{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Run one binary on your laptop for debugging"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"For debugging purposes you might want to run a single binary on your laptop to test a quick modification of the inlists, run_star_extras.f or run_binary_extras.f. Assume we want to run the same binary as in the previous tutorial. To use the POSYDON API to run a single binary, you can use the following command:\n",
"\n",
"```bash\n",
"posydon-setup-grid --grid-type fixed --inifile HMS-HMS_yggdrasil.ini --submission-type shell\n",
"```\n",
"\n",
"Similar to before, in our directorty we have:"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"binary\t\t grid_test.csv\t\tlaptop.ipynb star1\n",
"grid_command.sh HMS-HMS_yggdrasil.ini\tmk\t star2\n"
]
}
],
"source": [
"!ls"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We now export the `SLURM_ARRAY_TASK_ID` enviroment variable corresponding to the csv index of the `grid_test.csv` we want to run, `0` in this case in the temrinal:\n",
"\n",
"```bash\n",
"export $SLURM_ARRAY_TASK_ID=0\n",
"```\n",
"\n",
"We can now run the MESA binary simulation in the terminal with the following command:\n",
"\n",
"```bash\n",
"chmod +x grid_command.sh\n",
"./grid_command.sh\n",
"``````\n",
"\n",
"The terminal will not display an output, the screen output is saved to an `out.txt` file in the simulation directory."
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"binary\n",
"grid_command.sh\n",
"grid_test.csv\n",
"HMS-HMS_yggdrasil.ini\n",
"laptop.ipynb\n",
"mk\n",
"star1\n",
"star2\n",
"Zbase_0.0014_m1_30.0000_m2_21.0000_initial_z_1.4200e-03_initial_period_in_days_1.0000e+01_grid_index_0\n"
]
}
],
"source": [
"!ls"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"binary_history_columns.list inlist_grid_star1_binary_controls\n",
"binary_history.data\t inlist_grid_star2_binary_controls\n",
"history_columns.list\t LOGS1\n",
"initial_star1.mod\t LOGS2\n",
"initial_star2.mod\t out.txt\n",
"inlist\t\t\t profile_columns.list\n",
"inlist_grid_points\t tmp.hdf5\n"
]
}
],
"source": [
"!ls Zbase_0.0014_m1_30.0000_m2_21.0000_initial_z_1.4200e-03_initial_period_in_days_1.0000e+01_grid_index_0"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"\n",
" read /srv/beegfs/scratch/shares/astro/posydon/simone/documentation/running_mesa/running_on_laptop/binary/inlist_project\n",
" read inlist_grid_points\n",
" version_number 11701\n",
" read inlist_grid_star1_binary_controls\n",
" set_eos_PC_parameters\n",
" mass_fraction_limit_for_PC 1.0000000000000000D-03\n",
" logRho1_PC_limit 2.9990000000000001D+00\n",
" logRho2_PC_limit 2.7999999999999998D+00\n",
" log_Gamma_all_HELM 1.0000000000000000D+00\n",
" log_Gamma_all_PC 1.3010299956000000D+00\n",
" PC_Gamma_start_crystal 1.5000000000000000D+02\n",
" PC_Gamma_full_crystal 1.7500000000000000D+02\n",
" PC_min_Z 9.9900000000000000D-01\n",
" change rates preference to 2\n",
" set_initial_age 0.0000000000000000D+00\n",
" set_initial_model_number 0\n",
" change to \"approx21.net\"\n",
" number of species 21\n",
" new_rotation_flag T\n",
" new_surface_rotation_v 0 0.0000000000000000D+00 0.0000000000000000D+00\n",
" net name approx21.net\n",
" rotation_flag T\n",
" species\n",
" 1 neut \n",
" 2 h1 \n",
" 3 prot \n",
" 4 he3 \n",
" 5 he4 \n",
" 6 c12 \n",
" 7 n14 \n",
" 8 o16 \n",
" 9 ne20 \n",
" 10 mg24 \n",
" 11 si28 \n",
" 12 s32 \n",
" 13 ar36 \n",
" 14 ca40 \n",
" 15 ti44 \n",
" 16 cr48 \n",
" 17 cr56 \n",
" 18 fe52 \n",
" 19 fe54 \n",
" 20 fe56 \n",
" 21 ni56 \n",
"\n",
" kappa_file_prefix gs98\n",
" kappa_lowT_prefix lowT_fa05_gs98\n",
" OMP_NUM_THREADS 4\n",
"\n",
"\n",
"\n",
"\n",
" read inlist_grid_star2_binary_controls\n",
" set_eos_PC_parameters\n",
" mass_fraction_limit_for_PC 1.0000000000000000D-03\n",
" logRho1_PC_limit 2.9990000000000001D+00\n",
" logRho2_PC_limit 2.7999999999999998D+00\n",
" log_Gamma_all_HELM 1.0000000000000000D+00\n",
" log_Gamma_all_PC 1.3010299956000000D+00\n",
" PC_Gamma_start_crystal 1.5000000000000000D+02\n",
" PC_Gamma_full_crystal 1.7500000000000000D+02\n",
" PC_min_Z 9.9900000000000000D-01\n",
" change rates preference to 2\n",
