AMBER Archive (2009)

Subject: Re: [AMBER] Error in PMEMD run

From: Marek Malý (maly_at_sci.ujep.cz)
Date: Mon May 04 2009 - 21:19:20 CDT

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=192.168.0.15 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
SGE_EXECD_PORT=537
EDITOR=/bin/nano
SGE_QMASTER_PORT=536
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
SHLVL=1
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
GCC_SPECS=
CVS_RSH=ssh
SSH_CONNECTION=192.168.0.15 37849 192.168.0.13 22
MPI_HOME=/opt/intel/impi/3.1
LESSOPEN=|lesspipe.sh %s
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 <rduke_at_email.unc.edu>
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" <maly_at_sci.ujep.cz>
> To: <amber_at_ambermd.org>
> 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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