Version bump (fixes bug #220855).

(Portage version: 2.1.5_rc7)

3 files changed, 339 insertions, 443 deletions

diff --git a/sci-chemistry/gamess/files/gamess-20060907.4.gentoo.patch b/sci-chemistry/gamess/files/gamess-20060907.4.gentoo.patch
deleted file mode 100644
index 746f778de006..000000000000
--- a/sci-chemistry/gamess/files/gamess-20060907.4.gentoo.patch
+++ /dev/null
@@ -1,221 +0,0 @@
-diff -Naur gamess/comp gamess-new/comp
---- gamess/comp	2006-11-06 10:17:54.000000000 -0500
-+++ gamess-new/comp	2006-12-13 18:06:06.000000000 -0500
-@@ -11,8 +11,8 @@
- #      linux-ia64,linux-pc,mac32,macG5,necsx,sgi32,sgi64,sun32,sun64
- #  2. Choose your GAMESS directory tree.
- #
--set TARGET=ibm64
--chdir /u1/mike/gamess
-+set TARGET=linux-pc
-+#chdir /u1/mike/gamess
- #
- #    ---- and now the script begins...
- #
-@@ -300,6 +300,7 @@
- if ($MODULE == neomp2)  set NEOCMP=true
- if ($MODULE == neosym)  set NEOCMP=true
- if ($MODULE == neotrn)  set NEOCMP=true
-+if ($MODULE == neopos)  set NEOCMP=true
- if ($NEOCMP == true && $ACTONLY != true) set SRCDIR=qmnuc/neo
- #
- #   ----- Does this module need to be activated? -----
-@@ -701,7 +702,7 @@
-    switch ($FORTRAN)
- 
-    case gfortran:
--      set OPT='-O2'
-+      set gentoo-OPT = '-O2'
-       if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
-       if (($MODULE == qeigen) || ($MODULE == int2c)) then
-          mv $MODULE.f $MODULE.junk
-@@ -1148,7 +1149,7 @@
- #   The only thing you need to change is the next line.
- #   Note: you must make the analogous choice in compddi and lked, as well.
- #
--    set FORTRAN=g77       # choose from g77, gfortran, ifort, pgf77, f2c
-+    set FORTRAN=gentoo-g77       # choose from g77, gfortran, ifort, pgf77, f2c
- #
-     switch ($FORTRAN)
- #
-@@ -1167,7 +1168,7 @@
- #   Pentium II fractionally).  None of these optimizations are used below.
- #
-    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
- #
-@@ -1203,7 +1204,7 @@
- #      -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 == qeigen) || ($MODULE == int2c)) then
-       mv $MODULE.f $MODULE.junk
-@@ -1230,7 +1231,7 @@
- #    but that may cause certain ifort versions to fail on some files.
- #
-    case ifort:
--   set OPT = '-O3'
-+   set gentoo-OPT = '-O2'
-    if ($MODULE == delocl) set OPT='-O0'  # from Cheol
-    if ($MODULE == zheev)  set OPT='-O0'
-    set echo
-diff -Naur gamess/compall gamess-new/compall
---- gamess/compall	2006-11-19 18:02:49.000000000 -0500
-+++ gamess-new/compall	2006-12-13 09:13:42.000000000 -0500
-@@ -12,8 +12,8 @@
- #      linux-ia64,linux-pc,mac32,macG5,necsx,sgi32,sgi64,sun32,sun64
- #  2. Choose your GAMESS directory tree.
- #
--set TARGET=ibm64
--chdir /u1/mike/gamess
-+set TARGET=linux-pc
-+#chdir /u1/mike/gamess
- #
- #  ----- and now the script begins...
