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Fixes for SoA NEURON data structures #67

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merged 10 commits into from
May 2, 2023
Merged

Fixes for SoA NEURON data structures #67

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699c736
Append output .txt to gout for now.
olupton Dec 13, 2022
049c2b7
PRs for neuronsimulator/nrn#2027 compatibility.
olupton Dec 13, 2022
e963fbc
Add PR for 83344.
olupton Mar 24, 2023
921bad6
33975: hacky curation
olupton Mar 24, 2023
0a5e2df
105507: avoid printing times differently
olupton Mar 24, 2023
2855cff
better debug
olupton Apr 24, 2023
4e6e5ce
reduce diff
olupton Apr 28, 2023
a6c6531
reduce diff, most PRs are merged
olupton May 1, 2023
b7d1986
Update modeldb/modeldb-run.yaml
olupton May 1, 2023
97fd0ad
final PR is merged
olupton May 2, 2023
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21 changes: 16 additions & 5 deletions modeldb/modeldb-run.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -340,13 +340,26 @@
- cat mosinit.hoc >> temp
- mv temp mosinit.hoc
33975:
# The "interesting" feature of this model is that it produces an error message, roughly:
# We were unable to associate a PlayRecord item with a RANGE variable
# whose format changed after 8.2.2, and which went away in the data structure PR #2027.
# The error going away caused an (empty) gout file to be written, which also caused a diff.
# To avoid false positives, we regex away the error + traceback, and never produce a gout.
curate_patterns:
- pattern: 'hoc_run1: caught exception: hoc_execerror: We were unable to associate a PlayRecord item with a RANGE variable'
repl: ''
- pattern: '%neuron-executable%: We were unable to associate a PlayRecord item with a RANGE variable'
repl: ''
- pattern: ' in %model_dir%/driver.hoc near line 44'
repl: ''
- pattern: '^\s+(finitialize|init|run|stdinit)\((|-65)\)'
repl: ''
- pattern: '^\s+\^'
repl: ''
run:
- ringperf()
- run()
- verify_graph_()
# - verify_graph_()
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37856:
run:
- runiv()
Expand Down Expand Up @@ -692,15 +705,12 @@
- run()
- verify_graph_()
105507:
curate_patterns:
- pattern: '^([0-9.\-e]+) kilocycles$'
repl: '%some_count% kilocycles'
run:
- load_file("batch_.hoc")
- verify_graph_()
script:
# 424242: this is just avoiding a timing-related number being printed
- sed -i'.bak' -e 's/batch_flag=0/batch_flag=1/g;s/tstop = 1e3/tstop = 20/g;s#return tti/1e3#return 424242#g' batch_.hoc
- sed -i.bak -e 's/batch_flag=0/batch_flag=1/g;s/tstop = 1e3/tstop = 20/g;s#return tti/1e3#return 424242#g;s#print tti/.*#print "%some_time%"#g' batch_.hoc
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106551:
run:
- use_mcell_ran4(1)
Expand Down Expand Up @@ -1219,6 +1229,7 @@
comment: Tries to open bac6.ses, which does not exist
run: null
267384:
github: 'pull/2'
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model_dir: 'BBP_TTPC_EXAMPLE'
script:
# 12 is the largest value (runModel-template.hoc); this is a guess
Expand Down