In your virtual environment, install in editable mode:
pip install -e .
NOTE: You have to install NEURON by yourself (wheel, CMake install).
The following commands are now available:
-
getmodels
-> retrieve all or specified models from ModelDB.getmodels -h
-
runmodels
-> runnrn-modeldb-ci
for all or specified models.runmodels -h
Note that models have to be downloaded beforehand with
getmodels
. You can specify--virtual
so that NEURON GUI is run in headless mode. It requires a backend (n.r.Xvfb
). Re-running in the same--workdir
can mangle results. Please use--clean
if you wish to re-run in the same--workdir
. -
report2html
-> create an interactive HTML report for a given json report (obtained withrunmodels
)report2html -h
Note that the generated HTML file is self-contained.
-
diffgout
-> launchnrngui
and display the two gout files in different colors.diffgout -h
This can come in handy when comparing/investigating results from binary incompatible neuron versions.
-
diffreports2html
-> create an interactiveNEURONv1-vs-NEURONv2
HTML reportdiffreports2html -h
The differences that are taken into account:
nrn_run
andmoderr
from the json reports -> outputs side-by-side diffsgout
-> outputs git-like diffs; NOTE: this walks gout paths from json reportrun_info
, make sure they are present.
Note that the generated HTML file is self-contained.
-
modeldb-config
-> list configuration fornrn-modeldb-ci
:modeldb-config
Config Details ROOT_DIR location of nrn-modeldb-ci
installationMODELDB_ROOT_DIR path to modeldb
package insidenrn-modeldb-ci
MODELDB_RUN_FILE yaml file containing run instructions for models (required for runmodels
)MODELDB_METADATA_FILE yaml file containing model info for those downloaded with getmodels
MODELS_ZIP_DIR location of cache folder for models populated via getmodels
MDB_NEURON_MODELS_URL url used to get list of all NEURON model ids (necessary for getmodels
)MDB_MODEL_DOWNLOAD_URL url template used for model downloading (cf {model_id}
)
This is where the "black magic" lives, instructions on how to run models from ModelDB. Default handling is available in case there are no entries for a given model id.
All entries are optional:
yaml entry | special value | Details | Default handling |
---|---|---|---|
run | custom instructions used to effectively run the model | verify_graph_() * |
|
run | null | DoNotRun mode -> model is built but not run |
|
model_dir | custom location of mod sub-directory to compile |
*.mod @ root level |
|
model_dir | dir;dir | several custom mod sub-directories to compile |
*.mod @ root level |
skip | model is skipped from running alltogether | ||
comment | comment to be included in the report for skip or run: null |
||
script | bash script entries needed to adjust the model before running |
(*) verify_graph_()
saves all lines of all graphs to the gout
file in the model working directory.
The generated report following runmodels
contains te following info:
gout
- (optional) graph data from the neuron execution (must be run withrunmodels --gout
)logs
- logs regarding model setup, nrnivmodl, ...nrn_run
- command used to run the model and its outputrun_info
- model run informationrun_time
- model run time
For example, by running:
runmodels --gout --workdir=test3682 3682
we will generate report test3782.json
:
{
"0": {...} # runmodels stats, see next section
"3682": {
"gout": [
"Graphs 1\n",
"Graph[0]\n",
"lines 1\n",
"points 10001\n",
"xvec1\n",
"0\n",
"0.025\n",
".....", # truncated (can be HUGE)
"-57.9912\n",
"\n"
],
"logs": [
"",
"",
"/usr/bin/xcrun",
"%model_dir%",
"Mod files: \"%model_dir%/hh3.mod\" \"%model_dir%/rglu_score.mod\"",
"",
"Creating x86_64 directory for .o files.",
"",
"COBJS=''",
" -> \u001b[32mNMODL\u001b[0m %model_dir%/hh3.mod",
