[mesa-users] MESA problems - Segmentation fault when running rlo with ifort
Bill Paxton
paxton at kitp.ucsb.edu
Tue Jul 23 13:55:36 EDT 2013
On Jul 23, 2013, at 10:47 AM, Michael Zingale wrote:
> Bill, one magic flag that I've always had to use with ifort is "-mp", this tells the compiler not to do any optimizations that change the answer. You might want to see if using this + -O2 makes it happy. Generally, we've found ifort to be flaky.
>
> Mike
>
Hi Mike,
Gotta love those magic flags!
I'm looking for the one that enables intelligence, but so far it eludes me.
There are good arguments for making mesa work on as many compilers
as possible (Frank preaches this sermon to me regularly, but without effect).
But ifort is one windmill I'm not willing to take on.
If gfortran would just do a backtrace of the call stack after a crash I'd be happy.
Bill
>
> On Tue, Jul 23, 2013 at 1:43 PM, Bill Paxton <paxton at kitp.ucsb.edu> wrote:
> Hi Jonas,
>
> We have also had problems with the new ifort.
> In section B.11 of the new mesa instrument paper we report comparisons of results using ifort and gfortran on mac and linux. In order to get the tests to run at all with ifort we had to drop down to optimization -O1. Not a good sign. So I'd suggest either using gfortran with -O2 or ifort with -O1.
>
> -Bill
>
>
>
>
>
>
> On Jul 23, 2013, at 10:21 AM, Jonas Goliasch wrote:
>
>> Hello Bill,
>> I am in the group of Lorne Nelson, and I am having trouble running the MESA rlo module with mass loss. I am using version 4942 but a similar problem seems to also occur with the latest version (5118).
>> The mesa module is installed on a computing cluster using the most recent version ifort
>> $ ifort –version
>> ifort (IFORT) 12.1.3 20120212
>> Copyright (C) 1985-2012 Intel Corporation. All rights reserved.
>>
>> And I can run the standard ‘work’ module and most of the other modules I tested. And even with the rlo module I can produce a proper single star track (by setting a very large separation). However, a segmentation fault occurs whenever the star starts losing mass due to roche lobe overflow (please see attached segmentation fault output).
>> I have traced the occurrence of the crash to subroutine set_xa in adjust_mass.f (inside the ‘private’ folder of ‘star’). More specifically, it occurs in the first few lines of that routine when s% xa(j,k) is being updated (see the line ‘s% xa(j,k) = xa_old(j,k)
>> ‘ below)
>>
>> if (dbg_adjm) &
>> write(*,2) 'set_xa: k_const_mass', k_const_mass
>> if (k_const_mass < nz) then
>> ! for k >= k_const_mass have m_new(k) = m_old(k),
>> ! so no change in xa_new(:,k) for k > k_const_mass
>> do k=k_const_mass+1,nz
>> do j=1,species
>> s% xa(j,k) = xa_old(j,k)
>> end do
>> end do
>> end if
>>
>>
>> By placing a dummy statement inside this loop before the reassignment of s% xa(j,k), I can circumvent the segmentation fault which allows the code to run several hundred models further. But it eventually also gets itself into trouble (see attached output). So far I have not been able to get around this issue, which seems to be related to me using the ifort compiler. As mentioned above, I can successfully produce a complete single star evolutionary track using the rlo module.
>> Any suggestions or help to resolve this issue would be greatly appreciated. For completeness I’ve also attached the output when running the latest version of MESA. Note, I have also attached a pdf version of the code output in case the formatting of the e-mail becomes distorted.
