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Add documentation for the PNear ensemble metric #53

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1eed1f8
Adding ensemble metrics to sidebars.
vmullig Feb 8, 2022
9156829
Updating main RosettaScripts page.
vmullig Feb 8, 2022
35cb717
Adding page for CentralTendency metric.
vmullig Feb 8, 2022
cc023e6
Updating auto-generated docs.
vmullig Feb 8, 2022
a18aca6
Adding auto-generated ensemble metric docs.
vmullig Feb 8, 2022
3e8cc7f
Updating CentralTendency ensemble metric doc.
vmullig Feb 8, 2022
0e5918f
Working on documentation for EnsembleMetrics.
vmullig Feb 10, 2022
b3730e1
Fleshing out EnsembleMetric documentation.
vmullig Feb 10, 2022
97d7892
Updating auto-generated docs.
vmullig Feb 10, 2022
ca9eebd
Adding note about accessing named values.
vmullig Feb 10, 2022
bbfdb09
Adding note about filtering.
vmullig Feb 10, 2022
9dd6e89
Revising text slightly.
vmullig Feb 10, 2022
9629b4b
Adding note about MPI mode.
vmullig Feb 10, 2022
3301900
Adding example of internal generation mode.
vmullig Feb 10, 2022
a5778bb
Adding note about multithreading.
vmullig Feb 10, 2022
a045962
Updating note about multi-threading.
vmullig Feb 11, 2022
eb93e85
Adding example for mode 3.
vmullig Feb 11, 2022
62a9158
Add EnsembleFilter docs to filter list.
vmullig Feb 11, 2022
d38608f
Moving some filters that were in the wrong folder.
vmullig Feb 11, 2022
11215f2
Adding documentation for EnsembleFilter.
vmullig Feb 11, 2022
b7e9ef7
Minor typos.
vmullig Feb 11, 2022
fc6e674
Expanding note about mode.
vmullig Feb 11, 2022
08dc81e
Minor tweak.
vmullig Feb 11, 2022
0b2cc38
Merge remote-tracking branch 'origin/master' into vmullig/ensemble_me…
vmullig Feb 25, 2022
af0cded
Updating note about MPI.
vmullig Feb 25, 2022
41dacf1
Updating CentralTendency and FragmentScore auto-generated docs.
vmullig Feb 25, 2022
faa5e70
Merge branch 'vmullig/ensemble_metric_doc' into vmullig/ensemble_metr…
vmullig Feb 25, 2022
e0d4213
Add auto-generated docs for PNearEnsembleMetric.
vmullig Mar 11, 2022
5faa107
Add PNear ensemble metric to EnsembleMetrics documenation page.
vmullig Mar 11, 2022
d00043e
Updating CentralTendency.
vmullig Mar 11, 2022
f08de9e
Adding documentation for PNear ensemble metric.
vmullig Mar 11, 2022
f93b3be
Adding a little more description.
vmullig Mar 11, 2022
0801e4a
Adding MPI note.
vmullig Mar 11, 2022
22503cc
Merge remote-tracking branch 'origin/master' into vmullig/ensemble_me…
vmullig Mar 11, 2022
99146f7
Updating auto-generated docs.
vmullig Mar 11, 2022
e23b820
Merge branch 'vmullig/ensemble_metric_doc' into vmullig/ensemble_metr…
vmullig Mar 11, 2022
171afb3
Merge remote-tracking branch 'origin/vmullig/ensemble_metric_mpi_docs…
vmullig Mar 11, 2022
af0a491
Merge remote-tracking branch 'origin/master' into vmullig/ensemble_me…
vmullig Apr 18, 2022
4fa4729
Update documentation with mention of support in MPIFileBufJobDistribu…
vmullig Apr 18, 2022
2549d1b
Merge remote-tracking branch 'origin/master' into vmullig/ensemble_me…
vmullig Apr 27, 2022
bfe5514
Merge branch 'vmullig/ensemble_metric_doc' into vmullig/ensemble_metr…
vmullig Apr 27, 2022
f2cbac0
Merge remote-tracking branch 'origin/master' into vmullig/ensemble_me…
vmullig Jul 2, 2022
9c8700e
Merge branch 'vmullig/ensemble_metric_doc' into vmullig/ensemble_metr…
vmullig Jul 2, 2022
1bef5b8
Merge branch 'vmullig/ensemble_metric_mpi_docs' into vmullig/pnear_en…
vmullig Jul 2, 2022
802ce09
Merge remote-tracking branch 'origin/master' into vmullig/ensemble_me…
vmullig Oct 11, 2022
1aed331
Merge branch 'vmullig/ensemble_metric_doc' into vmullig/ensemble_metr…
vmullig Oct 11, 2022
07f0d4a
Merge branch 'vmullig/ensemble_metric_mpi_docs' into vmullig/pnear_en…
vmullig Oct 11, 2022
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Update documentation with mention of support in MPIFileBufJobDistribu…
…tor for ensemble metrics.
vmullig committed Apr 18, 2022
commit 4fa4729ea786438f99d56d0708755ac1b4c571e3
Original file line number Diff line number Diff line change
@@ -335,7 +335,7 @@ Note that if one simply wants the value produced by the EnsembleMetric to be rec

## 4. Note about running in MPI mode

The [[Message Passing Interface (MPI)|MPI]] permits massively parallel execution of a Rosetta protocol. If an EnsembleMetric is used in basic mode (Section 2.1) using the [[MPI build|Build-Documentation]] of Rosetta, all poses seen _by all processes_ are considered part of the ensemble that is being analysed. At the end of the protocol, all of the instances of the EnsembleMetric on worker processes will report back to the director process with the measurements needed to allow the director process to perform the analysis on the whole ensemble. This can be convenient for rapidly analysing very large ensembles generated in memory across a large cluster, without needing to write thousands or millions of structuers to disk. This functionality is currently only available in the [[JD2]] version of the [[RosettaScripts]] application, and only when the [[MPIWorkPoolJobDistributor|JD2]] (the default MPI JD2 job distributor) is used. Support for [[JD3|RosettaScripts-JD3]] is planned.
The [[Message Passing Interface (MPI)|MPI]] permits massively parallel execution of a Rosetta protocol. If an EnsembleMetric is used in basic mode (Section 2.1) using the [[MPI build|Build-Documentation]] of Rosetta, all poses seen _by all processes_ are considered part of the ensemble that is being analysed. At the end of the protocol, all of the instances of the EnsembleMetric on worker processes will report back to the director process with the measurements needed to allow the director process to perform the analysis on the whole ensemble. This can be convenient for rapidly analysing very large ensembles generated in memory across a large cluster, without needing to write thousands or millions of structuers to disk. This functionality is currently only available in the [[JD2]] version of the [[RosettaScripts]] application, and only when the [[MPIWorkPoolJobDistributor|JD2]] (the default MPI JD2 job distributor) or the MPIFileBufJobDistributor (the default MPI JD2 job distributor for use with Rosetta silent files) is used. Support for [[JD3|RosettaScripts-JD3]] is planned.

Note that EnsembleMetrics that run in different MPI processes, and which generate ensembles internally using either a generating protocol (Section 2.2) or a multiple pose mover (Section 2.3), report immediately on the ensemble seen locally _in that process_. In this case, no information is shared between processes.