Hi,
As Carlos suggested
(> try running it single processor as a test- sometimes if there is an
> error message on one of the non-master nodes it won't go in the output
> file.)
I am now trying to run the same job in a single processor. But as obvious
it is taking much time. So its still running without any error (For clustar
run, the mdout file ceased after 17000steps, so I think it will take time to
give error this time)
I didnt understand what Jason is suggesting. I am sorry for inconvenience
but how can I incorporate the stdout in a file. I googled the term as well
but didnt get any idea how to read from stdout file. Please elaborate in
this. Currently I am using mpi script. The sander command of which is as
mentioned below:
mpirun -np 16 sander.MPI -O -i eq1.in -p fab.parm7 -c min2.rst -r eq1.rst
-ref min2.rst -o eq1.out
On Fri, Jan 28, 2011 at 8:12 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Carlos raised a good point. All data is written to standard output which
> for the master node is the output file. Slave threads will output to
> stdout
> instead of mdout, so the error might be found in the stdout file (specified
> by #PBS -o output if you are using PBS scheduling). Can you include the
> output of this file?
>
> On Fri, Jan 28, 2011 at 9:23 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > try running it single processor as a test- sometimes if there is an
> > error message on one of the non-master nodes it won't go in the output
> > file.
> >
> >
> >
> > On Fri, Jan 28, 2011 at 9:18 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> > wrote:
> > > Yes, I checked for job status. and I found that it is still running. I
> > think
> > > that the amber installation in OK as all other jobs are running OK. I
> am
> > > runnning the job using MPI.
> > >
> > >
> > >
> > > On Fri, Jan 28, 2011 at 7:45 PM, Carlos Simmerling <
> > > carlos.simmerling.gmail.com> wrote:
> > >
> > >> it isn't clear that this is an amber problem.
> > >> did you check to see if the job is still running?
> > >> does your amber installation pass the test cases?
> > >>
> > >>
> > >> On Fri, Jan 28, 2011 at 8:58 AM, Hirdesh Kumar <
> hirdesh.iitd.gmail.com>
> > >> wrote:
> > >> > Hi All,
> > >> > I am tying to heat my system (protein + bound cofactor) slowly. I
> am
> > >> using
> > >> > ntt =3 with gamma_ln = 1.0, Below mentioned is the script which I
> am
> > >> using.
> > >> >
> > >> >
> > >> >
> > >> > Heating the system linearly with weak restraints
> > >> > &cntrl
> > >> > imin = 0,
> > >> > irest = 0,
> > >> > ntx = 1,
> > >> > ntb = 1,
> > >> > cut = 12,
> > >> > ntr = 1,
> > >> > ntc = 2,
> > >> > ntf = 2,
> > >> > tempi = 0.0,
> > >> > temp0 = 300.0,
> > >> > ntt = 3,
> > >> > ig = 20933
> > >> > gamma_ln = 1.0, nmropt=1,
> > >> > nstlim = 50000, dt = 0.002
> > >> > ntpr = 100, ntwx = 100, ntwr = 1000
> > >> > /
> > >> > &wt TYPE='TEMP0', istep1=0, istep2=40000,
> > >> > value1=0.1, value2=300.0, /
> > >> > &wt TYPE='DUMPFREQ',ISTEP1=10, /
> > >> > &wt TYPE='END' /
> > >> > Keep protein fixed
> > >> > 5.0
> > >> > RES 1 339
> > >> > END
> > >> > END
> > >> >
> > >> > The equilibration runs fine upto 9100 steps. After that there is* no
> > >> change
> > >> > in the mdout file* but the sander job is running. Previously I didnt
> > >> > included Ig value in my script so I thought that it may be due to Ig
> > >> value
> > >> > as I am using ntt=3. Next time I added the Ig value (a random
> number)
> > but
> > >> > this time also the run is upto 7100 steps after that there is no
> > change
> > >> in
> > >> > the mdout file.
> > >> >
> > >> > Below mentioned is the last line of my output file:
> > >> >
> > >> > NSTEP = 7000 TIME(PS) = 14.000 TEMP(K) = 49.27
> PRESS
> > =
> > >> > 0.0
> > >> > Etot = -211822.1441 EKtot = 5837.1249 EPtot =
> > >> > -217659.2690
> > >> > BOND = 323.1122 ANGLE = 956.0308 DIHED =
> > >> > 3200.9235
> > >> > 1-4 NB = 1056.0283 1-4 EEL = 14174.4148 VDWAALS =
> > >> > 35009.8809
> > >> > EELEC = -272523.6263 EHBOND = 0.0000 RESTRAINT =
> > >> > 143.9667
> > >> > EAMBER (non-restraint) = -217803.2357
> > >> > Ewald error estimate: 0.3030E-04
> > >> >
> > >>
> >
> ------------------------------------------------------------------------------
> > >> >
> > >> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
> > >> 0.000
> > >> >
> > >>
> >
> ===============================================================================
> > >> >
> > >> > NSTEP = 7100 TIME(PS) = 14.200 TEMP(K) = 50.36
> PRESS
> > =
> > >> > 0.0
> > >> > Etot = -211664.7202 EKtot = 5966.1111 EPtot =
> > >> > -217630.8314
> > >> > BOND = 312.2514 ANGLE = 957.5403 DIHED =
> > >> > 3192.0819
> > >> > 1-4 NB = 1062.4902 1-4 EEL = 14166.2999 VDWAALS =
> > >> > 34826.4805
> > >> > EELEC = -272299.1537 EHBOND = 0.0000 RESTRAINT =
> > >> > 151.1782
> > >> > EAMBER (non-restraint) = -217782.0095
> > >> > Ewald error estimate: 0.2147E-04
> > >> >
> > >>
> >
> ------------------------------------------------------------------------------
> > >> >
> > >> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
> > >> 0.000
> > >> >
> > >>
> >
> ===============================================================================
> > >> >
> > >> >
> > >> >
> > >> > Please suggest me where I am wrong..
> > >> >
> > >> > Thanks
> > >> > Hirdesh
> > >> > _______________________________________________
> > >> > AMBER mailing list
> > >> > AMBER.ambermd.org
> > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >
> > >>
> > >> _______________________________________________
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> > >>
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> > >
> >
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> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
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Received on Fri Jan 28 2011 - 09:00:06 PST
