[gmx-users] gromacs3.3 problem after installation
Erik Lindahl
lindahl at sbc.su.se
Thu Oct 13 16:12:43 CEST 2005
Try setting CFLAGS="-O0 -g" before running configure.
If the output is still garbled, run it under gdb:
1. gdb /path/to/pdb2gmx
2. "run <normal arguments to mdrun>"
3. check where it crashes with "backtrace"
Cheers,
Erik
On Oct 13, 2005, at 7:21 AM, Wang Zhun wrote:
> Hi, Erik,
>
> It seems to be a rather linux-related problem instead of gromacs-
> related one, I'm afraid.
>
>
>> Hi,
>>
>> We won't be able to help without details, details, details:
>>
>> * What type hardware do you have?
>>
>
> My pc is a Compaq AP400, with two PII CPUs and 128M RAM.
>
>
>> * Which operation system, and which version?
>>
>
> Mandrake 8.1
> [wzh at hewei bin]$ uname -a
> Linux hewei.cams.ac.cn 2.4.8-26mdksmp #1 SMP Tue Mar 5 12:10:41 EST
> 2002 i686 unknown
>
This is ancient by linux standards...
>
>> * How did you install Gromacs? Did you compile yourself or use a
>> package?
>>
>
> I compiled it.
>
>
>> * If you compiled it, which compiler and version (cc --version or
>> something) are you using?
>>
>
> gcc version: 3.4.1
>
Although this is pretty new, so the problem might very well be
related to package incompatibilities on your OS.
>
>> * Did you get any strange output/warnings when running configure?
>>
>
> There is no strange output and everything seems ok during the
> installation. And the config.log is attached .
>
>
>> * Were there any errors/warnings when building?
>>
>
> No.
>
>
>> * Did you have any earlier Gromacs version working?
>>
>
> I had installed version 3.2.1 and it worked in order. Later I tried
> 3.3 rc_3 and failed to get it work.
>
>
>> * Did you uninstall that before running "make install" (in case
>> you installed from source)
>>
>
> Before I install this version 3.3, I removed the gromacs folder
> under /usr/local directly. Is this the reason for my trouble?
>
>
>> * Do any other Gromacs commands work (e.g. "luck" that just
>> echoes one of the "cool quotes")
>>
>
> No. Luck does not output any quotes as before.
>
> [wzh at hewei wzh]$ cd /usr/local/gromacs/bin
> [wzh at hewei bin]$ ls
> anadock* g_clustsize* g_gyrate* g_order* highway*
> average* g_confrms* g_h2order* g_potential* luck*
> cdist* g_covar* g_hbond* g_rama* make_edi*
> completion.bash* g_density* g_helix* g_rdf* make_ndx*
> completion.csh* g_densmap* g_lie* g_rms* mdrun*
> completion.zsh* g_dielectric* g_mdmat* g_rmsdist* mk_angndx*
> disco* g_dih* g_mindist* g_rmsf* ngmx*
> do_dssp* g_dipoles* g_morph* grompp* pdb2gmx*
> editconf* g_disre* g_msd* g_rotacf* protonate*
> eneconv* g_dist* gmxcheck* g_saltbr* tpbconv*
> ffscan* g_dyndom* gmxdump* g_sas* trjcat*
> g_anaeig* genbox* GMXRC* g_sgangle* trjconv*
> g_analyze* genconf* GMXRC.bash* g_sham* trjorder*
> g_angle* g_enemat* GMXRC.csh* g_sorient* wheel*
> g_bond* g_energy* GMXRC.zsh* g_tcaf* x2top*
> g_bundle* genion* g_nmeig* g_traj* xpm2ps*
> g_chi* genpr* g_nmens* g_velacc* xrama*
> g_cluster* g_filter* g_nmtraj* g_wham*
> [wzh at hewei bin]$ ./luck
> K. Nemoto[wzh at hewei bin]$
>
> Man and info pdb2gmx show: pdb2gmx VERSION 3.3_beta_20050823. Is
> it right?
>
>
>>
>> Cheers,
>>
>> Erik
>>
>>
>> On Oct 12, 2005, at 7:35 PM, Wang Zhun wrote:
>>
>>
>>> Hi,
>>> I've installed version 3.3 but failed to get it work.
>>> Eg: pdb2gmx is in my path but cannot be found, and segmentation
>>> fault will occur if it's carried out.
>>> I don't know what's the problem.
>>>
>>>
>>> [wzh at hewei wzh]$ pdb2gmx -h
>>> tmpstrtrp[i]tmpstrtrp[i]tmpstrtra and K.
>>> Nemototmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstr
>>> tr p[i]tmpstrtrp[i]t of range
>>> (135930989)---------------------------------------------------------
>>> -- -
>>> No filetype (null)
>>> d argument rint help info for option (null)Segmentation fault
>>> [wzh at hewei wzh]$ whereis pdb2gmx
>>> pdb2gmx:
>>> [wzh at hewei wzh]$ ls /usr/local/gromacs/bin/pdb2gmx
>>> /usr/local/gromacs/bin/pdb2gmx*
>>> [wzh at hewei wzh]$ echo $PATH
>>> /usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/games:/usr/
>>> X11R6/ bin:/usr/games:/usr/X11R6/bin:/usr/games:/usr/X11R6/bin:/
>>> usr/ games:.:/usr/X11R6/bin:/usr/games:/usr/local/gromacs/bin:/
>>> home/wzh/ biolinux/autodock/bin:/home/wzh/bin
>>> [wzh at hewei wzh]$ /usr/local/gromacs/bin/pdb2gmx
>>> tmpstrtrp[i]tmpstrtrp[i]tmpstrtra and K.
>>> Nemototmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstrtrtmpstr
>>> tr p[i]tmpstrtrp[i]t of range
>>> (135930989)---------------------------------------------------------
>>> -- -
>>> No filetype (null)
>>> d argument rint help info for option (null)Segmentation fault
>>> _______________________________________________
>>> gmx-users mailing list
>>> gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
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>>> www interface or send it to gmx-users-request at gromacs.org.
>>>
>>>
>>>
>>
>> -----------------------------------------------------------
>> Erik Lindahl <lindahl at sbc.su.se>
>> Assistant Professor, Stockholm Bioinformatics Center
>> Stockholm University, SE 106 91 Stockholm
>> Phone: +46 8 5537 8564 Fax: +46 8 5537 8214
>>
>>
>>
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>>
>>
> Thanks for your help in advance. This problem has troubled me for
> morethan one week.
>
> Regards,
>
> wzh
>
[big attachment killed]
Cheers,
Erik
-----------------------------------------------------------
Erik Lindahl <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564 Fax: +46 8 5537 8214
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