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

From: Douglas Houston (DouglasR.Houston_at_ed.ac.uk)
Date: Fri Dec 19 2014 - 08:33:31 CST

Thanks Jim, I'll check out the new binary and let you know. It might
take a few days to generate 2GB.

Quoting Jim Phillips <jim_at_ks.uiuc.edu> on Thu, 18 Dec 2014 22:30:55
-0600 (CST):

> Hi Douglass,
>
> I'm guessing your DCD file just hit 2 GB. I've tweaked the large
> file support code for Windows. Please let me know if this binary
> fixes it:
>
> http://www.ks.uiuc.edu/~jim/tmp/NAMD_2.10_Win64-multicore.zip
>
> Jim
>
>
> On Thu, 18 Dec 2014, Douglas Houston wrote:
>
>>
>> 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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