Re: AW: FATAL ERROR: seek failed while writing DCD file: No such file or directory

From: Maxime Boissonneault (maxime.boissonneault_at_calculquebec.ca)
Date: Fri Dec 19 2014 - 08:18:38 CST

If the problem is 2GB size, it may very well be a limit of your
filesystem. Relatively many filesystems (including most older
filesystems like FAT32) have a file size limit of 2GB or less.
http://en.wikipedia.org/wiki/Comparison_of_file_systems

Maxime Boissonneault

Le 2014-12-19 03:12, Douglas Houston a écrit :
> So far, it has occurred once. That's not to say it won't occur again
> since I fully expect the .dcd file to hit 2GB during every run.
>
> Is the way NAMD handles I/O unusual in some way? I seem to be having
> "writing to file" problems on both Linux and on Windows.
>
>
>
> Quoting Norman Geist <norman.geist_at_uni-greifswald.de> on Fri, 19 Dec
> 2014 07:35:26 +0100:
>
>> Did this error occur more often than only this one time? If not,
>> ignore it.
>>
>> Norman Geist.
>>
>>> -----Ursprüngliche Nachricht-----
>>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>>> Auftrag von Douglas Houston
>>> Gesendet: Donnerstag, 18. Dezember 2014 21:40
>>> An: namd-l_at_ks.uiuc.edu
>>> Betreff: namd-l: FATAL ERROR: seek failed while writing DCD file: No
>>> such file or directory
>>>
>>>
>>> What might cause this error after 4 days of perfectly stable running?
>>>
>>>
>>>
>>> ENERGY: 46995750 11.9575 24.2251 13.3193
>>> 2.0010
>>> -7508.1727 660.7055 0.0000 0.0000
>>> 1292.5420
>>> -5503.4224 316.3603 -6795.9644 -5500.2671
>>> 309.1678
>>> 40.4566 74.5755 20513.9582 -13.2123
>>> -13.1010
>>>
>>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>>> Reason: FATAL ERROR: seek failed while writing DCD file: No such file
>>> or directory
>>>
>>> Charm++ fatal error:
>>> FATAL ERROR: seek failed while writing DCD file: No such file or
>>> directory
>>>
>>> PRESSURE: 46996000 515.269 -916.628 -377.656 -916.628 -425.468
>>> -292.049 -377.65
>>> 6 -292.049 1306.75
>>> GPRESSURE: 46996000 838.768 -953.714 96.0755 -560.366 -409.768
>>> -323.975 -1019.3
>>> 4 -150.47 1064.65
>>> PRESSAVG: 46996000 -4.66517 -78.6176 -210.973 -78.6176 -76.796 264.706
>>> -210.973
>>> 264.706 168.085
>>> GPRESSAVG: 46996000 -4.93746 -79.6884 -210.48 -78.943 -73.9752 267.019
>>> -209.898
>>> 265.595 165.364
>>> ENERGY: 46996000 7.8038 30.5784 14.2287
>>> 3.5330
>>> -7659.5336 751.1412 0.0000 0.0000
>>> 1325.1116
>>> -5527.1369 324.3320 -6852.2485 -5524.1883
>>> 314.2416
>>> 465.5161 497.8826 20432.6083 28.8746
>>> 28.8170
>>>
>>> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 46996000
>>> WRITING COORDINATES TO DCD FILE ionized_run2.dcd AT STEP 46996000
>>> FATAL ERROR: seek failed while writing DCD file: No such file or
>>> directory
>>>
>>>
>>>
>>> The file is there in the correct directory. I restarted the job and it
>>> appears to be running again quite happily.
>>>
>>> I'm running Windows 7 64 bit; reading/writing to a local drive;
>>> "NAMD_2.10_Win64-multicore/namd2 +p4 namdrun.conf" is the command I
>>> used.
>>>
>>>
>>>
>>> --
>>> The University of Edinburgh is a charitable body, registered in
>>> Scotland, with registration number SC005336.
>>
>>
>>
>>
>
>
>
>
> _____________________________________________________
> Dr. Douglas R. Houston
> Lecturer
> Institute of Structural and Molecular Biology
> Room 3.23, Michael Swann Building
> King's Buildings
> University of Edinburgh
> Edinburgh, EH9 3JR, UK
> Tel. 0131 650 7358
> http://tinyurl.com/douglasrhouston
>

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