AMBER Archive (2009)

Subject: RE: [AMBER] Error message for tutorial 1 (run in parallel)

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Mon May 04 2009 - 08:31:05 CDT

Dear Prof. Case,

 

Thank you. I solved this problem, as polyAT_wat_min2.rst was missing in the old directory. I redo the calculations again. This time the jobs start without problem. However, the works seems to stop at the location:

 

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 2968

 

--------------------------------------------------------------------------------------------------

 

I tried to do the calculations with single node, the jobs finished without an error. How can I double check if the jobs are visible to all the nodes?

 

Best regards & thanks,

 

 
> Date: Mon, 4 May 2009 08:40:36 -0400
> From: case_at_biomaps.rutgers.edu
> To: amber_at_ambermd.org
> Subject: Re: [AMBER] Error message for tutorial 1 (run in parallel)
>
> On Mon, May 04, 2009, Catein Catherine wrote:
> >
> > [supercomputer]$ mpirun -np 2 /share1/amber8/exe/sander -O -i
> > polyAT_wat_md1.in -o polyAT_wat_md1.out -p polyAT_wat.prmtop -c
> > polyAT_wat_min2.rst -r polyAT_wat_md1.rst -x polyAT_wat_md1.mdcrd -ref
> > polyAT_wat_min2.rst &
> > [1] 19207
> > [supercomputer]$
> > Unit 9 Error on OPEN: polyAT_wat_min2.rst
>
> This means that the indicated file could not be opened, either because
> it is not present, or because you do not have the correct permissions.
> Be sure your files are visible on all nodes, etc.
>
> >
> > Interestingly, when I do the calculations with the following command,
> > the job finished without error message using the same input files.
>
> I didn't see the difference between the invocation that worked and the
> one that did not; but if you can track down yourself what is different,
> that is probably a good clue.
>
> ...dac
>
>
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