- #
-diff -Naur gamess/ddi/compddi gamess-new/ddi/compddi
---- gamess/ddi/compddi	2006-08-30 09:34:15.000000000 -0400
-+++ gamess-new/ddi/compddi	2006-12-13 09:14:23.000000000 -0500
-@@ -14,7 +14,7 @@
- #      fuji-pp32,fuji-pp64,hpux32,hpux64,ibm32,ibm64,ibm64-sp,ibm-bg,
- #      linux-ia64,linux-pc,mac32,macG5,necsx,sgi32,sgi64,sun32,sun64
- #
--         set TARGET = ibm64
-+         set TARGET = linux-pc
- 
- #  2. Choose DDI communication layer, the only legal values are
- #                   sockets,mixed,mpi,shmem,lapi
-@@ -488,9 +488,9 @@
- #
-   if($TARGET == linux-pc) then
- 
--     set FORTRAN=g77       # choose from g77, gfortran, ifort, pgf77, f2c
-+     set FORTRAN=gentoo-g77       # choose from g77, gfortran, ifort, pgf77, f2c
- 
--     set CC = 'gcc'
-+     set gentoo-CC = 'gcc'
-      set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./include"
- 
-      switch ($FORTRAN)
-diff -Naur gamess/ddi/tools/ddikick/ddikick.c gamess-new/ddi/tools/ddikick/ddikick.c
---- gamess/ddi/tools/ddikick/ddikick.c	2006-06-05 03:15:09.000000000 -0400
-+++ gamess-new/ddi/tools/ddikick/ddikick.c	2006-12-13 09:13:42.000000000 -0500
-@@ -105,7 +105,7 @@
-           remoteshell = argv[++i];
-        } else {
-           if((remoteshell = getenv("DDI_RSH")) == NULL) {
--              remoteshell = (char *) strdup("rsh");
-+              remoteshell = (char *) strdup("ssh");
-           }
-        }
- 
-diff -Naur gamess/lked gamess-new/lked
---- gamess/lked	2006-11-19 18:02:58.000000000 -0500
-+++ gamess-new/lked	2006-12-13 09:13:42.000000000 -0500
-@@ -14,8 +14,8 @@
- #       linux-ia64,linux-pc,mac32,macG5,necsx,sgi32,sgi64,sun32,sun64
- #  2. Choose your GAMESS directory tree.
- #
--set TARGET=ibm64
--chdir /u1/mike/gamess
-+set TARGET=linux-pc
-+#chdir /u1/mike/gamess
- #
- #    ---- and now the script begins...
- #
-@@ -330,22 +330,22 @@
- #
- if ($TARGET == linux-pc) then
- #
--   set FORTRAN=g77       # choose from g77, gfortran, ifort, pgf77, f2c
-+   set FORTRAN=gentoo-g77       # choose from g77, gfortran, ifort, pgf77, f2c
- #
-    switch ($FORTRAN)
-      case g77:
-         set LDR='g77'
--        set LDOPTS=' '  # add '-Wl,-M' to see load map
-+        set gentoo-LDOPTS=' '  # add '-Wl,-M' to see load map
-         set LIBRARIES=' '
-         breaksw
-      case gfortran:
-         set LDR='gfortran'
--        set LDOPTS=' '
-+        set gentoo-LDOPTS=' '
-         set LIBRARIES=' '
-         breaksw
-      case ifort:
-         set LDR='ifort'
--        set LDOPTS=' '  # add '-Wl,-M' to see load map
-+        set gentoo-LDOPTS=' '  # add '-Wl,-M' to see load map
-         set LIBRARIES='-Vaxlib'
-         breaksw
-      case pgf77:
-diff -Naur gamess/runall gamess-new/runall
---- gamess/runall	2006-11-06 10:04:51.000000000 -0500
-+++ gamess-new/runall	2006-12-13 09:13:42.000000000 -0500
-@@ -10,7 +10,7 @@
- #  Edit this file to set the base path to GAMESS, and execute it to be
- #  sure all the jobs TERMINATED NORMALLY, and got correct numbers too.
- #
--chdir /u1/mike/gamess
-+#chdir /u1/mike/gamess
- set VERNO=00
- #
- foreach NUM ( 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 \
-diff -Naur gamess/rungms gamess-new/rungms
---- gamess/rungms	2006-11-19 18:09:11.000000000 -0500
-+++ gamess-new/rungms	2006-12-13 09:13:42.000000000 -0500
-@@ -54,7 +54,7 @@
- #       of using LoadLeveler via a "llgms" front end in ~/gamess/misc.
