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On 18.07.14 23:08, Xikai Jiang wrote:
No, I set a skin of 0.1.
I think I found the problem. The max_range is 3.4, while when I
use 16 cores, node_grid is 4 2 2, so on one box size it's 20/4=5
< 2*3.4, which cause the problem.
Ah, true, I also oversaw that 16 cores is already 2^4, not 2^3 :-).
So, reduce the number of cores to 12, and everything should be fine.
Or just run two simulations of 8 cores on a 16 core node.
Best regards,
Axel
Date: Thu, 17 Jul 2014 23:14:41 +0200
From: address@hidden
To: address@hidden; address@hidden
Subject: Re: [ESPResSo-users] minimum number of cells
On 17.07.14 20:23, Xikai Jiang
wrote:
Dr. Arnold:
Yes, it's an error, not warning, for "number of cells is
smaller than minimum". The simulation box sizes are 20, 20
and 19 and each side is larger than twice the r_cut. P3M
parameters are from automatic tuning.
That sounds weird, since r_cut is much smaller than the
simulation box. Do you set a large skin value? Otherwise,
there should be around 6 cells per dimensions, so you can use
up to approx 200 cores before getting the error.
It requires at least 2 cells per spatial
dimension, then "min_num_cells" is 8 on 1 core, and it's 1
on 8 cores. For 16 cores, if I set min_num_cells to 1, for
the whole system, the total min_num_cells is 1*16=16 and
it's safe for the simulation, is my understanding correct?
On 16 cores, min_num_cells is anyways 1, as you can check
using setmd. Check also what max_range, that should be p3m
skin + r_cut, or whatever else has the largest cutoff. If this
cutoff is larger than box_l/num_procs_per_dimension, then you
get a problem (or box_l/2 on a single core).
Axel
Date: Wed, 16 Jul 2014 22:12:01
+0200
From: address@hidden
To: address@hidden; address@hidden
Subject: Re: [ESPResSo-users] minimum number of cells
On 16.07.14 18:59, Xikai
Jiang wrote:
Dear all:
I have a question about the global variable
"minimum_num_cells".
Espresso seems to set "minimum_num_cells" to 8 by
default, but
when I use MPI and use more cores, it gives me a
warning saying
"number of cells is smaller than minimum". And I
found when I
increase number of cores, number of
cells decreases.
You don't get a warning, but an error message, since
Espresso would produce incorrect results. We need at
least two cells per spatial dimension to make the
minimum image convention unambiguous. minimum_num_cells
however counts per core, so if you have 2 cores, you
just need 4, and for 4 cores 2.
I'm using P3M algorithm and Coulomb cutoff is 3.3:
inter coulomb [expr 138.935485/$epsilonr/$T] p3m
3.3 100 7 1.1
Here I'm supposed not to change the interaction
range (r_cut) and
my question is, is it safe to manually set
"minimum_num_cells" to 0,
in order to avoid the warning and let me use more
cores?
No, first of all you cannot set minimum_num_cells to a
lower value, since ESPResSo wants to avoid computing
incorrect results. As a consequence, there is a limit to
the cutoff depending on the box size. You simply cannot
use r_cut 3.3 in a box smaller than 6.7. Either, you put
more particles to increase the box size, or you don't
insist on your parameters, but rather let P3M tune them.
Best,
Axel
--
JP Dr. Axel Arnold
ICP, Universität Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609
--
JP Dr. Axel Arnold
ICP, Universität Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609
--
JP Dr. Axel Arnold
ICP, Universität Stuttgart
Allmandring 3
70569 Stuttgart, Germany
Email: address@hidden
Tel: +49 711 685 67609
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