AMBER Archive (2009)

Subject: RE: [AMBER] MKL error ?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Feb 03 2009 - 23:22:48 CST

Hi Marek,

> In the case of "make test.serial" and "make test.parallel" I obtained
> error:
>
> --------------------------------------
> MLK func load error: /opt/intel/mkl/10.0.011/lib/em64t/libmkl_vml_mc.so:
> undefined symbol: vmlGetErrorCallBack
> ./Run.circdna: Program error
> make: *** [test.sander.GB] Error 1
> ------------------------------------
>
> In the case of "make test.serial.QMMM" and "make test.parallel.QMMM" it
> was similar error:
>
> ----------------------------------------
> MLK func load error: /opt/intel/mkl/10.0.011/lib/em64t/libmkl_vml_mc.so:
> undefined symbol: vmlGetErrorCallBack
> ./Run.1NLN_internal: Program error
> make: *** [test.sander.QMMM] Error 1
> ----------------------------------------
>

I believe that this is a bug in MKL itself, essentially Intel has the symbol
mapping incorrect (or we may be linking it wrong but I don't think so).
There are two possible solutions for this. The first is to try to compile
statically this 'should' make the problem go away.

The second is to explicitly set the environment variable OMP_NUM_THREADS=1 -
I haven't fully verified this second fix but I think it should solve the
problem. Essentially make sure this gets set in /etc/bashrc or a similar
location (run script etc) so that whatever shell runs the job inherits this
environment variable.

An alternative options is to try a different version of MKL. I currently use
10.0.018 and do not see this problem although I haven't extensively checked
it since I normally compile statically.

Good luck,
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| 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 |

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