openCARP issueshttps://git.opencarp.org/groups/openCARP/-/issues2022-08-22T13:35:32Zhttps://git.opencarp.org/openCARP/openCARP/-/issues/151Failing tests with Ginkgo backend2022-08-22T13:35:32ZAxel Loeweaxel.loewe@kit.eduFailing tests with Ginkgo backendSome test are failing when the Gingko numerical backend is used.
Example test log: https://git.opencarp.org/openCARP/openCARP/-/jobs/39485
We will [merge](https://git.opencarp.org/openCARP/openCARP/-/merge_requests/79) the `ginkgo_inte...Some test are failing when the Gingko numerical backend is used.
Example test log: https://git.opencarp.org/openCARP/openCARP/-/jobs/39485
We will [merge](https://git.opencarp.org/openCARP/openCARP/-/merge_requests/79) the `ginkgo_integration` branch anyway soon to expose the abstraction of the numerical backend. When running the PETSc, everything passes. This issue is to keep track of the work done with the Ginkgo backend to reach fully similar output.Terry CojeanTerry Cojeanhttps://git.opencarp.org/openCARP/experiments/-/issues/39Some comments on the "Single-cell APD restitution" experiment2023-01-09T13:00:03ZJoshua SteyerSome comments on the "Single-cell APD restitution" experiment- 1st task: When generating the APD vs. DI plots, the second figure (the one with the two images comparing APD and restitution slope) is not very readable in its standard output size (the x axis description of the upper image overlaps wi...- 1st task: When generating the APD vs. DI plots, the second figure (the one with the two images comparing APD and restitution slope) is not very readable in its standard output size (the x axis description of the upper image overlaps with the headline of the lower one). Only if the figure itself is enlarged, one may read the description better. I'd suggest to automatically adjust the distances, e.g., by setting bbox_inches='tight' or so
- 2nd task: "It should be well above 1.0 and look similar to Figure 5 in the Tusscher2006 paper." -> maybe specify which one is meant specifically, e.g., (5F)
- 2nd task: Even though in the text, 'G_Kr=0.172,G_Ks=0.441,G_pCa=0.8666,G_pK=0.00219,G_tf=2' (so in total five parameters) are to be changed, in the corresponding command line, only GKr=0.172 and GKs=0.441 are set.
- 2nd task: Neither Gtf nor G_tf seem to exist in the tenTusscherPanfilov model (at least according to when running bench --imp=tenTusscherPanfilov --imp-info)https://git.opencarp.org/openCARP/openCARP/-/issues/122Optical mapping post-processing2022-01-31T10:58:26ZGirish RamlugunOptical mapping post-processingHi,
Could the optical mapping post-processing from carp/carpentry be ported to opencarp?
Cheers,
Girish Ramlugun
### Intended users
This feature could be useful to researchers who would like to include simulation results to comple...Hi,
Could the optical mapping post-processing from carp/carpentry be ported to opencarp?
Cheers,
Girish Ramlugun
### Intended users
This feature could be useful to researchers who would like to include simulation results to complement their experimental studies or validate certain hypotheses from experimental data. It can also be used to generate synthetic data to develop and test optical mapping signal processing algorithms.
### Proposal
This feature existed in carp/[carpentry](https://carpentry.medunigraz.at/examples/devtests/devtests.bidomain.optical_mapping.run.html) based on [Bishop et al, 2006](https://www.sciencedirect.com/science/article/pii/S0006349506724742?via%3Dihub) and should therefore be reasonably straightforward to port to opencarp.https://git.opencarp.org/openCARP/openCARP/-/issues/120Evaluate hpc-container-maker2022-10-24T13:42:48ZAxel Loeweaxel.loewe@kit.eduEvaluate hpc-container-makerCan this tool be valuable to automate building and maintaining Docker files for multiple environments (e.g. different operating systems?)
https://github.com/NVIDIA/hpc-container-maker
Could be used for #119Can this tool be valuable to automate building and maintaining Docker files for multiple environments (e.g. different operating systems?)
https://github.com/NVIDIA/hpc-container-maker
Could be used for #119Marie HouillonMarie Houillonhttps://git.opencarp.org/openCARP/openCARP/-/issues/115Video: example using Docker2023-10-31T08:42:08ZAxel Loeweaxel.loewe@kit.eduVideo: example using DockerFrom user meeting 2021.