- #
- set TARGET=sockets
--set SCR=/scr/$USER
-+set SCR=`pwd`
- #
- set JOB=$1      # name of the input file xxx.inp, give only the xxx part
- set VERNO=$2    # revision number of the executable created by 'lked' step
-@@ -114,14 +114,14 @@
- #
- set echo
- #                        ASCII input files (see explanation above)
--setenv ERICFMT ~mike/gamess/ericfmt.dat
--setenv MCPPATH ~mike/gamess/mcpdata
-+setenv ERICFMT /usr/share/gamess/ericfmt/ericfmt.dat
-+setenv MCPPATH /usr/share/gamess/mcpdata
- setenv  EXTBAS /dev/null
- setenv  NUCBAS /dev/null
- #
--setenv IRCDATA ~$USER/scr/$JOB.irc
-+setenv IRCDATA $SCR/$JOB.irc
- setenv   INPUT $SCR/$JOB.F05
--setenv   PUNCH ~$USER/scr/$JOB.dat
-+setenv   PUNCH $SCR/$JOB.dat
- setenv  AOINTS $SCR/$JOB.F08
- setenv  MOINTS $SCR/$JOB.F09
- setenv DICTNRY $SCR/$JOB.F10
-@@ -151,8 +151,8 @@
- setenv  SOINTY $SCR/$JOB.F32
- setenv  SOINTZ $SCR/$JOB.F33
- setenv  SORESC $SCR/$JOB.F34
--setenv   SIMEN ~$USER/scr/$JOB.simen
--setenv  SIMCOR ~$USER/scr/$JOB.simcor
-+setenv   SIMEN $SCR/$JOB.simen
-+setenv  SIMCOR $SCR/$JOB.simcor
- setenv GCILIST $SCR/$JOB.F37
- setenv HESSIAN $SCR/$JOB.F38
- setenv SOCCDAT $SCR/$JOB.F40
-@@ -332,7 +332,7 @@
-    if ($os == HP-UX)   set GMSPATH=/zr/mike/gamess
-    if ($os == IRIX)    set GMSPATH=/home/hbar4/people/schmidt/gamess
-    if ($os == IRIX64)  set GMSPATH=/home/hbar4/people/schmidt/gamess
--   if ($os == Linux)   set GMSPATH=/cu/mike/gamess
-+   if ($os == Linux)   set GMSPATH=/usr/bin
-    if ($os == OSF1)    set GMSPATH=/au/mike/gamess
-    if ($os == SunOS)   set GMSPATH=/hf/mike/gamess
- #       special compilation for my old Sun (uname also replies SunOS)
diff --git a/sci-chemistry/gamess/files/gamess-20070324.1.gentoo.patch b/sci-chemistry/gamess/files/gamess-20070324.1.gentoo.patch
deleted file mode 100644
index 4d552d153f7f..000000000000
--- a/sci-chemistry/gamess/files/gamess-20070324.1.gentoo.patch
+++ /dev/null
@@ -1,222 +0,0 @@
-diff -Naur gamess/comp gamess-new/comp
---- gamess/comp	2007-03-24 18:21:35.000000000 -0400
-+++ gamess-new/comp	2007-04-17 15:02:02.000000000 -0400
-@@ -12,8 +12,8 @@
- #        sgi32,sgi64,sun32,sun64
- #  2. Choose your GAMESS directory tree.
- #
--set TARGET=ibm64
--chdir /u1/mike/gamess
-+set TARGET=linux32
-+#chdir /u1/mike/gamess
- #
- #    ---- and now the script begins...
- #
-@@ -1112,7 +1112,7 @@
- #   The only thing you need to change is the next line.
- #   Note: you must make the analogous choice in compddi and lked, as well.
- #
--    set FORTRAN=g77       # choose from g77, gfortran, ifort, pgf77, f2c
-+    set FORTRAN=gentoo-g77       # choose from g77, gfortran, ifort, pgf77, f2c
- #
-     switch ($FORTRAN)
- #
-@@ -1131,7 +1131,7 @@
- #   Pentium II fractionally).  None of these optimizations are used below.
- #
-    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
- #
-@@ -1167,7 +1167,7 @@
- #      -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 == qeigen) || ($MODULE == int2c)) then
-       mv $MODULE.f $MODULE.junk
-@@ -1194,7 +1194,7 @@
- #    but that may cause certain ifort versions to fail on some files.
- #
-    case ifort:
--   set OPT = '-O3'
-+   set gentoo-OPT = '-O2'
-    if ($MODULE == delocl) set OPT='-O0'  # from Cheol
-    if ($MODULE == zheev)  set OPT='-O0'
-    set echo
-diff -Naur gamess/compall gamess-new/compall
---- gamess/compall	2007-03-24 12:44:31.000000000 -0400
-+++ gamess-new/compall	2007-04-17 15:02:09.000000000 -0400
-@@ -13,8 +13,8 @@
- #      sgi32,sgi64,sun32,sun64
- #  2. Choose your GAMESS directory tree.
- #
--set TARGET=ibm64
--chdir /u1/mike/gamess
-+set TARGET=linux32
-+#chdir /u1/mike/gamess
- #
- #  ----- and now the script begins...
