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
>>>