Hello community,
here is the log from the commit of package gromacs
checked in at Wed Oct 8 11:46:14 CEST 2008.
--------
--- gromacs/gromacs.changes 2006-10-16 01:33:35.000000000 +0200
+++ /mounts/work_src_done/STABLE/gromacs/gromacs.changes 2008-10-07 20:55:20.949159000 +0200
@@ -1,0 +2,5 @@
+Tue Oct 7 20:32:58 CEST 2008 - kkaempf@suse.de
+
+- Fix buffer overflow (gcc static detection) in calcmu.c
+
+-------------------------------------------------------------------
calling whatdependson for head-i586
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ gromacs.spec ++++++
--- /var/tmp/diff_new_pack.y14379/_old 2008-10-08 11:45:28.000000000 +0200
+++ /var/tmp/diff_new_pack.y14379/_new 2008-10-08 11:45:28.000000000 +0200
@@ -1,24 +1,32 @@
#
# spec file for package gromacs (Version 3.3.1)
#
-# Copyright (c) 2006 SUSE LINUX Products GmbH, Nuernberg, Germany.
-# This file and all modifications and additions to the pristine
-# package are under the same license as the package itself.
+# Copyright (c) 2008 SUSE LINUX Products GmbH, Nuernberg, Germany.
#
+# All modifications and additions to the file contributed by third parties
+# remain the property of their copyright owners, unless otherwise agreed
+# upon. The license for this file, and modifications and additions to the
+# file, is the same license as for the pristine package itself (unless the
+# license for the pristine package is not an Open Source License, in which
+# case the license is the MIT License). An "Open Source License" is a
+# license that conforms to the Open Source Definition (Version 1.9)
+# published by the Open Source Initiative.
+
# Please submit bugfixes or comments via http://bugs.opensuse.org/
#
# norootforbuild
+
Name: gromacs
BuildRequires: fftw3-devel xorg-x11-devel
Version: 3.3.1
-Release: 10
+Release: 164
Summary: Molecular Dynamics Package
-URL: http://www.gromacs.org
-License: GPL
+Url: http://www.gromacs.org
+License: GPL v2 or later
Group: Productivity/Scientific/Chemistry
-Autoreqprov: on
+AutoReqProv: on
Source0: gromacs-%{version}.tar.bz2
Patch: gromacs-%{version}.dif
BuildRoot: %{_tmppath}/%{name}-%{version}-build
@@ -44,6 +52,7 @@
Erik Lindahl
%package devel
+License: GPL v2 or later
Summary: Molecular dynamics package
Group: Productivity/Scientific/Chemistry
Prefix: %{prefix}
@@ -122,42 +131,44 @@
%dir %{prefix}/include/gromacs
%{prefix}/include/gromacs/*
-%changelog -n gromacs
-* Mon Oct 16 2006 - schwab@suse.de
+%changelog
+* Tue Oct 07 2008 kkaempf@suse.de
+- Fix buffer overflow (gcc static detection) in calcmu.c
+* Mon Oct 16 2006 schwab@suse.de
- Use install-exec-hook instead of install-hook.
- Use AM_PROG_AS.
-* Wed Jul 19 2006 - kkaempf@suse.de
+* Wed Jul 19 2006 kkaempf@suse.de
- update to 3.3.1
see http://www.gromacs.org for a complete list of changes.
-* Mon Jun 19 2006 - schwab@suse.de
+* Mon Jun 19 2006 schwab@suse.de
- Set datadir.
-* Wed Jan 25 2006 - mls@suse.de
+* Wed Jan 25 2006 mls@suse.de
- converted neededforbuild to BuildRequires
-* Mon Dec 19 2005 - ro@suse.de
+* Mon Dec 19 2005 ro@suse.de
- added .so symlink to filelist
-* Wed Aug 11 2004 - kkaempf@suse.de
+* Wed Aug 11 2004 kkaempf@suse.de
- bugfix update to 3.2.1
-* Mon Feb 23 2004 - kkaempf@suse.de
+* Mon Feb 23 2004 kkaempf@suse.de
- rename 'disco' to 'g_disco' to avoid nameclash with package mono
- build with -fno-strict-aliasing
- return value from main()
-* Tue Feb 17 2004 - kkaempf@suse.de
+* Tue Feb 17 2004 kkaempf@suse.de
- remove obsolete libtool from "configure.ac".
- use proper automake syntax in "acinclude.m4".
