[CP2K-user] [CP2K:18836] Dipole moment segmentation fault

[Vladislav Sláma]

Hi, 
I'm including a small update from the run on different machine with 
differently compiled version of CP2K which provides a more detailed 
information about the source of the error:

Program received signal SIGSEGV: Segmentation fault - invalid memory 
reference.

Backtrace for this error:
#0  0x628b4ef in ???
        at 
/home/abuild/rpmbuild/BUILD/glibc-2.31/nptl/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0
#1  0xc9b71e in __qs_moments_MOD_build_local_moment_matrix
        at /home/krack/github/cp2k/cp2k-2023.1/src/qs_moments.F:253
#2  0xca0074 in __qs_moments_MOD_qs_moment_locop
        at /home/krack/github/cp2k/cp2k-2023.1/src/qs_moments.F:1874
#3  0xb923fe in __qs_scf_post_gpw_MOD_qs_scf_post_moments
        at /home/krack/github/cp2k/cp2k-2023.1/src/qs_scf_post_gpw.F:1262
#4  0xb93d18 in __qs_scf_post_gpw_MOD_scf_post_calculation_gpw
        at /home/krack/github/cp2k/cp2k-2023.1/src/qs_scf_post_gpw.F:376
#5  0x18ba70d in __qs_scf_post_scf_MOD_qs_scf_compute_properties
        at /home/krack/github/cp2k/cp2k-2023.1/src/qs_scf_post_scf.F:78
#6  0x1823e51 in __qs_scf_MOD_scf
        at /home/krack/github/cp2k/cp2k-2023.1/src/qs_scf.F:301
#7  0x11adb1b in __qs_energy_MOD_qs_energies
        at /home/krack/github/cp2k/cp2k-2023.1/src/qs_energy.F:111
#8  0xe2f6c0 in __force_env_methods_MOD_force_env_calc_energy_force
        at /home/krack/github/cp2k/cp2k-2023.1/src/force_env_methods.F:259
#9  0x5282c7 in rt_initial_guess
        at 
/home/krack/github/cp2k/cp2k-2023.1/src/motion/rt_propagation.F:460
#10  0x5282c7 in __rt_propagation_MOD_rt_prop_setup
        at 
/home/krack/github/cp2k/cp2k-2023.1/src/motion/rt_propagation.F:131
#11  0x478b8f in cp2k_run
        at /home/krack/github/cp2k/cp2k-2023.1/src/start/cp2k_runs.F:383
#12  0x47b672 in __cp2k_runs_MOD_run_input
        at /home/krack/github/cp2k/cp2k-2023.1/src/start/cp2k_runs.F:997
#13  0x468771 in cp2k
        at /home/krack/github/cp2k/cp2k-2023.1/src/start/cp2k.F:379
#14  0x405a4c in main
        at /home/krack/github/cp2k/cp2k-2023.1/src/start/cp2k.F:44
/var/spool/slurm/job299631/slurm_script: line 17:  1360 Segmentation fault 
     /home/vslama/software/cp2k-2023.1-Linux-gnu-x86_64.ssmp -i 
Au_NP_small_OT_RTP_z.in -o Au_NP_small_OT_RTP_z.out

I'll be glad for any suggestion how to overcome this error.

Best wishes,
Vladislav

Dne středa 24. května 2023 v 9:29:57 UTC+2 uživatel Vladislav Sláma napsal:

> Dear Matthias*,*
>
> Thank you for your suggestion. I was already using “ulimit -s unlimited”, 
> but adding “export OMP_STACKSIZE=16M” didn’t help and I’m still getting the 
> same segmentation fault. I’m including my submission script on CSCS cluster 
> to provide all the settings for the cp2k run.
>
>
> Best wishes,
>
> Vladislav
> Dne středa 24. května 2023 v 9:06:47 UTC+2 uživatel Krack Matthias napsal:
>
>> Hi Vladislav
>>
>>  
>>
>> Segmentation faults are often caused by an insufficient stack size. Try 
>> to set (assuming bash) “ulimit -s unlimited” and “export OMP_STACKSIZE=16M” 
>> before launching the cp2k run.
>>
>>  
>>
>> HTH
>>
>>  
>>
>> Matthias
>>
>>  
>>
>> *From: *cp... at googlegroups.com <cp... at googlegroups.com> on behalf of 
>> Vladislav Sláma <sla... at gmail.com>
>> *Date: *Tuesday, 23 May 2023 at 18:36
>> *To: *cp2k <cp... at googlegroups.com>
>> *Subject: *[CP2K:18833] Dipole moment segmentation fault
>>
>> Dear all,
>>
>> I’m trying to simulate optical spectra and plasmon resonance for 
>> different gold cluster sizes. In order to do that, I’m employing real time 
>> propagation after initial delta-pulse kick. For the smaller particle sizes 
>> (up to ~114 atoms) everything works well and I get reasonable spectra. 
>> However for the larger nanoparticle (178 atoms) I’m getting segmentation 
>> fault due to the calculation of the dipole moments. When I do not compute 
>> and print dipole moments, the real time propagation goes well without any 
>> problem. Could you please suggest me how to compute the dipole moment 
>> during the real time propagation to avoid this problem?
>>
>>  
>>
>> Thank you. Best wishes,
>>
>> Vladislav
>>
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>>
>

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