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
I am definitively getting lost :))
OK, first of all nor the original nor your config file for pmemd obtain
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:
all the others paths are listed in my previous email (please see below)
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 !
Dne Wed, 06 May 2009 19:30:43 +0200 Robert Duke <rduke_at_email.unc.edu>
> 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
> be acceptable for me
> now since as I wrote sooner. Now I am dealing just with explicit solvent
> 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 !
> Dne Tue, 05 May 2009 06:08:37 +0200 Robert Duke <rduke_at_email.unc.edu>
>> 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
>> 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
>> 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
>> this problem.
>> Thanks in advance !
>> SSH_CLIENT=192.168.0.15 37849 22
>> CONFIG_PROTECT_MASK=/etc/fonts/fonts.conf /etc/terminfo
>> LESS=-R -M --shift 5
>> SSH_CONNECTION=192.168.0.15 37849 192.168.0.13 22
>> LESSOPEN=|lesspipe.sh %s
>> Dne Tue, 05 May 2009 03:35:54 +0200 Robert Duke <rduke_at_email.unc.edu>
>>> 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
>>> 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
>>> this, let me know your version of MKL and I will dig up the
>>> 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
>>> 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
>>> phases) from SANDER
>>> to PMEMD, my calculation is broken starting with this error line:
>>> "symbol lookup error: /opt/amber/exe/pmemd: undefined symbol:
>>> 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
>>> 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
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
- application/octet-stream attachment: configure
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