[Mesa-users] Segfault when running tutorial
Rob Farmer
r.j.farmer at uva.nl
Wed Oct 31 04:50:33 EDT 2018
hi,
These are good questions for the mesa-users list (cc'ed), i can answer a
few.
> When I extend the brown dwarf test case to longer timeperiods, it
eventually dies of "too many retries". Admittedly, this is after 90
billion years and it's already quite cooled, but I'm curious to understand
why such problems would occur and how I should remedy them should I
encounter them again - just simply increasing max_number_retries? Or is
there some problem that's more fundamental that I need to address?
Yes max_number_retires is only useful for us developers when we are testing
the test suite, so it should be removed when doing science. You've provided
too little information to diagnose any problems with the physics, though
the first guess would be its gotten too cold and your having issues with
the EOS.
> It's not entirely clear (to me) which options are necessary for dealing
with various cases (brown dwarfs, high mass stars, neutron stars, etc)
The test suite is the place to look for where to start with different types
of stars.
Rob
On Wed, 31 Oct 2018 at 02:21, Karen Pease <karenpease at gmail.com> wrote:
> Thanks for this - I appreciate it!
>
> After reading through the docs and working through some examples, I have a
> couple quick questions / issues (if it's not too much to ask):
>
> * (Not question, just a suggestion!) The docs on the website are
> seemingly out of order. This confused me for a while, because it jumps
> right from how to do the basics straight to "extending MESA"... so from
> "beginner stuff" to "advanced stuff". I didn't realize for a while that
> "everything in-between" is after "FAQ" (the "defaults" sections).
>
> * Variable stars - I checked the inlist options and the "pulse" cases in
> the test suite but didn't see any obvious answer as to how to get changes
> in luminosity across their associated periods.
>
> * When I extend the brown dwarf test case to longer timeperiods, it
> eventually dies of "too many retries". Admittedly, this is after 90
> billion years and it's already quite cooled, but I'm curious to understand
> why such problems would occur and how I should remedy them should I
> encounter them again - just simply increasing max_number_retries? Or is
> there some problem that's more fundamental that I need to address?
>
> * It's not entirely clear (to me) which options are necessary for dealing
> with various cases (brown dwarfs, high mass stars, neutron stars, etc).
> E.g. if I just up the mass in the brown dwarf scenario to 15 solar masses,
> I see no signs of anything going on except deuterium burning because it's
> clearly not configured for that. I feel this whole aspect is sort of
> skipped over on the website - the various settings that can go in the
> inlists are documented en masse in the "defaults" pages, but they're more
> like a catalogue than a tutorial.
>
> Is it possible to set up a "general scenario" that functions for a wide
> range of stellar conditions? I have concerns that if I build isochrone
> tables using multiple disjoint scenarios (each with their own infiles based
> on test suite examples of similar stars) then there will be a discongruity
> between isochrones generated with each mechanism. Or... perhaps a better
> question: if you were seeking to build isochrone tables across a wide range
> of starting masses, from birth until cooling, how would you approach it?
> No complex edge cases, just straightforward stellar evolution runs with
> varying starting masses and metallicities.
>
> - kv, Karen
>
> þri., 30. okt. 2018 kl. 09:44 skrifaði Rob Farmer <r.j.farmer at uva.nl>:
>
>> Hi Karen,
>> As others have mentioned its ill advised to use an unreleased mesa
>> version. However the bug you ran into was fixed in 10618, what you can do
>> is in the following file $MESA_DIR/star/private/history.f90 line 383:
>>
>> replace line
>> if (write_flag) write(io,*)
>> with
>> if (open_close_log .and. write_flag) close(io)
>>
>> The reason it fails for you with a segmentation fault is this is an issue
>> that is only detected by the gfortran8 compiler, older versions of the
>> compiler don't seem to care.
>>
>> Rob
>>
>>
>> On Mon, 29 Oct 2018 at 22:23, Karen Pease via Mesa-users <
>> mesa-users at lists.mesastar.org> wrote:
>>
>>> Thanks for the reply! I actually fixed the problem on my own by
>>> upgrading MESA to the latest devel trunk. I guess it's very sensitive to
>>> which version goes with what! I am however encountering a new problem.
