AMBER Archive (2009)

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

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Wed May 06 2009 - 00:40:54 CDT

Dear Ross,

 

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.

 

If it is the case, what else should I check or change? When you mean file system (do you mean the amber/exe folder?)? Right now, I have the ownership for the test directory. Do I need to have permission to other directories as well? As I can do the jobs using single node, does it mean that I should have permission right to assess system folders too? Please kindly help to give me more details about how to change the setting for AMBER parallel runs, as I am new to administrative works on supercomputer sytems.

 

Best regards and many thanks in advanced,

 

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 20:37:28 -0700
>
> Hi Catein,
>
> This looks to me like you don't have write permission to the test directory.
> If this works in serial but not in parallel it probably means that your
> computer system is not setup correctly. Either whichever user account is
> running the job in parallel does not have write permission or the file
> system is mounted read only on the nodes the actual job is running on.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> > Behalf Of Catein Catherine
> > Sent: Tuesday, May 05, 2009 7:52 PM
> > To: amber_at_ambermd.org
> > Subject: [AMBER] Error message in "make test.sander"
> >
> >
> > > Dear All,
> > >
> > >
> > >
> > > We compile amber 8 on our supercomputer without error message.
> > However, we found we cannot run parallel (the jobs idle). So, I do the
> > test.parallel according to the manual. Here is the error message that I
> > found. Could you mind to let me know what's does it mean?
> > >
> > >
> > >
> > > Best regards & thanks,
> > >
> > >
> > >
> > > Cat
> > >
> > >
> > >
> > > [supercomputer]$ set DO_PARALLEL 'mpirun -np 4'
> > > [supercomputer]$ make test.sander
> > > cd dmp; ./Run.dmp
> > >
> > > Unit 6 Error on OPEN: mdout.dmp
> > > [0] MPI Abort by user Aborting program !
> > > [0] Aborting program!
> > > p0_7963: p4_error: : 1
> > > ./Run.dmp: Program error
> > > make: *** [test.sander.no_lmod] Error 1
> > > [supercomputer]$
> > >
> > >
> > > _________________________________________________________________
> > > Drag n' drop-Get easy photo sharing with Windows LiveT Photos.
> > >
> > >
> > http://www.microsoft.com/windows/windowslive/products/photos.aspx______
> > _________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _________________________________________________________________
> > Windows LiveT: Keep your life in sync. Check it out!
> > http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t1_allup_explore_01200
> > 9_______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_________________________________________________________________
Drag n’ drop—Get easy photo sharing with Windows Live™ Photos.

http://www.microsoft.com/windows/windowslive/products/photos.aspx_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber