[gmx-users] Re:Re: How to complie gromacs on sgi Altix450?

[Carsten Kutzner]

Hi,

there is an issue on the Altix with the assembly kernels which
you might suffer from. Your simulation would then get stuck
at time step 0, which could be the case from the status of the
run you are reporting.

Try to compile with the following extra options:

--disable-ia64-asm --enable-fortran

The fortran loops will be nearly as fast as the assembly kernels
on that machine.

Carsten


On Sep 15, 2009, at 5:05 PM, 石子枫 wrote:

> Hello, Martin
>
> I complied fftw3.2.2 and gromacs4.0.5 on the Altix450 workstation  
> again.
> I use these commands:
> not for parallel version
> ;for fftw3;
> ./configure --prefix=/opt/fftw3
> make
> make install
> make distclean
> export CPPFLAGS=-I/opt/fftw3/include
> epxort LDFLAGS=-L/opt/fftw3/lib
> for gromacs:
> ./configure --enable-float --prefix=/opt/fftw3
> make
> make install
> ;for gromacs;
> ./configure --disable-float --prefix=/opt/gmx
> make
> make install
> =============================================
> Have not briefed on mistake this time.
>
> But the procedure still can't produce the output files .
>
> The both the size of '*.trr' and '*.edr' are 0 bit.
>
> And the md.log file end is:
> =============================================
> ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> U. Essman, L. Perela, M. L. Berkowitz, T. Darden, H. Lee and L. G.  
> Pedersen
> A smooth particle mesh Ewald method
> J. Chem. Phys. 103 (1995) pp. 8577-8592
> -------- -------- --- Thank You --- -------- --------
> =============================================
> The nohup.out file end in:
> =============================================
> Back Off! I just backed up md.log to ./#md.log.1#
> Reading file sysion_em.tpr, VERSION 4.0.5 (double precision)
>
> Back Off! I just backed up emtest.trr to ./#emtest.trr.1#
>
> Back Off! I just backed up ener.edr to ./#ener.edr.1#
> Steepest Descents:
>    Tolerance (Fmax)   =  6.00000e+02
>    Number of steps    =        50000
>  =============================================
>
> This problem is really too strange.
>
> I have been perplexed for a long time by this question.
>
> Who can help me ?
>
>
> Best wishs
>
> Wenping Lv
>
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne