[gmx-developers] block_tx.c error on 3.3_rc3

[David]

On Tue, 2005-10-04 at 21:23 +0200, Yiannis wrote:
> Thanks for the reply,
> YEs I have more than one job to run, it was a kind of "exercice" to 
> test if it is possible, mainly because we have a few "old and slow" 
> machines that would be interesting to put together on one job and I 
> wanted first to test on two fast but different.
> About the grompp bug on 3.3_rc3, if grompp and mdrun work as usual I 
> can presume I am not concerned or is it a kind of bug that can pass 
> unnoticed?
> Ioannis
By the way, if you install the i686 OS on all boxes they should work
together fine. The network is probably the bottleneck. Check out the -
load option in grompp.

> 
> Le 4 oct. 05, à 08:42, Erik Lindahl a écrit :
> 
> > Hi,
> >
> > Your machines are both running different architectures (x86_64 and 
> > i686) and different operating systems.
> >
> > In theory it is still possible to use both of them, but you must make 
> > sure the correct mdrun_mpi binary compiled for each of them, you must 
> > take care to load balance due to the speed difference, etc.
> >
> > In practice I'm not sure it's worth it, since you probably have more 
> > jobs to run anyway.
> >
> > There is a bug in 3.3_rc3 affecting grompp on some machine/compiler 
> > combinations, which has been fixed in CVS.
> >
> > Cheers,
> >
> > Erik
> >
> >
> > On Oct 4, 2005, at 2:07 AM, Yiannis wrote:
> >
> >> Hello,
> >> I try to run in parallel between two different machines, both dual 
> >> Xeon, one is 2x2.8GHz i686 with Mandrake, the other is 2x3.2GHz 
> >> x86_64 with Suse.
> >> Is it possible to run on the 4 CPUs?
> >> After reading the thread on the list I installed the 3.3_rc3 tarball 
> >> but when I try:
> >>
> >> grompp -v -np 4
> >> mpirun -v -np4 mdrun_mpi -v -np 4
> >>
> >> on the d.villin benchmark I get the block_tx.c error:
> >>
> >> Reading file topol.tpr, VERSION 3.3_rc3 (single precision)
> >> -------------------------------------------------------
> >> Program mdrun_mpi, VERSION 3.3_rc3
> >> Source code file: block_tx.c, line: 74
> >>
> >> Fatal error:
> >> 0: size=672, len=840, rx_count=0
> >>
> >> -------------------------------------------------------
> >>
> >> I tried to run on two CPU on the same machine, it works with no 
> >> problem, I tried also to run on two CPUs, one in each machine and I 
> >> then have the same block_tx error.
> >>
> >> So, is the problem coming from the heterogeneous environment and I 
> >> should stop trying, or it is supposed to work and in that case how?
> >>
> >> Thanks for any help,
> >>
> >> Ioannis Nicolis
> >>
> >> _______________________________________________
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> >>
> >>
> >
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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