AMBER Archive (2009)

Subject: Re: [AMBER] Error in PMEMD run

From: Marek Malý (maly_at_sci.ujep.cz)
Date: Wed May 06 2009 - 13:51:03 CDT

Dear Ross,
I don't know if your suggestion is after Bob's last info still valid but
anyway, please
find attached my pmemd "config.h" file and if you have any idea how to
change it
to obtain functional pmemd binary file please do it and send it to me.

Thank you very much in advance !

Best,

   Marek

Dne Wed, 06 May 2009 19:07:01 +0200 Ross Walker <ross_at_rosswalker.co.uk>
napsal/-a:

> 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
>> >>
>> >>
>> >>
>> >
>>
>> --
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  • application/octet-stream attachment: config.h

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