QK/arnV89rWvm -jCe3J7jpoqUucSb9oBWESL5a+P84NSUI349cjgoD9fHY52v14tFmeYrBGYOsfTuZ -lKbNh0q0t1xM+t51GaJZy4YCuQ2W5hIJuY4hlg6BYQ6sdg2IE2xnQc+yXJqETV5R -DKQrFtXul0Z1fJupkGlHuJXnG4z8bc76784RHaDki77QVmKMaMvJffjkDJEb/UxQ -3NFjSerrLfXxm98KPu8YtclbpgZ2ZLSZWUhEFuR/Blh2K7vBKqWqmhqq+jbW2EpP -sf5Wxw+GnYgNnQGRjt2Ohq/e0hj3dm6G2HtOGNfQit8+krBgwTAYJ8S0qE9y71Qv -r5BPskvNDuRykQasVgAm -=BvFe +iQIcBAEBCAAGBQJOltKgAAoJEOf+E+/4L5LmFXoP/jADUlxmjXPpwYcRxCBBj4XU +1BIMKkaFAyo0LPD+nOFyYmpIlU+3DRnUpvoK/TdRw4DPVJ/Ymp7mVvapJGE7a/cq ++eNj7tGJcVO0H6iexHlENTfBuqMlHKXeKEOusAKUd+VrPYzH2rvuGSX00ARlbpf4 +0xKXOAyd0H5it1+dV1oad07BLC6Rjpp4PYq/unanfCuZ7P3WDJQHLuEUoWFtduEw +UirZp+zSF9rk9LS1fKRHHX51MMG99eI7fQr+LnB1L+Pg7sJxaJ1cNltHFasYQiQd +ffP6MLhajCB3I59kSX8kx4XSDSkx+lG680Rj9FdBwxB4FXf48KKXtRyZ8OU79xxt +5l1OZttcUxVqIuvJnlqxZDeNBiCRcBO4e0ll82h2fsgtRD0S22MHFwVwvRD/5onf +sprUwxNj9UETkzSuqpZZT+Zh88A7mtivH8lHIhFkVhhGMnbrGr4QFAKJsbZ+RgJ7 +DdIAaFVP+q/g6Cj7hQLgBOPDE4pQ1wGJk3dtXsdx6ucC0grLfnRSMclrJ5JdkPiJ +l82M1nB96NwgnrLwmuHQTIHIbIaOhiDt1nWBUMusFAXFjiBE0cos0Asswv6GtUhi +Z9Mg/2u/MkHXv7Mbl+XqgPyub+VwdmvX7AECUvHeSnsNMKR7A5CoQO6+WAXEJofo +PPiFLuPgMC67MxlaJo1N +=KUzP -----END PGP SIGNATURE----- diff --git a/sci-chemistry/gamess/files/gamess-20101001.3.gentoo.patch b/sci-chemistry/gamess/files/gamess-20110811.1.gentoo.patch similarity index 51% rename from sci-chemistry/gamess/files/gamess-20101001.3.gentoo.patch rename to sci-chemistry/gamess/files/gamess-20110811.1.gentoo.patch index fe352395565a..adf2e3583c6d 100644 --- a/sci-chemistry/gamess/files/gamess-20101001.3.gentoo.patch +++ b/sci-chemistry/gamess/files/gamess-20110811.1.gentoo.patch @@ -1,7 +1,7 @@ diff -urN gamess.orig/comp gamess/comp ---- gamess.orig/comp 2010-08-05 19:04:54.000000000 +0400 -+++ gamess/comp 2010-12-07 20:29:13.000000000 +0300 -@@ -1390,7 +1390,7 @@ +--- gamess.orig/comp 2011-08-11 17:37:48.000000000 +0200 ++++ gamess/comp 2011-10-11 15:17:23.349829478 +0200 +@@ -1444,7 +1444,7 @@ # g77 does not support FORTRAN logical units above 99, or 128 bit math. # case g77: @@ -10,7 +10,7 @@ diff -urN gamess.orig/comp gamess/comp 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 -@@ -1420,7 +1420,7 @@ +@@ -1474,7 +1474,7 @@ # -std=legacy suppresses warnings about use of f77 constructs. # case gfortran: @@ -19,37 +19,37 @@ diff -urN gamess.orig/comp gamess/comp if ($MODULE == zheev) set OPT='-O0' # defensive compiling if ($MODULE == pcmcv2) set OPT='-O1' # EFP+CPCM, ala Francois, v4.1.2 if (($MODULE == qeigen) || ($MODULE == int2c)) then -@@ -1446,7 +1446,7 @@ +@@ -1500,7 +1500,7 @@ # optimizations in 32 bit mode, as a function of the ifort version. # case ifort: - set OPT = '-O3' + set gentoo-OPT = '-O2' if ($MODULE == delocl) set OPT='-O0' # from Cheol + if ($MODULE == prpamm) set OPT='-O0' # for exam13 if ($MODULE == zheev) set OPT='-O0' - set echo -@@ -1558,7 +1558,7 @@ +@@ -1617,7 +1617,7 @@ case gfortran: # -finit-real= could be interesting debug opt # -fno-automatic forces static storage of all local variables - set OPT='-O2' + set gentoo-OPT = '-O2' + if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS" if ($MODULE == zheev) set OPT='-O0' # defensive compiling if (($MODULE == qeigen) || ($MODULE == int2c)) then - mv -f $MODULE.f $MODULE.junk -@@ -1587,7 +1587,7 @@ +@@ -1648,7 +1648,7 @@ # -WB means warn but don't fail on out-of-bounds array references # -ftz flushes underflow results to zero # - set OPT = '-O2' + set gentoo-OPT = '-O2' + if (".