Added benchmark command line tool

[gtribello]

This tool runs plumed using a trajectory that is hard coded in the source code. It essentially works very much like driver, except the trajectory is fixed. You can use this to benchmark plumed calculations. The advantage of having the separate code is the the profiles you get from this tool are not influenced by lots of I/O.

Description

Added tool for benchmarking plumed

Target release

I would like my code to appear in release v2.10

Type of contribution

• [ x] 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

• [x ] 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

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

[gtribello]

Hi @GiovanniBussi

Here is a PR with the benchmark tool that I wrote for plumed. Please feel free to modify it in whatever way you see fit.

[codecov-commenter]

Codecov Report

Attention: 60 lines in your changes are missing coverage. Please review.

Comparison is base (0ae3da5) 84.18% compared to head (433f809) 84.11%. Report is 70 commits behind head on master.

:exclamation: Current head 433f809 differs from pull request most recent head cc36bb8. Consider uploading reports for the commit cc36bb8 to get more accurate results

Files	Patch %	Lines
src/cltools/Benchmark.cpp	25.53%	35 Missing :warning:
src/cltools/GenExample.cpp	0.00%	3 Missing :warning:
src/core/Action.h	70.00%	3 Missing :warning:
src/core/PlumedMain.cpp	91.89%	3 Missing :warning:
src/cltools/Driver.cpp	0.00%	2 Missing :warning:
src/core/TargetDist.cpp	0.00%	2 Missing :warning:
src/core/WithCmd.h	71.42%	2 Missing :warning:
src/core/Action.cpp	75.00%	1 Missing :warning:
src/core/ActionShortcut.h	0.00%	1 Missing :warning:
src/core/ActionToGetData.h	0.00%	1 Missing :warning:
... and 7 more

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Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #1014 +/- ## ========================================== - Coverage 84.18% 84.11% -0.08% ========================================== Files 612 614 +2 Lines 56476 56646 +170 ========================================== + Hits 47547 47649 +102 - Misses 8929 8997 +68 ```

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[gtribello]

Hello @GiovanniBussi

What is the status with this? It looks like you did a lot of commits on this PR. I think a lot of them are from a merge of master after you added the PyCV stuff?

Do you want me to look at anything here?

[GiovanniBussi]

I am fixing a few stuff then I'll merge in master. I already merged master into this branch, and for some reasons, github doesn't understand that the only difference between this branch and master is the Benchmark.cpp file.

I added the possibility to load a previous version of the kernel, to do comparisons, and to run "forever" (until ctrl-C). I would like to also add the possibility to run with domain decomposition and MPI, because it's crucial for some other tests I am doing (see #1025)

I'll merge this in master today.

[gtribello]

OK that is great. Thanks.