AMBER Archive (2006)

Subject: RE: AMBER: Error while running test.serial in Amber9

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed May 03 2006 - 10:21:42 CDT

Hi Priti,

Can you let me know some more details about your system please. That is the
operating system version, processor type (is it an Intel chip? P4 or
P4_EM64T?) and most importantly the compiler version you are using. If you
are using ifort do:

ifort -V and let me know what it says.

I have seen problems with the targetted MD test cases due to buggy
compilers. The intel compilers are notorious for being buggy. Especially any
of the version 8.0 ones. I recommend either:

v9.0.033 or v8.1.023

Both of these versions work fine for me.

Also let me know the options you used for configure (or alternatively copy
me your $AMBERHOME/src/config.h file).

Anyway, if you can send me more details I can try and help some more.

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Priti Hansia
> Sent: Wednesday, May 03, 2006 05:02
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Error while running test.serial in Amber9
>
>
> I had looked at the .dif files and only some values were differnet. I
> actually wanted to point out the last error:
>
> >>cd tgtmd/minimize; ./Run.tgtmin
> >>SANDER: Targeted minimization
> >> ./Run.tgtmin: Program error
> >>make: *** [test.sander.BASIC] Error 1
>
> I checked the 'tgtmin.out' file and following was written at
> the end of
> the file:
>
>
> 5. REFERENCE ATOM COORDINATES
>
>
> | INFO: Old style inpcrd file read
>
> Error in group input::atommask.f::residue_numlist
> error reading residue number
>
> I have no idea why it gave problem why test run. Should I fix
> something
> before running it ?
>
> Thanks,
>
> -Priti
>
>
>
> > did you look at the output .dif files as it is
> > telling you? what are the differences?
> >
> > Priti Hansia wrote:
> >
> >>Dear users,
> >>
> >>I have successfully installed Amber9 (serial) on my pc.
> After that I was
> >>testing the basic AMBER distribution as instructed. It was
> doing fine
> >>until it gave the following problem:
> >>
> >>cd tgtmd/change_target; ./Run.tgtmd
> >>SANDER: Targeted MD with changing target
> >>diffing tgtmd.out.save with tgtmd.out
> >>possible FAILURE: check tgtmd.out.dif
> >>==============================================================
> >>cd tgtmd/change_target.rms; ./Run.tgtmd
> >>SANDER: Targeted MD with changing target and fit/rmsd
> >> to different regions
> >>diffing tgtmd.out.save with tgtmd.out
> >>possible FAILURE: check tgtmd.out.dif
> >>==============================================================
> >>cd tgtmd/change_target.ntr; ./Run.tgtmd
> >>SANDER: Targeted MD with changing target and restraints
> >>diffing tgtmd.out.save with tgtmd.out
> >>PASSED
> >>==============================================================
> >>cd tgtmd/conserve_ene; ./Run.tgtmd
> >>SANDER: Targeted MD energy conservation test
> >>diffing tgtmd.out.save with tgtmd.out
> >>possible FAILURE: check tgtmd.out.dif
> >>==============================================================
> >>cd tgtmd/minimize; ./Run.tgtmin
> >>SANDER: Targeted minimization
> >> ./Run.tgtmin: Program error
> >>make: *** [test.sander.BASIC] Error 1
> >>
> >>and it didnt complete the test run. Can anybody please tell
> me why it has
> >>happened ?
> >>
> >>Thanks in advance.
> >>
> >>-Priti
>
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