AMBER Archive (2007)

Subject: Re: AMBER: Re: Amber_ifort_x86_64 test error

From: Ilya Chorny (ichorny_at_gmail.com)
Date: Sun Dec 09 2007 - 12:11:52 CST

I only have one version of MKL( I do have different version for differetn
architechtures (i.e. 32, 64, and emt64). In the make log and in the error,
the linking is to the emt64.

Has anyone successfully compiled Amber 9 with MKL 10?

Thanks,

Ilya

On Dec 9, 2007 10:01 AM, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Hi Ilya,
>
> If this is for running production jobs then yes you should be using ifort
> over gfortran. That makes a 30% or more difference in performance. If it is
> only for local 'debugging / testing' on your local machine then you are fine
> sticking with gfortran.
>
> Note, while Dave says that MKL doesn't make much of a difference it can
> depend on what type of simulation you run, GB sims benefit more than PME
> sims. The QMMM calculations benefit quite a bit from MKL and in AMBER 10
> will benefit a signficantly (read > 50% for systems with more than 90 QM
> atoms) from MKL10 and other math libraries that have optimized diagonalizers
> in them.
>
> What seems weird with the error you are seeing below is that this is a
> runtime error that should have been picked up at compile time. Hence it
> looks to me like you are using a different version of MKL at runtime than
> you linked against at compile time. If this is a cluster you should probably
> check that each of the nodes has identical versions of MKL installed (in the
> same paths) as the login node. You should also check your environment
> variables are the same on the compute nodes as the one you compiled on.
>
> I would also suggest trying to compile statically so you don't run into
> these problems. This sometimes work, sometimes doesn't depending on whether
> statically linkable libraries are available. For MKL this is generally okay
> but I haven't tried it with v10 yet.
>
> Good luck,
>
> 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
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>
>
> ------------------------------
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Ilya Chorny
> *Sent:* Sunday, December 09, 2007 09:22
> *To:* amber_at_scripps.edu
> *Subject:* Re: AMBER: Re: Amber_ifort_x86_64 test error
>
> should I even be using ifort?
>
> On Dec 9, 2007 9:13 AM, David A. Case <case_at_scripps.edu> wrote:
>
> > On Sun, Dec 09, 2007, Ilya Chorny wrote:
> > >
> > >
> > > cd circ_dna; ./Run.circdna
> > >
> > > MKL func load error:
> > > /data0/software/intel/mkl/10.0.1.014/lib/em64t/libmkl_vml_mc.so:
> > undefined
> > > symbol: vmlGetErrorCallBack
> > > ./Run.circdna: Program error
> > > make: *** [test.sander.GB] Error 1
> > >
> >
> > Amber 9 was released before Intel had version 10 of the MKL libraries,
> > and
> > the calling sequences have been changed. Someone on the list who has
> > access
> > to version 10 might be able to post a bug-fix here.
> >
> > In the meantime, please realize the MKL has very little impact on
> > overall
> > performance, and you should probably just un-define your MKL_HOME
> > variable and
> > re-configure.
> >
> > ...dac
> >
> > -----------------------------------------------------------------------
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>
>
>
> --
> Ilya Chorny Ph.D.
>
> 

-- 
Ilya Chorny Ph.D.

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