- add missing FF.dat as advised on gromacs-users mailing list.
-* Tue Feb 03 2004 - kkaempf@suse.de
+* Tue Feb 03 2004 kkaempf@suse.de
- update to 3.2
-* Sat Jan 10 2004 - adrian@suse.de
+* Sat Jan 10 2004 adrian@suse.de
- add %%run_ldconfig
-* Fri Jun 13 2003 - kukuk@suse.de
+* Fri Jun 13 2003 kukuk@suse.de
- Add missing directories to filelist and fix permissions
-* Thu Nov 21 2002 - ro@suse.de
+* Thu Nov 21 2002 ro@suse.de
- work around automake problem
-* Fri Nov 15 2002 - uli@suse.de
+* Fri Nov 15 2002 uli@suse.de
- removed lesstif from neededforbuild (not used)
-* Mon Nov 11 2002 - ro@suse.de
+* Tue Nov 12 2002 ro@suse.de
- changed neededforbuild <xf86 xshared xdevel> to <x-devel-packages>
-* Tue Oct 29 2002 - ro@suse.de
+* Tue Oct 29 2002 ro@suse.de
- removed own libtool hacks from acinclude.m4
-* Mon Jul 29 2002 - kkaempf@suse.de
+* Mon Jul 29 2002 kkaempf@suse.de
- Initial version 3.1.4
++++++ gromacs-3.3.1.dif ++++++
--- /var/tmp/diff_new_pack.y14379/_old 2008-10-08 11:45:28.000000000 +0200
+++ /var/tmp/diff_new_pack.y14379/_new 2008-10-08 11:45:28.000000000 +0200
@@ -1,16 +1,6 @@
---- Makefile.am
-+++ Makefile.am
-@@ -17,7 +17,7 @@
-
- EXTRA_DIST = config/depcomp
-
--install-hook:
-+install-exec-hook:
- @echo ""
- @echo "GROMACS is installed under $(prefix)."
- @echo "Make sure to update your PATH and MANPATH to find the"
---- acinclude.m4
-+++ acinclude.m4
+diff -wruN ../orig-gromacs-3.3.1/acinclude.m4 ./acinclude.m4
+--- ../orig-gromacs-3.3.1/acinclude.m4 2006-04-06 21:21:44.000000000 +0200
++++ ./acinclude.m4 2008-10-07 20:26:39.000000000 +0200
@@ -1268,6423 +1268,3 @@
fi
AC_LANG_RESTORE
@@ -6435,8 +6425,9 @@
-AC_MSG_RESULT([$SED])
-])
-
---- admin/programs.txt
-+++ admin/programs.txt
+diff -wruN ../orig-gromacs-3.3.1/admin/programs.txt ./admin/programs.txt
+--- ../orig-gromacs-3.3.1/admin/programs.txt 2006-03-30 19:27:33.000000000 +0200
++++ ./admin/programs.txt 2008-10-07 20:26:39.000000000 +0200
@@ -56,8 +56,8 @@
g_confrms|fits two structures and calculates the rmsd
g_cluster|clusters structures
@@ -6459,8 +6450,9 @@
anadock|cluster structures from Autodock runs
END
---- configure.ac
-+++ configure.ac
+diff -wruN ../orig-gromacs-3.3.1/configure.ac ./configure.ac
+--- ../orig-gromacs-3.3.1/configure.ac 2006-04-06 21:16:00.000000000 +0200
++++ ./configure.ac 2008-10-07 20:26:39.000000000 +0200
@@ -314,6 +314,7 @@
@@ -6478,8 +6470,21 @@
AC_SUBST(CCAS)
AC_SUBST(CCASFLAGS)
---- man/man1/cdist.1
-+++ man/man1/cdist.1
+diff -wruN ../orig-gromacs-3.3.1/Makefile.am ./Makefile.am
+--- ../orig-gromacs-3.3.1/Makefile.am 2006-03-08 15:03:54.000000000 +0100
++++ ./Makefile.am 2008-10-07 20:26:39.000000000 +0200
+@@ -17,7 +17,7 @@
+
+ EXTRA_DIST = config/depcomp
+
+-install-hook:
++install-exec-hook:
+ @echo ""
+ @echo "GROMACS is installed under $(prefix)."
+ @echo "Make sure to update your PATH and MANPATH to find the"
+diff -wruN ../orig-gromacs-3.3.1/man/man1/cdist.1 ./man/man1/cdist.1
+--- ../orig-gromacs-3.3.1/man/man1/cdist.1 2005-08-29 21:39:39.000000000 +0200
++++ ./man/man1/cdist.1 2008-10-07 20:26:39.000000000 +0200
@@ -38,7 +38,7 @@
.SH DESCRIPTION
cdist read a
@@ -6516,8 +6521,9 @@
.BI "-[no]vir" " no"
Use virtual particles
---- man/man1/disco.1
-+++ man/man1/disco.1
+diff -wruN ../orig-gromacs-3.3.1/man/man1/disco.1 ./man/man1/disco.1
+--- ../orig-gromacs-3.3.1/man/man1/disco.1 2005-08-29 21:39:39.000000000 +0200
++++ ./man/man1/disco.1 2008-10-07 20:26:39.000000000 +0200
@@ -1,9 +1,9 @@
-.TH disco 1 "Mon 29 Aug 2005"
+.TH g_disco 1 "Mon 29 Aug 2005"
@@ -6553,8 +6559,9 @@
master-slave approach. Slaves work asynchronously, and it is no
problem when nodes are not equally fast, or when a node dies,
unless it is the master node.
---- scripts/completion.bash
-+++ scripts/completion.bash
+diff -wruN ../orig-gromacs-3.3.1/scripts/completion.bash ./scripts/completion.bash
+--- ../orig-gromacs-3.3.1/scripts/completion.bash 2005-09-06 10:01:54.000000000 +0200
++++ ./scripts/completion.bash 2008-10-07 20:26:39.000000000 +0200
@@ -44,7 +44,7 @@
-keep) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-viol) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
@@ -6564,8 +6571,9 @@
shopt -s extglob
_do_dssp_compl() {
local p c
---- scripts/completion.csh
-+++ scripts/completion.csh
+diff -wruN ../orig-gromacs-3.3.1/scripts/completion.csh ./scripts/completion.csh
+--- ../orig-gromacs-3.3.1/scripts/completion.csh 2005-09-06 10:01:54.000000000 +0200
++++ ./scripts/completion.csh 2008-10-07 20:26:39.000000000 +0200
@@ -1,6 +1,6 @@
complete anadock "n/-f/f:*.pdb{,.gz,.Z}/" "n/-ox/f:*.pdb{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( f ox od of g h nice noxvgr free norms cutoff)/"
complete cdist "n/-sm/( none tri tetra)/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-q/f:*.pdb{,.gz,.Z}/" "n/-d/f:*.dat{,.gz,.Z}/" "n/-o/f:*.dat{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-dom/f:*.ndx{,.gz,.Z}/" "c/-/( s g q d o n dom h nice noengh bm am pm rr ar er vm lm il dm im nm hm hb nobon nonb measure maxdist add vir sm)/"
@@ -6574,8 +6582,9 @@
complete do_dssp "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ssdump/f:*.dat{,.gz,.Z}/" "n/-map/f:*.map{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "n/-sc/f:*.xvg{,.gz,.Z}/" "n/-a/f:*.xpm{,.gz,.Z}/" "n/-ta/f:*.xvg{,.gz,.Z}/" "n/-aa/f:*.xvg{,.gz,.Z}/" "c/-/( f s n ssdump map o sc a ta aa h nice b e dt tu w noxvgr sss)/"
complete editconf "n/-bt/( tric cubic dodecahedron octahedron)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,esp,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent,esp}{,.gz,.Z}/" "n/-mead/f:*.pqr{,.gz,.Z}/" "n/-bf/f:*.dat{,.gz,.Z}/" "c/-/( f n o mead bf h nice w ndef bt box angles d c center translate rotate princ scale density novol pbc grasp rvdw sig56 vdwread atom legend label)/"
