AMBER Archive (2009)

Subject: Re: [AMBER] Error in PMEMD run

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon May 04 2009 - 23:08:37 CDT

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" <maly_at_sci.ujep.cz>
To: "AMBER Mailing List" <amber_at_ambermd.org>
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=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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