From: xiaojing gong (gongxiaojing1981_at_yahoo.com.cn)
Date: Thu Jun 29 2006 - 23:56:51 CDT
Hi,
when I run the NAMD, it would run some time and gave me an error message saying FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE.
Then I used VMD to see the structure of my protein, I saw the last line saying syntax error, I use the confinement to Arg197 residues, Did the error caused by the confinement?
Dong Luo <us917_at_yahoo.com> 写道：
Ok, I noticed your NAMD is a MPI version, that means
there is no need to use charmrun to initiate the job.
Alternately, just use the one available in your MPI
system. And also you may not need to use the script to
find available nodes as the system may do it
automatically. You can check this link:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/3344.html
In my case, poe is used.
--- xiaojing gong
wrote:
> Thank you for your attention, the following is the
> lsf file, I bsub the lsf file to run my programm.
>
> Dong Luo 写道： Since you are
> using bsub, I think there is no need to
> use nodelist. In your case, NAMD took the first
> option
> as input configuration file, that's not what you
> want.
> Could you show me your submitted job file?
>
> --- xiaojing gong
> wrote:
>
> > Dear all,
> > When I run NAMD on cluster, it will
> > becoming run at one cpu after some time, BUT I
> bsub
> > the job on 8 cpus, and the following is the error
> > messages.
> > can you give me some suggestions?
> > Info: NAMD 2.5 for Linux-amd64-MPI
> > Info:
> > Info: Please visit
> > http://www.ks.uiuc.edu/Research/namd/
> > Info: and send feedback or bug reports to
> > namd_at_ks.uiuc.edu
> > Info:
> > Info: Please cite Kale et al., J. Comp. Phys.
> > 151:283-312 (1999)
> > Info: in all publications reporting results
> obtained
> > with NAMD.
> > Info:
> > Info: Based on Charm++/Converse 0143160 for
> > mpi-linux-gm2-opteron
> > Info: Built Mon Jan 17 21:19:25 CST 2005 by fgf on
> > gbnode002
> > Info: Sending usage information to NAMD developers
> > via UDP. Sent data is:
> > Info: 1 NAMD 2.5 Linux-amd64-MPI 8 ganode002
> > tzhang
> > Info: Running on 8 processors.
> > Info: 2100 kB of memory in use.
> > Measuring processor speeds... Done.
> > Info: Found 3 config files.
> > Info: Configuration file is ++nodelist
> > FATAL ERROR: Simulation config file is not
> > accessible.
> > FATAL ERROR: Simulation config file is not
> > accessible.
> > [0] MPI Abort by user Aborting program !
> > [0] Aborting program!
> >
> >
> >
> > ---------------------------------
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APP_NAME=fourcpus
> NP=20
> NP_PER_NODE=4
> RUN="RAW"
>
> rm -f $PWD/namd2.nodelist
>
>
> #start creating .nodelist
> echo 'group main' >$PWD/namd2.nodelist
>
> for i in `echo $LSB_HOSTS`
> do
> echo "host "$i >> $PWD/namd2.nodelist
> done
>
>
> echo
> "------------------------------------------------"
> /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/charmrun
> /home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/namd2
> +p20 ++nodelist $PWD/namd2.nodelist
>
/home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/13_APRIL/compare_sys_HSE/md1.config>/home/user/siap/Gong_NAMD_2.6b1_Linux-amd64/13_APRIL/compare_sys_HSE/log1.log
>
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