[gmx-users] more than 2 step*.pdb files?
aldo jongejan
jongejan at few.vu.nl
Wed Jun 4 14:33:01 CEST 2003
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.
>>
>>
>
>
--
###########################################
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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