* Install Docker
* Install openCARP container
* Launch container
* Run example experiment
* Access result data from host systemFrom user meeting 2021.
* Install Docker
* Install openCARP container
* Launch container
* Run example experiment
* Access result data from host systemYung-Lin HuangYung-Lin Huanghttps://git.opencarp.org/openCARP/experiments/-/issues/33Video tutorial: build first own experiment2021-10-04T11:33:34ZAxel Loeweaxel.loewe@kit.eduVideo tutorial: build first own experimentBased on https://git.opencarp.org/openCARP/experiments/-/tree/master/tutorials/02_EP_tissue/22_simple
Could be the example from the modeling challenge.
Show openCARP parameter documentation and carputils doxygen documentation in video....Based on https://git.opencarp.org/openCARP/experiments/-/tree/master/tutorials/02_EP_tissue/22_simple
Could be the example from the modeling challenge.
Show openCARP parameter documentation and carputils doxygen documentation in video.
@hermenegild / Simula offered to also contribute some examples.Jorge SanchezJorge Sanchezhttps://git.opencarp.org/openCARP/openCARP/-/issues/113Video: installation / compilation2021-10-04T11:25:38ZAxel Loeweaxel.loewe@kit.eduVideo: installation / compilationFrom user meeting 2021From user meeting 2021Yung-Lin HuangYung-Lin Huanghttps://git.opencarp.org/openCARP/openCARP/-/issues/112Add verbose output that prints values of all parameters2022-11-25T15:25:31ZAxel Loeweaxel.loewe@kit.eduAdd verbose output that prints values of all parametersFrom user meeting 2021:
> Add flag that outputs all parameter values (including those where default values are being used).From user meeting 2021:
> Add flag that outputs all parameter values (including those where default values are being used).https://git.opencarp.org/openCARP/experiments/-/issues/32Documentation on lookup tables in ionic models2021-10-04T11:19:29ZAxel Loeweaxel.loewe@kit.eduDocumentation on lookup tables in ionic modelsFrom user meeting 2021:
> More information about how lookup tables can be used for ionic models. What should one look out for? Does the model formulation matter for speed or accuracy?
Add to https://git.opencarp.org/openCARP/experiments...From user meeting 2021:
> More information about how lookup tables can be used for ionic models. What should one look out for? Does the model formulation matter for speed or accuracy?
Add to https://git.opencarp.org/openCARP/experiments/-/blob/master/tutorials/01_EP_single_cell/05_EasyML/run.py to be shown on https://opencarp.org/documentation/examples/01_ep_single_cell/05_easymlKristian Gregorius HustadKristian Gregorius Hustadhttps://git.opencarp.org/openCARP/openCARP/-/issues/110Unify calling of external and shipped models2022-02-04T12:36:34ZAxel Loeweaxel.loewe@kit.eduUnify calling of external and shipped modelsCollected during user meeting 2021:
> Unify the use of external ionic models and models included in openCARP/bench so one does not have to specify if the model is external or not.Collected during user meeting 2021:
> Unify the use of external ionic models and models included in openCARP/bench so one does not have to specify if the model is external or not.Kristian Gregorius HustadKristian Gregorius Hustadhttps://git.opencarp.org/openCARP/experiments/-/issues/30Example how to visualize fibers2021-09-21T12:30:00ZAxel Loeweaxel.loewe@kit.eduExample how to visualize fibersIt would be nice to add an example demonstrating how to visualize fibers using meshalyzer. The recording of Ed's talk during the 4th openCARP User Meeting can be a good starting point. The video should be online soon.It would be nice to add an example demonstrating how to visualize fibers using meshalyzer. The recording of Ed's talk during the 4th openCARP User Meeting can be a good starting point. The video should be online soon.https://git.opencarp.org/openCARP/openCARP/-/issues/93Make rt library for run-time external function2021-01-25T16:34:58ZLuca AzzolinMake rt library for run-time external function### Problem to solve with the new feature
Use of run-time external function is currently not possible.
### Intended users
openCARP users who wants to track specific variables in run-time
### Further details
E.g. track specific variable...### Problem to solve with the new feature
Use of run-time external function is currently not possible.
### Intended users
openCARP users who wants to track specific variables in run-time
### Further details
E.g. track specific variables in run-time
### Proposal
E.g: Include the make_rt_lib.sh previously present in CARP and add test case
### Testing
It should not affect the performance or quality of openCARP.
