AMBER Archive (2009)

Subject: Re: [AMBER] Error in PMEMD run

From: Robert Duke (
Date: Mon May 04 2009 - 20:35:54 CDT

This looks to me like an MKL linkage problem. If you don't need generalized
Born, you can make this go away by simply not choosing to use MKL when you
run pmemd configure. Otherwise, we do have more recent directions that work
with the latest versions of MKL. If you want to use this, let me know your
version of MKL and I will dig up the appropriate new version of pmemd
configure that should work (I think I have posted fixed versions to the list
before; we should probably release a patch, but in the meantime I can dig
out the last posting if you want GB support with MKL).
Best Regards - Bob Duke
----- Original Message -----
From: "Marek Malý" <>
To: <>
Sent: Monday, May 04, 2009 9:23 PM
Subject: [AMBER] Error in PMEMD run

Dear amber users,

I have installed Amber10 in our cluster some time ago. Now I started
with some calculations and I have problem with PMEMD.

When I try to switch (after minimisation, heating and density equilibrium
phases) from SANDER
to PMEMD, my calculation is broken starting with this error line:

"symbol lookup error: /opt/amber/exe/pmemd: undefined symbol: __svml_cos2"

Without switching to PMEMD everything is OK, it means SANDER works
perfectly but since
I am working on big systems (hundreds thousands of atoms ) typically 32-64
CPUs jobs,
I would like to use PMEMD for my equil/production runs.

I would be grateful for any useful info.

With the best wishes


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