AMBER Archive (2009)

Subject: RE: [AMBER] Error in PMEMD run

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed May 06 2009 - 12:07:01 CDT

Hi Marek,

Try forcing static compilation that should, I hope, fix it - Add -static
after each entry of ifort (or mpif90) in the config.h file and make clean /
make

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Marek Malý
> Sent: Wednesday, May 06, 2009 8:59 AM
> To: AMBER Mailing List
> 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
> calculations.
>
> 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 !
>
> Best,
>
> Marek
>
>
>
>
>
>
>
> Dne Tue, 05 May 2009 06:08:37 +0200 Robert Duke <rduke_at_email.unc.edu>
> napsal/-a:
>
> > 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/int
> el/fce/10.1.012/man:/usr/local/share/man:/usr/share/man:/usr/share/binu
> tils-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/licen
> ses:/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/e
> m64t:/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/fc
> e/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/i
> ntel/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/10.1.01
> 2/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
> >>
> >>
> >>
> >
>
> --
> Tato zpráva byla vytvořena převratným poštovním klientem Opery:
> http://www.opera.com/mail/
>
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