AMBER Archive (2009)

Subject: RE: [AMBER] Error message in "make test.sander"

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Wed May 06 2009 - 01:58:04 CDT

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

 
> From: ross_at_rosswalker.co.uk
> To: amber_at_ambermd.org
> Subject: RE: [AMBER] Error message in "make test.sander"
> Date: Tue, 5 May 2009 23:28:01 -0700
>
> Hi Catherine,
>
> > I have the owership to the test directory, and I run the jobs in the
> > test directory. I tried to open the mdout.dmp file and write some
> > words and save the files. It seems to me that I have the right to
> > write to this file too.
> >
>
> The issue is not whether you have write permission to the file on the login
> node but that the user account that runs the parallel calculation on the
> 'compute' node has permission to write to this file. How this is setup and
> specifically how this works is likely specific to your supercomputer setup.
> Who setup the machine for you? Can you check with them to make sure you have
> write permission on compute nodes to the $AMBERHOME/test directory?
>
> Try running a calculation manually in your home directory - you can take one
> of the DNA inputs from tutorial B1 on http://ambermd.org/tutorials/
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
>
>
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