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

Wei Fu fuwei at adrik.bchs.uh.edu
Thu Jan 8 01:54:01 CET 2004

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?

Parallelized PME sum used.
Using the FFTW library (Fastest Fourier Transform in the West)
   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)

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 --- -------- --------

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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