Fabien -
Well, your interpretation would be my first guess, but this is the sort of
stuff that does not get messed with a lot. If you would make a gzipped
tarball of all your input files and send it to me via email
(rduke.email.unc.edu) I will do a bit of debugging. What version of pmemd
are you using? Would that version of sander do the same sort of thing if
you did a small test run on 4 processors on the same machine?
Thanks - Bob Duke
----- Original Message -----
From: "Fabien Cailliez" <Fabien.Cailliez.ibpc.fr>
To: "AMBER" <amber.scripps.edu>
Sent: Thursday, January 20, 2005 5:39 AM
Subject: AMBER: pmemd and distance restraint
> Dear all,
>
> I am using pmemd to run a distance-restrained simulation on a. I have a
> weird message.
> I am running this simulation on 16 processors on SGI Origin 3800.
> The information output is :
> JID OWNER COMMAND
> ------------------ -------------- --------------
> 0x783d00000000d8a5 cailliez /usr/local/lsf4.1/etc/res -d
> /usr/local/lsf4.1/etc -m athena /home/caill
> iez/.ls
>
> LIMIT NAME USAGE HIGH USAGE CURRENT LIMIT MAX LIMIT
> ------------------ -------------- -------------- --------------
> --------------
> cputime 0 0 unlimited unlimited
> datasize 2480k 2480k unlimited unlimited
> files 14 19 8000 12000000
> vmemory 7440k 8224k unlimited unlimited
> ressetsize 3552k 4368k 8000000k 16g
> threads 0 0 unlimited unlimited
> processes 4 4 unlimited unlimited
> physmem 3552k 4368k unlimited unlimited
>
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
> Warning: Error opening "New" file from subroutine OPNMRG
> File =
>
> The simulation does not stop and everything seems to go well (except this
> message).
> There are 15 times the same repeat in the message an I am running my
> simulation on 16 processors.
> Can it be that all the processors want to open the same file ?
> Do I need to worry about this message ?
>
> Yours sincerely,
> Fabien
>
> My input files are :
> *************************************************************************
> ***************************** md.in *****************************
> *************************************************************************
> 100 ps MD production at constant T= 300K & P= 1Atm and coupling = 5.0
> &cntrl
> imin=0, ntx=7, ntpr=500, ntwr=500, ntwx=500, ntwe=500,
> nscm=500,
> ntf=2, ntc=2,
> ntb=2, ntp=1, tautp=5.0, taup=5.0,
> nstlim=50000, t=0.0, dt=0.002,
> cut=9.0,
> ntt=1,nmropt=1,
> irest=1
> &end
> # Distance restraint
> &wt type='DUMPFREQ', istep1=10, &end
> &wt type='END', &end
> DISANG=dist.900.in
> DUMPAVE=dist900_vs_t
>
> and the file DISANG is :
> #
> # 2 TRP CD2 37 ILE N 10
> &rst
> iat=36, 599, r1= 0.0, r2 = 9.0, r3 = 9.0, r4 = 999.0,
> rk2=50.0, rk3=50.0, ir6=0, ialtd=0,
> &end
>
> --
> __________________________________________________________________
> Fabien Cailliez Tel : 01 58 41 51 63 Laboratoire de Biochimie Théorique
> e-mail : cailliez.ibpc.fr
> IBPC 13, rue Pierre et Marie Curie 75005 Paris
> __________________________________________________________________
>
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Received on Thu Jan 20 2005 - 12:53:00 PST