- #
-@@ -412,7 +412,7 @@
- #
- #      optional Nuclear-Electronic Orbital method, using NEO code
- #
--set NEO=false
-+set NEO=true
- if ($NEO == true) then
-    ./comp neo
-    ./comp neobas
-diff -Naur gamess/ddi/compddi gamess-new/ddi/compddi
---- gamess/ddi/compddi	2007-03-19 13:51:55.000000000 -0400
-+++ gamess-new/ddi/compddi	2007-04-17 15:02:48.000000000 -0400
-@@ -15,7 +15,7 @@
- #      linux32,linux64,linux-ia64,mac32,macG5,necsx,
- #      sgi32,sgi64,sun32,sun64
- #
--         set TARGET = ibm64
-+         set TARGET = linux32
- 
- #  2. Choose DDI communication layer, the only legal values are
- #                   sockets,mixed,mpi,shmem,lapi,armci
-@@ -535,9 +535,9 @@
- #
-   if($TARGET == linux32) then
- 
--     set FORTRAN=g77       # choose from g77, gfortran, ifort, pgf77, f2c
-+     set FORTRAN=gentoo-g77       # choose from g77, gfortran, ifort, pgf77, f2c
- 
--     set CC = 'gcc'
-+     set gentoo-CC = 'gcc'
-      set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./include"
- 
-      switch ($FORTRAN)
-diff -Naur gamess/ddi/tools/ddikick/ddikick.c gamess-new/ddi/tools/ddikick/ddikick.c
---- gamess/ddi/tools/ddikick/ddikick.c	2006-06-05 03:15:09.000000000 -0400
-+++ gamess-new/ddi/tools/ddikick/ddikick.c	2007-04-17 15:03:01.000000000 -0400
-@@ -105,7 +105,7 @@
-           remoteshell = argv[++i];
-        } else {
-           if((remoteshell = getenv("DDI_RSH")) == NULL) {
--              remoteshell = (char *) strdup("rsh");
-+              remoteshell = (char *) strdup("ssh");
-           }
-        }
- 
-diff -Naur gamess/lked gamess-new/lked
---- gamess/lked	2007-03-24 12:44:22.000000000 -0400
-+++ gamess-new/lked	2007-04-17 15:04:16.000000000 -0400
-@@ -15,8 +15,8 @@
- #       sgi32,sgi64,sun32,sun64
- #  2. Choose your GAMESS directory tree.
- #
--set TARGET=ibm64
--chdir /u1/mike/gamess
-+set TARGET=linux32
-+#chdir /u1/mike/gamess
- #
- #    ---- and now the script begins...
- #
-@@ -285,22 +285,22 @@
- #
- if ($TARGET == linux32) then
- #
--   set FORTRAN=g77       # choose from g77, gfortran, ifort, pgf77, f2c
-+   set FORTRAN=gentoo-g77       # choose from g77, gfortran, ifort, pgf77, f2c
- #
-    switch ($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 LIBRARIES=' '
-         breaksw
-      case gfortran:
-         set LDR='gfortran'
--        set LDOPTS=' '
-+        set gentoo-LDOPTS=' '
-         set LIBRARIES=' '
-         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 LIBRARIES='-Vaxlib'
-         breaksw
-      case pgf77:
-diff -Naur gamess/runall gamess-new/runall
---- gamess/runall	2007-03-05 16:59:51.000000000 -0500
-+++ gamess-new/runall	2007-04-17 15:04:31.000000000 -0400
-@@ -10,7 +10,7 @@
- #  Edit this file to set the base path to GAMESS, and execute it to be
- #  sure all the jobs TERMINATED NORMALLY, and got correct numbers too.
- #
--chdir /u1/mike/gamess
-+#chdir /u1/mike/gamess
- set VERNO=00
- #
- foreach NUM ( 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 \
-diff -Naur gamess/rungms gamess-new/rungms
---- gamess/rungms	2007-03-14 18:23:34.000000000 -0400
-+++ gamess-new/rungms	2007-04-17 15:06:23.000000000 -0400
-@@ -54,7 +54,7 @@
- #       of using LoadLeveler via a "llgms" front end in ~/gamess/misc.
