[gmx-users] Re:installation probem on Tru64 supercomputer

[David van der Spoel]

On Thu, 2004-01-08 at 01:06, Wei Fu wrote:
> Hi, David, 
> 
> I did a test with "mdrun -nice 0", and it does not work either.
> 
> I checked md.log file, and the following information, it does not give any
> error information. I don't know what is this kind of problem, the compling
> problem or the configure problem or the mathine problem?
> 
Hm, maybe you could start with a system withou PME (use plain cut-off).
Does it run on a single processor? Do you get any core dumps or
something like that?



> _______________________________________________________________________
> Parallelized PME sum used.
> Using the FFTW library (Fastest Fourier Transform in the West)
> PARALLEL FFT DATA:
>    local_nx:                  45  local_x_start:                   0
>    local_ny_after_transpose:  49  local_y_start_after_transpose    0
>    total_local_size:         379260
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
>   0:  Protein, initial mass: 48627
>   1:  rest, initial mass: 703806
> There are: 60764 Atom
> Removing pbc first time
> Done rmpbc
> 
> Constraining the starting coordinates (step -2)
> 
> ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
> H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
> Molecular dynamics with coupling to an external bath
> J. Chem. Phys. 81 (1984) pp. 3684-3690
> -------- -------- --- Thank You --- -------- --------
> 
> 
> ++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
> S. Miyamoto and P. A. Kollman
> SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
> Water Models
> J. Comp. Chem. 13 (1992) pp. 952-962
> -------- -------- --- Thank You --- -------- --------
> __________________________________________________________________
> 
> 
> 
>   > Dear users,
> > 
> >     I have installed gromacs on tru64 supercomputer (Compaq,
> alpha-ev68), there is some abnomal installation problem (like Making all
> in man1
> > No suffix list.), but all commands seem to work after finishing
> installation. When I submit job by using qsub (I calculate at lemieux
> mathine, and use prun instead of mpirun to submit paralell job), the MD is
> terminated before it begins to run. No error infomation, the md.log is
> finished with:
> > 
> > *****************************************************
> > starting mdrun 'Protein in water'
> > 20000 steps,     40.0 ps.
> > 
> > 
> > Back Off! I just backed up 3.trr to ./#3.trr.1#
> > *****************************************************
> > 
> 
> try mdrun -nice 0
> 
> Have you checked the log files?
> 
> >     I check the ener.edr and traj.trr file, it did not begin to run MD
> at all.
> > 
> >     Does anybody have experience on the installation or calculation of
> GROMACS on Tru64 supercomputer? Any suggestion is appreciated!
> > 
> > Happy new year!
> > 
> > Fu, Wei
> > 2004-01-07A
> 
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-- 
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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