Small optimization in CoordinationBase

[Iximiel]

Description

I changed how the couples are traversed in the CoordinationBase calculate() method, by passing from a "striped" traversal to a "block" one.
I get a 3%-5% speedup on my local machine.

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Here are some results I got on my workstation, the graph show the time spent in calculate() relative to the time spent in calculate in the master branch

for 4 mpi processes and 2 threads each one

for 1 process with 8 threads (Here I did not expect performance improvement)

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Before removing the draft status I'd like to see if it is possible to not store the couples in the neighbor list if the user asks for a fixed list

Target release

I would like my code to appear in release 2.10 (but I think this can rebased on 2.9)

Type of contribution

• changes to code or doc authored by PLUMED developers, or additions of code in the core or within the default modules
• changes to a module not authored by you
• new module contribution or edit of a module authored by you

Copyright

• I agree to transfer the copyright of the code I have written to the PLUMED developers or to the author of the code I am modifying.

• the module I added or modified contains a COPYRIGHT file with the correct license information. Code should be released under an open source license. I also used the command cd src && ./header.sh mymodulename in order to make sure the headers of the module are correct.

Tests

• I added a new regtest or modified an existing regtest to validate my changes.
• I verified that all regtests are passed successfully on GitHub Actions.

[GiovanniBussi]

I think you get an improvement also with pure openmp because also in that case the access to continuous memory is faster

[Iximiel]

Before removing the draft status I'd like to see if it is possible to not store the couples in the neighbor list if the user asks for a fixed list

I think it may be a better idea to do that in a separate PR

If you think it may be better to try another benchmark I'll do it, otherwise, I think it can be merged/rebased on 2.9

[GiovanniBussi]

I think we can merge it. It can even go to v2.9 because the change is minimal.

[Iximiel]

Ok, then I'm rebasing this to the v2.9

[Iximiel]

I changed the base and I pushed for the CI. while the CI is running I'm also comparing the branch with the master v2.9