" -> \u001b[32mCompiling\u001b[0m mod_func.cpp",
" -> \u001b[32mNMODL\u001b[0m %model_dir%/rglu_score.mod",
"Translating hh3.mod into %model_dir%/x86_64/hh3.c",
"Notice: VERBATIM blocks are not thread safe",
"Translating rglu_score.mod into %model_dir%/x86_64/rglu_score.c",
"Notice: This mechanism cannot be used with CVODE",
"Notice: VERBATIM blocks are not thread safe",
"Notice: Assignment to the GLOBAL variable, \"inf\", is not thread safe",
"Notice: This mechanism cannot be used with CVODE",
"Notice: Assignment to the GLOBAL variable, \"Rtau_AMPA\", is not thread safe",
"Notice: Assignment to the GLOBAL variable, \"Rinf_AMPA\", is not thread safe",
"Notice: Assignment to the GLOBAL variable, \"Rtau_NMDA\", is not thread safe",
"Notice: Assignment to the GLOBAL variable, \"Rinf_NMDA\", is not thread safe",
"Warning: Default 37 of PARAMETER celsius will be ignored and set by NEURON.",
"Warning: Default -100 of PARAMETER ek will be ignored and set by NEURON.",
"Warning: Default 40 of PARAMETER ena will be ignored and set by NEURON.",
" -> \u001b[32mCompiling\u001b[0m hh3.c",
" -> \u001b[32mCompiling\u001b[0m rglu_score.c",
" => \u001b[32mLINKING\u001b[0m shared library ./libnrnmech.dylib",
" => \u001b[32mLINKING\u001b[0m executable ./special LDFLAGS are: ",
"Successfully created x86_64/special",
"INFO : Using neuron-nightly Package (Developer Version)",
""
],
"nrn_run": [
"RUNNING -> ./x86_64/special -nobanner %model_dir%/mosinit.hoc %model_dir%/driver.hoc",
"\t0 ",
"\t1 ",
"\t1 ",
"\t1 ",
"\t1 ",
"\t1 ",
"\t1 ",
"\t1 ",
"\t1 ",
"\t1 ",
"\t1 ",
"Spike at 40.5 ",
"Spike at 81.15 ",
"Spike at 108 ",
"Spike at 133.65 ",
"Spike at 180.775 ",
"Spike at 201.3 ",
"Total spikes: 6 ",
"\t1 ",
"\t1 ",
""
],
"run_info": {
"driver": "/Users/savulesc/Workspace/nrn-modeldb-ci/test3682/synmap/driver.hoc",
"init": "/Users/savulesc/Workspace/nrn-modeldb-ci/test3682/synmap/mosinit.hoc",
"model_dir": "/Users/savulesc/Workspace/nrn-modeldb-ci/test3682/synmap",
"script": [
"echo 'use_mcell_ran4(1)' > temp",
"cat mosinit.hoc >> temp",
"mv temp mosinit.hoc"
],
"start_dir": "/Users/savulesc/Workspace/nrn-modeldb-ci/test3682/synmap"
},
"run_time": "7.595794515"
}
}
Every runmodels
report will hold out run statistics in the "0"
key:
"0": {
"NEURON version": "8.0a-743-g3871f82a",
"Stats": {
"Failed models": {
"Accession numbers": [
20212,
97868,
144549,
186768,
244262
],
"Count": 5
},
"Failed runs": {
"Accession numbers": [
194897
],
"Count": 1
},
"No. of models run": 659
}
},
For every model there is a <model.id>.yaml
that is dumped in the model run directory.
This is used in case the model is re-run in --inplace
mode (also useful for debugging).
(venv) nrn-modeldb-ci$ cat test3682/synmap/3682.yaml
driver: /home/savulesc/Workspace/nrn-modeldb-ci/test3682/synmap/driver.hoc
init: /home/savulesc/Workspace/nrn-modeldb-ci/test3682/synmap/mosinit.hoc
model_dir: /home/savulesc/Workspace/nrn-modeldb-ci/test3682/synmap
script:
- echo 'use_mcell_ran4(1)' > temp
- cat mosinit.hoc >> temp
- mv temp mosinit.hoc
start_dir: /home/savulesc/Workspace/nrn-modeldb-ci/test3682/synmap
(venv) savulesc@bbd-cjngk03:~/Workspace/nrn-modeldb-ci$
nrn-modeldb-ci
is developed in a joint collaboration between the Blue Brain Project and Yale University. This work is supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology, NIH grant number R01NS11613 (Yale University), the European Union Seventh Framework Program (FP7/20072013) under grant agreement n◦ 604102 (HBP) and the European Union’s Horizon 2020 Framework Programme for Research and Innovation under Specific Grant Agreement n◦ 720270 (Human Brain Project SGA1), n◦ 785907 (Human Brain Project SGA2) and n◦ 945539 (Human Brain Project SGA3).
Copyright (c) 2022 Yale University & Blue Brain Project/EPFL