>>
>> Kind Regards,
>>
>> Jonas Goliasch
>>
>>
>>
>>
>> Segmentation fault output:
>> [goliasch at ip10 make_mdot_work]$ ./rn
>> svn: '.' is not a working copy
>> DATE: 2013-07-23
>> TIME: 10:10:10
>> saved initial &star_job inlist values: star_job_namelist.out
>> version_number 4942
>> read inlist_test_rlo
>>
>> maccretor 1.0000000000000000D-02
>> mdonor 1.0000000000000000D+00
>> initial_period_in_days 1.3999999999999999D+00
>> jdot_multiplier 1.0000000000000000D+00
>> fr 1.0000000000000001D-01
>> gr_only F
>>
>> net name basic.net
>> use small_mtx_decsol bcyclic_dble 8 100
>> kappa_file_prefix gn93
>> kappa_lowT_prefix lowT_fa05_gs98
>> eos_file_prefix mesa
>> OMP_NUM_THREADS 8
>> _________________________________________________________________________________________________________________________________________________
>>
>> step lg_Tcntr Teff lg_LH lg_Lnuc Mass H_rich H_cntr N_cntr Y_surf X_avg eta_cntr pts retry
>> lg_dt_yr lg_Dcntr lg_R lg_L3a lg_Lneu lg_Mdot H_poor He_cntr O_cntr Z_surf Y_avg gam_cntr iters bckup
>> age lg_Pcntr lg_L lg_LZ lg_Psurf lg_Dsurf He_poor C_cntr Ne_cntr Z_cntr Z_avg v_div_cs dt_limit
>> __________________________________________________________________________________________________________________________________________________
>> 10 7.136146 5616.538 -0.139799 -0.139799 1.000000 1.000000 0.699287 0.001903 0.280000 0.699880 -1.769666 823 0
>> 5.631147 1.888831 -0.052838 -47.216113 -1.678073 -99.000000 0.000000 0.280585 0.009363 0.020000 0.280109 0.078966 2 0
>> 2.1894E+06 17.154144 -0.154319 -15.954590 4.847007 -6.702862 0.000000 0.002675 0.002100 2.013E-02 2.001E-02 -0.742E-11 lgTeff
>> …
>> 60 7.133184 5622.820 -0.147634 -0.147634 1.000000 1.000000 0.697882 0.003809 0.280000 0.699705 -1.727568 804 0
>> 4.995777 1.901966 -0.049065 -47.342103 -1.745142 -99.000000 0.000000 0.281718 0.009362 0.020000 0.280269 0.080374 2 0
>> 2.3787E+07 17.163974 -0.144832 -15.653560 4.841842 -6.708605 0.000000 0.001042 0.002100 2.040E-02 2.003E-02 0.415E-12 max_dt
>>
>> 70 7.133155 5623.302 -0.147276 -0.147276 1.000000 1.000000 0.697830 0.003862 0.280000 0.699699 -1.726333 804 0
>> 4.767965 1.902440 -0.049013 -47.342361 -1.746117 -99.000000 0.000000 0.281762 0.009362 0.020000 0.280275 0.080410 2 0
>> 2.4538E+07 17.164406 -0.144578 -99.000000 4.841707 -6.708778 0.000000 0.000996 0.002100 2.041E-02 2.003E-02 0.406E-12 max_dt
>>
>> limit_retention_by_mdot_edd 1.00000000000000
>>
>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> Image PC Routine Line Source
>> star_rlo_implicit 000000000055F236 adjust_mass_mp_do 247 adjust_mass.f
>> star_rlo_implicit 0000000000502953 evolve_mp_do_evol 233 evolve.f
>> star_rlo_implicit 0000000000421743 star_lib_mp_star_ 370 star_lib.f
>> star_rlo_implicit 000000000042ECE0 run_star_support_ 2275 run_star_support.f
>> star_rlo_implicit 0000000000421368 run_star_mp_do_ru 29 run_star.f
>> star_rlo_implicit 0000000000421462 MAIN__ 43 run.f
>> star_rlo_implicit 000000000040412C Unknown Unknown Unknown
>> libc.so.6 000000326001D994 Unknown Unknown Unknown
>> star_rlo_implicit 0000000000403FB9 Unknown Unknown Unknown
>> DATE: 2013-07-23
>> TIME: 10:10:19
>> [goliasch at ip10 make_mdot_work]$
>>
>>
>> Output when circumventing segmentation fault:
>>
>> [goliasch at ip10 make_mdot_work]$ ./rn
>> svn: '.' is not a working copy
>> DATE: 2013-07-23
>> TIME: 10:23:22
>> saved initial &star_job inlist values: star_job_namelist.out
>> version_number 4942
>> read inlist_test_rlo