- #
- set TARGET=sockets
--set SCR=/scr/$USER
-+set SCR=`pwd`
- #
- set JOB=$1      # name of the input file xxx.inp, give only the xxx part
- set VERNO=$2    # revision number of the executable created by 'lked' step
-@@ -119,14 +119,14 @@
- #
- set echo
- #                        ASCII input files (see explanation above)
--setenv ERICFMT ~mike/gamess/ericfmt.dat
--setenv MCPPATH ~mike/gamess/mcpdata
-+setenv ERICFMT /usr/share/gamess/ericfmt/ericfmt.dat
-+setenv MCPPATH /usr/share/gamess/mcpdata
- setenv  EXTBAS /dev/null
- setenv  NUCBAS /dev/null
- #
--setenv IRCDATA ~$USER/scr/$JOB.irc
-+setenv IRCDATA $SCR/$JOB.irc
- setenv   INPUT $SCR/$JOB.F05
--setenv   PUNCH ~$USER/scr/$JOB.dat
-+setenv   PUNCH $SCR/$JOB.dat
- setenv  AOINTS $SCR/$JOB.F08
- setenv  MOINTS $SCR/$JOB.F09
- setenv DICTNRY $SCR/$JOB.F10
-@@ -156,8 +156,8 @@
- setenv  SOINTY $SCR/$JOB.F32
- setenv  SOINTZ $SCR/$JOB.F33
- setenv  SORESC $SCR/$JOB.F34
--setenv   SIMEN ~$USER/scr/$JOB.simen
--setenv  SIMCOR ~$USER/scr/$JOB.simcor
-+setenv   SIMEN $SCR/$JOB.simen
-+setenv  SIMCOR $SCR/$JOB.simcor
- setenv GCILIST $SCR/$JOB.F37
- setenv HESSIAN $SCR/$JOB.F38
- setenv SOCCDAT $SCR/$JOB.F40
-@@ -242,7 +242,7 @@
-     if (null$4 == null) set ELGNAME=ELGFILE
-     set echo
-     setenv AOINTS   $SCR/$ELGNAME.F08
--    setenv ELGDOS   ~$USER/scr/$JOB.ldos
-+    setenv ELGDOS   $SCR/$JOB.ldos
-     setenv ELGDAT   $SCR/$ELGNAME.F71
-     setenv ELGPAR   $SCR/$ELGNAME.F72
-     setenv ELGCUT   $SCR/$ELGNAME.F74
-@@ -343,7 +343,7 @@
-    if ($os == AIX)     set GMSPATH=/u1/mike/gamess
-    if ($os == Darwin)  set GMSPATH=/Users/mike/desktop/gamess
-    if ($os == HP-UX)   set GMSPATH=/zr/mike/gamess
--   if ($os == Linux)   set GMSPATH=/cu/mike/gamess
-+   if ($os == Linux)   set GMSPATH=/usr/bin
-    if ($os == OSF1)    set GMSPATH=/in/mike/gamess
-    if ($os == SunOS)   set GMSPATH=/hf/mike/gamess
- #       special compilation for Sun E450 uSPARC       (uname also= SunOS)
diff --git a/sci-chemistry/gamess/files/gamess-20080411.1.gentoo.patch b/sci-chemistry/gamess/files/gamess-20080411.1.gentoo.patch
new file mode 100644
index 000000000000..38f2fe553f74
--- /dev/null
+++ b/sci-chemistry/gamess/files/gamess-20080411.1.gentoo.patch
@@ -0,0 +1,339 @@
+diff -Naur gamess/comp gamess.new/comp
+--- gamess/comp	2008-03-19 19:56:14.000000000 -0400
++++ gamess.new/comp	2008-05-08 09:12:01.000000000 -0400
+@@ -12,8 +12,8 @@
+ #        sgi32,sgi64,sun32,sun64
+ #  2. Choose your GAMESS directory tree.
+ #
+-set TARGET=ibm64
+-chdir /u1/mike/gamess
++set TARGET=gentoo-target
++#chdir /u1/mike/gamess
+ #
+ #    ---- and now the script begins...
+ #
+@@ -100,9 +100,7 @@
+ #      1st is Fedora Core's, 2nd is ASCI download from ORNL, 3rd is Atlas
+ #      the names of the latter two files on your system might well be
+ #      different from these, edit here and in 'lked' to match your paths.
+-if (($TARGET == linux32) && (-e /usr/lib/libblas.a))            set BLAS3=true
+-if (($TARGET == linux32) && (-e /usr/local/bin/libblas-asci.a)) set BLAS3=true
+-if (($TARGET == linux32) && (-e /usr/local/lib/libatlas.a))     set BLAS3=true
++if ($TARGET == linux32)      set BLAS3=true
+ #      For next two, assume that a math library will exist when
+ #      we arrive at the link step: MKL or Atlas or ACML....
+ if  ($TARGET == linux64)      set BLAS3=true
+@@ -1112,7 +1110,7 @@
+ #   The only thing you need to change is the next line.
+ #   Note: you must make the analogous choice in compddi and lked, as well.
+ #
+-    set FORTRAN=g77       # choose from g77, gfortran, ifort, pgf77, f2c
++    set FORTRAN=gentoo-g77       # choose from g77, gfortran, ifort, pgf77, f2c
+ #
+     switch ($FORTRAN)
+ #
+@@ -1131,7 +1129,7 @@
+ #   Pentium II fractionally).  None of these optimizations are used below.
+ #
+    case g77:
+-   set OPT = '-O2'
++   set gentoo-OPT = '-O2'
+    if ($MODULE == ormas1) set OPT='-O2 -fno-move-all-movables' # RH9, g77 3.3
+    if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
+ #
+@@ -1167,7 +1165,7 @@
+ #      -std=legacy  suppresses warnings about use of f77 constructs.
