[Mesa-users] Switching MESA-r9798 to the newest version r24.3.01

Kit Yu Lau kityulau.rita at gmail.com
Wed Jul 24 03:42:46 UTC 2024 

Hi all,

We doubt that the running time is so slow because different usage of
network solver (NOT network, but network solver for ns_h). Can anyone tell
me what network solver is the newest version using? Thank you very much.

Regards,
Rita


On Wed, Jul 17, 2024 at 4:00 AM Ebraheem Farag <ekfarag at asu.edu> wrote:

> Hi Rita,
>
> Thanks for sharing your inlists!
>
> Since you're modeling something quite specific and unique, I would advise
> against sharing disparate inlists where it is unclear when each is used,
> and where the loaded .mod file is not included. I would instead always
> recommend sharing a self contained clean model directory so it is easy for
> someone to unzip/untar ./clean, ./mk. and ./rn your model without worrying
> about how to put the pieces together. A clean directory should be <1Mb
> typically so it's relatively easy to share. shmesa
> <https://github.com/MESAHub/mesa/tree/main/scripts/shmesa> is now
> included with MESA r24.03.1+ which contains commands to do this for you,
> although it can be done by hand relatively easily as well.
>
> Nonetheless, since you're using rp.net with 303 isotopes, I can imagine
> this is quite an expensive run. I think the biggest clues will lie in
> whether your model is struggling to find solutions. Can you share the
> terminal output (as a singular txt file) from your runs in both versions,
> as I do not have the bandwidth to test these inlists. We can directly
> compare the terminal outputs to see if anything particularly different is
> happening for both runs, which should give some insight into the
> differences.
>
> Another extremely useful way to diagnose any issues or differences would
> be to generate pgstar pngs every 1-10 timesteps and then compress them into
> a movie (e.g. "images_to_movie "png/*.png" movie.mp4"). The pgstar movie is
> an extremely useful diagnostic for numerics, not just physics! See
> https://docs.mesastar.org/en/release-r24.03.1/test_suite/ns_h.html. In
> fact I often use pgstar to diagnose issues for runs that have to be done on
> a cluster, so there is a visible track record of what my model has done
> that I can review after the fact, and before post-processing or analyzing
> my results for their scientific merit. as far as your plots go, they look
> good, but I have questions like "how many model numbers did this take, how
> many retries, how many solver iterations", things that are not communicated
> by this plot but relate more directly to your question of "why is my model
> running slow?". It could be useful also to compare your models and their
> run time to the test_cases ns_h, ns_he, as you can switch the test cases to
> the larger network you're adopting and see if this issue is related to your
> inlist setup in the current MESA version or not.
>
> Lastly, OMP_NUM_THEADS=64 sounds like a lot of cores, which might not be
> giving you too much of a speed up, and could potentially slow your model
> down. MESA does not parallelize very well past 12-16 threads, so it might
> be worth saving some cluster resources and reducing the number of threads?
> I personally used 16 for most models, so it would be interesting to know if
> your model runs faster or slower with OMP_NUM_THREADS=16 as opposed to 64?
>
> I hope this helps!
>
> -EbF
>
> On Tue, Jul 16, 2024 at 7:27 AM Kit Yu Lau via Mesa-users <
> mesa-users at lists.mesastar.org> wrote:
>
>> Hi all,
>>
>> Thanks for replying to my emails.  I attached the inlist files and
>> run_star_extras.f90 files in the email. My OMP_NUM_THREADS is 64. Thank
>> you!
>>
>> Regards,
>> Rita
>>
>> On Tue, Jul 16, 2024 at 8:54 PM Francis Timmes <fxt44 at mac.com> wrote:
>>
>>> hi rita,
>>>
>>> thanks for the plot - looks reasonable. i will repeat eb's suggestion to
>>> post your inlist(s) and any associated run_star_extras, otherwise its
>>> impossible to offer any suggestions for potentially improving the run time.
>>> in addition, please give the value of your OMP_NUM_THREADS environment
>>> variable.
>>>
>>> fxt
>>>
>>>
>>>
>>>
>>>
>>> On Jul 16, 2024, at 1:08 AM, Kit Yu Lau via Mesa-users <