>> maccretor 1.0000000000000000D-02
>> mdonor 1.0000000000000000D+00
>> initial_period_in_days 1.3999999999999999D+00
>> jdot_multiplier 1.0000000000000000D+00
>> fr 1.0000000000000001D-01
>> gr_only F
>> net name basic.net
>> use small_mtx_decsol bcyclic_dble 8 100
>> kappa_file_prefix gn93
>> kappa_lowT_prefix lowT_fa05_gs98
>> eos_file_prefix mesa
>> OMP_NUM_THREADS 8
>> evolve_loop i= 1
>> __________________________________________________________________________________________________________________________________________________
>> step lg_Tcntr Teff lg_LH lg_Lnuc Mass H_rich H_cntr N_cntr Y_surf X_avg eta_cntr pts retry
>> lg_dt_yr lg_Dcntr lg_R lg_L3a lg_Lneu lg_Mdot H_poor He_cntr O_cntr Z_surf Y_avg gam_cntr iters bckup
>> age lg_Pcntr lg_L lg_LZ lg_Psurf lg_Dsurf He_poor C_cntr Ne_cntr Z_cntr Z_avg v_div_cs dt_limit
>> 10 7.136146 5616.538 -0.139799 -0.139799 1.000000 1.000000 0.699287 0.001903 0.280000 0.699880 -1.769666 823 0
>> 5.631147 1.888831 -0.052838 -47.216113 -1.678073 -99.000000 0.000000 0.280585 0.009363 0.020000 0.280109 0.078966 2 0
>> 2.1894E+06 17.154144 -0.154319 -15.954590 4.847007 -6.702862 0.000000 0.002675 0.002100 2.013E-02 2.001E-02 -0.742E-11 lgTeff
>> …
>> 70 7.133155 5623.302 -0.147276 -0.147276 1.000000 1.000000 0.697830 0.003862 0.280000 0.699699 -1.726333 804 0
>> 4.767965 1.902440 -0.049013 -47.342361 -1.746117 -99.000000 0.000000 0.281762 0.009362 0.020000 0.280275 0.080410 2 0
>> 2.4538E+07 17.164406 -0.144578 -99.000000 4.841707 -6.708778 0.000000 0.000996 0.002100 2.041E-02 2.003E-02 0.406E-12 max_dt
>> …
>> limit_retention_by_mdot_edd 1.00000000000000
>> 80 7.133147 5623.581 -0.147068 -0.147068 1.000000 1.000000 0.697799 0.003893 0.280000 0.699695 -1.725684 805 0
>> 4.540227 1.902700 -0.048982 -47.342139 -1.746666 -99.000000 0.000000 0.281789 0.009362 0.020000 0.280278 0.080429 2 0
>> 2.4982E+07 17.164649 -0.144430 -99.000000 4.841628 -6.708879 0.000000 0.000970 0.002100 2.041E-02 2.003E-02 0.410E-12 max_dt
>> …
>> 200 7.133133 5624.563 -0.146889 -0.146889 0.999998 0.999998 0.697756 0.003936 0.280000 0.699690 -1.724669 804 0
>> 1.704756 1.903102 -0.048986 -47.342260 -1.747449 -7.907379 0.000000 0.281826 0.009362 0.020000 0.280283 0.080458 2 0
>> 2.5609E+07 17.165027 -0.144135 -15.954590 4.842993 -6.709504 0.000000 0.000933 0.002100 2.042E-02 2.003E-02 0.348E-06 max_dt
>> …
>> 400 7.132610 5623.574 -0.153945 -0.153945 0.997556 0.997556 0.697754 0.003937 0.280000 0.699689 -1.724631 798 0
>> 1.322512 1.902343 -0.051336 -47.370921 -1.752430 -7.000000 0.000000 0.281828 0.009362 0.020000 0.280284 0.080508 2 0
>> 2.5634E+07 17.163740 -0.149140 -99.000000 4.845181 -6.707216 0.000000 0.000932 0.002100 2.042E-02 2.003E-02 0.116E-05 max_dt
>> …
>> 450 7.132586 5623.382 -0.154267 -0.154267 0.997446 0.997446 0.697754 0.003937 0.280000 0.699689 -1.724626 799 0
>> 1.380211 1.902309 -0.051457 -47.372230 -1.752657 -7.000000 0.000000 0.281828 0.009362 0.020000 0.280284 0.080511 2 0
>> 2.5635E+07 17.163683 -0.149442 -15.954590 4.845320 -6.707062 0.000000 0.000932 0.002100 2.042E-02 2.003E-02 0.105E-05 max_dt
>>
>> bad angular_momentum_j -1.6607253567366117D+48
>> 450 7.132587 5623.372 -0.154261 -0.154261 0.997449 0.997449 0.697754 0.003937 0.280000 0.699689 -1.724625 799 1
>> 1.229696 1.902311 -0.051455 -47.372212 -1.752653 -99.000000 0.000000 0.281828 0.009362 0.020000 0.280284 0.080511 2 0
>> 2.5635E+07 17.163687 -0.149440 -99.000000 4.845320 -6.707061 0.000000 0.000932 0.002100 2.042E-02 2.003E-02 -0.186E-09 varcontrol
