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.rosswalker.co.uk
> To: amber.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.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.
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_________________________________________________________________
Show them the way! Add maps and directions to your party invites.
http://www.microsoft.com/windows/windowslive/products/events.aspx
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 20 2009 - 14:50:32 PDT
