AMBER Archive (2009)

Subject: Re: [AMBER] Error in PMEMD run

From: Robert Duke (
Date: Wed May 06 2009 - 12:30:43 CDT

Hi Marek,
Well, I have been plowing around in the intel MKL libraries, and the
unresolved symbol you list is not defined in either MKL 8 or 10, so that is
why trying to fix the mkl does not work. It is instead defined in (for shared libs) and libsvml.a (for static libs). Normally you
get the shared lib linked in by including
-lsvml in the link line, which should be happening in your config file (if
you look at the config data files, this happens for everything except
linux_p3_athlon.ifort, which is probably now broken, but also probably now
completely unused (hence folks are not complaining - any chance you were
using this one?)). SO this is NOT an mkl problem, but a problem getting to
an svml function, perhaps called by some other function. Okay, so first
question - are you setting up the ifort environment in the manner specified
by the compiler (you source something like
/opt/intel/fc/10.whatever/bin/ifortvars.csh or depending on
which shell you use). You need to do an equivalent thing for MKL, by the
way. Then if you did not specify linux_p3_athlon, what exactly did you use
when you ran configure? We are finally narrowing it down... Sorry I did
not pick up on this right away - so many math function linkage problems
source from the chaos surrounding the interface to MKL.
Best Regards - Bob

----- Original Message -----
From: "Marek Malý" <>
To: "AMBER Mailing List" <>
Sent: Wednesday, May 06, 2009 11:58 AM
Subject: Re: [AMBER] Error in PMEMD run

Dear Bob,

unfortunately your "configure patch" didn't help me.

I tried just configure pmemd with your new configure file and run
the simulation (with still the same error), then I also made a new
compilation of of the pmemd after configuration with new cofigure file,
but there is again the same error (undefined symbol: __svml_cos2).

Anyway regarding to your question about version of our ifort compiler.
Our actual version is this: "Intel(R) 64, Version 10.1 Build 20080112
Package ID: l_fc_p_10.1.012"

If you have no other idea, probably will be for this moment the best
solution to use pmemd without
MKL. If pmemd uses MKL just for the implicit solvent calculations, it will
be acceptable for me
now since as I wrote sooner. Now I am dealing just with explicit solvent

So please tell me what all (lines/sentences) I should delete from the
configure file to prevent
linking pmemd with MKL and which configure file (original or your's) I
have to use now.
I assume that in this situation doesn't matter.

  Thank you very much in advance !



Dne Tue, 05 May 2009 06:08:37 +0200 Robert Duke <>

> Okay, attempt at a late-night fix. Attached is a tar ball for pmemd
> configuration, basically with two files. If you untar this, it will
> expand
> into a config_stuff dir. This then contains a new "configure" and a new
> config_data/interconnect.intelmpi (which you maybe can use if you really
> have intel mpi). So copy the two files into your existing pmemd tree
> (saving old files first, just in case), and rerun ./configure in the
> pmemd
> directory, and hopefully all will be well.
> Regards - Bob
> ----- Original Message -----
> From: "Marek Malý" <>
> To: "AMBER Mailing List" <>
> Sent: Monday, May 04, 2009 10:19 PM
> Subject: Re: [AMBER] Error in PMEMD run
> Dear Bob,
> actually we have installed MKL version 10.0.011 as it is clear from the
> "env list" below. Recently I would like to use PMEMD just
> for the explicit solvent simulations, but of course I would be happy to
> have possibility use PMEMD also for the implicit
> solvent calculations. So I will appreciate any idea which can help to fix
> this problem.
> Thanks in advance !
> Best,
> Marek
> MANPATH=/opt/intel/mkl/10.0.011/man:/opt/intel/cce/9.1.043/man:/opt/intel/fce/10.1.012/man:/usr/local/share/man:/usr/share/man:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.16.1/man:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.1/man
> INTEL_LICENSE_FILE=/opt/intel/fce/10.1.012/licenses:/opt/intel/licenses:/home/mmaly/intel/licenses:/Users/Shared/Library/Application
> Support/Intel/Licenses:/opt/intel/cce/9.1.043/licenses:/opt/intel/licenses:/home/mmaly/intel/licenses
> TERM=xterm
> SHELL=/bin/bash
> SSH_CLIENT= 37849 22
> LIBRARY_PATH=/opt/intel/mkl/10.0.011/lib/em64t
> SGE_CELL=default
> FPATH=/opt/intel/mkl/10.0.011/include
> SSH_TTY=/dev/pts/3
> USER=mmaly
> LD_LIBRARY_PATH=/opt/intel/impi/3.1/lib64:/opt/intel/mkl/10.0.011/lib/em64t:/opt/intel/cce/9.1.043/lib:/opt/intel/fce/10.1.012/lib::/opt/intel/impi/3.1/lib64
> LS_COLORS=no=00:fi=00:di=01
> CPATH=/opt/intel/mkl/10.0.011/include
> PAGER=/usr/bin/less
> CONFIG_PROTECT_MASK=/etc/fonts/fonts.conf /etc/terminfo
> MAIL=/var/mail/mmaly
> PATH=/opt/intel/impi/3.1/bin64:/opt/intel/cce/9.1.043/bin:/opt/intel/fce/10.1.012/bin:/usr/local/bin:/usr/bin:/bin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.1.1:/opt/intel/cce/9.1.043/bin:/opt/intel/fce/10.1.012/bin:/opt/intel/impi/3.1/bin:/opt/intel/idbe/9.1.043/bin:/opt/intel/idbe/10.1.012/bin:/opt/intel/etc:/opt/amber/exe:/opt/sge/bin/lx24-amd64
> PWD=/home/mmaly
> EDITOR=/bin/nano
> SGE_ROOT=/opt/sge
> MKL_HOME=/opt/intel/mkl/10.0.011
> INTEL_PATHS=/opt/intel/cce/9.1.043/bin:/opt/intel/fce/10.1.012/bin:/opt/intel/impi/3.1/bin:/opt/intel/idbe/9.1.043/bin:/opt/intel/idbe/10.1.012/bin:/opt/intel/etc
> HOME=/home/mmaly
> DYLD_LIBRARY_PATH=/opt/intel/fce/10.1.012/lib
> PYTHONPATH=/usr/lib64/portage/pym
> LESS=-R -M --shift 5
> LOGNAME=mmaly
> CVS_RSH=ssh
> SSH_CONNECTION= 37849 22
> MPI_HOME=/opt/intel/impi/3.1
> INFOPATH=/usr/share/info:/usr/share/binutils-data/x86_64-pc-linux-gnu/2.16.1/info:/usr/share/gcc-data/x86_64-pc-linux-gnu/4.1.1/info:/usr/share/info/emacs-22
> INCLUDE=/opt/intel/mkl/10.0.011/include
> AMBERHOME=/opt/amber
> _=/usr/bin/env
> Dne Tue, 05 May 2009 03:35:54 +0200 Robert Duke <>
> napsal/-a:
>> 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
>> Marek

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