[mesa-users] MESA problems - Segmentation fault when running rlo with ifort
Michael Zingale
michael.zingale at stonybrook.edu
Tue Jul 23 13:59:22 EDT 2013
Also, add -fbacktrace to the compile line for crash backtraces
On Tue, Jul 23, 2013 at 1:58 PM, Michael Zingale <
michael.zingale at stonybrook.edu> wrote:
> Ah... gfortran has a magic intrinsic extension:
>
> http://gcc.gnu.org/onlinedocs/gfortran/BACKTRACE.html
>
> just
>
> call backtrace
>
> fun!!
>
> (4.8 and higher)
>
>
> On Tue, Jul 23, 2013 at 1:55 PM, Bill Paxton <paxton at kitp.ucsb.edu> wrote:
>
>>
>> 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>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> See everything from the browser to the database with AppDynamics
>>> Get end-to-end visibility with application monitoring from AppDynamics
>>> Isolate bottlenecks and diagnose root cause in seconds.
>>> Start your free trial of AppDynamics Pro today!
>>>
>>> http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> mesa-users mailing list
>>> mesa-users at lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>
>>>
>>
>>
>> --
>> 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
>>
>>
>>
>
>
> --
> 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
>
--
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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