>>>
>>> First off, my goal: It's not particularly complicated; I've found plenty
>>> of tables of isochrone data for various initial masses and metallicities
>>> (for example, MIST_v1.2_vvcrit0.4_full_isos), but every dataset I've
>>> found A) does not extend down to brown dwarfs, and B) maxes out at ages
>>> that leave low-mass stars still alive (for example, the aforementioned
>>> dataset maxes out at 10^10,3 years). I'm just looking to - at least roughly
>>> - "fill in the gaps", so to speak, so that I can proceed to my actual goal
>>> of fitting the data to piecewise functions for rapid / low memory lookups.
>>>
>>> So, while the tutorial (using initial_mass = 15) runs fine, when I try
>>> to run it at initial_mass = 0.05, 0.07, or 0.09 it always ends up
>>> bombing out with "stopping because of problems dt <
>>> min_timestep_limit". The biggest increase in dt (in the 0.05 case) can be
>>> seen here:
>>>
>>> ------
>>> retry 234
>>> 234 5.702752 2831.216 -15.315204 -15.315204 0.050000
>>> 0.050000 0.700000 0.001008 0.280000 0.700000 -1.716322 633
>>> 37
>>> -5.342341 -0.127476 -0.069871 -99.000000 -16.712899 -99.000000
>>> 0.000000 0.280000 0.009360 0.020000 0.280000 0.455574 10
>>> 1
>>> 2.9281E+05 13.668138 -1.378369 3.276602 4.441925 -6.644122
>>> 0.000000 0.003442 0.002099 2.000E-02 2.000E-02 0.000E+00
>>> retry
>>>
>>> retry 235
>>> 235 5.702752 2831.216 -15.315204 -15.315204 0.050000
>>> 0.050000 0.700000 0.001008 0.280000 0.700000 -1.716322 633
>>> 38
>>> -5.564190 -0.127476 -0.069871 -99.000000 -16.712899 -99.000000
>>> 0.000000 0.280000 0.009360 0.020000 0.280000 0.455574 14
>>> 1
>>> 2.9281E+05 13.668138 -1.378369 3.276602 4.441925 -6.644122
>>> 0.000000 0.003442 0.002099 2.000E-02 2.000E-02 0.000E+00
>>> retry
>>>
>>> retry 236
>>> retry 236
>>> backup 236
>>> retry 235
>>> retry 235
>>> backup 235
>>> retry 235
>>> retry 235
>>> backup 235
>>> retry 235
>>> retry 235
>>> backup 235
>>> 235 5.702752 2831.213 -15.315204 -15.315204 0.050000
>>> 0.050000 0.700000 0.001008 0.280000 0.700000 -1.716322 633
>>> 46
>>> -11.505609 -0.127476 -0.069871 -99.000000 -16.712899 -99.000000
>>> 0.000000 0.280000 0.009360 0.020000 0.280000 0.455574 5
>>> 5
>>> 2.9281E+05 13.668138 -1.378371 3.276602 4.441926 -6.644119
>>> 0.000000 0.003442 0.002099 2.000E-02 2.000E-02 0.000E+00
>>> backup
>>>
>>> 236 5.702752 2831.210 -15.315204 -15.315204 0.050000
>>> 0.050000 0.700000 0.001008 0.280000 0.700000 -1.716322 633
>>> 46
>>> -11.505609 -0.127476 -0.069871 -99.000000 -16.712899 -99.000000
>>> 0.000000 0.280000 0.009360 0.020000 0.280000 0.455574 5
>>> 5
>>> 2.9281E+05 13.668138 -1.378372 3.276602 4.441928 -6.644116
>>> 0.000000 0.003442 0.002099 2.000E-02 2.000E-02 0.000E+00
>>> hold
>>> ------
>>>
>>> .... and the run ends suchly:
>>>
>>> ------
>>> 253 5.702752 2831.182 -15.315204 -15.315204 0.050000
