Ensure simpoints default of 200 in all programs like lims

[doluk]

No description provided.

[demeler]

Have you checked 2DSA, PCSA and GA to make sure they also use the same simulation numbers when generating models?

[demeler]

Checked the changed files. Please also make sure they are consistent with the fitting programs on the desktop and on the remote LIMS that generate the methods.

[doluk]

Have you checked 2DSA, PCSA and GA to make sure they also use the same simulation numbers when generating models?

I checked the 2DSA one with multiple models. I had no PCSA and GA model at hand, because the Konstanz instance is out of disk. But at the end this is always a setting the user can change in the advanced dialog, we are just changing the default

[demeler]

I meant the programs, not the models. us_pcsa, us_2dsa, etc...and the LIMS us_mpi versions thereof.

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On Fri, Nov 22, 2024 at 4:48 AM Lukas Dobler ***@***.***> wrote: Have you checked 2DSA, PCSA and GA to make sure they also use the same simulation numbers when generating models? I checked the 2DSA one with multiple models. I had no PCSA and GA model at hand, because the Konstanz instance is out of disk. But at the end this is always a setting the user can change in the advanced dialog, we are just changing the default — Reply to this email directly, view it on GitHub <#158 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB2N726UFRGZOH3KAWPAIL32B4KYDAVCNFSM6AAAAABSJA4FKGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOJTGU3TGNJSGA> . You are receiving this because your review was requested.Message ID: ***@***.***>

[doluk]

us_astfem_sim uses 200

ultrascan3/programs/us_astfem_sim/us_astfem_sim.cpp

Line 235 in 491f103

simparams.simpoints = 200; // Initialized number of radial grid points

us_mwl_species_sim uses 200

ultrascan3/programs/us_mwl_species_sim/us_mwl_species_sim.cpp

Line 675 in 491f103

simparams.simpoints = 200; // Initialized number of radial grid points

Programs relying on the data loader from US_AnalysisBase2 uses 200 (us_2dsa, us_pcsa) (the simparameters of the datasets are initialized while loading, but simparams.simpoints never gets overwritten)

ultrascan3/utils/us_simparms.cpp

Line 23 in 4906d21

simpoints = 200;

us_autoflow_analysis uses 200

ultrascan3/programs/us_autoflow_analysis/us_autoflow_analysis.cpp

Line 2688 in 491f103

adv_vals[ "simpoints" ] = "200";

us_fematch uses now 200

ultrascan3/programs/us_fematch/us_fematch.cpp

Line 400 in 491f103

adv_vals[ "simpoints" ] = "200";

us_reporter uses now 200

ultrascan3/programs/us_reporter_gmp/us_reporter_gmp.cpp

Line 3858 in 491f103

adv_vals[ "simpoints" ] = "200";

us_mpi_analysis relies on the job file generated by lims

ultrascan3/programs/us_mpi_analysis/us_mpi_parse.cpp

Line 323 in efdf514

if ( xml.name() == "simpoints" )

LIMS uses 200 as default (the slider created in the linked code is used in 2DSA, PCSA, DMGA, 2DSA-CG and GA) https://github.com/ehb54/us3lims_dbinst/blob/0271f107f11e72e8780e08cbd0b57fbe077a892b/lib/controls.php#L135

[doluk]

@demeler I haven't found any other usage of simpoints or initialization of something with 500 (But I didn't search for any other number except 200 and 500)

[ehb54]

Code changes seem fine, approved.

[demeler]

Did a quick test on demeler9 - running a 2DSA model on usiab-node0 and displaying it in the us_fematch module. Checking the RMSD levels from both systems provided identical RMSDs (2DSA remote):
Residual RMS Deviation:
0.00459557
Model-reported RMSD:
0.00459557

Observed the same for the local 2DSA:
Residual RMS Deviation:
0.00463817
Model-reported RMSD:
0.00463817

Also ran a PCSA (remote):
Residual RMS Deviation:
0.00455346
Model-reported RMSD:
0.00455346

PCSA (local):

Residual RMS Deviation:
0.00454871
Model-reported RMSD:
0.00454871

and a GA model (remote):

Residual RMS Deviation:
0.0045777
Model-reported RMSD:
0.00457197

Only the GA method showed a minor difference in the model RMSD. It's probably OK, but we should check why. The GA is not part of the GMP package.

[doluk]

I tested the 2DSA with MC, where it still deviates sometimes with the MC stuff. But this is now something purely with MC. The first MC single gives the same value. But we know this already
For me GA worked fine.
Residual RMS Deviation:
0.0164342
Model-reported RMSD:
0.0164342

[demeler]

For the MC analysis, it may be related as to what is considered the representative model in each module. In the LIMS, it probably just takes the RMSD from the last iteration, in the us_fematch routine it may be taking the average of all models and using that for the RMSD determination.

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On Fri, Nov 29, 2024 at 3:41 AM Lukas Dobler ***@***.***> wrote: I tested the 2DSA with MC, where it still deviates sometimes with the MC stuff. But this is now something purely with MC. The first MC single gives the same value. But we know this already For me GA worked fine. Residual RMS Deviation: 0.0164342 Model-reported RMSD: 0.0164342 — Reply to this email directly, view it on GitHub <#158 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB2N727VCGGQN74THSDCYF32DBAF3AVCNFSM6AAAAABSJA4FKGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKMBXGU2DEOBWGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[doluk]

Yeah the RMSD is the last mc single in the model file when you run it on lims