AMBER Archive (2006)

Subject: RE: AMBER: Re: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031

From: amit_at_mbu.iisc.ernet.in
Date: Wed May 10 2006 - 02:06:46 CDT

Dear Ross,
I have corrected my 1pfy.md.in file by removing one flag (npscale=1). Its
a retired flag in AMBER9. With the corrected md.in file I am getting a
different error while submitting the job in PBS enviorment (without PBS
working fine)
/altix_home/scratch/amit/amber9/exe/sander.MPI: relocation error:
/altix_home/scratch/amit/amber9/exe/sander.MPI: undefined symbol:
__powr8i4

sorry for replying late. Yesterday night I went to bed after submitting
the bug.
                    1pfy.md.in
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Equlibriation
 &cntrl
    imin=0,
    ntx=7, irest=1,
    ntpr=50, ntwr=500, iwrap=1, ntwx=500, ntwe=50,
    ntf=2, ntb=2, igb=0, scnb=2.0, scee=1.2,
    cut=10.0,
    nscm=50,
    nstlim=5000, dt=0.002,
    tempi=300., temp0=300., ntt=1, tautp=0.5, dtemp=0.,
    ntp=1, taup=0.5,
    ntc=2, tol=0.00001,
 &end
 &ewald
    vdwmeth=1,
 &end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

thanks in advance,
amit

> Dear Amit,
>
>> After compilation of amber9 (with intel compiler 9.0.033)
>> test.parallel
>> and test.serial went fine. I am getting following error when I have
>> submitted my own job as mpirun -np 8 sander.PMI -O -i 1pfy.md.in -o
>> 1pfy.110.out -p 1pfy.prm.top -c 1pfy.100.res -r 1pfy.110.res -x
>> 1pfy.110.crd
>>
>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> %%%%%%%%%%%%%%%%
>> forrtl: severe (19): invalid reference to variable in
>> NAMELIST input, unit
>> 5, file /altix_home/scratch/amit/MD/1pfy.md.in, line 11, position 28
>> MPI: MPI_COMM_WORLD rank 0 has terminated without calling
>> MPI_Finalize()
>> MPI: aborting job
>
> Does this calculation run in serial? It is always best to make sure your
> calculation will run at least a couple of steps in serial before trying to
> run a large parallel job.
>
> I suspect it is a problem with your input file. Either a typo, missing
> comma
> etc. Can you post the 1pfy.md.in file?
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | 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.
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu