AMBER Archive (2009)

Subject: Re: [AMBER] Error in PMEMD run

From: Marek Malý (maly_at_sci.ujep.cz)
Date: Wed May 06 2009 - 13:30:43 CDT

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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