>>
>> limit_retention_by_mdot_edd 3.214841505531817E-003
>>
>> bad angular_momentum_j -3.2131373377825206D+51
>> bad angular_momentum_j -2.2718819925086352D+51
>> num_backups 11
>> max_number_backups 10
>>
>> stopping because of convergence problems num_backups > max_number_backups
>>
>> save LOGS/profile3.data for model 457
>> save photos/x457 for model 457
>>
>> runtime, retries, backups, steps 1.686900 2.000000 12 11 457
>> 457 7.132585 5623.375 -0.154261 -0.154274 0.997449 0.997449 0.697754 0.003937 0.280000 0.699689 0.146E+18 799 12
>> -1.851937 1.902312 -0.051455 -47.372218 -1.752654 -99.000000 0.000000 0.281828 0.009362 0.020000 0.280284 0.855E+14 4 11
>> 2.5635E+07 17.163682 -0.149439 -99.000000 4.845320 0.000000 0.000000 0.000932 0.002100 2.042E-02 2.003E-02 0.000E+00 hold
>>
>> DATE: 2013-07-23
>> TIME: 10:28:23
>> [goliasch at ip10 make_mdot_work]$
>>
>>
>> Output of segmentation fault when running the latest version of MESA:
>>
>>
>> [goliasch at ip10 binary_donor_only]$ ./rn
>> DATE: 2013-07-23
>> TIME: 10:35:15
>>
>>
>> version_number 5118
>> donor_controls
>>
>> maccretor 8.0000000000000004D-01
>> mdonor 1.0000000000000000D+00
>> initial_period_in_days 5.0000000000000000D-01
>> jdot_multiplier 1.0000000000000000D+00
>> fr 1.0000000000000001D-01
>> gr_only F
>>
>> set_net basic.net
>> net name basic.net
>> extra_terminal_output_file: log1
>> use small_mtx_decsol bcyclic_dble 8 100
>> kappa_file_prefix gn93
>> kappa_lowT_prefix lowT_fa05_gs98
>> eos_file_prefix mesa
>> OMP_NUM_THREADS 8
>> donor_startup
>>
>>
>> star model age mass (r-rl)/rl last photo
>> 1 0 0.000000000E+00 1.000000000E+00 Infinity
>> __________________________________________________________________________________________________________________________________________________
>>
>> step lg_Tcntr Teff lg_LH lg_Lnuc Mass H_rich H_cntr N_cntr Y_surf X_avg eta_cntr pts retry
>> lg_dt_yr lg_Dcntr lg_R lg_L3a lg_Lneu lg_Mdot H_poor He_cntr O_cntr Z_surf Y_avg gam_cntr iters bckup
>> age lg_Pcntr lg_L lg_LZ lg_Psurf lg_Dsurf He_poor C_cntr Ne_cntr Z_cntr Z_avg v_div_cs dt_limit
>> __________________________________________________________________________________________________________________________________________________
>>
>> forrtl: severe (408): fort: (7): Attempt to use pointer S_ACCRETOR when it is not associated with a target
>>
>> Image PC Routine Line Source
>> star_binary_donor 0000000000B50F5A Unknown Unknown Unknown
>> star_binary_donor 0000000000B4FA56 Unknown Unknown Unknown
>> star_binary_donor 0000000000AF7060 Unknown Unknown Unknown
>> star_binary_donor 0000000000A9524F Unknown Unknown Unknown
>> star_binary_donor 0000000000A95771 Unknown Unknown Unknown
>> star_binary_donor 000000000042BD5B run_binarydo_run_ 477 run_binary.f
>> star_binary_donor 0000000000429291 run_binary_mp_do_ 356 run_binary.f
>> star_binary_donor 000000000043D62E MAIN__ 4 run.f
>> star_binary_donor 000000000040418C Unknown Unknown Unknown
>> libc.so.6 000000326001D994 Unknown Unknown Unknown
>> star_binary_donor 0000000000404019 Unknown Unknown Unknown
>> DATE: 2013-07-23
>> TIME: 10:35:22
>> [goliasch at ip10 binary_donor_only]$
>> <code_output.pdf>
>
>
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> --
> Michael Zingale
> Associate Professor
>
> Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800
> phone: 631-632-8225
> e-mail: Michael.Zingale at stonybrook.edu
> web: http://www.astro.sunysb.edu/mzingale
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