$GMS_DEBUG_FLAGS" != .) set OPT="$GMS_DEBUG_FLAGS" # alas, I'm so tired of hearing about so many versions failing to # diagonalize, that this time critical code is run w/o optimization. - # Very many (all?) ifort versions have problems with eigen.src. diff -urN gamess.orig/compall gamess/compall ---- gamess.orig/compall 2010-10-01 19:37:31.000000000 +0400 -+++ gamess/compall 2010-12-07 20:21:55.000000000 +0300 -@@ -84,15 +84,14 @@ +--- gamess.orig/compall 2011-05-17 22:53:33.000000000 +0200 ++++ gamess/compall 2011-10-11 12:13:30.041087251 +0200 +@@ -84,12 +84,11 @@ endif endif if ($TARGET == linux32) set extraflags='-DLINUX32' @@ -65,15 +65,11 @@ diff -urN gamess.orig/compall gamess/compall + if ($chip == ia64) set extraflags='-DLINUX64' # this always 64 bits endif if ($TARGET == mac32) set extraflags='-DLINUX32' --if ($TARGET == mac64) set extraflags='-DLINUX64 -m64 -I/usr/include/malloc' -+if ($TARGET == mac64) set extraflags='-DLINUX64 -m64 -I/usr/include/malloc' - if ($TARGET == necsx) set extraflags='-DNECSX -size_t64' - if ($TARGET == sgi32) set extraflags='-DSGI32 -n32' - if ($TARGET == sgi64) set extraflags='-DSGI64 -64' + if ($TARGET == mac64) set extraflags='-DLINUX64 -m64 -I/usr/include/malloc' diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi ---- gamess.orig/ddi/compddi 2010-06-24 02:35:20.000000000 +0400 -+++ gamess/ddi/compddi 2010-12-07 20:21:55.000000000 +0300 -@@ -628,7 +628,7 @@ +--- gamess.orig/ddi/compddi 2011-02-15 21:31:30.000000000 +0100 ++++ gamess/ddi/compddi 2011-10-11 12:23:45.513796580 +0200 +@@ -634,7 +634,7 @@ set FORTRAN=$GMS_FORTRAN # might be g77, gfortran, ifort, pgf77, f2c @@ -82,7 +78,7 @@ diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./" set CLIBS = "-lpthread" -@@ -681,7 +681,7 @@ +@@ -687,7 +687,7 @@ set ARCH='-m64' if (`uname -p` == ia64) set ARCH='' @@ -92,8 +88,8 @@ diff -urN gamess.orig/ddi/compddi gamess/ddi/compddi set CLIBS = "-lpthread" diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess/ddi/kickoff/ddikick.c ---- gamess.orig/ddi/kickoff/ddikick.c 2008-05-06 14:16:12.000000000 +0400 -+++ gamess/ddi/kickoff/ddikick.c 2010-12-07 20:21:55.000000000 +0300 +--- gamess.orig/ddi/kickoff/ddikick.c 2008-05-06 12:16:12.000000000 +0200 ++++ gamess/ddi/kickoff/ddikick.c 2011-10-11 12:25:11.862714681 +0200 @@ -105,7 +105,7 @@ remoteshell = argv[++i]; } else { @@ -104,8 +100,8 @@ diff -urN gamess.orig/ddi/kickoff/ddikick.c gamess/ddi/kickoff/ddikick.c } diff -urN gamess.orig/lked gamess/lked ---- gamess.orig/lked 2010-10-01 19:37:05.000000000 +0400 -+++ gamess/lked 2010-12-07 20:26:57.000000000 +0300 +--- gamess.orig/lked 2011-08-11 17:41:02.000000000 +0200 ++++ gamess/lked 2011-10-11 12:26:38.564634821 +0200 @@ -53,7 +53,7 @@ # # 3. optional Nuclear-Electronic Orbital method, using NEO code @@ -114,7 +110,7 @@ diff -urN gamess.orig/lked gamess/lked +set NEO=true # # 4. optional Nvidia/CUDA code, for closed shell SCF Fock construction - # see ~/gamess/libqc/aaa.readme.1st for more information + # see ~/gamess/libcchem/aaa.readme.1st for more information @@ -356,17 +356,17 @@ switch ($GMS_FORTRAN) case g77: @@ -174,7 +170,7 @@ diff -urN gamess.orig/lked gamess/lked # this auxiliary library seems to have disappeared in ifort 10 set FORTLIBS=' ' if($GMS_IFORT_VERNO < 10) set FORTLIBS='-Vaxlib' -@@ -549,12 +544,7 @@ +@@ -556,12 +551,7 @@ # ln -s liblapack_atlas.so.3.0 liblapack.so # ln -s liblapack.so.3.0 liblapack.so # It is strange the RPM's don't do these soft links for us. @@ -189,8 +185,8 @@ diff -urN gamess.orig/lked gamess/lked breaksw diff -urN gamess.orig/runall gamess/runall ---- gamess.orig/runall 2009-02-28 02:57:18.000000000 +0300 -+++ gamess/runall 2010-12-07 20:21:55.000000000 +0300 +--- gamess.orig/runall 2009-02-28 00:57:18.000000000 +0100 ++++ gamess/runall 2011-10-11 12:27:32.195586568 +0200 @@ -10,7 +10,6 @@ # # Only the following two lines need to be customized: @@ -209,8 +205,8 @@ diff -urN gamess.orig/runall gamess/runall @ i++ end diff -urN gamess.orig/rungms gamess/rungms ---- gamess.orig/rungms 2010-08-17 17:46:59.000000000 +0400 -+++ gamess/rungms 2010-12-07 20:36:43.000000000 +0300 +--- gamess.orig/rungms 2011-08-04 21:03:11.000000000 +0200 ++++ gamess/rungms 2011-10-11 12:30:05.244448126 +0200 @@ -55,7 +55,7 @@ # one for LoadLeveler "ll-gms" on the IBM SP line. # @@ -220,18 +216,16 @@ diff -urN gamess.orig/rungms gamess/rungms # 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 -@@ -139,22 +139,22 @@ - # c) The NUCBAS directory is for the NEO plug-in code, see its documentation - # Note that you must edit a+b, but will probably skip c+d. - # ASCII input files (see explanation above) +@@ -144,7 +144,7 @@ + # used by the NEO method. See NEO's documentation for more details. + # + set echo -setenv AUXDATA ~mike/gamess/auxdata +setenv AUXDATA /usr/share/gamess setenv EXTBAS /dev/null setenv NUCBAS /dev/null - # - set echo - # - setenv ERICFMT $AUXDATA/ericfmt.dat + setenv POSBAS /dev/null +@@ -153,12 +153,12 @@ setenv MCPPATH $AUXDATA/MCP setenv BASPATH $AUXDATA/BASES setenv QUANPOL $AUXDATA/QUANPOL @@ -249,7 +243,7 @@ diff -urN gamess.orig/rungms gamess/rungms setenv AOINTS $SCR/$JOB.F08 setenv MOINTS $SCR/$JOB.F09 setenv DICTNRY $SCR/$JOB.F10 -@@ -321,7 +321,7 @@ +@@ -347,7 +347,7 @@ if (null$4 == null) set ELGNAME=ELGFILE set echo setenv AOINTS $SCR/$ELGNAME.F08 @@ -258,7 +252,7 @@ diff -urN gamess.orig/rungms gamess/rungms setenv ELGDAT $SCR/$ELGNAME.F71 setenv ELGPAR $SCR/$ELGNAME.F72 setenv ELGCUT $SCR/$ELGNAME.F74 -@@ -474,7 +474,7 @@ +@@ -500,7 +500,7 @@ if ($os == AIX) set GMSPATH=/u1/mike/gamess if ($os == Darwin) set GMSPATH=/Users/mike/desktop/gamess if ($os == HP-UX) set GMSPATH=/zr/mike/gamess @@ -267,144 +261,3 @@ diff -urN gamess.orig/rungms gamess/rungms if ($os == OSF1) set GMSPATH=/in/mike/gamess if ($os == SunOS) set GMSPATH=/hf/mike/gamess # special compilation for Sun E450 uSPARC (uname also= SunOS) -@@ -543,85 +543,6 @@ - set HOSTLIST=(`hostname`) - endif - # --# 2. This is an example of how to run on a 4-way