AMBER Archive (2005)

Subject: RE: Re[2]: AMBER: AMBER compilation with -DREM

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Nov 30 2005 - 10:26:29 CST

Hi Sergey,

> Then, I tried to test parallel AMBER8 installation. I did the
> following:
> cd /usr/local/amber8/test
> make test.sander
> I've got the following:
>
> cd cytosine; ./Run.cytosine
> 2 - MPI_BCAST : Message truncated
> [2] Aborting program !
> [2] Aborting program!
> p2_3013: p4_error: : 14
> Broken pipe
> Broken pipe
> diffing cytosine.out.save with cytosine.out
> possible FAILURE: check cytosine.out.diff

What are you setting the environment variable DO_PARALLEL to? This needs to
be set to what you use to start a parallel job on your machine. If your
system requires you to do some kind of queue submission for parallel jobs
then you may have trouble running the test cases.

> Further, I tried to run usual job like the following:
>
> bsub -o lsf33.log -n 18 sander -O -i 4.in -o 4.out -p
> 1.prmtop -c 3.rst -r 4.rst -x 4.mdcrd
 
> and this is working.

Is this what you did for DO_PARALLEL with the test cases? What is bsub? It
must be part of your queuing system. It is probably best that you speak to
the person who setup the machine and queue so they can take a look at
things...
 
> However, when I tried to run usual simulation with the
> following command:
>
> mpirun -np 18 sander -O -i 4.in -o 4.out -p 1.prmtop -c 3.rst
> -r 4.rst -x 4.mdcrd
>
> I've got the following:
>
> Warning: Command line arguments for program should be given
> after the program name. Assuming -O is a

You may need to provide the full path to the sander executable. E.g.

mpirun -np 18 /usr/local/amber8/exe/sander -O .....

Note running a regular MD job with a non power of 2 number of processors is
not recommended. And in AMBER 8 will not work. For and REMD job it is fine,
just for regular MD it is not...

Note, all nodes must be able to see the sander executable in the same place
and also see the input and prmtop file in the same place. Make sure this is
the case.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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