complete eneconv "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-o/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( f o h nice b e dt offset settime nosort scalefac noerror)/"
---- scripts/completion.zsh
-+++ scripts/completion.zsh
+diff -wruN ../orig-gromacs-3.3.1/scripts/completion.zsh ./scripts/completion.zsh
+--- ../orig-gromacs-3.3.1/scripts/completion.zsh 2005-09-06 10:01:54.000000000 +0200
++++ ./scripts/completion.zsh 2008-10-07 20:26:39.000000000 +0200
@@ -1,6 +1,6 @@
compctl -x 's[-]' -s " f ox od of g h nice noxvgr free norms cutoff" - 'c[-1,-f]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-ox]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- anadock
compctl -x 's[-]' -s " s g q d o n dom h nice noengh bm am pm rr ar er vm lm il dm im nm hm hb nobon nonb measure maxdist add vir sm" - 'c[-1,-sm]' -s " none tri tetra" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-dom]' -g '*.ndx(|.gz|.Z) *(/)' -- cdist
@@ -6584,8 +6593,9 @@
compctl -x 's[-]' -s " f s n ssdump map o sc a ta aa h nice b e dt tu w noxvgr sss" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ssdump]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-map]' -g '*.map(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-sc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-ta]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-aa]' -g '*.xvg(|.gz|.Z) *(/)' -- do_dssp
compctl -x 's[-]' -s " f n o mead bf h nice w ndef bt box angles d c center translate rotate princ scale density novol pbc grasp rvdw sig56 vdwread atom legend label" - 'c[-1,-bt]' -s " tric cubic dodecahedron octahedron" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|esp|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent|esp)(|.gz|.Z) *(/)' - 'c[-1,-mead]' -g '*.pqr(|.gz|.Z) *(/)' - 'c[-1,-bf]' -g '*.dat(|.gz|.Z) *(/)' -- editconf
compctl -x 's[-]' -s " f o h nice b e dt offset settime nosort scalefac noerror" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- eneconv
---- share/html/online.html
-+++ share/html/online.html
+diff -wruN ../orig-gromacs-3.3.1/share/html/online.html ./share/html/online.html
+--- ../orig-gromacs-3.3.1/share/html/online.html 2005-09-06 10:05:59.000000000 +0200
++++ ./share/html/online.html 2008-10-07 20:26:39.000000000 +0200
@@ -48,7 +48,7 @@
<br>
<br><a href=online/anadock.html>anadock</a>
@@ -6617,8 +6627,9 @@
<TR><TD><A HREF="online/anadock.html">anadock</A></TD><TD>cluster structures from Autodock runs</TD>
</TABLE>
---- share/top/Makefile.am
-+++ share/top/Makefile.am
+diff -wruN ../orig-gromacs-3.3.1/share/top/Makefile.am ./share/top/Makefile.am
+--- ../orig-gromacs-3.3.1/share/top/Makefile.am 2005-10-11 13:55:04.000000000 +0200
++++ ./share/top/Makefile.am 2008-10-07 20:26:39.000000000 +0200
@@ -50,7 +50,7 @@
export.dlg bonds.dlg ss.map ps.m2p \
table6-10.xvg table6-11.xvg table6-12.xvg table6-8.xvg \
@@ -6628,3 +6639,342 @@
EXTRA_DIST = ${topol_DATA}
+diff -wruN ../orig-gromacs-3.3.1/src/gmxlib/nonbonded/nb_kernel/Makefile.am ./src/gmxlib/nonbonded/nb_kernel/Makefile.am
+--- ../orig-gromacs-3.3.1/src/gmxlib/nonbonded/nb_kernel/Makefile.am 2005-09-01 21:20:57.000000000 +0200
