AMBER Archive (2009)

Subject: [AMBER] Error message in "make test.sander" Is amber compatible with dual processors?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Wed May 06 2009 - 08:08:49 CDT

Dear Ross,

 

I asked the personel responsible for setup the supercomputers, they said they have done the setting correctly.

 

On the other hand, they suspect amber 8 did not compatible with dual processor, while amber 10 maybe OK. Is it true? Could you mind to let me know if the error message only happens in amber8?

 

Best regards,

 

Annie
 
> 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
>
>
> > 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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>
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