[gmx-users] more than 2 step*.pdb files?

[aldo jongejan]

Hi all,

Just to follow up; I am this colleague of Anton and I was running
on 9 CPU's. Crashes give me hell of a lot of step*.pdb and #step*.pdb 
files (each about ~13 MB, so indeed filling up disk space rapidly..)

It indeed seems as if each CPU decides to write his(her?) job to write
a file. Probably it is a simple bug...

with kind regards,

aldo

Tsjerk Wassenaar wrote:
> 
> Hmm, come to think of it, it occured to me too, though with two 
> step*.pdb files, but also two #step*.pdb# files. It didn't really strike 
> me, and was not much of a problem, running only on two processors.
> 
> The system in my case is also a receptor in a bilayer in water. If you 
> want more details, just mention.
> 
> Groetjes ;)
> 
> Tsjerk
> 
> Anton Feenstra wrote:
> 
>> Hi All,
>>
>>
>> My run of protein, ligand and water crashed, leaving three step*.pdb
>> files, in stead of the two (crash and pre-crash) that I expect. What
>> is more, there are three backup files (#step*.pdb.[12]#), one for one
>> of the step*.pdb and two for another. I'm running on 6 CPU's, so it
>> seems it is connected to the paralellism, maybe all CPU's think it
>> is their job to write the files? If so, they should be marked by CPU
>> #, so they don't overwrite each other.
>>
>> Anyone had this before?
>>
>> A coleague of mine had encountered this error before, but now I see it
>> myself also (for the first time). His system is a bilayer, receptor and
>> water and he gets many step*.pdb files (tens, or more). I'm not sure
>> how many CPU's he uses. In his case, this has resulted in a full disk
>> at least once, so there is a problem.
>>
>>
> 
> 



-- 
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Aldo Jongejan
Molecular Modeling Group
Dept. of Pharmacochemistry
Free University of Amsterdam
De Boelelaan 1083
1081 HV Amsterdam
The Netherlands

e-mail: jongejan at chem.vu.nl
tlf:    +31 (0)20 4447612
fax:    +31 (0)20 4447610

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