AMBER Archive (2007)

Subject: RE: AMBER: Re: Amber_ifort_x86_64 test error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Dec 09 2007 - 12:01:57 CST

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
 

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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.

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