++++ ./src/gmxlib/nonbonded/nb_kernel/Makefile.am 2008-10-07 20:32:16.000000000 +0200
+@@ -148,7 +148,7 @@
+
+
+
+-BUILD_COMPILE = $(CC_FOR_BUILD) $(DEFS) $(DEFAULT_INCLUDES)
++BUILD_COMPILE = $(CC_FOR_BUILD) $(DEFS) $(DEFAULT_INCLUDES) $(CCFLAGS)
+
+
+
+diff -wruN ../orig-gromacs-3.3.1/src/gmxlib/nonbonded/nb_kernel/Makefile.am~ ./src/gmxlib/nonbonded/nb_kernel/Makefile.am~
+--- ../orig-gromacs-3.3.1/src/gmxlib/nonbonded/nb_kernel/Makefile.am~ 1970-01-01 01:00:00.000000000 +0100
++++ ./src/gmxlib/nonbonded/nb_kernel/Makefile.am~ 2005-09-01 21:20:57.000000000 +0200
+@@ -0,0 +1,214 @@
++
++AM_CPPFLAGS= -I$(top_srcdir)/include -DGMXLIBDIR=\"$(datadir)/top\"
++
++noinst_LTLIBRARIES = libnb_kernel.la
++
++
++FORTRAN_KERNEL_OBJS = \
++ nb_kernel010_f.lo nb_kernel020_f.lo nb_kernel030_f.lo nb_kernel100_f.lo \
++ nb_kernel101_f.lo nb_kernel102_f.lo nb_kernel103_f.lo nb_kernel104_f.lo \
++ nb_kernel110_f.lo nb_kernel111_f.lo nb_kernel112_f.lo nb_kernel113_f.lo \
++ nb_kernel114_f.lo nb_kernel120_f.lo nb_kernel121_f.lo nb_kernel122_f.lo \
++ nb_kernel123_f.lo nb_kernel124_f.lo nb_kernel130_f.lo nb_kernel131_f.lo \
++ nb_kernel132_f.lo nb_kernel133_f.lo nb_kernel134_f.lo nb_kernel200_f.lo \
++ nb_kernel201_f.lo nb_kernel202_f.lo nb_kernel203_f.lo nb_kernel204_f.lo \
++ nb_kernel210_f.lo nb_kernel211_f.lo nb_kernel212_f.lo nb_kernel213_f.lo \
++ nb_kernel214_f.lo nb_kernel220_f.lo nb_kernel221_f.lo nb_kernel222_f.lo \
++ nb_kernel223_f.lo nb_kernel224_f.lo nb_kernel230_f.lo nb_kernel231_f.lo \
++ nb_kernel232_f.lo nb_kernel233_f.lo nb_kernel234_f.lo nb_kernel300_f.lo \
++ nb_kernel301_f.lo nb_kernel302_f.lo nb_kernel303_f.lo nb_kernel304_f.lo \
++ nb_kernel310_f.lo nb_kernel311_f.lo nb_kernel312_f.lo nb_kernel313_f.lo \
++ nb_kernel314_f.lo nb_kernel320_f.lo nb_kernel321_f.lo nb_kernel322_f.lo \
++ nb_kernel323_f.lo nb_kernel324_f.lo nb_kernel330_f.lo nb_kernel331_f.lo \
++ nb_kernel332_f.lo nb_kernel333_f.lo nb_kernel334_f.lo nb_kernel400_f.lo \
++ nb_kernel410_f.lo nb_kernel420_f.lo nb_kernel430_f.lo
++
++FORTRAN_KERNEL_SOURCES = \
++ nb_kernel010_f.f nb_kernel020_f.f nb_kernel030_f.f nb_kernel100_f.f \
++ nb_kernel101_f.f nb_kernel102_f.f nb_kernel103_f.f nb_kernel104_f.f \
++ nb_kernel110_f.f nb_kernel111_f.f nb_kernel112_f.f nb_kernel113_f.f \
++ nb_kernel114_f.f nb_kernel120_f.f nb_kernel121_f.f nb_kernel122_f.f \
++ nb_kernel123_f.f nb_kernel124_f.f nb_kernel130_f.f nb_kernel131_f.f \
++ nb_kernel132_f.f nb_kernel133_f.f nb_kernel134_f.f nb_kernel200_f.f \
++ nb_kernel201_f.f nb_kernel202_f.f nb_kernel203_f.f nb_kernel204_f.f \
++ nb_kernel210_f.f nb_kernel211_f.f nb_kernel212_f.f nb_kernel213_f.f \
++ nb_kernel214_f.f nb_kernel220_f.f nb_kernel221_f.f nb_kernel222_f.f \
++ nb_kernel223_f.f nb_kernel224_f.f nb_kernel230_f.f nb_kernel231_f.f \
++ nb_kernel232_f.f nb_kernel233_f.f nb_kernel234_f.f nb_kernel300_f.f \
++ nb_kernel301_f.f nb_kernel302_f.f nb_kernel303_f.f nb_kernel304_f.f \
++ nb_kernel310_f.f nb_kernel311_f.f nb_kernel312_f.f nb_kernel313_f.f \
++ nb_kernel314_f.f nb_kernel320_f.f nb_kernel321_f.f nb_kernel322_f.f \
