[gmx-users] problem with icc compiler

Thomas Schlesier schlesi at uni-mainz.de
Wed Mar 10 17:04:43 CET 2010


Gromacs was compiled on a xeon (woodcrest). for the simulations i used 
an old xeon (don't know what chip, but also 64bit system) and a i7.

About static / dynamic libraries:
I used there default settings. At the end of the configure command it 
tells me the following:
* On most platforms you can save 10X space with dynamic libraries, 
although the binaries might be less portable. Why not try --enable-shared?
So i think the libraries are static.

I tried Mark's suggestion and compiled a new version, where i change 
'--with-fft=mkl' with '--enable-fft=fftpack' (the restr of the configure 
command was the same then before). With that, the error didn't appear.
Does that mean that the linking to mkl did not work for mdrun, but 
worked for mdrun_mpi (because there the temperature was right)?

One thing for  the temperature jump:
Temperature starts at around 300 K (from 'gen_temp') then goes in 1-2ps 
up to around 425 K and then stays there. the simulation was 100ps long, 
in the end i had an average value of about 425 K (from log file).

Here are the first 20ps from g_energy
     0.000000  305.240509
     1.000000  381.614166
     2.000000  410.572906
     3.000000  434.954956
     4.000000  414.660400
     5.000000  394.799591
     6.000000  389.087128
     7.000000  414.893982
     8.000000  449.444183
     9.000000  417.877472
    10.000000  442.470306
    11.000001  446.170258
    12.000001  448.844666
    13.000001  412.847473
    14.000001  454.549744
    15.000001  447.908478
    16.000000  404.607422
    17.000000  404.629944
    18.000000  441.559448
    19.000000  396.328400
    20.000000  421.386017
and:
Energy       Average       RMSD     Fluct.      Drift  Tot-Drift
----------------------------------------------------------------
Temperature  424.625    21.7645    21.6696  0.0703201    7.03215



> 
> On 10/03/2010 12:21 AM, Thomas Schlesier wrote:
>> Could anybody reproduce that error or has an idea what is happening?
>> Or i am alone with that problem?
> 
> Nothing looks obviously wrong, but it's hard to be sure in the absence
> of information about your hardware. The most likely issue is some kind
> of dynamically-linked library mismatch. This can happen if your
> execution environment differs from your linking environment. Try forcing
> linking to static versions of the libraries, which will prevent this.
> 
> Also try disabling things until you get sensible behaviour in all cases,
> like --enable-fft=fftpack. That would reveal that the problem was with
> linking to mkl.
> 
> Also 1-2ps is a bit too short to expect convergence of temperature -
> check the plot of T against t with g_energy.
> 
> Mark
> 
>>> Date: Fri, 5 Mar 2010 23:11:45 +0100
>>> From: Thomas Schlesier <schlesi at uni-mainz.de>
>>> Subject: [gmx-users] problem with icc compiler
>>> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>>> Message-ID: <4B9181A1.7060106 at uni-mainz.de>
>>> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed
>>>
>>> Hi,
>>> i observed the following problem. if i simulate water (spc or tip4p)
>>> with gromacs 4.0.5 i get with v-rescale or berendsen thermostat the
>>> wrong temperature (ref_t = 300K -> average around 425K, in about 1-2ps),
>>> but only in serial, not in parallel runs.
>>> non-water molecules or nose-hoover thermostat make no problems.
>>> see also
>>> http://lists.gromacs.org/pipermail/gmx-users/2010-March/049248.html
>>> for mdp and log file.
>>>
>>> gromacs was compiled with the following comands:
>>> and in the file 'configure' all '-lmkl' were deleted (don't ask me why,
>>> i don't really understand that stuff, the command were from our previous
>>> phd student).
>>>
>>> ./configure CC="icc" CPPFLAGS="-I/share/apps/intel/mkl/10.0.011/include"
>>> LDFLAGS="-L/share/apps/intel/mkl/10.0.011/lib/em64t
>>> -lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64
>>> -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-fft=mkl
>>> --prefix="/share/apps/gromacs/4.0.5"
>>> make
>>> make install
>>> make clean
>>> ./configure CC="icc" CPPFLAGS="-I/share/apps/intel/mkl/10.0.011/include"
>>> LDFLAGS="-L/share/apps/intel/mkl/10.0.011/lib/em64t
>>> -lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64
>>> -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread" --with-fft=mkl
>>> --prefix="/share/apps/gromacs/4.0.5" --enable-mpi --disable-nice
>>> --program-suffix=_mpi
>>> make mdrun
>>> make install-mdrun
>>>
>>> for gromacs 4.0.5 i used the icc 9.1.046 compiler.
>>>
>>> i also tried gromacs 4.0.7 with icc 9.1.046 and icc 10.1.008 with spc
>>> water, v-rescale thermostat.
>>> -> serial: too high temperature 425K iso 300K
>>> -> parallel: no problems
>>> with non-water (mesitylene) i have no problem in serial.
>>>
>>> the problem does not come from grompp because i can use same tpr-file
>>> for serial and parallel runs with the above results.
>>>
>>> if someone needs more informations about this please tell me.
>>>
>>> greetings
>>> thomas
>>>



More information about the gromacs.org_gmx-users mailing list