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Hi Matt,<br>
<br>
Thanks for your answer. I will try the analytic Poisson solver.<br>
<br>
Regards,<br>
Pierre<br>
<br>
<div class="moz-cite-prefix">On 22/09/2020 16:22, Matt W wrote:<br>
</div>
<blockquote type="cite"
cite="mid:24cc9df4-0eda-4c...@googlegroups.com">
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There are no timings for the gas phase run but it looks like the
pw operations are dominating - they don't really care how many
atoms are involved just the box size (you have nearly 8x more grid
points). With the wavelet poisson solver you only need around 5A
space around the system to be OK but having to be cubic means you
are limited by the largest dimension of your molecule. If it is
very much bigger in one direction you might be better with
analytic poisson solver and a non-cubic box.
<div><br>
</div>
<div>Matt<br>
<br>
</div>
<div class="gmail_quote">
<div dir="auto" class="gmail_attr">On Tuesday, September 22,
2020 at 3:14:58 PM UTC+1 <a class="moz-txt-link-abbreviated" href="mailto:pier...@gmail.com">pier...@gmail.com</a> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex;
border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div> Dear Marcella,<br>
<br>
Please find as attached document two output files. The first
aco-mo.inp contains the results for a crystal made of 78
atoms. This is a normal condensed phase calculation. The
second opt.out is for the gas phase system made of 75 atoms.
The systems have nothing in common.<br>
<br>
I would like to attract your attention that the grid cutoffs
of aco-mo.inp are much larger than those of opt.inp, and yet
aco-mo.inp is much faster than opt.inp.<br>
<br>
I am also running the gas phase system on a single node of a
cluster with 40 MPI tasks. The calculation is obviously
faster than on my workstation but still frustratingly slow.<br>
<br>
Regards,<br>
Pierre</div>
<div><br>
<br>
<div>On 22/09/2020 14:00, Marcella Iannuzzi wrote:<br>
</div>
</div>
<div>
<blockquote type="cite"> Dear Pierre,
<div><br>
</div>
<div>from the timings in the output you should be able to
determine where the calculation is spending most of the
time and compare to the condensed matter calculation.
Most probably OMP is not the most efficient in this case
to parallelise. Have you tried with 8 tasks instead. </div>
<div>Regards</div>
<div>Marcella</div>
<div><br>
<br>
</div>
<div class="gmail_quote">
<div dir="auto" class="gmail_attr">On Tuesday, September
22, 2020 at 1:53:36 PM UTC+2 <a href=""
data-email-masked="" rel="nofollow"
moz-do-not-send="true">pier...@gmail.com</a>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
<div> Hi Marcella,<br>
<br>
I am trying to run the calculation on my workstation
with just OMP (8 threads). This usually works for
condensed phase with a two hundred atoms so I
thought it would be fine for just 75 atoms. Anyway,
I reduced the cutoffs and it seems to be helping a
lot but it is still slow and require a lot of
memory. Please find as attached document the input
file I am using.<br>
<br>
Regards,<br>
Pierre</div>
<div><br>
<br>
<div>On 22/09/2020 11:06, Marcella Iannuzzi wrote:<br>
</div>
</div>
<div>
<blockquote type="cite"> Dear Pierre,
<div><br>
</div>
<div>Without additional information, like input,
output, scaling with the number of processors
..., </div>
<div>it is not possible fo provide any help.</div>
<div>Regards</div>
<div>Marcella</div>
<div><br>
<br>
</div>
<div class="gmail_quote">
<div dir="auto" class="gmail_attr">On Monday,
September 21, 2020 at 1:09:03 PM UTC+2 <a
rel="nofollow" moz-do-not-send="true">pier...@gmail.com</a>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0
0 0 0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">Dear CP2K
users,
<div><br>
</div>
<div>I would like to know how to perform a gas
phase calculation with CP2K. I tried to
follow some of the examples available in the
tutorials but they lead to very slow and
heavy calculations for a system with only 75
atoms.</div>
<div><br>
</div>
<div>I used wavelet for the Poisson solver, I
set periodic none for both the solver and
the cell. The cell is cubic with a size of
26.250 A. I am using DFT (PBE) with OT.
Should the number of grid be changed
compared to a condensed phase? What about
the cutoffs?</div>
<div><br>
</div>
<div>Alternatively, I tried the periodic
approach with a larger cell so that the
molecule "does not interact" with its
periodic image .Yet again, the calculation
is extremely demanding in terms of memory
which makes the OS kill the job.</div>
<div><br>
</div>
<div>Is there a solution to these problems?<br>
</div>
<div><br>
</div>
<div>Regards,</div>
<div>Pierre</div>
</blockquote>
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<pre cols="72">--
Dr Pierre Cazade, PhD
AD3-023, Bernal Institute,
University of Limerick,
Plassey Park Road,
Castletroy, co. Limerick,
Ireland</pre>
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<pre cols="72">--
Dr Pierre Cazade, PhD
AD3-023, Bernal Institute,
University of Limerick,
Plassey Park Road,
Castletroy, co. Limerick,
Ireland</pre>
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<pre class="moz-signature" cols="72">--
Dr Pierre Cazade, PhD
AD3-023, Bernal Institute,
University of Limerick,
Plassey Park Road,
Castletroy, co. Limerick,
Ireland</pre>
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