Hi Marek,
Sorry for slow response - I am getting tied up in other things in the middle
of all this. Here's the deal. If you see the -lsvml in the config.h (you
are right - that was where you needed to look), then I strongly suspect you
are not setting up the environment right for ifort, or your ifort install is
bad somehow. Do you have a "source <path to ifort>/bin/ifortvars.csh" in
your .login file (for tcsh or csh) - or it should be to ifortvars.sh in
.bash_profile if you use bash? This script needs to be sourced before you
run your configure or compiles, and then the ifort library components can be
found. Now, actually, I would suspect all sorts of problems would arise if
this is not done, so maybe your ifort install is bad (libsvml.so is
missing). Perhaps you should do the following:
enter csh or tcsh (to put you in a csh session) if you don't already use csh
or tcsh as your login shell.
do a "source <path to ifort>/bin/ifortvars.csh" if this has not yet been
done
if you want to use mkl be sure you have sourced the file for it too...
Simpler to not do this for now though, and not use mkl or bintraj for that
matter.
do a "printenv >& printenv.out" and send output
redo the ./configure <your args> under pmemd dir - send the config.h
do a make clean under pmemd dir
do a make >& make.out under pmemd/src
It should have worked... If it doesn't, send various outputs.
Sorry this is such a pain; always hard to know details about remote hardware
and software.
Best Regards - Bob
----- Original Message -----
From: "Marek Malý" <maly.sci.ujep.cz>
To: "AMBER Mailing List" <amber.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.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.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.sci.ujep.cz>
>> To: "AMBER Mailing List" <amber.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.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.sci.ujep.cz>
>>> To: "AMBER Mailing List" <amber.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.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.sci.ujep.cz>
>>>> To: <amber.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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Received on Wed May 20 2009 - 14:55:44 PDT
