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libRoadRunner: A high-performance SBML simulator
http://libroadrunner.org/
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Memory can't be released when using the auto.execute() #1231

Open ZiyiiiLiu opened 2 months ago

ZiyiiiLiu commented 2 months ago

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!

hsauro commented 1 month 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!

— 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: @.***>

ZiyiiiLiu commented 1 month 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! — 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?

ZiyiiiLiu commented 1 month ago

Also, I used the newest version of roadrunner

adelhpour commented 1 month ago

Hi @ZiyiiiLiu, Is it possible for you to send us the Python script you are using that leads to this memory issue for you?

ZiyiiiLiu commented 1 month ago

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?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.

Message ID: @.***>

adelhpour commented 1 month ago

@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.

luciansmith commented 1 month ago

If it contains private information, though, feel free to email lpsmith (at) uw.edu directly.

ZiyiiiLiu commented 1 month ago

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!

luciansmith commented 1 month ago

Sigh, sorry about that. Try lucianoelsmitho at gmail.com instead.

ZiyiiiLiu commented 1 month ago

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.

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

ZiyiiiLiu commented 1 month ago

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