[gmx-developers] Contribution to Gromacs

[Oliver Lange]

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
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> 
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-- 
Oliver Lange
MPI for biophysical Chemistry
olange at gwdg.de
Fax: +495512012302
Tel: +495512012305