1GB on board
51092 atoms
46110 atoms belong to water (15370 molecules)
4976 atoms of protein (2503 heavy atoms)
BEFORE APPLYING THE PATCH pmemd.cuda had performance 3.84 ns/day (285) and
slightly more than 12 ns for 580.
NOW launch failed (segfault)
Langevin thermostat (2 ps-1) + pressure control (relaxation time 2 ps).
Switching to Berendsen thermostat (and removing gamma_ln) allows to execute
pmemd.cuda successfully. Again, this system plays a role of test, because it
ran well before.
Previous version printed error message about lack of memory in cases when
system was too large, so the error I have faced is definitely new. 'Line 9'
in the error message corresponds to the code of executable file, not script
(it is occurred in the line 18 of bash script).
2011/8/21 Scott Le Grand <varelse2005.gmail.com>
> Questions:
> GPU? Assuming 285 with 2 GB? (don't actually have one anymore as they all
> died of old age)
> Number of atoms?
>
> > >
> > > In my case GPU memory isn't loaded very much. nvidia-smi reports about
> > 16%
> > is utilized with ntt=1, that means it will be enough space on board.
> tests
> > were passed (if memory amount was sufficient), but simulations that went
> > fine previously now do not (re-)launch because of that segfault...
> > Amber11 / at15 / patches till 17th...
> >
>
--
Sincerely,
Dmitry Mukha
Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
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Received on Sun Aug 21 2011 - 13:30:02 PDT
