Dear Dr.Ross,
The results continues to be same even with NTX = 5. The error log
file shows the following -
forrtl: severe (64): input conversion error, unit 9, file
/mnt/home/singhvij/mdout800_1.rst
Image PC Routine Line Source
sander.MPI 00000000007E2492 Unknown Unknown Unknown
sander.MPI 00000000007E1692 Unknown Unknown Unknown
sander.MPI 0000000000798246 Unknown Unknown Unknown
sander.MPI 000000000074D63E Unknown Unknown Unknown
sander.MPI 000000000074CC5A Unknown Unknown Unknown
sander.MPI 000000000076D3A9 Unknown Unknown Unknown
sander.MPI 00000000004F4556 Unknown Unknown Unknown
sander.MPI 00000000004B8854 Unknown Unknown Unknown
sander.MPI 00000000004B2BAD Unknown Unknown Unknown
sander.MPI 0000000000405E32 Unknown Unknown Unknown
libc.so.6 00002BA629E1A154 Unknown Unknown Unknown
sander.MPI 0000000000405D6A Unknown Unknown Unknown
forrtl: error (78): process killed (SIGTERM)
Image PC Routine Line Source
sander.MPI 000000000073763F Unknown Unknown Unknown
sander.MPI 0000000000736740 Unknown Unknown Unknown
I have no idea of how to proceed from here.Incase needed, I am attaching the
"mdout800_1.rst" file for your perusal.
Thanks a lot,
Vijay
On Jan 11, 2008 3:04 PM, Vijay Singh <vijayratan.singh.gmail.com > wrote:
> Hi,
>
> Thanks for the response. I actually tried NTX = 5 too. Result was same
> as that with NTX=7. But, I will go ahead and try once again and may be wait
> a little more longer to see if the output file updates properly.
>
> Thanks again,
> Vijay
>
>
> On Jan 11, 2008 2:56 PM, Ross Walker < ross.rosswalker.co.uk> wrote:
>
> > Hi Vijay,
> >
> > The issue is that you are running a non-periodic simulation here (ntb=0)
> > but when you restart you are setting ntx=7 which tells sander to expect box
> > information from the input coordinate file. Since your input coordinate file
> > does not have any box info the code is hanging there waiting for that
> > information to be appended to the file. I realize we should probably find a
> > better way to do this in the code so it fails gracefully rather than just
> > hanging but this isn't always easy in parallel.
> >
> > Anyway, to answer your problem set ntx=5 and everything should be good.
> > Also note that with Amber 9 you can always set NTX=5 and it will auto load
> > the box info if you are running a periodic simulation. Thus ntx=7 is
> > actually deprecated as an option hence why it is no longer in the manual.
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Assistant Research Professor |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> > not be read every day, and should not be used for urgent or sensitive
> > issues.
> >
> >
> > ------------------------------
> > *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> > Behalf Of *Vijay Singh
> > *Sent:* Friday, January 11, 2008 09:30
> > *To:* amber.scripps.edu
> > *Subject:* AMBER: problems with restart of MD
> >
> > Hi,
> >
> >
> > Not sure if my messages are reaching the right destination. I did not
> > get any response on 2 different occasions earlier. Neverthless, another try.
> >
> > I am using amber9 and doing some very basic MD.I am having some trouble
> > with the restart of MD production run. Not sure where I am going wrong.
> > After initial minimization, the first part of run is fine
> >
> > The input files looks -
> >
> >
> > &cntrl
> > imin = 0, ntb = 0, irest = 0,
> > igb = 1, ntpr = 10000, ntwx = 1000,
> > ntt = 3, gamma_ln = 1.0,
> > temp0 = 800.0,tempi = 800.0,
> > nstlim = 40000000, dt = 0.001,
> > cut = 999
> > /
> >
> > mpiexec $AMBERHOME/exe/sander.MPI -O -i md_800k_1.in -o md800_1.out -c
> > t57c_min.rst -p t57c.prmtop -r mdout800_1.rst -x mdout800_1.mdcrd
> >
> >
> > Till this point I get all the output as needed. But the 2nd step below
> > is where I get stuck on the restart part, the input is as follows -
> >
> >
> > &cntrl
> > imin = 0, ntb = 0, irest = 1, ntx = 7,
> > igb = 1, ntpr = 10000, ntwx = 1000,
> > ntt = 3, gamma_ln = 1.0,
> > temp0 = 800.0,
> > nstlim =40000000, dt = 0.001,
> > cut = 999
> > /
> >
> > #mpiexec $AMBERHOME/exe/sander.MPI -O -i md_800k_2.in -o md800_2.out -c
> > mdout800_1.rst -p t57c.prmtop -r mdout800_2.rst -x mdout800_2.mdcrd
> >
> > From here I don't get any output. The mdout file stops with -
> >
> > Langevin dynamics temperature regulation:
> > ig = 71277
> > temp0 = 800.00000, tempi = 0.00000, gamma_ln= 1.00000
> > | INFO: Old style inpcrd file read
> >
> > ----------------------------------------------------------------------------
> > ----
> > 3. ATOMIC COORDINATES AND VELOCITIES
> > ----------------------------------------------------------------------------
> > ----
> >
> >
> > Could someone please help me on that.
> >
> > Regards
> > Vijay
> >
> >
>
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Received on Sun Jan 13 2008 - 06:07:33 PST