SMP enclosure, --# where all CPUs (aka COREs) are inside a -single- NODE. --# The example is repeated for some nodes we use as 2-way's. --# At other locations, you may wish to consider some of the examples --# that follow below, after commenting out this ISU specific part. -- if ($NCPUS > 1) then -- switch (`hostname`) -- case ti.msg.chem.iastate.edu: -- case cd.msg.chem.iastate.edu: -- case zn.msg.chem.iastate.edu: -- case ni.msg.chem.iastate.edu: -- case co.msg.chem.iastate.edu: -- case pb.msg.chem.iastate.edu: -- case bi.msg.chem.iastate.edu: -- case po.msg.chem.iastate.edu: -- case at.msg.chem.iastate.edu: -- case sc.msg.chem.iastate.edu: -- if ($NCPUS > 4) set NCPUS=4 -- set NNODES=1 -- set HOSTLIST=(`hostname`:cpus=$NCPUS) -- breaksw -- case se.msg.chem.iastate.edu: -- case sb.msg.chem.iastate.edu: -- case br.msg.chem.iastate.edu: -- if ($NCPUS > 2) set NCPUS=2 -- set NNODES=1 -- set HOSTLIST=(`hostname`:cpus=$NCPUS) -- breaksw -- default: -- echo I do not know how to run this node in parallel. -- exit 20 -- endsw -- endif --# --# 3. How to run in a single computer, namely the "localhost", so --# this computer needn't have a proper Internet name. --# This example also presumes SysV was deliberately *not* chosen --# when DDI was compiled, so that host names have to be repeated, --# instead of using the simpler localhost:cpus=$NCPU form. --# --# This example is appropriate for use with the pre-compiled --# Apple binary from our web site, provided it is uncommented, --# and the passage #2 just above is deleted or commented out. --# --#-- set HOSTLIST=() --#-- @ n=1 --#-- while ($n <= $NCPUS) --#-- set HOSTLIST=($HOSTLIST localhost) --#-- @ n++ --#-- end --#-- set NNODES=$NCPUS --# --# 4. A phony example, of four dual processors (arbitrary names) --# Since their names never change, we just can just specify them. --# Note that we can use a short name like 'bb' if and only if --# system name resolution can map them onto the true host names. -- if (`hostname` == aa.msg.chem.iastate.edu) then -- set NCPUS=8 -- set NNODES=4 -- set HOSTLIST=(aa:cpus=2 bb:cpus=2 cc:cpus=2 dd:cpus=2) -- endif --# --# 5. An example of 16 uniprocessor boxes in a Beowulf-type cluster. --# Because they are uniprocessors, we just set NNODES = NCPUS. --# Their host names fall into the pattern fly1 to fly16, --# which we can turn into a HOSTLIST with a small loop. -- if (`hostname` == fly1.fi.ameslab.gov) then -- set NNODES=$NCPUS -- set HOSTLIST=() -- set nmax=$NCPUS -- if ($nmax > 16) set nmax=16 -- @ CPU=1 -- while ($CPU <= $nmax) -- set HOSTLIST=($HOSTLIST fly$CPU) -- @ CPU++ -- end -- unset $CPU -- endif --# - # 6. Scalable Computing Lab's clusters running PBS batch queues. - # Here the task is to manipulate the dynamically assigned host - # names into the HOSTLIST string for the kickoff program, -@@ -604,8 +530,6 @@ - # - # The IBM cluster has two Gigabit adapters in each 4-way SMP, - # while the AXP cluster is based on a Myrinet network. -- if (`uname` == AIX) set NETEXT=".gig,.gig2" -- if (`uname` == Linux) set NETEXT=".myri" - # - # repeated host names in the PBS host file indicate being assigned - # CPUs in the same