AMBER Archive (2009)

Subject: Re: [AMBER] Error in PMEMD run

From: Robert Duke (rduke_at_email.unc.edu)
Date: Wed May 06 2009 - 14:29:41 CDT

Hi Marek,
As an additional note, I did look at your config.h, and it looks to me like
the ifort setup should be fine, so I am pretty puzzled as to what is going
on. If it still doesn't work, please send some additional info about your
hardware setup; I would note that I use ifort 10.1.021 all the time without
problems, but don't know if there is something odd about 012 or not.
Best Regards - Bob

----- Original Message -----
From: "Marek Malý" <maly_at_sci.ujep.cz>
To: "AMBER Mailing List" <amber_at_ambermd.org>
Sent: Wednesday, May 06, 2009 2:42 PM
Subject: Re: [AMBER] Error in PMEMD run

Sorry now I realised that you probably talked about "config.h" not about
configure file,
so please find this pmemed config file attached - there is "-lsvml"
present.

So if it is necessary to modify this file please tell me how or please
edit it and send
back.

   Thanks a lot !

    Best,

      Marek

Dne Wed, 06 May 2009 20:30:43 +0200 Marek Malý <maly_at_sci.ujep.cz>
napsal/-a:

> Dear Bob,
>
> I am definitively getting lost :))
>
> OK, first of all nor the original nor your config file for pmemd obtain
> "-lsvml" parameter.
> Simply this string doesn't exist in this file please see the attached
> file
> "configure" (this is that your
> last version which you sent me). In confiuguration file for Amber -
> please
> see attached file "configure_amber"
> there is one occurrence of this parameter in part "IA32 Intel compilers".
>
> Here is the whole path to our ifort compiler:
>
> /opt/intel/fce/10.1.012/bin/ifort
>
> all the others paths are listed in my previous email (please see below)
> there
> is list after performing "env" command.
>
> My config line for pmemd is this:
>
> ./configure linux_em64t ifort intelmpi pubfft bintraj
>
> If I can provide you more useful information please just let me know.
>
> For this moment thank you veru much for your time and effort !
>
> Best,
>
> Marek
>
>
>
>
>
>
> Dne Wed, 06 May 2009 19:30:43 +0200 Robert Duke <rduke_at_email.unc.edu>
> napsal/-a:
>
>> 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
>> libsvml.so (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
>> ifortvars.sh 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" <maly_at_sci.ujep.cz>
>> To: "AMBER Mailing List" <amber_at_ambermd.org>
>> 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
>> 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/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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