Open ZiyiiiLiu opened 2 months ago
Something is leaking memory in this part of the code. Lucian or Adel can take a look.
Herbert Sauro
Herbert Sauro, Professor Director: NIH Center for model reproducibility University of Washington, Bioengineering 206-685-2119, www.sys-bio.org, http://reproduciblebiomodels.org/ Mobile: 206-880-8093 @.*** Books: http://books.analogmachine.org/
On Sat, Jul 6, 2024 at 10:37 PM ZiyiiiLiu @.***> wrote:
Hi, I am running a code that need to go through lots of parameter sets, and I apply bifurcation analysis for all sets. But every time I running the auto.execute() it consumes some RAM and my program will be killed because the RAM is not enough. Do you know how to release the RAM it comsumes for each parameter set?
Thanks!
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Something is leaking memory in this part of the code. Lucian or Adel can take a look. Herbert Sauro Herbert Sauro, Professor Director: NIH Center for model reproducibility University of Washington, Bioengineering 206-685-2119, www.sys-bio.org, http://reproduciblebiomodels.org/ Mobile: 206-880-8093 @. Books: http://books.analogmachine.org/ … On Sat, Jul 6, 2024 at 10:37 PM ZiyiiiLiu @.> wrote: Hi, I am running a code that need to go through lots of parameter sets, and I apply bifurcation analysis for all sets. But every time I running the auto.execute() it consumes some RAM and my program will be killed because the RAM is not enough. Do you know how to release the RAM it comsumes for each parameter set? Thanks! — Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/sys-bio/roadrunner/issues/1231__;!!K-Hz7m0Vt54!jhiJUs3iNtjjEMslh4rrJ3J8Avsa6t9xE12nHJs3tRA2VW4nmQgWw-zFqJgM3MvlTaupmfl16q9YTqiFaHWYaqjhT8uQgA$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AAIBSDQ4PDBH27N2QZH6DCLZLDH2RAVCNFSM6AAAAABKPBUD4GVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM4TGOJQGIZDINQ__;!!K-Hz7m0Vt54!jhiJUs3iNtjjEMslh4rrJ3J8Avsa6t9xE12nHJs3tRA2VW4nmQgWw-zFqJgM3MvlTaupmfl16q9YTqiFaHWYaqjZyN8BPw$ . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Thanks for the reply! I am using python, do you know whether there are any methods that I can added to the auto2000 python code to release the RAM this code uses?
Also, I used the newest version of roadrunner
Hi @ZiyiiiLiu, Is it possible for you to send us the Python script you are using that leads to this memory issue for you?
Sure! Which email can I send my code?
Thanks! Ziyi
---Original--- From: "Adel @.> Date: Thu, Jul 11, 2024 16:27 PM To: @.>; Cc: @.**@.>; Subject: Re: [sys-bio/roadrunner] Memory can't be released when using theauto.execute() (Issue #1231)
Hi @ZiyiiiLiu, Is it possible for you to send us the Python script you are using that leads to this memory issue for you?
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@ZiyiiiLiu I believe If you could just paste it or attach the file (as a zip file) here, that would be very helpful for referencing it in the future.
If it contains private information, though, feel free to email lpsmith (at) uw.edu directly.
Hi, I sent the zip code and separated py files to your email, but both of them were blocked as 'The response from the remote server was: 550 5.7.0 The attachment type is not permitted. Please contact help@uw.edu if you have questions or need assistance (FW)', do you know how to solve this? Thanks!
Sigh, sorry about that. Try lucianoelsmitho at gmail.com instead.
Sent! Thanks!
---Original--- From: "Lucian @.> Date: Tue, Jul 16, 2024 14:39 PM To: @.>; Cc: @.**@.>; Subject: Re: [sys-bio/roadrunner] Memory can't be released when using theauto.execute() (Issue #1231)
Sigh, sorry about that. Try lucianoelsmitho at gmail.com instead.
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Hi, I found that we don't need to use my code (because its not a direct example to show the problem), but just use one of your simple example about ode numerical solution and bifurcation diagram, and we can see that the memory isn't released
Hi, I am running a code that need to go through lots of parameter sets, and I apply bifurcation analysis for all sets. But every time I running the auto.execute() it consumes some RAM and my program will be killed because the RAM is not enough. Do you know how to release the RAM it comsumes for each parameter set?
Thanks!