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 <[email protected]>
Subject: [gmx-users] problem with icc compiler
To: "[email protected]" <[email protected]>
Message-ID: <[email protected]>
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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