AMBER Archive (2009)

Subject: [AMBER] Error in parallel run

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Wed May 06 2009 - 21:46:02 CDT

> From: askamber23_at_hotmail.com
> To: amber_at_ambermd.org
> Subject: RE: [AMBER] Error message in "make test.sander"
> Date: Wed, 6 May 2009 14:58:04 +0800
>
>
> Dear Ross,
>
>
>
> Thank you very much for your help. I tried to do a tutorial test in my home directory.
>
>
>
> [home directory]$ ls
> polyAT_wat_md1.in polyAT_wat_min2.rst polyAT_wat.prmtop
> [home directory]$ 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 &
>
>
>
> This time no error message appears, but the job (polyAT_wat_md1.out) hang at
>
>
> --------------------------------------------------------------------------------
> 3. ATOMIC COORDINATES AND VELOCITIES
> --------------------------------------------------------------------------------
>
>
> begin time read from input coords = 0.000 ps
>
> Number of triangulated 3-point waters found: 2968
>
>
> Under the same directory, I change the command line to "mpirun /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 &"
>
>
>
> The jobs finished quickly when only one node was used.
>
>
>
> I tried to compare the first (2 nodes) and the second (1 node) polyAT_wat_md1.out files, the first file hang before the following sentence:
>
>
>
> Running AMBER/MPI version on 1 nodes
>
>
> What is the indication of this error message? Should I make other changes to the system to solve this problem?
>
>
>
> Best regards,
>
>
>
> Cat
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