[Mesa-users] Segfault when running tutorial
Karen Pease
karenpease at gmail.com
Mon Oct 29 17:23:55 EDT 2018
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
> >
>
>
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