From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 19 2014 - 12:10:47 CST

I saw that Jim committed a change to the NAMD CVS for DCD writing on
Windows, so I'm guessing this is fixed in the latest nightly builds.

Cheers,
  John Stone

On Fri, Dec 19, 2014 at 09:45:26AM +0100, Norman Geist wrote:
> 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.
>
>

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