FileNotFoundError

[JK9057]

I am a beginner of Python.

I tried test command.

from biomass import Model, optimize
from biomass.models import Nakakuki_Cell_2010

model = Model(Nakakuki_Cell_2010.package).create()

optimize(model, x_id=range(1, 11))

but, it didn't work

error occerd.

FileNotFoundError: [Errno 2] No such file or directory: 'biomass\models\Nakakuki_Cell_2010\set_model.py'

I couldn't find the solution.

Could you give me some advise?

Thank you.

[himoto]

Hello @JK9057, thank you for your inquiry, and great thanks for using BioMASS!

I guess you installed BioMASS via pip. Can you please install biomass via git clone?

$ git clone https://github.com/biomass-dev/biomass
$ cd biomass

Or download zip and work in biomass-master folder.

Then, you can run:

from biomass import Model, optimize
from biomass.models import Nakakuki_Cell_2010

model = Model(Nakakuki_Cell_2010.__package__).create()

optimize(model, x_id=range(1, 11))

I hope this helps resolve the issue. If the problem still persists, please do let me know.

Thanks,
Hiroaki

[JK9057]

Dear Hiroaki
Thank you for your advice
I really appericate your comment.

It is needed an options (overwrite : True) ! it is very simple but I couldn't imagine.

I retry it.

My PC is not a good performance. It maybe takes a few days.

I will check that it is finished without any problems.

I am looking forward to being able to use this program.

Best regards, JK.

[himoto]

@JK9057,

I recommend you to use the following options:

optimize(
    model, x_id=range(1, 11), options={
        "popsize": 3,
        "max_generation": 100,
        "allowable_error": 0.5,
        "local_search_method": "DE",
        "maxiter": 50,
        "workers": 1,
        "overwrite": True,
    }
)

The computation time will also depend on these parameters, especially max_generation and allowable_error.
Please refer to https://biomass-core.readthedocs.io/en/latest/api/core.html for the description of each parameter.

Please do let me know anytime if you have any questions, I'd be delighted to try to answer questions about BioMASS!

[JK9057]

Hello Hiroaki

I appreciate for your comment.
I tried your advice to test, but it took many hours to optimze.
And finally I couldn't finish it.

I think my PC spec is weak, so I changed the parameter.

from biomass import optimize

optimize(
model, x_id=1, options={
"popsize": 3,
"max_generation": 10,
"allowable_error": 0.5,
"local_search_method": "DE",
"maxiter": 50,
"overwrite": True}
)

Today I found some error messages,
I understood message meanings but I couldn't solve it.

So I hope that you give me some advice.

The message is

C:\Users\XXXX\biomass\biomass\models\Nakakuki_Cell_2010\set_model.py:136: RuntimeWarning: invalid value encountered in double_scalars
x[C.V57] * y[V.pcFOSn] ** x[C.n57] / (x[C.Km57] ** x[C.n57] + y[V.pcFOSn] ** x[C.n57])
C:\Users\XXXX\biomass\biomass\models\Nakakuki_Cell_2010\set_model.py:107: RuntimeWarning: invalid value encountered in double_scalars

• (y[V.Fn] / x[C.KF31]) ** x[C.nF31]

py:107: is repeated some time.

Best regards, JK.

[himoto]

Hi @JK9057, thank you for your report.

C:\Users\XXXX\biomass\biomass\models\Nakakuki_Cell_2010\set_model.py:136: RuntimeWarning: invalid value encountered in double_scalars
x[C.V57] * y[V.pcFOSn] ** x[C.n57] / (x[C.Km57] ** x[C.n57] + y[V.pcFOSn] ** x[C.n57])
C:\Users\XXXX\biomass\biomass\models\Nakakuki_Cell_2010\set_model.py:107: RuntimeWarning: invalid value encountered in double_scalars

While estimating parameters, biomass generates multiple parameter candidates. Occasionally they are not suitable for the model to numerically solve ODE. For me, it is reasonable to see this warning during parameter estimation. Since such parameter sets are weeded out during optimization, you do not have to care about this warning right now.

[JK9057]

Hello Hioaki,

Thank you for your answer.
I understood that these warnings are not needed to mention.

I am just waiting for finish the optimizing, ain't I?

I would like to know whether BioMass is powerful tool as soon as possible.