" set_initial_age 0.0000000000000000D+00\n",
" set_initial_model_number 0\n",
" change to \"approx21.net\"\n",
" number of species 21\n",
" new_rotation_flag T\n",
" new_surface_rotation_v 0 0.0000000000000000D+00 0.0000000000000000D+00\n",
" net name approx21.net\n",
" rotation_flag T\n",
" species\n",
" 1 neut \n",
" 2 h1 \n",
" 3 prot \n",
" 4 he3 \n",
" 5 he4 \n",
" 6 c12 \n",
" 7 n14 \n",
" 8 o16 \n",
" 9 ne20 \n",
" 10 mg24 \n",
" 11 si28 \n",
" 12 s32 \n",
" 13 ar36 \n",
" 14 ca40 \n",
" 15 ti44 \n",
" 16 cr48 \n",
" 17 cr56 \n",
" 18 fe52 \n",
" 19 fe54 \n",
" 20 fe56 \n",
" 21 ni56 \n",
"\n",
" kappa_file_prefix gs98\n",
" kappa_lowT_prefix lowT_fa05_gs98\n",
" OMP_NUM_THREADS 4\n",
"\n",
"\n",
"\n",
"\n",
"\n",
" m2 2.1000000000000000D+01\n",
" m1 3.0000000000000000D+01\n",
" initial_period_in_days 1.0000000000000000D+01\n",
" initial_separation_in_Rsun 7.2417496333000003D+01\n",
" jdot_multiplier 1.0000000000000000D+00\n",
" fr 1.0000000000000000D-02\n",
"\n",
"\n",
"\n",
" The binary terminal output contains the following information\n",
"\n",
" 'step' is the number of steps since the start of the run,\n",
" 'lg_dt' is log10 timestep in years,\n",
" 'age_yr' is the simulated years since the start run,\n",
" 'M1+M2' is the total mass of the system (Msun),\n",
" 'M1' is the mass of the primary (Msun)\n",
" 'M2' is the mass of the secondary (Msun)\n",
" 'separ' is the semi-major axis of the orbit (Rsun),\n",
" 'R1' is the radius of the primary (Rsun)\n",
" 'R2' is the radius of the secondary (Rsun)\n",
" 'Porb' is the orbital period (days),\n",
" 'P1' is the rotation period of star 1 (days, zero if not modeling rotation),\n",
" 'P2' is the rotation period of star 2 (days, zero if not modeling rotation),\n",
" 'e' orbital eccentricity,\n",
" 'dot_e' time derivative of e (1/yr),\n",
" 'Eorb' orbital energy G*M1*M2/2*separation (ergs),\n",
" 'M2/M1' mass ratio,\n",
" 'vorb1' orbital velocity of star 1 (km/s),\n",
" 'vorb2' orbital velocity of star 2 (km/s),\n",
" 'pm_i' index of star evolved as point mass, zero if both stars are modeled,\n",
" 'RL1' Roche lobe radius of star 1 (Rsun),\n",
" 'Rl2' Roche lobe radius of star 2 (Rsun),\n",
" 'donor_i' index of star taken as donor,\n",
" 'RL_gap1' (R1-Rl1)/Rl1,\n",
" 'RL_gap2' (R2-Rl2)/Rl2,\n",
" 'dot_Mmt', mass transfer rate (Msun/yr),\n",
" 'dot_M1', time derivative for the mass of star 1 (Msun/yr),\n",
" 'dot_M2', time derivative for the mass of star 2 (Msun/yr),\n",
" 'eff', mass transfer efficiency, computed as -dot_M2/dot_M1 (zero if dot_M1=0),\n",
" 'dot_Medd', Eddington accretion rate (Msun/yr),\n",
" 'L_acc', accretion luminosity when accreting to a point mass (ergs/s),\n",
" 'Jorb', orbital angular momentum (g*cm^2/s)\n",
" 'spin1', spin angular momentum of star 1 (g*cm^2/s),\n",
" 'spin2', spin angular momentum of star 2 (g*cm^2/s),\n",
" 'dot_J', time derivative of Jorb (g*cm^2/s^2),\n",
" 'dot_Jgr', time derivative of Jorb due to gravitational waves (g*cm^2/s^2),\n",
" 'dot_Jml', time derivative of Jorb due to mass loss (g*cm^2/s^2),\n",
" 'dot_Jmb', time derivative of Jorb due to magnetic braking (g*cm^2/s^2),\n",
" 'dot_Jls', time derivative of Jorb due to spin-orbit coupling (g*cm^2/s^2),\n",
" 'rlo_iters', number of iterations for implicit calculation of mass transfer,\n",
"\n",
" All this and more can be saved in binary_history.data during the run.\n",
" num_steps_to_relax_rotation 50\n",
" relax to omega: wanted-current, current, wanted 1 7.2722052166430393D-06 0.0000000000000000D+00 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 2 7.1239371671217664D-06 1.4826804952127298D-07 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 3 6.9775031537422630D-06 2.9470206290077610D-07 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 4 6.8325228134160023D-06 4.3968240322703724D-07 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 5 6.6880335934326623D-06 5.8417162321037739D-07 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 6 6.5429720944820478D-06 7.2923312216099155D-07 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 7 6.3960414376057951D-06 8.7616377903724423D-07 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 8 6.2481185101766360D-06 1.0240867064664032D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 9 6.0988144371784416D-06 1.1733907794645978D-06 7.2722052166430393D-06\n",
