There are three main standard streams in UNIX (and Windows, too, I
believe). These are the standard input, standard output, and standard
error. Each has its own default *place* that it writes to or reads from.
By default, standard output and standard error both write to the screen but
they can, in principle, be separated.
Many batch systems (like torque, moab, other PBS queuing systems) allow you
to specify a file that the different output streams are sent to. Everything
printed to standard output by the master thread is sent to the mdout file,
but slave threads send their output to the device's standard output (or
standard error). This is, by default, the screen. However, in cluster
computing environments this is often redirected to another file.
If you are running on a cluster, the documentation describing how to run on
the cluster should say where the stdout and stderr goes. If it doesn't, one
of your system administrators should be able to help you with this question
(they should know what I'm talking about).
Good luck!
Jason
On Fri, Jan 28, 2011 at 11:33 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>wrote:
> 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
> > > >> >
> > > >>
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 28 2011 - 09:00:09 PST
