AMBER Archive (2009)

Subject: Re: [AMBER] Error in PMEMD run

From: Marek Malý (maly_at_sci.ujep.cz)
Date: Wed May 06 2009 - 14:48:26 CDT

Dear Bob,

before I will try all the things you recommended regarding ifort.

I have simple question.

How is it possible, that compilation of serial Amber version proceeds
without any problem

here is the relevant config line: ./configure_amber ifort

and how is it possible that also parallel version of Amber was compiled
without
any problem ?

here is the relevant config line: ./configure_amber -intelmpi ifort

I would assume that if there were no problems in this cases there
shouldn't be
any problem with ifort compiler in case of pmemd or am I wrong ?

But OK I have compilled everything before 2 months so something could
happen in between,
but I would at least assume some warnings/errors during pmemd compilation
but it was OK ...

Anyway I will try to understand realise your instructions but I am not an
administrator
so I can just change files in my home and on the amber dir to be able
compile and change
all necessary files.

I don't know, maybe it would be the quickest solution that I provide you
for necessary time
acces to my account to allow you check all the necessary things personaly.
It could
save us lot of time I thing. So please let me know your opinion ...

Anyway thanks for this moment.

Best

   Marek

Dne Wed, 06 May 2009 21:20:37 +0200 Robert Duke <rduke_at_email.unc.edu>
napsal/-a:

> 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_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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