[gmx-users] Re: problem with icc compiler

Mark Abraham Mark.Abraham at anu.edu.au
Tue Mar 9 22:54:34 CET 2010

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.


>> 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

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