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lanl / PyBNF

An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuristic optimization algorithms, and an adaptive Markov chain Monte Carlo (MCMC) sampling algorithm.
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error during test with example egfr_nf #325

Closed nchorton closed 1 year ago

nchorton commented 1 year ago

Hello, I'm just starting to use bionetfit and had it installed on our HPC computers. The demo tests ran fine, but I've had trouble with some other examples and I don't understand the errors. With egfr_nf.conf, I get an error and this log file:

egfr_nf_logfile

Thanks!

wshlavacek commented 1 year ago

I get the same errorWe need to figure out what’s wrongThis job worked fine in the past and the job setup files haven’t changed Sent from my iPhoneOn Feb 15, 2023, at 9:16 PM, nchorton @.***> wrote: Hello, I'm just starting to use bionetfit and had it installed on our HPC computers. The demo tests ran fine, but I've had trouble with some other examples and I don't understand the errors. With egfr_nf.conf, I get an error and this log file:

Thanks!

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wshlavacek commented 1 year ago

The problem I found was that the definition of the Clusters observable is incompatible with BioNetGen version 2.8.4. I don't know why the latest release of BioNetGen doesn't like the observable definition - I reported the issue to the BNG help list. I commented out the observable and redefined Clusters as a global function, Clusters(). This change required replacing "Clusters" with "Clusters()" in 4 function definitions. After these changes, the job runs.

nchorton commented 1 year ago

Hi Bill,

Should I reinstall PyBNF or install a patch?

Thanks, Nancy

On Tue, Feb 28, 2023 at 3:30 PM Bill Hlavacek @.***> wrote:

The problem I found was that the definition of the Clusters observable is incompatible with BioNetGen version 2.8.4. I don't know why the latest release of BioNetGen doesn't like the observable definition - I reported the issue to the BNG help list. I commented out the observable and redefined Clusters as a global function, Clusters(). This change required replacing "Clusters" with "Clusters()" in 4 function definitions. After these changes, the job runs.

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wshlavacek commented 1 year ago

Jacob updated PyBNF recently to fix several issuesYou should probably upgrade/re-installThe example problem you had trouble with is fixed - at the GitHub repo Sent from my iPhoneOn Feb 28, 2023, at 5:49 PM, nchorton @.***> wrote: Hi Bill,

Should I reinstall PyBNF or install a patch?

Thanks, Nancy

On Tue, Feb 28, 2023 at 3:30 PM Bill Hlavacek @.***> wrote:

The problem I found was that the definition of the Clusters observable is incompatible with BioNetGen version 2.8.4. I don't know why the latest release of BioNetGen doesn't like the observable definition - I reported the issue to the BNG help list. I commented out the observable and redefined Clusters as a global function, Clusters(). This change required replacing "Clusters" with "Clusters()" in 4 function definitions. After these changes, the job runs.

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