Hi Bob,
here is the content of the LD_LIBRARY_PATH variable:
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
here is the answer after aplying the "which ifort" command.
/opt/intel/fce/10.1.012/bin/ifort
so it seems to me OK since LD_LIBRARY_PATH contain
/opt/intel/fce/10.1.012/lib
which is in my opinion dir. with ifort libraries or am I wrong ?
Anyway thanks very much, tomorrow I will probably try Ross idea to adopt
pmemed a litle Amber way. If Amber has no problems with MKL cosine
implementation
I hope that pmemd will be also OK with this after that little changes.
Best,
Marek
Dne Wed, 06 May 2009 22:40:29 +0200 Robert Duke <rduke.email.unc.edu>
napsal/-a:
> Hi Marek,
> It may be something subtle in the setup of the different builds, and I
> will have to go back over a bunch of stuff to understand exactly what is
> going on. PMEMD uses what is called the "rpath" mechanism to add
> library directories to search paths; could be this fails differently
> than whatever sander is doing (could be just use of LD_LIBRARY_PATH). I
> am actually very puzzled by all this because the pmemd mechanism has
> been working very well for probably about 3-4 years now, but with
> configuring unix systems, there are a number of subtle things that can
> happen. Speaking of LD_LIBRARY_PATH, do check and see if the ifort lib
> directory is listed as part of it...
> Regards - Bob
> ----- Original Message ----- From: "Marek Malý" <maly.sci.ujep.cz>
> To: "AMBER Mailing List" <amber.ambermd.org>
> Sent: Wednesday, May 06, 2009 4:26 PM
> Subject: Re: [AMBER] Error in PMEMD run
>
>
> Hi Bob,
>
> thanks again. What I do not understand in the light of your last comment
> is
> why the parallel version of Amber which I compilled on the same node as
> pmemd is
> possible to use on any node of our cluster without any problems. It works
> perfectly,
> I have now 3 calculations on 32CPUs/job ( = each job on four 8 CPUs nodes
> ) and it works,
> it is running from Monday without problem (minimisation, and MD -
> explicit
> solvent).
>
> So where could be so big difference here. Is it that Amber uses different
> shared libraries
> that pmemd ?
>
> Best
>
> Marek
>
>
> Dne Wed, 06 May 2009 22:08:56 +0200 Robert Duke <rduke.email.unc.edu>
> napsal/-a:
>
>> Hi Marek,
>> I think you are probably going to need to get somebody involved on your
>> end that understands the intricacies of runtime loading of shared
>> libraries; it is probably best to go this route rather than hacking the
>> build, which is known to work if you don't mess with it (maybe not on
>> your setup at the moment, but that is because something is not being
>> set up correctly). The key here is being able to handle getting at
>> the ifort shared libraries from all nodes in the cluster. Sorry again
>> this has been so hard.
>> Regards - Bob
>> ----- Original Message ----- From: "Marek Malý" <maly.sci.ujep.cz>
>> To: "AMBER Mailing List" <amber.ambermd.org>
>> Sent: Wednesday, May 06, 2009 4:02 PM
>> Subject: Re: [AMBER] Error in PMEMD run
>>
>>
>> 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.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.ambermd.org [mailto:amber-bounces.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.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/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.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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>>>>
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>>>> ---------
>>>>
>>>>
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>>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>> >
>>>>
>>>>
>>>>
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>>>
>>>
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Received on Wed May 20 2009 - 14:56:58 PDT
