[gmx-developers] Contribution to Gromacs
Erik Lindahl
lindahl at sbc.su.se
Tue Feb 8 16:07:06 CET 2005
Hi Oliver,
I'm sure we can setup an account for you if you plan to have more
contributions in the future.
However, the easiest way to get something added immediately is just to
create a diff file, either of the whole Gromacs tree or a single file,
between your version and vanilla CVS. The command to use is e.g.
diff -r -u -N gromacs-vanilla gromacs-flooding > flooding.patch
where gromacs-vanilla and gromacs-flooding are directories (or files)
with the respective versions. This way David or I can just add
everything with a single "patch -p0 < flooding.patch" command.
Cheers,
Erik
On Feb 8, 2005, at 3:58 PM, Oliver Lange wrote:
>
> Hi Erik and David,
>
> as you suggested i patched the flooding code into the new CVS version.
> I removed the tools from compilation, since they do not affect the
> Flooding stuff. (->LAPACK error)
>
> I compiled and tested, everything works fine.
>
> How should we proceed ?
> Do you want to give me a cvs - account, so that i can upload the stuff
> ?
>
> Documentation:
> Some first aid help is already included with the -h option. I can
> write a chapter for the manual when i am back from California in the
> beginning of March.
>
> As for the LAPACK:
> The error prevails. even with update -A
>
> Oliver
>
>
> Erik Lindahl wrote:
>> Hi,
>> Try a 'cvs update -A', since we recently added a bunch of stuff (i.e.
>> new directories). If that still doesn't work I'll look more into it.
>> This code is a semi-automatic translation by f2c, but it's fairly
>> easy for me to edit the labels if they make the compiler choke.
>> Cheers,
>> Erik
>> On Feb 7, 2005, at 5:44 PM, Oliver Lange wrote:
>>> Hi Paul,
>>>
>>> i updated once again,
>>> did a make distclean
>>> and compiled again.
>>>
>>> Same error.
>>>
>>> It seems that i have a problem with my Linux setup.
>>>
>>> Any hint, what i can do about it ?
>>>
>>> Anyway, i excluded most of the tools from compilation and that
>>> works, for now.
>>>
>>> But one should keep in mind that there can be problems with the
>>> installation of the LAPACK libraries, would be good to tackle that
>>> before the distribution comes out.
>>>
>>> Regards
>>> Oliver
>>>
>>>
>>>
>>> System: Linux Suse 9.0, gcc 3.3.1,
>>>
>>> bin/sh ../../libtool --mode=link cc -g -O3 -fomit-frame-pointer
>>> -finline-functions -Wall -Wno-unused -malign-double
>>> -funroll-all-loops -L/home/olange/packages/fftw-linux/lib -o
>>> g_cluster g_cluster.o libgmxana.la ../mdlib/libmd.la
>>> ../gmxlib/libgmx.la -L/usr/X11R6/lib -lnsl -lrfftw -lfftw -lm
>>> -lSM -lICE -lX11
>>> cc -g -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
>>> -malign-double -funroll-all-loops -o g_cluster g_cluster.o
>>> -L/home/olange/packages/fftw-linux/lib ./.libs/libgmxana.a
>>> -L/usr/X11R6/lib ../mdlib/.libs/libmd.a ../gmxlib/.libs/libgmx.a
>>> -lnsl /home/olange/packages/fftw-linux//lib/librfftw.a
>>> /home/olange/packages/fftw-linux//lib/libfftw.a -lm -lSM -lICE -lX11
>>> ../gmxlib/.libs/libgmx.a(ilasrt2.o)(.debug_info+0x1b3):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ ilasrt2.c:201: undefined reference to `.L10'
>>> ../gmxlib/.libs/libgmx.a(ilasrt2.o)(.debug_info+0x1bc):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ ilasrt2.c:201: undefined reference to `.L23'
>>> ../gmxlib/.libs/libgmx.a(ilasrt2.o)(.debug_info+0x1c5):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ ilasrt2.c:26: undefined reference to `.L37'
>>> ../gmxlib/.libs/libgmx.a(ilasrt2.o)(.debug_info+0x1ce):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ ilasrt2.c:71: undefined reference to `.L53'
>>> ../gmxlib/.libs/libgmx.a(ilasrt2.o)(.debug_info+0x1d7):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ ilasrt2.c:73: undefined reference to `.L54'
>>> ../gmxlib/.libs/libgmx.a(ilasrt2.o)(.debug_info+0x1e0):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ ilasrt2.c:73: undefined reference to `.L56'
>>> ../gmxlib/.libs/libgmx.a(ilasrt2.o)(.debug_info+0x1e9):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ ilasrt2.c:74: undefined reference to `.L62'
>>> ../gmxlib/.libs/libgmx.a(ilasrt2.o)(.debug_info+0x1f2):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ ilasrt2.c:76: undefined reference to `.L63'
>>> ../gmxlib/.libs/libgmx.a(ilasrt2.o)(.debug_info+0x1fb):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ ilasrt2.c:79: undefined reference to `.L65'
>>> ../gmxlib/.libs/libgmx.a(slasrt2.o)(.debug_info+0x1b2):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ slasrt2.c:58: undefined reference to `.L10'
>>> ../gmxlib/.libs/libgmx.a(slasrt2.o)(.debug_info+0x1bb):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ slasrt2.c:29: undefined reference to `.L58'
>>> ../gmxlib/.libs/libgmx.a(slasrt2.o)(.debug_info+0x1c4):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ slasrt2.c:29: undefined reference to `.L59'
>>> ../gmxlib/.libs/libgmx.a(slasrt2.o)(.debug_info+0x1cd):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ slasrt2.c:30: undefined reference to `.L62'
>>> ../gmxlib/.libs/libgmx.a(slasrt2.o)(.debug_info+0x1d6):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ slasrt2.c:34: undefined reference to `.L69'
>>> ../gmxlib/.libs/libgmx.a(slasrt2.o)(.debug_info+0x1df):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ slasrt2.c:37: undefined reference to `.L70'
>>> ../gmxlib/.libs/libgmx.a(slasrt2.o)(.debug_info+0x1e8):/mnt/wombat1/
>>> olange/gromacs_src/test_patching/gromacs-3.2.1/src/gmxlib/
>>> gmx_lapack/ slasrt2.c:204: undefined reference to `.L73'
>>> collect2: ld returned 1 exit status
>>> make[3]: *** [g_cluster] Error 1
>>>
>>>
>>>
>>>
>>>
>>>
>>> Paul van Maaren wrote:
>>>
>>>> +++ Oliver Lange [Mon, Feb 07, 2005 at 11:23:59AM +0100]:
>>>>
>>>>> i cannot compile the CVS version.
>>>>
>>>> Did you do a cvs update before the compilation? I did this this
>>>> morning and
>>>> it compiles fine for me.
>>>
>>>
>>> --
>>> Oliver Lange
>>> MPI for biophysical Chemistry
>>> olange at gwdg.de
>>> Fax: +495512012302
>>> Tel: +495512012305
>>> _______________________________________________
>>> gmx-developers mailing list
>>> gmx-developers at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-developers
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-developers-request at gromacs.org.
>> ----------------------------------------------------------------------
>> --
>> _______________________________________________
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
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>
> --
> Oliver Lange
> MPI for biophysical Chemistry
> olange at gwdg.de
> Fax: +495512012302
> Tel: +495512012305
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-developers-request at gromacs.org.
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