>>> mesa-users at lists.mesastar.org> wrote:
>>>
>>> This is the luminosity plot I got for the new version. It takes 1  week
>>> to get the following resutls:<image.png>
>>>
>>> On Tue, Jul 16, 2024 at 12:29 AM Ebraheem Farag <ekfarag at asu.edu> wrote:
>>>
>>>> Hello Kit,
>>>>
>>>> Please share your inlists or some sort of output comparison (perhaps
>>>> attach txt files of the terminal output from both of your runs or the logs
>>>> or a pgstar) if you want comment. It's nearly impossible to speculate
>>>> otherwise except to say that the current version of MESA is much more
>>>> careful  in a variety of respects and takes extra solver iterations to
>>>> ensure good numerical convergence with respect to previous versions
>>>> including the use energy conservation to maintain numerical accuracy
>>>> (something not done in mesa-r9798). Much of this is documented in MESA
>>>> IV
>>>> <https://urldefense.com/v3/__https://ui.adsabs.harvard.edu/abs/2018ApJS..234...34P/abstract__;!!IKRxdwAv5BmarQ!a123359XKv1btj2551_X1jOESvLwTfWENBGaMxuC1YXMIsVGlvfTQGkxleBAQeXzmPiaVX75ND4fs8ReScK_KXftMcH-QA$>
>>>> and MESA V
>>>> <https://urldefense.com/v3/__https://ui.adsabs.harvard.edu/abs/2019ApJS..243...10P/abstract__;!!IKRxdwAv5BmarQ!a123359XKv1btj2551_X1jOESvLwTfWENBGaMxuC1YXMIsVGlvfTQGkxleBAQeXzmPiaVX75ND4fs8ReScK_KXc7sFpJyQ$>
>>>> .
>>>>
>>>> -EbF
>>>>
>>>> On Mon, Jul 15, 2024 at 6:40 AM Kit Yu Lau via Mesa-users <
>>>> mesa-users at lists.mesastar.org> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> I used the most updated version of mesa to run X-ray bursts. Comparing
>>>>> with the old version (mesa-r9798) . It is much slower. I spent 10 days for
>>>>> the new version to get 2 bursts but the old version I spent 3 days to get 5
>>>>> bursts. All the input files are the same for both versions. Is there any
>>>>> way to speed up the new version? Thank you very much.
>>>>>
>>>>> Regards,
>>>>> Rita Lau
>>>>>
>>>>> On Wed, Jun 19, 2024 at 1:48 PM Frank Timmes <fxtimmes at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> hi rita,
>>>>>>
>>>>>> mesa has always used an evolving patchwork of eos modules to cover
>>>>>> the rho-t plane. this eos patchwork for recent versions is shown in figure
>>>>>> 7 of section 4 in mesa vi (jermyn et al 2023), also described at
>>>>>> https://docs.mesastar.org/en/release-r24.06.1-rc1/eos/overview.html
>>>>>> <https://urldefense.com/v3/__https://docs.mesastar.org/en/release-r24.06.1-rc1/eos/overview.html__;!!IKRxdwAv5BmarQ!YEDGoBxIue5Bt2R-BRTkPSG-6fl2vcTcqMub_4ovLO-Q0TQt9hld6JxESGO8MaIX13vdzJfkkDBMN5Tyzs2O_6pMof9Osw$> with
>>>>>> inlist controls at
>>>>>> https://docs.mesastar.org/en/release-r24.06.1-rc1/eos/defaults.html#eos-module-controls
>>>>>> <https://urldefense.com/v3/__https://docs.mesastar.org/en/release-r24.06.1-rc1/eos/defaults.html*eos-module-controls__;Iw!!IKRxdwAv5BmarQ!YEDGoBxIue5Bt2R-BRTkPSG-6fl2vcTcqMub_4ovLO-Q0TQt9hld6JxESGO8MaIX13vdzJfkkDBMN5Tyzs2O_6qY4lMFmA$> . the
>>>>>> current eos patchwork cannot be easily changed to the eos patchwork used in
>>>>>> 2017 for r9798.
>>>>>>
>>>>>> fxt
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Jun 17, 2024, at 11:23 PM, Kit Yu Lau via Mesa-users <
>>>>>> mesa-users at lists.mesastar.org> wrote:
>>>>>>
>>>>>> Hi everyone,
>>>>>>
>>>>>> I was using mesa-r9798 and I am switching to the newest version.
>>>>>> However, there was no eos in mesa-r9798. I think I was using helm_table.dat
>>>>>> for the old version. How do I change the newest version to use the same
>>>>>> eos? I tried not to command anything in eos and it seems that it is using
>>>>>> eos_free. How do I change the eos to helm_table.dat? Thank you very much.
>>>>>>
>>>>>> Regards,
>>>>>> Rita
>>>>>> _______________________________________________
>>>>>> mesa-users at lists.mesastar.org
>>>>>> https://lists.mesastar.org/mailman/listinfo/mesa-users
>>>>>> <https://urldefense.com/v3/__https://lists.mesastar.org/mailman/listinfo/mesa-users__;!!IKRxdwAv5BmarQ!YEDGoBxIue5Bt2R-BRTkPSG-6fl2vcTcqMub_4ovLO-Q0TQt9hld6JxESGO8MaIX13vdzJfkkDBMN5Tyzs2O_6oc-vzPzw$>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>> mesa-users at lists.mesastar.org
>>>>>
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>>>>>
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