[gmx-users] x86 SSE
David van der Spoel
spoel at xray.bmc.uu.se
Sat Dec 27 09:42:01 CET 2003
On Fri, 26 Dec 2003, Osmany Guirola Cruz wrote:
>I COMPILE BOTH (FFT AND GGROMACS) WHITH DOUBLE PRECISION
>AN MY CLUSTER IS DUAL PIII
Ok, but you could still have different libraries installed, can you try
with
ldd `which mdrun`
to see which libraries are used?
>KA
>
>-----Original Message-----
>From: David van der Spoel [mailto:spoel at xray.bmc.uu.se]
>Sent: Friday, December 26, 2003 2:23 PM
>To: gmx-users at gromacs.org
>Subject: RE: [gmx-users] x86 SSE
>
>
>On Fri, 26 Dec 2003, Osmany Guirola Cruz wrote:
>
>>Sorry.. these problem exists on single CPU and multiple CPUs
>>These problem exist when I use PME.... When I use cutt-off the
>>simulation runs whitout problem
>
>what CPU is this?
>
>could be trouble with fft libraries. some linux come preinstalled with
>the
>double prec. fftw.
>>
>>
>>
>>
>>
>>
>>-----Original Message-----
>>From: David van der Spoel [mailto:spoel at xray.bmc.uu.se]
>>Sent: Friday, December 26, 2003 11:21 AM
>>To: gmx-users at gromacs.org
>>Subject: Re: [gmx-users] x86 SSE
>>
>>
>>On Fri, 26 Dec 2003, Osmany Guirola Cruz wrote:
>>
>>>Hi
>>> I am doing a simulation on multiple machine 8 and my md.log give me
>>these error
>>>
>>Does the problem exist on single CPU as well?
>>Did you check your starting structure? It looks like a close contact.
>>
>>>
>>>Started mdrun on node 0 Fri Dec 26 02:53:28 2003
>>>Initial temperature: 299.966 K
>>>Grid: 24 x 24 x 24 cells
>>>
>>>Testing x86 processor CPUID...
>>>
>>>Testing x86 SSE2 capabilities...
>>>No SSE2 support found for this CPU.
>>> Step Time Lambda Annealing
>>> 0 0.00000 0.00000 1.00000
>>>
>>> Rel. Constraint Deviation: Max between atoms RMS
>>> Before LINCS 0.014437 61 62 nan
>>> After LINCS 0.000000 1 2 nan
>>>
>>> Energies (kJ/mol)
>>> G96Angle Proper Dih. Improper Dih. LJ-14
>>Coulomb-14
>>> 3.52659e+03 1.82274e+03 1.09959e+03 6.50594e+02
>>2.68827e+04
>>> LJ (SR) Coulomb (SR) Coulomb (LR) Potential
>Kinetic
>>En.
>>> 2.77323e+05 -4.45936e+06 nan nan
>>nan
>>> Total Energy Temperature Pressure (bar)
>>> nan nan nan
>>>
>>>Grid: -2147483648 x -2147483648 x -2147483648 cells
>>>Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 210]
>>>
>>>WHAT CAN I DO
>>>
>>>
>>>
>>
>>
>
>
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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