AMBER Archive (2006)

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

From: amit_at_mbu.iisc.ernet.in
Date: Tue May 09 2006 - 13:32:52 CDT

Dear Ross,
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
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

thanks in advance,
amit

> Hi All,
>
> Seeing as a number of people seem to be having problems with Amber 9 on
> SGI
> Altix and other IA64 machines I thought I would post the following
> information that myself and Roberto Gomperts have been able to glean...
>
> First of all if you are trying to compile AMBER 9 on an IA64 machine using
> version 9.0 of the Intel compilers up to and including:
>
> F: Version 9.0 Build 20051201 Package ID: l_fc_c_9.0.031
> C: Version 9.0 Build 20051201 Package ID: l_cc_c_9.0.030
>
> You will have problems with Amber 9. The newer compilers .033 and later
> seem
> to be okay as do the 8.1 compilers. Just to clarify here: THIS IS INTEL'S
> FAULT - IT IS A BUG IN THEIR COMPILERS...
>
> My advice is to try and obtain the latest version of the compilers from
> http://premier.intel.com and use this to build Amber 9.
>
> A "temporary" work around is to do the following:
>
> cd $AMBERHOME/src/sander
>
> Change line 484 of the file depend from
>
> $(FC) -c $(FOPTFLAGS) -o $@ _ene.f
> to
> $(FC) -c $(FFLAGS) -o $@ _ene.f
>
> Then do 'make clean' and then rebuild Amber.
>
> 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.
>
>
>

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