+ #
+    case gfortran:
+-   set OPT='-O2'
++   set gentoo-OPT = '-O2'
+    if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
+    if ($MODULE == pcmcv2) set OPT='-O1'  # EFP+CPCM, ala Francois, v4.1.2
+    if (($MODULE == qeigen) || ($MODULE == int2c)) then
+@@ -1197,7 +1195,7 @@
+ #    optimizations in 32 bit mode, as a function of the ifort version.
+ #
+    case ifort:
+-   set OPT = '-O3'
++   set gentoo-OPT = '-O2'
+    if ($MODULE == delocl) set OPT='-O0'  # from Cheol
+    if ($MODULE == zheev)  set OPT='-O0'
+    set echo
+@@ -1344,12 +1342,12 @@
+ #   Note: you must make the analogous choice in compddi and lked, as well.
+ #   If you wish to use ifort in 64 bit mode, use only target=linux-ia64.
+ #
+-   set FORTRAN=gfortran      # choose from gfortran, pgf77, pathf90
++   set FORTRAN=gentoo-g77      # choose from gfortran, pgf77, pathf90
+ #
+    switch ($FORTRAN)
+ 
+    case gfortran:
+-      set OPT='-O2'
++      set gentoo-OPT = '-O2'
+       if ($MODULE == zheev)  set OPT='-O0'  # defensive compiling
+       if (($MODULE == qeigen) || ($MODULE == int2c)) then
+          mv $MODULE.f $MODULE.junk
+diff -Naur gamess/compall gamess.new/compall
+--- gamess/compall	2008-04-11 14:47:57.000000000 -0400
++++ gamess.new/compall	2008-05-08 09:12:01.000000000 -0400
+@@ -13,8 +13,8 @@
+ #      sgi32,sgi64,sun32,sun64
+ #  2. Choose your GAMESS directory tree.
+ #
+-set TARGET=ibm64
+-chdir /u1/mike/gamess
++set TARGET=gentoo-target
++#chdir /u1/mike/gamess
+ #
+ #  ----- and now the script begins...
+ #
+@@ -139,8 +139,8 @@
+ if ($TARGET == axp64)      ./comp blas
+ if ($TARGET == ibm64)      ./comp blas
+ if ($TARGET == ibm-bg)     ./comp blas
+-if ($TARGET == linux32)    ./comp blas
+-if ($TARGET == linux64)    ./comp blas
++#if ($TARGET == linux32)    ./comp blas
++#if ($TARGET == linux64)    ./comp blas
+ if ($TARGET == linux-ia64) ./comp blas
+ if ($TARGET == sun32)      ./comp blas
+ if ($TARGET == sun64)      ./comp blas
+@@ -428,7 +428,7 @@
+ #
+ #      optional Nuclear-Electronic Orbital method, using NEO code
+ #
+-set NEO=false
++set NEO=true
+ if ($NEO == true) then
+    ./comp neo
+    ./comp neobas
+diff -Naur gamess/ddi/compddi gamess.new/ddi/compddi
+--- gamess/ddi/compddi	2008-03-05 09:21:30.000000000 -0500
++++ gamess.new/ddi/compddi	2008-05-08 09:12:01.000000000 -0400
+@@ -15,7 +15,7 @@
+ #      linux32,linux64,linux-ia64,mac32,mac64,macG5,necsx,
+ #      sgi32,sgi64,sun32,sun64
+ #
+-         set TARGET = ibm64
++         set TARGET = gentoo-target
+ 
+ #  2. Choose DDI communication layer, the only legal values are
+ #                   sockets,mixed,mpi,shmem,lapi,armci
+@@ -537,9 +537,9 @@
+ #
+   if($TARGET == linux32) then
+ 
+-     set FORTRAN=g77       # choose from g77, gfortran, ifort, pgf77, f2c
++     set FORTRAN=gentoo-g77       # choose from g77, gfortran, ifort, pgf77, f2c
+ 
+-     set CC = 'gcc'
++     set gentoo-CC = 'gcc'
+      set CFLAGS = "-DLINUX -O3 -fstrict-aliasing -I./include"
+ 
+      switch ($FORTRAN)
+@@ -578,12 +578,12 @@
+ 
+ #        for generic 64 bit Linux, choose one of the following,
+ #           gfortran, pgf77, pathf90
+-     if ($TARGET == linux64)    set FORTRAN=gfortran
++     if ($TARGET == linux64)    set FORTRAN=gentoo-g77
+ #
+ #        for linux-ia64, leave the choice set to ifort (do not change!)
+      if ($TARGET == linux-ia64) set FORTRAN=ifort
+ 
+-     set CC = 'gcc'
++     set gentoo-CC = 'gcc'
+ 
+      if ($TARGET == linux64) then
+         set CFLAGS = "-DLINUX -m64 -O3 -fstrict-aliasing -I./include"
+diff -Naur gamess/ddi/tools/ddikick/ddikick.c gamess.new/ddi/tools/ddikick/ddikick.c
+--- gamess/ddi/tools/ddikick/ddikick.c	2006-06-05 03:15:09.000000000 -0400
++++ gamess.new/ddi/tools/ddikick/ddikick.c	2008-05-08 09:12:01.000000000 -0400
+@@ -105,7 +105,7 @@
+           remoteshell = argv[++i];
+        } else {
+           if((remoteshell = getenv("DDI_RSH")) == NULL) {
+-              remoteshell = (char *) strdup("rsh");
++              remoteshell = (char *) strdup("ssh");
+           }
+        }
+ 
+diff -Naur gamess/lked gamess.new/lked
+--- gamess/lked	2008-04-11 14:47:43.000000000 -0400
++++ gamess.new/lked	2008-05-08 09:12:01.000000000 -0400
+@@ -15,8 +15,8 @@
+ #       sgi32,sgi64,sun32,sun64
+ #  2. Choose your GAMESS directory tree.
+ #
+-set TARGET=ibm64
+-chdir /u1/mike/gamess
++set TARGET=linux32
++#chdir /u1/mike/gamess
+ #
+ #    ---- and now the script begins...
+ #
+@@ -299,22 +299,22 @@
+ #
+ if ($TARGET == linux32) then
+ #
+-   set FORTRAN=g77       # choose from g77, gfortran, ifort, pgf77, f2c
++   set FORTRAN=gentoo-g77       # choose from g77, gfortran, ifort, pgf77, f2c
+ #
+    switch ($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 LIBRARIES=' '
+         breaksw
+      case gfortran:
+         set LDR='gfortran'
+-        set LDOPTS=' '
++        set gentoo-LDOPTS=' '
+         set LIBRARIES=' '
+         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 LIBRARIES='-Vaxlib'
+         breaksw
+      case pgf77:
+@@ -344,22 +344,22 @@
+ #  Additional libraries not considered here are 32 bit versions
+ #  of Atlas, MKL, or ACML, they are perfectly reasonable choices.
+ #
+-   set BLASLIBRARY=' '
+-   set BLAS='blas.o'  # turn this off if a math library exists...
++   set BLASLIBRARY=`pkg-config --libs blas`
++   set BLAS=''  
+ #
+-   if (-e /usr/lib/libblas.a) then
+-      set BLASLIBRARY="-lblas"
+-      set BLAS=' '
+-   endif
+-   if (-e /usr/local/bin/libblas-asci.a) then
+-      set BLASLIBRARY="/usr/local/bin/libblas-asci.a"
+-      set BLAS=' '
+-   endif
+-   if (-e /usr/local/lib/libatlas.a) then
+-      set BLASLIBRARY="/usr/local/lib/libf77blas.a"
+-      set BLASLIBRARY="$BLASLIBRARY /usr/local/lib/libatlas.a"
+-      set BLAS=' '
+-   endif
++#   if (-e /usr/lib/libblas.a) then
++#      set BLASLIBRARY="-lblas"
++#      set BLAS=' '
++#   endif
++#   if (-e /usr/local/bin/libblas-asci.a) then
++#      set BLASLIBRARY="/usr/local/bin/libblas-asci.a"
++#      set BLAS=' '
++#   endif
++#   if (-e /usr/local/lib/libatlas.a) then
++#      set BLASLIBRARY="/usr/local/lib/libf77blas.a"
++#      set BLASLIBRARY="$BLASLIBRARY /usr/local/lib/libatlas.a"
++#      set BLAS=' '
++#   endif
+ #
+    if ($BLAS == 'blas.o') then
+       echo " "
+diff -Naur gamess/runall gamess.new/runall
+--- gamess/runall	2008-03-18 16:18:58.000000000 -0400
++++ gamess.new/runall	2008-05-08 09:12:01.000000000 -0400
+@@ -10,7 +10,7 @@
+ #  Edit this file to set the base path to GAMESS, and execute it to be
+ #  sure all the jobs TERMINATED NORMALLY, and got correct numbers too.
+ #
+-chdir /u1/mike/gamess
++#chdir /u1/mike/gamess
+ set VERNO=00
+ #
+ foreach NUM ( 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 \
+diff -Naur gamess/rungms gamess.new/rungms
+--- gamess/rungms	2008-03-13 19:56:18.000000000 -0400
++++ gamess.new/rungms	2008-05-08 09:14:03.000000000 -0400
+@@ -54,7 +54,7 @@
+ #       of using LoadLeveler via a "llgms" front end in ~/gamess/misc.
+ #
+ set TARGET=sockets
+-set SCR=/scr/$USER
++set SCR=`pwd`
+ #
+ set JOB=$1      # name of the input file xxx.inp, give only the xxx part
+ set VERNO=$2    # revision number of the executable created by 'lked' step
+@@ -119,15 +119,15 @@
+ #
+ set echo
+ #                        ASCII input files (see explanation above)
+-setenv ERICFMT ~mike/gamess/ericfmt.dat
+-setenv MCPPATH ~mike/gamess/mcpdata
++setenv ERICFMT /usr/share/gamess/ericfmt/ericfmt.dat
++setenv MCPPATH /usr/share/gamess/mcpdata
+ setenv  EXTBAS /dev/null
+ setenv  NUCBAS /dev/null
+ #
+-setenv  MAKEFP ~$USER/scr/$JOB.efp
+-setenv IRCDATA ~$USER/scr/$JOB.irc
++setenv  MAKEFP $SCR/$JOB.efp
++setenv IRCDATA $SCR/$JOB.irc
+ setenv   INPUT $SCR/$JOB.F05
+-setenv   PUNCH ~$USER/scr/$JOB.dat
++setenv   PUNCH $SCR/$JOB.dat
+ setenv  AOINTS $SCR/$JOB.F08
+ setenv  MOINTS $SCR/$JOB.F09
+ setenv DICTNRY $SCR/$JOB.F10
+@@ -157,8 +157,8 @@
+ setenv  SOINTY $SCR/$JOB.F32
+ setenv  SOINTZ $SCR/$JOB.F33
+ setenv  SORESC $SCR/$JOB.F34
+-setenv   SIMEN ~$USER/scr/$JOB.simen
+-setenv  SIMCOR ~$USER/scr/$JOB.simcor
++setenv   SIMEN $SCR/$JOB.simen
++setenv  SIMCOR $SCR/$JOB.simcor
+ setenv GCILIST $SCR/$JOB.F37
+ setenv HESSIAN $SCR/$JOB.F38
+ setenv SOCCDAT $SCR/$JOB.F40
+@@ -303,7 +303,7 @@
+     if (null$4 == null) set ELGNAME=ELGFILE
+     set echo
+     setenv AOINTS   $SCR/$ELGNAME.F08
+-    setenv ELGDOS   ~$USER/scr/$JOB.ldos
++    setenv ELGDOS   $SCR/$JOB.ldos
+     setenv ELGDAT   $SCR/$ELGNAME.F71
+     setenv ELGPAR   $SCR/$ELGNAME.F72
+     setenv ELGCUT   $SCR/$ELGNAME.F74
+@@ -406,7 +406,7 @@
+    if ($os == AIX)     set GMSPATH=/u1/mike/gamess
+    if ($os == Darwin)  set GMSPATH=/Users/mike/desktop/gamess
+    if ($os == HP-UX)   set GMSPATH=/zr/mike/gamess
+-   if ($os == Linux)   set GMSPATH=/cu/mike/gamess
++   if ($os == Linux)   set GMSPATH=/usr/bin
+    if ($os == OSF1)    set GMSPATH=/in/mike/gamess
+    if ($os == SunOS)   set GMSPATH=/hf/mike/gamess
+ #       special compilation for Sun E450 uSPARC       (uname also= SunOS)
+diff -Naur gamess/.rungms.rej.swo gamess.new/.rungms.rej.swo
+--- gamess/.rungms.rej.swo	1969-12-31 19:00:00.000000000 -0500
++++ gamess.new/.rungms.rej.swo	2008-05-08 09:13:01.000000000 -0400
+@@ -0,0 +1 @@
++b0VIM 7.1
+\ No newline at end of file
+diff -Naur gamess/source/zunix.c gamess.new/source/zunix.c
+--- gamess/source/zunix.c	2007-05-07 10:44:22.000000000 -0400
++++ gamess.new/source/zunix.c	2008-05-08 09:12:01.000000000 -0400
+@@ -331,6 +331,7 @@
+ #ifdef LINUX32
+ 
+ #include <stdlib.h>
++#include <string.h>
+ int memget_(nwords) int *nwords;
+    { int nbytes;
+      nbytes = (*nwords+2)*8;
+@@ -412,6 +413,7 @@
+ 
+ #include <stdlib.h>
+ #include <malloc.h>
++#include <string.h>
+ 
+ #define FORTINT long
+