>>> 0.050000 0.700000 0.001008 0.280000 0.700000 -1.716322 633
>>> 52
>>> -12.519976 -0.127476 -0.069871 -99.000000 -16.712899 -99.000000
>>> 0.000000 0.280000 0.009360 0.020000 0.280000 0.455574 5
>>> 7
>>> 2.9281E+05 13.668138 -1.378389 3.276602 4.441940 -6.644091
>>> 0.000000 0.003442 0.002099 2.000E-02 2.000E-02 0.000E+00
>>> hold
>>>
>>> retry 254
>>> retry 254
>>> backup 254
>>> 253 5.702752 2831.182 -15.315204 -15.315204 0.050000
>>> 0.050000 0.700000 0.001008 0.280000 0.700000 -1.716322 633
>>> 54
>>> -13.122036 -0.127476 -0.069871 -99.000000 -16.712899 -99.000000
>>> 0.000000 0.280000 0.009360 0.020000 0.280000 0.455574 5
>>> 8
>>> 2.9281E+05 13.668138 -1.378389 3.276602 4.441940 -6.644091
>>> 0.000000 0.003442 0.002099 2.000E-02 2.000E-02 0.000E+00
>>> backup
>>>
>>> 254 5.702752 2831.182 -15.315204 -15.315204 0.050000
>>> 0.050000 0.700000 0.001008 0.280000 0.700000 -1.716322 633
>>> 54
>>> -13.122036 -0.127476 -0.069871 -99.000000 -16.712899 -99.000000
>>> 0.000000 0.280000 0.009360 0.020000 0.280000 0.455574 5
>>> 8
>>> 2.9281E+05 13.668138 -1.378389 3.276602 4.441940 -6.644091
>>> 0.000000 0.003442 0.002099 2.000E-02 2.000E-02 0.000E+00
>>> hold
>>>
>>> 255 5.702752 2831.182 -15.315204 -15.315204 0.050000
>>> 0.050000 0.700000 0.001008 0.280000 0.700000 -1.716322 633
>>> 54
>>> -13.122036 -0.127476 -0.069871 -99.000000 -16.712899 -99.000000
>>> 0.000000 0.280000 0.009360 0.020000 0.280000 0.455574 5
>>> 8
>>> 2.9281E+05 13.668138 -1.378389 3.276602 4.441940 -6.644091
>>> 0.000000 0.003442 0.002099 2.000E-02 2.000E-02 0.000E+00
>>> hold
>>>
>>> 256 5.702752 2831.182 -15.315204 -15.315204 0.050000
>>> 0.050000 0.700000 0.001008 0.280000 0.700000 -1.716322 633
>>> 54
>>> -13.122036 -0.127476 -0.069871 -99.000000 -16.712899 -99.000000
>>> 0.000000 0.280000 0.009360 0.020000 0.280000 0.455574 5
>>> 8
>>> 2.9281E+05 13.668138 -1.378389 3.276602 4.441940 -6.644091
>>> 0.000000 0.003442 0.002099 2.000E-02 2.000E-02 0.000E+00
>>> hold
>>>
>>> retry 257
>>> retry 257
>>> dt
>>> 5.9568293960300256D-07
>>> min_timestep_limit
>>> 9.9999999999999995D-07
>>>
>>> stopping because of problems dt < min_timestep_limit
>>> ------
>>>
>>> I don't encounter this problem when running however with the default initial_mass
>>> of 15.
>>>
>>> It's odd, as I'd (perhaps naively) assume that a brown dwarf would be
>>> one of the easiest cases the software could face. Suggestions?
>>>
>>> - kv, Karen
>>>
>>>
>>>
>>>
>>> mán., 29. okt. 2018 kl. 01:26 skrifaði Francis Timmes <fxt44 at mac.com>:
>>>
>>>> hi karen,
>>>>
>>>> i see you are trying a development version of the mesasdk.
>>>> try recompiling r10398 with the current release version
>>>>
>>>> http://www.astro.wisc.edu/~townsend/resource/download/mesasdk/mesasdk-x86_64-linux-20180822.tar.gz
>>>>
>>>> for the record, i’m unable to reproduce this error
>>>> although i am using a different architecture.