SMP enclosure, which we must count up correctly. -@@ -636,12 +560,11 @@ - @ NNODES = 1 - @ NSMPCPU = 1 - set spacer1=":cpus=" -- set spacer2=":netext=" - while($IPROC <= $nmax) - set MYPROC=`sed -n -e "$IPROC p" $PBS_NODEFILE` - set MYPROC=`echo $MYPROC | awk '{split($0,a,"."); print a[1]}'` - if($MYPROC != $MYNODE) then -- set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU$spacer2$NETEXT) -+ set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU) - set MYNODE=$MYPROC - @ NSMPCPU = 0 - @ NNODES++ -@@ -649,13 +572,13 @@ - @ IPROC++ - @ NSMPCPU++ - end -- set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU$spacer2$NETEXT) -+ set HOSTLIST = ($HOSTLIST $MYNODE$spacer1$NSMPCPU) - endif - # - # we have now finished setting up a correct HOSTLIST. - # uncomment the next two if you are doing script debugging. --#--echo "The generated host list is" --#--echo $HOSTLIST -+ echo "The generated host list is" -+ echo $HOSTLIST - # - - # One way to be sure that the master node of each subgroup -diff -urN gamess.orig/tools/checktst/checktst gamess/tools/checktst/checktst ---- gamess.orig/tools/checktst/checktst 2008-12-30 18:33:09.000000000 +0300 -+++ gamess/tools/checktst/checktst 2010-12-07 20:21:55.000000000 +0300 -@@ -3,11 +3,6 @@ - # Compare the results of GAMESS sample jobs to pre-stored correct values. - # This script can be executed from any directory with write permissions. - # Written by D. G. Fedorov, AIST, July 20, 2004. --# --# Only the path name in the very next line needs to be customized. --# --set GMSPATH=~/gamess -- - # The Ntest outputs are assumed to be named exam01.log, exam02.log, ... - # but the user will be allowed to specify the directory containing them. - # diff --git a/sci-chemistry/gamess/files/gamess-checktst.patch b/sci-chemistry/gamess/files/gamess-checktst.patch index ee986d09d2ea..9fc1547e4540 100644 --- a/sci-chemistry/gamess/files/gamess-checktst.patch +++ b/sci-chemistry/gamess/files/gamess-checktst.patch @@ -1,6 +1,14 @@ ---- /usr/share/gamess/tests/checktst 2011-08-19 18:08:16.000000000 +0200 -+++ ./checktst 2011-08-20 00:45:59.613091738 +0200 -@@ -61,8 +61,8 @@ +--- gamess.orig/tools/checktst/checktst 2008-12-30 16:33:09.000000000 +0100 ++++ gamess/tools/checktst/checktst 2011-10-11 22:06:26.019798622 +0200 +@@ -6,7 +6,6 @@ + # + # Only the path name in the very next line needs to be customized. + # +-set GMSPATH=~/gamess + + # The Ntest outputs are assumed to be named exam01.log, exam02.log, ... + # but the user will be allowed to specify the directory containing them. +@@ -66,8 +65,8 @@ setenv tolW 0.1 setenv tolX 0.00001 diff --git a/sci-chemistry/gamess/files/gamess-neo-fix.patch b/sci-chemistry/gamess/files/gamess-neo-fix.patch deleted file mode 100644 index 299b4a0db72d..000000000000 --- a/sci-chemistry/gamess/files/gamess-neo-fix.