posting to log file

Raitis

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Jul 4, 2019, 9:41:13 AM7/4/19

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Hi,

I am new to the cp2k and I am trying to calculate the Raman spectra by following this tutorial. I am having several questions about cp2k performance/way of calculating things:

1. Is it normal that for several first hours of my calculations there are nearly no output in the log file (it prints all the cp2k and quickstep related information and then nothing for a while). Is it supposed be like that or something might be wrong? What is happening during this time.

2. The walltime on my server is 2 days and I cannot finish all the simulation in this time, therefore I am continuing it using the .restart file. But than again, once I restart the simulation, there is this long few hour time were nothing is written in the log file, and only later the actual simulation data are printed.

Raitis

equilibration.in

Patrick Gono

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Jul 6, 2019, 7:05:48 AM7/6/19

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Dear Raitis,

Could you please attach the output file as well? So that we can get some idea of the timings.

How many nodes are you using? Is it possible to use more, to speed up the calculations? Are you limited by memory or the lack of CPUs?

Finally, if you have to restart a calculation, especially an MD, you should choose to start from an already computed wavefunction file (if you're not already doing it):

&DFT

...

WFN_RESTART_FILE_NAME *project name*-RESTART.wfn ! default naming convention

&SCF
SCF_GUESS RESTART

...

&END SCF

...

&END DFT

This should speed up any restarted simulation, as you don't have to solve the KS equations from scratch at the beginning.

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Raitis

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Jul 6, 2019, 8:36:37 AM7/6/19

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Thank you for the answer, Patrick.

Here is the output of one of the simulations (i cut out most of the non-interesting data as the file was to large to attach).

I am running on 1 node with 12 cores. I tried to to run on more nodes, but by running with mpirun -np 36 cp2k.popt it was even slower. I will get in touch with our server administrator to understand how to run it properly on more than one node.

Thank you for the suggestion. I thought that this might have something to do with wave function recalculations at the restart, but i could not figure out how to write this information from the first simulation. Will modify the input and try it this way.

Raitis

On Saturday, July 6, 2019 at 2:05:48 PM UTC+3, Patrick Gono wrote:

Dear Raitis,

Could you please attach the output file as well? So that we can get some idea of the timings.

How many nodes are you using? Is it possible to use more, to speed up the calculations? Are you limited by memory or the lack of CPUs?

Finally, if you have to restart a calculation, especially an MD, you should choose to start from an already computed wavefunction file (if you're not already doing it):

&DFT
...
WFN_RESTART_FILE_NAME *project name*-RESTART.wfn ! default naming convention
&SCF
SCF_GUESS RESTART
...
&END SCF
...
&END DFT

This should speed up any restarted simulation, as you don't have to solve the KS equations from scratch at the beginning.

On Thu, 4 Jul 2019 at 15:41, Raitis <raitis...@gmail.com> wrote:

Hi,

I am new to the cp2k and I am trying to calculate the Raman spectra by following this tutorial. I am having several questions about cp2k performance/way of calculating things:

1. Is it normal that for several first hours of my calculations there are nearly no output in the log file (it prints all the cp2k and quickstep related information and then nothing for a while). Is it supposed be like that or something might be wrong? What is happening during this time.

2. The walltime on my server is 2 days and I cannot finish all the simulation in this time, therefore I am continuing it using the .restart file. But than again, once I restart the simulation, there is this long few hour time were nothing is written in the log file, and only later the actual simulation data are printed.

Raitis

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output.out

Patrick Gono

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Jul 6, 2019, 11:31:34 AM7/6/19

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Dear Raitis,

given the scale of your calculation, you should be well within optimal scaling with only 3 nodes (36 cores). Make sure you have a correctly compiled version of CP2K and a correctly written submission script (do you spawn 36 mpi processes on a single 12 core node, by any chance?). With 300 atoms and at the semilocal level of theory, I expect you should see linear speed-up with up to 10 nodes. And certainly, even adding more nodes beyond that should not slow down the calculation, quite the opposite, actually.

Good luck!

Yours sincerely,

Patrick Gono

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