[gmx-users] Debugging

[Andrey V Golovin]

Dear Kirill,

Once i had a similar crash, just in middle of line all outputs was
stopped. Reason was .. =) i run out of disk space =) and once the same
thing was than i run out of 2Gb limit. So it's jus a idea =).

KT> Erik,
>> 0. What Gromacs version, hardware, and operating system version are you
>> using?  
KT> I'm using the current version of GMX posted on the website running
KT> under Linux Kernel 2.6 on an  P4.
>> 1. By "stop running", do you mean crash, or a freeze where the step
>> count stops updating?
KT> That's exactly it: simulations just stop running.  No error messages,
KT> md.log stops in the middle of a line.

KT> Does this give any clues?

KT> thanks

>> 2. If it is a Mac (using Altivec) or x86 (using SSE/SSE2/3DNow), try
>> disabling assembly loop support by setting the environment variable
>> NOASSEMBLYLOOPS (to anything) before starting mdrun.
>> 
>> Cheers,
>> 
>> Erik
>> 
>> On Feb 17, 2005, at 2:00 PM, Kirill Titievsky wrote:
>> 
>> > Dear All,
>> >
>> > Gromacs seems to just stop running in the middle of half of my
>> > simulations.  No error messages.  Where do I start debugging?  Is
>> > there a debug reporting level in Gromacs?
>> >
>> > Symptoms:
>> > The logs get cut off in the middle of a line.  It appears that this
>> > has something to do with atoms ending up outside the box -- the
>> > trajectory files show some files to be outside and restarting the
>> > simulation shows NaN forces on some atoms, even though I'm using soft,
>> > finite potentials.
>> >
>> >
>> > Many thanks
>> >
>> > Kirill Titievsky
>> > Chemical Engineering
>> > MIT
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>> 
>> 
>>
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-- 
Best regards, Andrey

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Andrey V. Golovin 
Ph.D,Professor assistant    tel: (095) 939-5305  
Bioengineering and 
Bioinformatics Department              
Moscow State University     fax: (095) 939-3181 
119899 Moscow            E-mail: golovin at genebee.msu.su 
Russia                      web: http://rnp-group.genebee.msu.su 
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