++ nb_kernel323_f.f nb_kernel324_f.f nb_kernel330_f.f nb_kernel331_f.f \
++ nb_kernel332_f.f nb_kernel333_f.f nb_kernel334_f.f nb_kernel400_f.f \
++ nb_kernel410_f.f nb_kernel420_f.f nb_kernel430_f.f
++
++
++#
++
++C_KERNEL_OBJS = \
++ nb_kernel010_c.lo nb_kernel020_c.lo nb_kernel030_c.lo nb_kernel100_c.lo \
++ nb_kernel101_c.lo nb_kernel102_c.lo nb_kernel103_c.lo nb_kernel104_c.lo \
++ nb_kernel110_c.lo nb_kernel111_c.lo nb_kernel112_c.lo nb_kernel113_c.lo \
++ nb_kernel114_c.lo nb_kernel120_c.lo nb_kernel121_c.lo nb_kernel122_c.lo \
++ nb_kernel123_c.lo nb_kernel124_c.lo nb_kernel130_c.lo nb_kernel131_c.lo \
++ nb_kernel132_c.lo nb_kernel133_c.lo nb_kernel134_c.lo nb_kernel200_c.lo \
++ nb_kernel201_c.lo nb_kernel202_c.lo nb_kernel203_c.lo nb_kernel204_c.lo \
++ nb_kernel210_c.lo nb_kernel211_c.lo nb_kernel212_c.lo nb_kernel213_c.lo \
++ nb_kernel214_c.lo nb_kernel220_c.lo nb_kernel221_c.lo nb_kernel222_c.lo \
++ nb_kernel223_c.lo nb_kernel224_c.lo nb_kernel230_c.lo nb_kernel231_c.lo \
++ nb_kernel232_c.lo nb_kernel233_c.lo nb_kernel234_c.lo nb_kernel300_c.lo \
++ nb_kernel301_c.lo nb_kernel302_c.lo nb_kernel303_c.lo nb_kernel304_c.lo \
++ nb_kernel310_c.lo nb_kernel311_c.lo nb_kernel312_c.lo nb_kernel313_c.lo \
++ nb_kernel314_c.lo nb_kernel320_c.lo nb_kernel321_c.lo nb_kernel322_c.lo \
++ nb_kernel323_c.lo nb_kernel324_c.lo nb_kernel330_c.lo nb_kernel331_c.lo \
++ nb_kernel332_c.lo nb_kernel333_c.lo nb_kernel334_c.lo nb_kernel400_c.lo \
++ nb_kernel410_c.lo nb_kernel420_c.lo nb_kernel430_c.lo
++
++
++C_KERNEL_SOURCES = \
++ nb_kernel010_c.c nb_kernel020_c.c nb_kernel030_c.c nb_kernel100_c.c \
++ nb_kernel101_c.c nb_kernel102_c.c nb_kernel103_c.c nb_kernel104_c.c \
++ nb_kernel110_c.c nb_kernel111_c.c nb_kernel112_c.c nb_kernel113_c.c \
++ nb_kernel114_c.c nb_kernel120_c.c nb_kernel121_c.c nb_kernel122_c.c \
++ nb_kernel123_c.c nb_kernel124_c.c nb_kernel130_c.c nb_kernel131_c.c \
++ nb_kernel132_c.c nb_kernel133_c.c nb_kernel134_c.c nb_kernel200_c.c \
++ nb_kernel201_c.c nb_kernel202_c.c nb_kernel203_c.c nb_kernel204_c.c \
++ nb_kernel210_c.c nb_kernel211_c.c nb_kernel212_c.c nb_kernel213_c.c \
++ nb_kernel214_c.c nb_kernel220_c.c nb_kernel221_c.c nb_kernel222_c.c \
++ nb_kernel223_c.c nb_kernel224_c.c nb_kernel230_c.c nb_kernel231_c.c \
++ nb_kernel232_c.c nb_kernel233_c.c nb_kernel234_c.c nb_kernel300_c.c \
++ nb_kernel301_c.c nb_kernel302_c.c nb_kernel303_c.c nb_kernel304_c.c \
++ nb_kernel310_c.c nb_kernel311_c.c nb_kernel312_c.c nb_kernel313_c.c \
++ nb_kernel314_c.c nb_kernel320_c.c nb_kernel321_c.c nb_kernel322_c.c \
++ nb_kernel323_c.c nb_kernel324_c.c nb_kernel330_c.c nb_kernel331_c.c \
++ nb_kernel332_c.c nb_kernel333_c.c nb_kernel334_c.c nb_kernel400_c.c \
++ nb_kernel410_c.c nb_kernel420_c.c nb_kernel430_c.c
++
++
++
++if GMX_FORTRAN
++ KERNEL_OBJS = $(FORTRAN_KERNEL_OBJS) nb_kernel_f77sync.lo
++else
++ KERNEL_OBJS = $(C_KERNEL_OBJS)
++endif
++
++#
++# This is a virtual target for all the kernels, to ensure it is only run
++# by one CPU even if you run make in parallel.
