[sci-chemistry/gamess] Version bump. Fixed bugs #375803 #386839

(Portage version: 2.2.0_alpha67/cvs/Linux x86_64)

6 files changed, 66 insertions, 224 deletions

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 <alexxy@gentoo.org>
+  -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 <alexxy@gentoo.org> gamess-20101001.3-r1.ebuild:
   Fix patch name
diff --git a/sci-chemistry/gamess/files/gamess-20101001.3.gentoo.patch b/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 ($MODULE == zheev)  set OPT='-O0'
-    set echo
-@@ -1558,7 +1558,7 @@
+@@ -1617,7 +1617,7 @@
     case gfortran:
  #           -finit-real=<zero|inf|-inf|nan>  could be interesting debug opt
  #           -fno-automatic forces static storage of all local variables
 -      set OPT='-O2'
 +      set gentoo-OPT = '-O2'
+       if (".$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
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 @@
 	<herd>sci-chemistry</herd>
 	<use>
 		<flag name='neo'>Enable NEO for nuclear basis support</flag>
+		<flag name='pax_kernel'>Make this package work on PAX kernels</flag>
 		<flag name='qmmm-tinker'>Enable tinker qmmm code</flag>
 	</use>
 </pkgmetadata>