[Mesa-users] Segfault when running tutorial
Aaron Dotter
aaron.dotter at gmail.com
Mon Oct 29 17:32:59 EDT 2018
Hi Karen,
I'd advise against using the latest revision of MESA in the svn
unless/until you're a seasoned MESA user. Stick with the public releases,
such as 10398, until then. You never know what might not be working, or be
different from advertised in a development version.
Brown dwarfs aren't easy to model well. The parts of the problem that
require special attention are much different than those that make a 15
solar mass model challenging so I'd advise against trying to use a 15M
inlist for BDs.
There are a couple of cases in the test suite that deal with brown dwarfs,
see for example mesa/star/test_suite/brown_dwarf that will give you
something to start with.
Cheers,
Aaron
On Mon, Oct 29, 2018 at 5:24 PM 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
>
>
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