### Links / referenceshttps://git.opencarp.org/openCARP/openCARP/-/issues/91gvec[] doesn't work with plugins2021-01-23T06:58:06ZPatrick Boylegvec[] doesn't work with plugins<!---
Please read this!
Before opening a new issue, make sure to search for keywords in the issues
filtered by the "Bug" label:
- https://git.opencarp.org/groups/openCARP/-/issues?label_name=Bug
and verify the issue you're about to su...<!---
Please read this!
Before opening a new issue, make sure to search for keywords in the issues
filtered by the "Bug" label:
- https://git.opencarp.org/groups/openCARP/-/issues?label_name=Bug
and verify the issue you're about to submit isn't a duplicate.
--->
### Summary
When the gvec[] interface is used to attempt to output data from a state variable (SV) in a plugin, the program instead outputs SV data from the main ionic model.
### What version of openCARP are you using?
master branch as of time of posting:
SHA1 ID: 68e34868e5358bddf6d40fe4150d0d9239a48d91
### What operating system and processor architecture are you using?
```
> uname -a
Linux frazier 4.15.0-130-generic #134-Ubuntu SMP Tue Jan 5 20:46:26 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
```
### Steps to reproduce
I attached a tarball with minimal examples. I have reproduced this bug with two plugins, one built-in (MacCannell_Fb_plug) and one dynamically loaded via the external_imp[] interface (my own IChR2 implementation).
[GVecProblemWithPlugins.tgz](/uploads/18a69507cf8265e8d29d52e7b1650521/GVecProblemWithPlugins.tgz)
### What is the current *bug* behavior?
Consider the following example:
```
num_gvecs = 2
gvec[0].ID = Ca_i
gvec[0].name = TT2.Ca_i
gvec[1].imp = MacCannell_Fb_plug
gvec[1].ID = V_fb
gvec[1].name = FbPlug.Vm
```
The resulting output files are binary identical (they should not be!):
```
> diff GVecProblemTest/FbPlug.Vm.igb GVecProblemTest/TT2.Ca_i.igb
>
```
They are identical because I cherry-picked the Ca_i variable from the TT2. When I opened the GVecProblemTest/FbPlug.Vm.igb and I saw that the initial condition in all nodes was 0.07 (same as default value for Ca_i in uM), I suspected something was up. If you change the .ID parameters to different SV names, the igb files will differ.
I think what is happening is that the size of the memory block where base ionic model SVs live is not being taken into account when the gvec[] code tries to index into the memory where plugin SVs live.
### What is the expected *correct* behavior?
The values over time of the requested SV in the plugin should be output :)
### Relevant logs and/or screenshots
See attached + above.
### Possible fixes
If I'm not mistaken, the issue is on/around L461 of physics/ionics.cc. If the requested SV is in plugin N, I think the memory offset needs to be added to the whole byte size of miif->iontypes[idx] plus the size of any preceding miif->plugtypes[idx][k] (where k < N). I have no idea how to fix this though, function pointers terrify me.https://git.opencarp.org/openCARP/openCARP/-/issues/87Merge general modeling intro with content from carpentry web page2020-12-21T14:16:09ZAxel Loeweaxel.loewe@kit.eduMerge general modeling intro with content from carpentry web pageThe content in chapters 3-7 of the [openCARP manual](https://opencarp.org/documentation/user-manual) should be merged with additional (or updated) information on the [carpentry page](https://carpentry.medunigraz.at/carputils/knowledge-ba...The content in chapters 3-7 of the [openCARP manual](https://opencarp.org/documentation/user-manual) should be merged with additional (or updated) information on the [carpentry page](https://carpentry.medunigraz.at/carputils/knowledge-base/index.html)
#86 would then not only include this information in the PDF manual but also deploy it to pages on the website.https://git.opencarp.org/openCARP/openCARP/-/issues/86Documentation: deploy web version2020-12-21T14:15:54ZAxel Loeweaxel.loewe@kit.eduDocumentation: deploy web versionIt would be nice to deploy the documentation not only to the [PDF](https://opencarp.org/documentation/user-manual) but also to pages of the web site.
The LaTeX -> pandoc -> Markdown workflow should support this in combination with the ...It would be nice to deploy the documentation not only to the [PDF](https://opencarp.org/documentation/user-manual) but also to pages of the web site.
