AMBER Archive (2007)

Subject: RE: AMBER: MPI error message

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jul 23 2007 - 12:56:35 CDT

Hi Taryn,
 
The first error is correct it is your prmtop file that has problems - take a
look at it and see if you can see anything wrong. How did you copy this over
to the machine you are running on? Check it didn't get converted to DOS
format or anything strange during the transfer.
 
I would also suggest just trying to run it interactively first on the
machine - for 10 seconds or so, just to check it works okay. Often when you
use a queuing system the errors can get printed to a different file or lost
altogether making hard to work out what went wrong. This is even more so
when running in parallel so you should always verify that you can run, at
least a couple of MD steps, in serial before running in parallel.
 
With regards to the tutorials I will attempt to update these. These were
originally written for Amber 8 where both the serial and parallel versions
were called sander - (so that you had to compile them in different
directories). In Amber 9 the serial version is called sander and the
parallel version (sander.MPI) such that it can all be built in one
directory.
 
I'll add a note to this effect to the tutorials.
 
All the best
Ross
 

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Taryn Hartley
Sent: Monday, July 23, 2007 10:39
To: amber_at_scripps.edu
Subject: AMBER: MPI error message

Regarding using Sander on Amber9 to run an MD simulation, my pbs script
included AMBERHOME/exe/sander and was receiving this error message:
MPI: co-compute1: 0x34b5000042df8b72: forrtl: severe (64): input conversion
error, un
it 8, file /u/ac/thartley/test/bundlewat.prmtop
MPI: co-compute1: 0x34b5000042df8b72: Image PC
Routine
         Line Source
MPI: co-compute1: 0x34b5000042df8b72: sander 4000000000C91390
Unknown
            Unknown Unknown
MPI: co-compute1: 0x34b5000042df8b72: sander 4000000000C8C560
Unknown
            Unknown Unknown
MPI: co-compute1: 0x34b5000042df8b72: sander 4000000000C34250
Unknown
            Unknown Unknown
MPI: co-compute1: 0x34b5000042df8b72: sander 4000000000B882E0
Unknown
            Unknown Unknown
MPI: co-compute1: 0x34b5000042df8b72: sander 4000000000B87810
Unknown
            Unknown Unknown
MPI: co-compute1: 0x34b5000042df8b72: sander 4000000000BCB6B0
Unknown
            Unknown Unknown
MPI: co-compute1: 0x34b5000042df8b72: sander 40000000001B13C0
Unknown
            Unknown Unknown
MPI: co-compute1: 0x34b5000042df8b72: sander 400000000018B850
Unknown
            Unknown Unknown
MPI: co-compute1: 0x34b5000042df8b72: sander 40000000001874F0
Unknown
            Unknown Unknown
MPI: co-compute1: 0x34b5000042df8b72: sander 4000000000003D40
Unknown
            Unknown Unknown
MPI: co-compute1: 0x34b5000042df8b72: libc.so.6.1 2000000001D0DC50
Unknown
            Unknown Unknown
MPI: co-compute1: 0x34b5000042df8b72: sander 4000000000003A80
Unknown
            Unknown Unknown
MPI: could not run executable (case #4)

It was suggested to me to add .MPI after sander (AMBERHOME/exe/sander.MPI),
which I did, and now my error message reads as follows:
set_SCR: using existing PBS job directory /scratch/batch/204612
forrtl: severe (64): input conversion error, unit 8, file
/u/ac/thartley/test/bundlewat.prmtop
Image PC Routine Line Source

  
sander.MPI 40000000007F3CD0 Unknown Unknown Unknown
sander.MPI 40000000007EEEA0 Unknown Unknown Unknown
sander.MPI 4000000000796B90 Unknown Unknown Unknown
sander.MPI 40000000006EEEE0 Unknown Unknown Unknown
sander.MPI 40000000006EE410 Unknown Unknown Unknown
sander.MPI 4000000000731DF0 Unknown Unknown Unknown
sander.MPI 40000000001CAA00 Unknown Unknown Unknown
sander.MPI 40000000001A4650 Unknown Unknown Unknown
sander.MPI 4000000000194BC0 Unknown Unknown Unknown
sander.MPI 4000000000004840 Unknown Unknown Unknown
libc.so.6.1 2000000005791C50 Unknown Unknown Unknown
sander.MPI 4000000000004580 Unknown Unknown Unknown
MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
MPI: aborting job

Is it my .prmtop file as the 2nd line indicates? .MPI was not used in the
PBS script in the tutorials (which I executed successfully before attempting
my own project) and that is what I am using as my guide. Help?

-Taryn

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