>>>>
>>>> fxt
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> > On Oct 28, 2018, at 1:43 PM, Karen Pease via Mesa-users <
>>>> mesa-users at lists.mesastar.org> wrote:
>>>> >
>>>> > [meme at chmmr tutorial]$ ./rn
>>>> > DATE: 2018-10-28
>>>> > TIME: 20:27:32
>>>> > version_number 10398
>>>> > read inlist_project
>>>> >
>>>> >
>>>> > The terminal output contains the following information
>>>> >
>>>> > 'step' is the number of steps since the start of the run,
>>>> > 'lg_dt' is log10 timestep in years,
>>>> > 'age_yr' is the simulated years since the start run,
>>>> > 'lg_Tcntr' is log10 center temperature (K),
>>>> > 'lg_Dcntr' is log10 center density (g/cm^3),
>>>> > 'lg_Pcntr' is log10 center pressure (ergs/cm^3),
>>>> > 'Teff' is the surface temperature (K),
>>>> > 'lg_R' is log10 surface radius (Rsun),
>>>> > 'lg_L' is log10 surface luminosity (Lsun),
>>>> > 'lg_LH' is log10 total PP and CNO hydrogen burning power (Lsun),
>>>> > 'lg_L3a' is log10 total triple-alpha helium burning power
>>>> (Lsun),
>>>> > 'lg_LZ' is log10 total burning power excluding LH and L3a and
>>>> photodisintegrations (Lsun),
>>>> > 'lg_LNuc' is log10 nuclear power excluding photodisintegration
>>>> (Lsun),
>>>> > 'lg_LNeu' is log10 total neutrino power (Lsun),
>>>> > 'lg_Psurf' is log10 surface pressure (gas + radiation),
>>>> > 'Mass' is the total stellar baryonic mass (Msun),
>>>> > 'lg_Mdot' is log10 magnitude of rate of change of mass
>>>> (Msun/year),
>>>> > 'lg_Dsurf' is log10 surface density (g/cm^3),
>>>> > 'H_env' is the amount of mass where H is the most abundant iso,
>>>> > 'He_core' is the largest mass where He is most abundant iso.
>>>> > 'C_core' is the largest mass where C is most abundant iso.
>>>> > 'H_cntr' is the center H1 mass fraction,
>>>> > 'He_cntr' is the center He4 mass fraction,
>>>> > 'C_cntr' is the center C12 mass fraction,
>>>> > 'N_cntr' is the center N14 mass fraction,
>>>> > 'O_cntr' is the center O16 mass fraction,
>>>> > 'Ne_cntr' is the center Ne20 mass fraction,
>>>> > 'X_avg' is the star average hydrogen mass fraction,
>>>> > 'Y_avg' is the star average helium mass fraction,
>>>> > 'Z_avg' is the star average metallicity,
>>>> > 'gam_cntr' is the center plasma interaction parameter,
>>>> > 'eta_cntr' is the center electron degeneracy parameter,
>>>> > 'zones' is the number of zones in the current model,
>>>> > 'iters' is the number of newton iterations for the current step,
>>>> > 'retry' is the number of step retries required during the run,
>>>> > 'bckup' is the number of step backups required during the run,
>>>> > 'dt_limit' is an indication of what limited the timestep.
>>>> >
>>>> > All this and more are saved in the LOGS directory during the run.