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -urN gamess.orig/qmnuc/neo/neogrd.src gamess/qmnuc/neo/neogrd.src ---- gamess.orig/qmnuc/neo/neogrd.src 2010-06-16 22:46:15.000000000 +0400 -+++ gamess/qmnuc/neo/neogrd.src 2011-01-23 15:35:56.000000000 +0300 -@@ -1435,20 +1435,10 @@ - C - DO 790 IC = 1,MAXIC - IF(ICHARM.EQ.0) THEN -- IF(IC.LE.NAT) THEN - ZNUC = -ZAN(IC) --C ZNUC = ZAN(IC) - CX = C(1,IC) - CY = C(2,IC) - CZ = C(3,IC) -- ELSE -- IAZ=IATSP(IC-NAT) -- ZNUC = -COSZAN(IC-NAT) --C ZNUC = COSZAN(IC-NAT) -- CX = CORZAN(1,IC-NAT) -- CY = CORZAN(2,IC-NAT) -- CZ = CORZAN(3,IC-NAT) -- END IF - ELSE - ZNUC = -QCHM(ICHARM) - CX = XCHM(ICHARM) diff --git a/sci-chemistry/gamess/gamess-20101001.3-r1.ebuild b/sci-chemistry/gamess/gamess-20110811.1.ebuild similarity index 94% rename from sci-chemistry/gamess/gamess-20101001.3-r1.ebuild rename to sci-chemistry/gamess/gamess-20110811.1.ebuild index 26af09370674..354274a5001f 100644 --- a/sci-chemistry/gamess/gamess-20101001.3-r1.ebuild +++ b/sci-chemistry/gamess/gamess-20110811.1.ebuild @@ -1,10 +1,10 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/gamess-20101001.3-r1.ebuild,v 1.2 2011/10/08 11:50:31 alexxy Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/gamess/gamess-20110811.1.ebuild,v 1.1 2011/10/13 12:00:38 alexxy Exp $ EAPI="4" -inherit eutils fortran-2 toolchain-funcs flag-o-matic +inherit eutils fortran-2 flag-o-matic pax-utils toolchain-funcs DESCRIPTION="A powerful quantum chemistry package" LICENSE="gamess" @@ -20,12 +20,11 @@ SLOT="0" # 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="hardened mpi neo qmmm-tinker" +IUSE="mpi neo pax_kernel qmmm-tinker" CDEPEND=" virtual/fortran app-shells/tcsh - hardened? ( sys-apps/paxctl ) mpi? ( virtual/mpi ) virtual/blas" DEPEND="${CDEPEND} @@ -38,7 +37,7 @@ S="${WORKDIR}/${PN}" RESTRICT="fetch" GAMESS_DOWNLOAD="http://www.msg.ameslab.gov/GAMESS/License_Agreement.html" -GAMESS_VERSION="1 OCT 2010 (R3)" +GAMESS_VERSION="1 AUG 2011 (R1)" pkg_nofetch() { echo @@ -120,7 +119,7 @@ src_prepare() { # for hardened-gcc let't turn off ssp, since it breakes # a few routines - if use hardened && [[ ${FCOMP} == g77 ]]; then + if use pax_kernel && [[ ${FCOMP} == g77 ]]; then FFLAGS="${FFLAGS} -fno-stack-protector-all" fi @@ -136,7 +135,6 @@ src_prepare() { # enable NEO if use neo; then - epatch "${FILESDIR}/${PN}-neo-fix.patch" sed -e "s:NEO=false:NEO=true:" -i compall lked || \ die "Failed to enable NEO code" else @@ -233,9 +231,8 @@ src_compile() { # for hardened (PAX) users and ifc we need to turn # MPROTECT off - if [[ ${FCOMP} == "ifort" ]] && use hardened; then - /sbin/paxctl -PemRxS actvte.x 2> /dev/null || \ - die "paxctl failed on actvte.x" + if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then + pax-mark -PemRxS actvte.x fi # build gamess @@ -252,9 +249,8 @@ src_compile() { # for hardened (PAX) users and ifc we need to turn # MPROTECT off - if [[ ${FCOMP} == "ifort" ]] && use hardened; then - /sbin/paxctl -PemRxS ${PN}.00.x 2> /dev/null || \ - die "paxctl failed on actvte.x" + if [[ ${FCOMP} == "ifort" ]] && use pax_kernel; then + pax-mark -PemRxS ${PN}.00.x fi } diff --git a/sci-chemistry/gamess/metadata.xml b/sci-chemistry/gamess/metadata.xml index 1ef8f6bcb3c5..6ea2f9c7e978 100644 --- a/sci-chemistry/gamess/metadata.xml +++ b/sci-chemistry/gamess/metadata.xml @@ -8,6 +8,7 @@ sci-chemistry Enable NEO for nuclear basis support + Make this package work on PAX kernels Enable tinker qmmm code -- 2.26.2