" 10 7.649681 4.541E+04 5.083637 5.083787 30.000000 30.000000 0.746765 0.000508 0.251100 0.747141 -6.159624 2598 0\n",
" 3.021836 0.768039 0.749893 -23.011309 3.935137 -99.000000 0.000000 0.251795 0.000441 0.001420 0.251427 0.009963 3 0\n",
" 2.3543E+03 16.667399 5.081908 1.622938 4.361599 -8.707435 0.000000 0.000004 0.000133 0.000071 1.432E-03 0.000E+00 max increase\n",
"\n",
" relax to omega: wanted-current, current, wanted 10 5.9494923842667907D-06 1.3227128323762491D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 11 5.8047902383525235D-06 1.4674149782905158D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 12 5.6656472219130140D-06 1.6065579947300258D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 13 5.5253850379006039D-06 1.7468201787424357D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 14 5.3813998139082310D-06 1.8908054027348084D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 15 5.2360332812183832D-06 2.0361719354246558D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 16 5.0905569484589031D-06 2.1816482681841367D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 17 4.9451036922867509D-06 2.3271015243562889D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 18 4.7996593421142631D-06 2.4725458745287766D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 19 4.6542152662843934D-06 2.6179899503586464D-06 7.2722052166430393D-06\n",
" 20 7.648797 4.525E+04 5.069089 5.069239 30.000000 30.000000 0.746765 0.000508 0.251100 0.747141 -6.164975 2613 0\n",
" 6.032136 0.764405 0.746596 -23.057888 3.920548 -99.000000 0.000000 0.251795 0.000441 0.001420 0.251427 0.009955 2 0\n",
" 2.1539E+06 16.663052 5.069239 1.607921 4.359365 -8.704639 0.000000 0.000004 0.000133 0.000071 1.432E-03 0.000E+00 max increase\n",
"\n",
" relax to omega: wanted-current, current, wanted 20 4.5087711728839026D-06 2.7634340437591372D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 21 4.3633267819036798D-06 2.9088784347393599D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 22 4.2178823225008446D-06 3.0543228941421948D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 23 4.0724377789053992D-06 3.1997674377376405D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 24 3.9269931252400189D-06 3.3452120914030209D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 25 3.7815483288686108D-06 3.4906568877744285D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 26 3.6361034654341649D-06 3.6361017512088744D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 27 3.4906587737615971D-06 3.7815464428814422D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 28 3.3452144110082463D-06 3.9269908056347930D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 29 3.1997702456217982D-06 4.0724349710212411D-06 7.2722052166430393D-06\n",
" 30 7.648797 4.525E+04 5.069078 5.069228 30.000000 30.000000 0.746765 0.000508 0.251100 0.747141 -6.164960 2610 0\n",
" 9.042435 0.764409 0.746606 -23.057923 3.920536 -99.000000 0.000000 0.251795 0.000441 0.001420 0.251427 0.009955 2 0\n",
" 2.2053E+09 16.663054 5.069228 1.607910 4.359335 -8.704658 0.000000 0.000004 0.000133 0.000071 1.432E-03 0.000E+00 max increase\n",
"\n",
" relax to omega: wanted-current, current, wanted 30 3.0543261335993711D-06 4.2178790830436683D-06 7.2722052166430393D-06\n",
" relax to omega: wanted-current, current, wanted 31 2.9088820289801618D-06 4.3633231876628776D-06 7.2722052166430393D-06\n"
]
}
],
"source": [
"!head -n 200 Zbase_0.0014_m1_30.0000_m2_21.0000_initial_z_1.4200e-03_initial_period_in_days_1.0000e+01_grid_index_0/out.txt"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Congratulation, you now know how to harvast the power of POSYDON to run a grid of simulations on a supercomputer!"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "posydon_env",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.5"
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"nbformat": 4,
"nbformat_minor": 2
}