++# The mknb program will generate the kernel-stamp file when done.
++#
++BUILT_SOURCES = kernel-stamp
++
++libnb_kernel_la_LIBADD = $(KERNEL_OBJS)
++libnb_kernel_la_DEPENDENCIES = $(KERNEL_OBJS)
++
++
++libnb_kernel_la_SOURCES = \
++ nb_kernel010.h nb_kernel020.h nb_kernel030.h nb_kernel100.h \
++ nb_kernel101.h nb_kernel102.h nb_kernel103.h nb_kernel104.h \
++ nb_kernel110.h nb_kernel111.h nb_kernel112.h nb_kernel113.h \
++ nb_kernel114.h nb_kernel120.h nb_kernel121.h nb_kernel122.h \
++ nb_kernel123.h nb_kernel124.h nb_kernel130.h nb_kernel131.h \
++ nb_kernel132.h nb_kernel133.h nb_kernel134.h nb_kernel200.h \
++ nb_kernel201.h nb_kernel202.h nb_kernel203.h nb_kernel204.h \
++ nb_kernel210.h nb_kernel211.h nb_kernel212.h nb_kernel213.h \
++ nb_kernel214.h nb_kernel220.h nb_kernel221.h nb_kernel222.h \
++ nb_kernel223.h nb_kernel224.h nb_kernel230.h nb_kernel231.h \
++ nb_kernel232.h nb_kernel233.h nb_kernel234.h nb_kernel300.h \
++ nb_kernel301.h nb_kernel302.h nb_kernel303.h nb_kernel304.h \
++ nb_kernel310.h nb_kernel311.h nb_kernel312.h nb_kernel313.h \
++ nb_kernel314.h nb_kernel320.h nb_kernel321.h nb_kernel322.h \
++ nb_kernel323.h nb_kernel324.h nb_kernel330.h nb_kernel331.h \
++ nb_kernel332.h nb_kernel333.h nb_kernel334.h nb_kernel400.h \
++ nb_kernel410.h nb_kernel420.h nb_kernel430.h \
++ nb_kernel.c nb_kernel.h
++
++
++
++EXTRA_libnb_kernel_la_SOURCES = nb_kernel_f77sync.c
++
++
++# sources built at compile time
++nodist_EXTRA_libnb_kernel_la_SOURCES = $(FORTRAN_KERNEL_SOURCES) $(C_KERNEL_SOURCES)
++
++
++
++# mknb is special - we cant use a noinst_PROGRAMS target, since it might have
++# to be compiled with a non-MPI compiler whose files can be executed by make:
++
++EXTRA_DIST = \
++ mknb.c \
++ mknb_metacode.c mknb_metacode.h \
++ mknb_common.c mknb_common.h \
++ mknb_declarations.c mknb_declarations.h \
++ mknb_outerloop.c mknb_outerloop.h \
++ mknb_innerloop.c mknb_innerloop.h \
++ mknb_interactions.c mknb_interactions.h
++
++
++
++
++BUILD_COMPILE = $(CC_FOR_BUILD) $(DEFS) $(DEFAULT_INCLUDES)
++
++
++
++mknb.o: mknb.c
++ $(BUILD_COMPILE) -c -o $@ $<
++mknb_common.o: mknb_common.c
++ $(BUILD_COMPILE) -c -o $@ $<
++mknb_metacode.o: mknb_metacode.c
++ $(BUILD_COMPILE) -c -o $@ $<
++mknb_declarations.o: mknb_declarations.c
++ $(BUILD_COMPILE) -c -o $@ $<
++mknb_outerloop.o: mknb_outerloop.c
++ $(BUILD_COMPILE) -c -o $@ $<
++mknb_innerloop.o: mknb_innerloop.c
++ $(BUILD_COMPILE) -c -o $@ $<
++mknb_interactions.o: mknb_interactions.c
++ $(BUILD_COMPILE) -c -o $@ $<
++
++MKNB_OBJ = \
++ mknb.o mknb_metacode.o mknb_common.o mknb_declarations.o \
++ mknb_outerloop.o mknb_innerloop.o mknb_interactions.o
++
++mknb: $(MKNB_OBJ)
++ $(BUILD_COMPILE) -o $@ $(MKNB_OBJ)
++
++
++if GMX_DOUBLE
++ DOUBLEFLAG = -double
++endif
++
++if GMX_THREAD
++ THREADFLAG = -threads
++endif
++
++if GMX_SOFTWARE_SQRT
++ SQRTFLAG = -software_invsqrt
++endif
++
++if GMX_PREFETCH_FORCES
++ PREFETCHFLAG = -prefetch_forces
++endif
++
++if GMX_FORTRAN
++ FORTRANFLAG = -fortran
++endif
++
++MKNB_FLAGS = $(DOUBLEFLAG) $(THREADFLAG) $(SQRTFLAG) \
++ $(PREFETCHFLAG) $(FORTRANFLAG)
++
++#
++# The kernels should only be built once, instead of once per
++# source file when using parallel builds (make -j N). To solve this
++# the mknb program writes out a stamp file after the kernels, which
++# we use as a dummy/virtual target.
