AMBER Archive (2009)

Subject: Re: [AMBER] Error in PMEMD run

From: Marek Malý (maly_at_sci.ujep.cz)
Date: Wed May 06 2009 - 15:02:11 CDT

Hi Ross,

I just tested pmemd on the same (calculation) node where I have compilled
it, still with the same
error.

I also found in my personal notices that

compilation with this -static flag didn't proceed.

  ./configure_amber -intelmpi ifort -static

I can eventually try again to sent you which errors appeared during
compilation ...

But anyway thank you for your suggestions.

  Best,

    Marek

Dne Wed, 06 May 2009 21:41:10 +0200 Ross Walker <ross_at_rosswalker.co.uk>
napsal/-a:

> Hi Marek,
>
> Here is my take on what is going on here. It may be right it may not be
> but
> this is what I guess it is.
>
> 1) When you compile PMEMD with MKL it always links in the static
> libraries.
> Thus it doesn't matter what the environment is at run time, just at build
> time.
>
> 2) When it links svml it links the shared version of svml. This is part
> of
> the ifort compiler suite.
>
> Thus you have statically linked mkl and dynamically linked svml.
>
> My guess then would be that when you run the code your environment is
> different in some way, either the shell is different, the paths are
> different, or it is a different node with different versions of the intel
> compiler installed. Either way this is messing up the dynamic link to
> svml.
>
> To fix this you either need to find out what is wrong with your
> environment
> (i.e. what is different between when you build and when you run) or
> build a
> statically linked version of pmemd.
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
>> Behalf Of Robert Duke
>> Sent: Wednesday, May 06, 2009 12:30 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] Error in PMEMD run
>>
>> 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/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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