>>>> > create pre-main-sequence model
>>>> > use_eosPTEH_for_low_density T
>>>> > use_eosPTEH_for_high_Z T
>>>> > species mass 8
>>>> 1.5000000000000000D+01
>>>> > read /scratch/MESA/data/eosDT_data/mesa-eosPTEH_z0.02_x0.7.data
>>>> > write /scratch/MESA/data/eosDT_data/cache/mesa-eosPTEH_z0.02_x0.7.bin
>>>> >
>>>> > relax_num_steps
>>>> >
>>>> > retry log10(dt/yr), log10(dt), retry_factor 1 1
>>>> -5.602060 1.897052 0.500000
>>>> > first model is slow to converge: num tries 70
>>>> > first model is slow to converge: num tries 80
>>>> > first model is slow to converge: num tries 90
>>>> > first model is slow to converge: num tries 100
>>>> > first model is slow to converge: num tries 110
>>>> > first model is slow to converge: num tries 120
>>>> > first model is slow to converge: num tries 130
>>>> > 1 5.479739 3327.593 -21.749180 -21.749180 15.000000
>>>> 15.000000 0.700000 0.001008 0.280000 0.700000 -12.925080 1077
>>>> 1
>>>> > -5.301030 -5.414822 2.521541 -99.000000 -23.147049 -99.000000
>>>> 0.000000 0.280000 0.009360 0.020000 0.280000 0.013156 137
>>>> 0
>>>> > 5.0000E-06 8.245848 4.085084 -99.000000 3.083430 -8.231930
>>>> 0.000000 0.003442 0.002099 2.000E-02 2.000E-02 0.290E+04
>>>> retry
>>>> >
>>>> >
>>>> > Program received signal SIGSEGV: Segmentation fault - invalid memory
>>>> reference.
>>>> >
>>>> > Backtrace for this error:
>>>> > #0 0x7f28c0a93a7f in ???
>>>> > #1 0x54313f in do_history_info
>>>> > at ../private/history.f90:383
>>>> > #2 0x54ec64 in get_hist_values
>>>> > at /scratch/MESA/star/make/pgstar.f90:1641
>>>> > #3 0x54ec64 in __pgstar_MOD_update_pgstar_data
>>>> > at /scratch/MESA/star/make/pgstar.f90:1619
>>>> > #4 0x589662 in __relax_MOD_do_internal_evolve
>>>> > at ../private/relax.f90:3838
>>>> > #5 0x58a95b in __relax_MOD_do_relax_num_steps
>>>> > at ../private/relax.f90:3243
>>>> > #6 0x599eac in model_builder
>>>> > at ../private/init.f90:1282
>>>> > #7 0x59abd4 in __init_MOD_create_pre_ms_model
>>>> > at ../private/init.f90:1041
>>>> > #8 0x41a6e8 in __star_lib_MOD_star_create_pre_ms_model
>>>> > at ../public/star_lib.f90:372
>>>> > #9 0x42b740 in __run_star_support_MOD_do_load1_star
>>>> > at ../job/run_star_support.f90:1800
>>>> > #10 0x431bca in __run_star_support_MOD_before_evolve_loop
>>>> > at ../job/run_star_support.f90:325
>>>> > #11 0x432438 in __run_star_support_MOD_run1_star
>>>> > at ../job/run_star_support.f90:98
>>>> > #12 0x416ad0 in __run_star_MOD_do_run_star
>>>> > at /scratch/MESA/star/job/run_star.f:26
>>>> > #13 0x416b73 in run
>>>> > at ../src/run.f:16
>>>> > #14 0x416baa in main
>>>> > at ../src/run.f:2
>>>> > ./rn: line 9: 14112 Segmentation fault (core dumped) ./star
>>>> > DATE: 2018-10-28
>>>> > TIME: 20:33:21
>>>> >
>>>> > [meme at chmmr tutorial]$ echo $MESA_DIR
>>>> > /scratch/MESA
>>>> > [meme at chmmr tutorial]$ echo $MESASDK_ROOT
>>>> > /scratch/mesasdk
>>>> > [meme at chmmr tutorial]$ /scratch/mesasdk/bin/mesasdk_version.sh
>>>> > x86_64-linux-20181007
>>>> >
>>>> > Since this is "right out of the box", any suggestions on what I
>>>> should try? Obviously (since I'm working on the tutorial) I'm totally new
>>>> to MESA :)
>>>> >
>>>> > - kv, Karen
>>>> >
>>>> >
>>>> > _______________________________________________
>>>> > mesa-users at lists.mesastar.org
>>>> > https://lists.mesastar.org/mailman/listinfo/mesa-users
>>>> >
>>>>
>>>> _______________________________________________
>>> mesa-users at lists.mesastar.org
>>> https://lists.mesastar.org/mailman/listinfo/mesa-users
>>>
>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.mesastar.org/pipermail/mesa-users/attachments/20181031/09f8d03f/attachment.html>
More information about the Mesa-users
mailing list