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ISSUES.txt
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This file is intended to be a running list of open and resolved issues for CellBlender.
Some of this functionality is in the various "issue trackers" that come with a particular
repository host (Google Code, GitHub, GitLab), but those "issue trackers" may be specific
to each platform and are not part of what's downloaded when a repository is cloned.
=== Open Issues ===
1 <Done?> Better user interface for the text output overlay
Added poll methods to gray out task control buttons as appropriate.
Changed text label of text update delay and moved to settings panel.
Drew only one of the "Show Text" or "Hide Text" buttons at a time.
Added an icon to the "Home" button.
Removed global variable: accumulate_text - no longer needed.
2 Opening a parameter-driven swept geometry blend file doesn't display the right geometry.
3 <DONE?> Can't use a parameter value for time step with MCellR
(it may need to be converted to a numeric value for use with export or BNGL suite?)
Note that this reported problem may be due to another cause.
Commit 6202f0703bf30d95076586a4dd1ce342b4e8ee9f was written to generate
TIME_STEP (and others) from the parameters and write them with fixed values
before writing the parameters (the current "typical" MDLR format).
However, this failed to reliably solve the problem.
Also, on further testing, writing parameters before TIME_STEP (and others) did
work sometimes. So it's not clear what's going on.
For that reason, this task may be considered done, but another task may be required.
4 When sweeping (MCellR only?), the task list doesn't update until the last few are run.
5 The plot setting to always generate all files seems to be stuck on (MCellR only?).
6 <DONE> Adding new release sites sometimes duplicates the default name (Release_Site_2 for example).
This was happening when a user manually (or sometimes via Data Model import) created
release site names that would end up being duplicated by the auto-naming system.
For example, creating an initial release site and naming it "Release_Site_5" would
cause a problem when 4 more release sites were added (auto-generating a duplicate).
This was fixed for Release Sites, Release Patterns, and Molecules by searching for
conflicts in the current list before choosing an auto-generated name.
A similar problem may exist for BNGL Molecule components which are also auto-named,
but it is less likely for a user to use those auto-generated names. In fact, that's
why the release sites were the first to be noticed. They generate names that are often
not changed by the user and remain in the likely to be conflicting pattern. This is less
likely to happen for BNGL component names which generally have meaning to the user.
7 It would be nice to not have to define reflective surface classes for everything (MCellR).
8 Creating an MCellR project from scratch and running works, but sometimes the .blend file
needs to be re-opened to show the mol-viz data. This seems to happen when deleting all
CellBlender data and regenerating the project from a script. When a new project is
created (with File/New) that doesn't seem to happen. It might have something to do
with the proxy molecules? The errors are:
Saving dynamic and script name for objects
Done saving dynamic and script name for objects
save post handler: cellblender_mol_viz.viz_data_save_post() called
New file name = .../bind_unbind_from_script.blend
Viz not manually selected
Blend: .../bind_unbind_from_script.blend
Viz: .../bind_unbind_from_script_files/mcell/output_data/viz_data/seed_00001
Refreshing/Reloading the Parameters, Molecules, and Geometry ...
Error: Array length mismatch (expected 300000, got 3000)
***** RuntimeError reading file: .../bind_unbind_from_script_files/mcell/output_data/viz_data/seed_00001/Scene.cellbin.0842.dat
str(error):
internal error setting the array
Error Type: <class 'RuntimeError'>
Error Value: internal error setting the array
=== Traceback Start ===
File ".../addons/cellblender/cellblender_mol_viz.py", line 916, in mol_viz_file_read
mol_pos_mesh.vertices.foreach_set("co", mol_pos)
=== Traceback End ===
Error: Array length mismatch (expected 303000, got 3000)
***** RuntimeError reading file: .../bind_unbind_from_script_files/mcell/output_data/viz_data/seed_00001/Scene.cellbin.0384.dat
str(error):
internal error setting the array
Error Type: <class 'RuntimeError'>
Error Value: internal error setting the array
=== Traceback Start ===
File ".../addons/cellblender/cellblender_mol_viz.py", line 916, in mol_viz_file_read
mol_pos_mesh.vertices.foreach_set("co", mol_pos)
=== Traceback End ===
Error: Array length mismatch (expected 306000, got 3000)
9 Do we need reactions and observables to run MCellR?
=============================================================================================
Running Scene.mdlr
There is an issue with the observables section in the mdlr file
Traceback (most recent call last):
File ".../addons/cellblender/extensions/mdlr2mdl.py", line 165, in <module>
namespace.input, namespace.nfsim)
File ".../addons/cellblender/extensions/read_mdl.py", line 285, in construct_bng_from_mdlr
reactions = process_reaction_rules(sections['reactions'])
File ".../2.78/python/lib/python3.5/site-packages/pyparsing.py", line 393, in __getitem__
return self.__tokdict[i][-1][0]
KeyError: 'reactions'
There is an issue with the observables section in the mdlr file
Traceback (most recent call last):
File ".../addons/cellblender/extensions/mdlr2mdl.py", line 165, in <module>
namespace.input, namespace.nfsim)
File ".../addons/cellblender/extensions/read_mdl.py", line 285, in construct_bng_from_mdlr
reactions = process_reaction_rules(sections['reactions'])
File ".../2.78/python/lib/python3.5/site-packages/pyparsing.py", line 393, in __getitem__
return self.__tokdict[i][-1][0]
KeyError: 'reactions'
=============================================================================================
Running Scene.mdlr
There is an issue with the observables section in the mdlr file
Traceback (most recent call last):
File ".../addons/cellblender/extensions/mdlr2mdl.py", line 165, in <module>
namespace.input, namespace.nfsim)
File ".../addons/cellblender/extensions/read_mdl.py", line 291, in construct_bng_from_mdlr
final_bngl_str.write(observables)
UnboundLocalError: local variable 'observables' referenced before assignment
There is an issue with the observables section in the mdlr file
Traceback (most recent call last):
File ".../addons/cellblender/extensions/mdlr2mdl.py", line 165, in <module>
namespace.input, namespace.nfsim)
File ".../addons/cellblender/extensions/read_mdl.py", line 291, in construct_bng_from_mdlr
final_bngl_str.write(observables)
UnboundLocalError: local variable 'observables' referenced before assignment
=============================================================================================
10 Testing ... we need lots of test cases to test various combinations of features.
This is especially important for testing lots of features with MCellR.
11 <DONE?> CPU usage by CellBlender goes up after several runs.
This may be connected display updating.
Further testing shows that this only happens when running MCellR models.
When CellBlender runs a simulation, Blender's CPU usage will go up and down during
various phases (export, running, finished). Blender's CPU usage should return to its
resting state after any number of runs. However, when running MCellR runs, Blender's
CPU usage will show a higher number after each successive MCellR run.
12 <DONE> Seed isn't being displayed properly in Simulation Process's list (show # of seeds rather than seed).
13 Check seed propagation from CellBlender to BioNetGen/MCellR (any repeatability issues?).
=== Resolved Issues ===
- In the Objects panel: selecting "Display From: Exported Files" doesn't work.
This option doesn't make sense for static scripted objects.
The logic was re-worked to produce sensible options for this case.
- Display engine output (text) to the 3D view during run.
Completed
- Move the "start_time.txt" file into the <project>_files directory.
start_time.txt is now in the <project>_files directory.
- Doesn't seem to support sweeping ...
Completed
- Can't seem to add plain (non-BNGL) molecules to an MCellR simulation.
This was an "operator error". Released molecules use a syntax like: @CP::x()
They work fine without any components, but do need to be referenced properly.
- Check for mcell path in extensions folder and use as the default if not already set
(it should default to the extensions folder: extensions/mcell)
- Check for bionetgen path in extensions folder and use as the default if not already set
(it should default to the extensions folder: extensions/bng2/BNGL2.pl)
- Add MCellR support to the "MCell Local" Engine/Runner.
This is partially implemented, and being tested.
Should we default to hiding the "mol_surface_proxy" and "mol_volume_proxy" molecules?
Sometimes a model needs to be run twice for MCell to run (race condition in files?).
- When looping over run commands (rather than looping over seeds), the seed value is
found in "run_cmd[5]". That's the value to use in the status line for the process name.
- CPU usage was increasing when tasks terminated abnormally because the percent done timers
for those tasks kept running (waiting for a "100% complete" detection in their streams).