VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Dec 19 2014 - 02:45:26 CST

So you connect this problem to the dcd file hitting the 2GB mark? What file
system do you use?

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: Douglas Houston [mailto:DouglasR.Houston_at_ed.ac.uk]
> Gesendet: Freitag, 19. Dezember 2014 09:13
> An: Norman Geist
> Cc: namd-l_at_ks.uiuc.edu
> Betreff: Re: AW: namd-l: FATAL ERROR: seek failed while writing DCD
> file: No such file or directory
>
> 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.