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 pier...@gmail.com 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">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">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>
</div>
</blockquote>
</div>
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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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To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/afec8cd6-9834-4e05-bdee-3637cb366dd2n%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank" rel="nofollow" data-saferedirecturl="https://www.google.com/url?hl=en&q=https://groups.google.com/d/msgid/cp2k/afec8cd6-9834-4e05-bdee-3637cb366dd2n%2540googlegroups.com?utm_medium%3Demail%26utm_source%3Dfooter&source=gmail&ust=1600873802046000&usg=AFQjCNGFkhN99dBZs0n-2If0dy-SUocahQ">https://groups.google.com/d/msgid/cp2k/afec8cd6-9834-4e05-bdee-3637cb366dd2n%40googlegroups.com</a>.<br>
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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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