[mesa-users] MESA problems - Segmentation fault when running rlo with ifort
Michael Zingale
michael.zingale at stonybrook.edu
Tue Jul 23 13:58:55 EDT 2013
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>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
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>> mesa-users at lists.sourceforge.net
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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
>
>
>
--
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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