++#
++kernel-stamp: mknb
++ rm -f kernel-stamp
++ ./mknb $(MKNB_FLAGS)
++
++
++
++CLEANFILES = *.la *~ \\\#* mknb nb_kernel*_f.f nb_kernel*_c.c cg kernel-stamp
++
+diff -wruN ../orig-gromacs-3.3.1/src/mdlib/calcmu.c ./src/mdlib/calcmu.c
+--- ../orig-gromacs-3.3.1/src/mdlib/calcmu.c 2005-03-01 10:00:38.000000000 +0100
++++ ./src/mdlib/calcmu.c 2008-10-07 20:29:43.000000000 +0200
+@@ -82,7 +82,7 @@
+ /* For backward compatibility */
+ real mmm[4];
+
+- if (fread(mmm,(size_t)(4*sizeof(mmm)),1,fp) != 1)
++ if (fread(mmm,(size_t)(4*sizeof(real)),1,fp) != 1)
+ return FALSE;
+
+ copy_rvec(mmm,mu);
+diff -wruN ../orig-gromacs-3.3.1/src/mdlib/calcmu.c~ ./src/mdlib/calcmu.c~
+--- ../orig-gromacs-3.3.1/src/mdlib/calcmu.c~ 1970-01-01 01:00:00.000000000 +0100
++++ ./src/mdlib/calcmu.c~ 2005-03-01 10:00:38.000000000 +0100
+@@ -0,0 +1,93 @@
++/*
++ * $Id: calcmu.c,v 1.11 2005/03/01 09:00:38 hess Exp $
++ *
++ * This source code is part of
++ *
++ * G R O M A C S
++ *
++ * GROningen MAchine for Chemical Simulations
++ *
++ * VERSION 3.2.0
++ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
++ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
++ * Copyright (c) 2001-2004, The GROMACS development team,
++ * check out http://www.gromacs.org for more information.
++
++ * This program is free software; you can redistribute it and/or
++ * modify it under the terms of the GNU General Public License
++ * as published by the Free Software Foundation; either version 2
++ * of the License, or (at your option) any later version.
++ *
++ * If you want to redistribute modifications, please consider that
++ * scientific software is very special. Version control is crucial -
++ * bugs must be traceable. We will be happy to consider code for
++ * inclusion in the official distribution, but derived work must not
++ * be called official GROMACS. Details are found in the README & COPYING
++ * files - if they are missing, get the official version at www.gromacs.org.
++ *
++ * To help us fund GROMACS development, we humbly ask that you cite
++ * the papers on the package - you can find them in the top README file.
++ *
++ * For more info, check our website at http://www.gromacs.org
++ *
++ * And Hey:
++ * GROwing Monsters And Cloning Shrimps
++ */
++/* This file is completely threadsafe - keep it that way! */
++#ifdef HAVE_CONFIG_H
++#include
++#endif
++
++#include
++#include
++#include "typedefs.h"
++#include "network.h"
++#include "vec.h"
++#include "fatal.h"
++#include "physics.h"
++#include "nsb.h"
++#include "main.h"
++
++void calc_mu(t_nsborder *nsb,rvec x[],real q[],real qB[],
++ bool bFreeEnergy,
++ rvec mu,rvec mu_B)
++{
++ int i,start,end,m;
++ /* temporary double prec. to maintain precision */
++ dvec tmpmu;
++
++ start = START(nsb);
++ end = start + HOMENR(nsb);
++
++ clear_dvec(tmpmu);
++ for(i=start; (i