From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Fri Dec 19 2014 - 02:12:48 CST
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
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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