The LaTeX -> pandoc -> Markdown workflow should support this in combination with the [openCARP-CI scripts](https://git.opencarp.org/openCARP/openCARP-CI).
* The [parameters](https://opencarp.org/documentation/opencarp-parameters) are already deployed to the web page and could be skipped.
* The [installation](https://opencarp.org/download/installation) is also already on the webpage and could be sourced from there for generating the PDF to remove the duplicate description (and the need to maintain 2 texts).
* Related issue #87 merge content of former carpentry rst description into remaining chaptershttps://git.opencarp.org/openCARP/openCARP/-/issues/80Limpet Metadata extension2024-03-14T12:13:25ZAxel Loeweaxel.loewe@kit.eduLimpet Metadata extension* [ ] Add fields for species and location
* [ ] Output condensed metadata with `--list-imps` (in a table?)
* [ ] Output full metadata with `--imp-info` (in a table?)
* [x] Fix doi output (interpreted as a floating point number).* [ ] Add fields for species and location
* [ ] Output condensed metadata with `--list-imps` (in a table?)
* [ ] Output full metadata with `--imp-info` (in a table?)
* [x] Fix doi output (interpreted as a floating point number).Ionic model library overhaulJorge SanchezJorge Sanchez2022-02-16https://git.opencarp.org/openCARP/carputils/-/issues/8Move from stimulus[] to stim[]2021-04-27T05:58:27ZAxel Loeweaxel.loewe@kit.eduMove from stimulus[] to stim[]openCARP throws a deprecation warning for stimulus[] commands
https://git.opencarp.org/openCARP/carputils/blob/master/carputils/model/stimulus.py#L25openCARP throws a deprecation warning for stimulus[] commands
https://git.opencarp.org/openCARP/carputils/blob/master/carputils/model/stimulus.py#L25https://git.opencarp.org/openCARP/experiments/-/issues/2603A_study_prep_tuneCV output inconsistent with web page2020-11-04T15:20:10ZAxel Loeweaxel.loewe@kit.edu03A_study_prep_tuneCV output inconsistent with web pageReported by @rafael.sebastian:
We have realized that outputs for 03A_study_prep_tuneCV are not the same as in the web page. However, we follow exactly the steps in the script, so probably the example has changed? We have also detected in...Reported by @rafael.sebastian:
We have realized that outputs for 03A_study_prep_tuneCV are not the same as in the web page. However, we follow exactly the steps in the script, so probably the example has changed? We have also detected in this example an incompatibility with the parameter Lumping. In the web page it gives two options True/False (it is read automatically from args), but in the example if you choose the option compareMassLumping, even if you set Lumping to False fails. We believe that the problem is due to the existence (even if set to False) of the variable Lumping in the arguments of the run.py. Could you check it out?https://git.opencarp.org/openCARP/carputilsgui/-/issues/22Integrate help page within carputilsGUI more inline with the webpage layout2020-11-02T16:38:39ZGunnar SeemannIntegrate help page within carputilsGUI more inline with the webpage layout@D_Serra @jochen: Maybe we can think about a strategy to show the "nice" example page of the opencarp.org website in the help window of carputilsGUI. One can even think about a specific parsing (or editing of the rst) so that only necess...@D_Serra @jochen: Maybe we can think about a strategy to show the "nice" example page of the opencarp.org website in the help window of carputilsGUI. One can even think about a specific parsing (or editing of the rst) so that only necessary content for carputilsGUI is shown (`cd to/some/folder` e.g., is not necessary in the WebApp). This is more a midterm task and not high priority for the workshophttps://git.opencarp.org/openCARP/carputilsgui/-/issues/21Start paraview web with standard scaling and color bar2020-11-02T16:32:04ZGunnar SeemannStart paraview web with standard scaling and color barCurrently, I need to rescale the results for simulation in paraview web when the window opens and need to turn on the color bar every time. It would be good for an easy use (also here for the workshop) if paraview would be started with a...Currently, I need to rescale the results for simulation in paraview web when the window opens and need to turn on the color bar every time. It would be good for an easy use (also here for the workshop) if paraview would be started with a scaling either between the upper and lower bound of the simulation or fixed values (e.g. -90 ... 20).Dolors SerraDolors Serra