is_outputting_averaged_fields issue #15

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1. tan2 commented on Dec 6, 2023

   

   tan2

   on Dec 6, 2023 via email

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   Hi Lam, A quick confirmation, what is the revision id of the code you are using? You can check it with the following command: git log -1 HEAD The most recent revision is: commit 5420830

   …

   On Wed, Dec 6, 2023 at 3:37 AM R.C. Lam ***@***.***> wrote: Recently I was running a program and wanted to set is_outputting_averaged_fields = yes for my simulation. I received an error message and the program was killed. I checked to see if the same thing happened when I ran the original benchmark code oedometer-2d.cfg. When the option was set to no, it ran fine. When I changed it to yes, then I got the same error message. Screen.Shot.2023-12-05.at.1.28.43.PM.png (view on web) <https://github.com/tan2/DynEarthSol/assets/75513951/e6ffe092-e65c-46cd-a87a-e0f5b4d30c5f> Checking it with valgrind (shown below), it seems that there is leakage occurring. Could someone check their own fork and see if they have the same problem? Screen.Shot.2023-12-05.at.1.30.44.PM.png (view on web) <https://github.com/tan2/DynEarthSol/assets/75513951/c7ea01c9-eb20-42d5-8f8f-2da33de8b229> — Reply to this email directly, view it on GitHub <https://github.com/tan2/DynEarthSol/issues/15>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABWQQRCLWUTAI2WMPGPGULYH5ZYRAVCNFSM6AAAAABAIHEUN6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGAZDMOJYGYZDEMQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>
2. rclam commented on Dec 6, 2023

   

   rclam

   on Dec 6, 2023

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   `commit b380249 (HEAD, EhTan/master)
   Merge: ac1a328 b071cc6
   Author: Eunseo Choi echoi@users.noreply.github.com
   Date: Mon Oct 23 08:25:07 2023 -0500

   Merge pull request #12 from chaseshyu/merge_openacc
   
   Preparation of test case, flag, and consistency for merge openacc`
   
3. chaseshyu commented on Dec 7, 2023

   

   chaseshyu

   on Dec 7, 2023

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   Hi @rclam,

   Sorry, I cannot reproduce the Invalid free() / delete / delete[] / realloc() in commit tan2/DynEarthSol@b380249 with valgrind.
   Can you provide the commands you are using to compile and debug? And what the compiler do you use?
   For instance, my comiler version is: g++ (GCC) 4.8.5 .
   I am using following commands to

   Compile

   make ndims=2 BOOST_ROOT_DIR=/path/to/boost/62 -j4 opt=0

   Debug

   valgrind --leak-check=full --show-leak-kinds=all --log-file="valgrind-out.txt" ./dynearthsol2d oedometer-2d.cfg
4. chaseshyu commented on Jan 4, 2024

   

   chaseshyu

   on Jan 4, 2024

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   Hi @rclam,

   With
   max_steps = 200
is_outputting_averaged_fields = yes
quality_check_step_interval = 40

   I have run commit tan2/DynEarthSol@b380249 and commit tan2/DynEarthSol@0d20bd9 (the commit before merge).

   b380249
   
   0d20bd9
   

   Debug of commits both do not have invaild free() memory access.
5. rclam commented on Jan 12, 2024

   

   rclam

   on Jan 12, 2024

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   Chase, thanks for looking into this. When I last re-ran the same problem using valgrind, it was stuck and didn't give any outputs (just constantly reiteratively trying to do output 1 maybe); when I ran it without valgrind, it gave the same error and killed itself immediately. It's possible the change is because Nefertiti might have had a compiler update between when I submitted the bug and when I checked the compiler versions. How should I approach the issue again? I was thinking to ask someone else on Nefertiti to try running it so I can see if the error is on my version only and I've somehow messed with something (and need to git pull the original all over) or we can see if it's related to Nefertiti's set-up. What do you think? Is there something else I need to check?