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

[Yiannis]

Ok, if I find time I will do some tests and I'll let you know. Thanks,
Ioannis

Le 4 oct. 05, à 22:07, David a écrit :

> 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
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