AMICI

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AMICI, OpenMP and conda

1

I get a `SIGABRT` which is apparently due to OpenMP. ``` __pthread_kill 0x00007fff6eac833a pthread_kill 0x00007fff6eb84e60 abort 0x00007fff6ea4f808 __kmp_abort_process 0x0000000120d34440 __kmp_fatal 0x0000000120cf5d17 __kmp_register_library_startup() 0x0000000120cfd500 __kmp_do_serial_initialize() 0x0000000120cf6362 __kmp_get_global_thread_id_reg 0x0000000120cf6321 amici::AmiciApplication::runAmiciSimulations(amici::Solver const&, std::__1::vector...

lcontento

Split expressions into static and dynamic

1

static expressions don't depend on time/states and only need to be evaluated after reinitialization, not at every timepoint.

FFroehlich

Add option to disable printing to stdout

1

Currently there is no clean way to hide AMICI warnings and errors when using the Python interface. This should be changed. Using the Python `warnings` library would be ideal, but...

dweindl

Python package installation from python/sdist/ broken

6

Only the development installation with `pip -e` or via sdist works. This is due to the symlink to README.md. Needs to be cleaned up somehow.

dweindl

Speed up Python import of small models

2

Import time for small models is determined mostly by compiling and especially linking. Pretty sure there is room for improvement... Potential starting points: - [ ] reduce swig interface -...

dweindl

Generate model code for all test models in Python

3

Currently AMICI C++ code is pre-generated from Matlab. For proper testing, models should be imported on the fly. Requires: - [x] Allow for import of raw ODEs (YAML) #654 #857...

dweindl

residuals ignore events

3

only account for time-resolved observables :/

FFroehlich

_Originally posted by @FFroehlich in https://github.com/AMICI-dev/AMICI/issues/1451#issuecomment-794872534_ >> Reports missed expectations, but does not fail. Currently, '/model_steadystate/sensifwdbyhandpreeq' reports wrong sx0, sx, sy and sllh, independently of these changes. > That's one...

dweindl

Exploit structures for models with particular datasets

2

I just had the idea, that models with only 1 data point per simulation condition allows for many, many simplifications... (e.g., comouting the FIM from the gradient). Does it make...

paulstapor

DAE integration fails

6

I have a problem with a simple published model (5 states, 8 parameters): I would like to have it as a DAE, but AMICI fails to do the simulation then,...

yannikschaelte