<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"> <head> <meta http-equiv="Content-Type" content="text/html; charset=windows-1250"> <meta name="Generator" content="Microsoft Word 15 (filtered medium)"> <style></style> </head> <body lang="en-CH" link="blue" vlink="purple" style="word-wrap:break-word"> <div class="WordSection1"> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US">I suggest to open <a href="https://github.com/cp2k/cp2k/issues">an issue on github</a> for this and to address the author of the routine.<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:12.0pt;margin-left:36.0pt"> <b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">cp2k@googlegroups.com <cp2k@googlegroups.com> on behalf of Vladislav Sláma <slamavl@gmail.com><br> <b>Date: </b>Wednesday, 24 May 2023 at 10:20<br> <b>To: </b>cp2k <cp2k@googlegroups.com><br> <b>Subject: </b>Re: [CP2K:18836] Dipole moment segmentation fault<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Hi, <o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">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:<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Program received signal SIGSEGV: Segmentation fault - invalid memory reference.<br> <br> Backtrace for this error:<br> #0 0x628b4ef in ???<br> at /home/abuild/rpmbuild/BUILD/glibc-2.31/nptl/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0<br> #1 0xc9b71e in __qs_moments_MOD_build_local_moment_matrix<br> at /home/krack/github/cp2k/cp2k-2023.1/src/qs_moments.F:253<br> #2 0xca0074 in __qs_moments_MOD_qs_moment_locop<br> at /home/krack/github/cp2k/cp2k-2023.1/src/qs_moments.F:1874<br> #3 0xb923fe in __qs_scf_post_gpw_MOD_qs_scf_post_moments<br> at /home/krack/github/cp2k/cp2k-2023.1/src/qs_scf_post_gpw.F:1262<br> #4 0xb93d18 in __qs_scf_post_gpw_MOD_scf_post_calculation_gpw<br> at /home/krack/github/cp2k/cp2k-2023.1/src/qs_scf_post_gpw.F:376<br> #5 0x18ba70d in __qs_scf_post_scf_MOD_qs_scf_compute_properties<br> at /home/krack/github/cp2k/cp2k-2023.1/src/qs_scf_post_scf.F:78<br> #6 0x1823e51 in __qs_scf_MOD_scf<br> at /home/krack/github/cp2k/cp2k-2023.1/src/qs_scf.F:301<br> #7 0x11adb1b in __qs_energy_MOD_qs_energies<br> at /home/krack/github/cp2k/cp2k-2023.1/src/qs_energy.F:111<br> #8 0xe2f6c0 in __force_env_methods_MOD_force_env_calc_energy_force<br> at /home/krack/github/cp2k/cp2k-2023.1/src/force_env_methods.F:259<br> #9 0x5282c7 in rt_initial_guess<br> at /home/krack/github/cp2k/cp2k-2023.1/src/motion/rt_propagation.F:460<br> #10 0x5282c7 in __rt_propagation_MOD_rt_prop_setup<br> at /home/krack/github/cp2k/cp2k-2023.1/src/motion/rt_propagation.F:131<br> #11 0x478b8f in cp2k_run<br> at /home/krack/github/cp2k/cp2k-2023.1/src/start/cp2k_runs.F:383<br> #12 0x47b672 in __cp2k_runs_MOD_run_input<br> at /home/krack/github/cp2k/cp2k-2023.1/src/start/cp2k_runs.F:997<br> #13 0x468771 in cp2k<br> at /home/krack/github/cp2k/cp2k-2023.1/src/start/cp2k.F:379<br> #14 0x405a4c in main<br> at /home/krack/github/cp2k/cp2k-2023.1/src/start/cp2k.F:44<br> /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<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">I'll be glad for any suggestion how to overcome this error.<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Best wishes,<o:p></o:p></span></p> </div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Vladislav<o:p></o:p></span></p> </div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Dne středa 24. května 2023 v 9:29:57 UTC+2 uživatel Vladislav Sláma napsal:<o:p></o:p></span></p> </div> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <p style="mso-margin-top-alt:5.0pt;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt"> Dear <span lang="EN-US">Matthias<u>,</u></span><o:p></o:p></p> <p style="mso-margin-top-alt:5.0pt;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt"> <span lang="EN-US">Thank you for your suggestion. I was already using </span>“<span lang="EN-US">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.</span><o:p></o:p></p> <p style="mso-margin-top-alt:5.0pt;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt"> <o:p> </o:p></p> <p style="mso-margin-top-alt:5.0pt;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt"> <span lang="EN-US">Best wishes,</span><o:p></o:p></p> <p style="mso-margin-top-alt:5.0pt;margin-right:0cm;margin-bottom:0cm;margin-left:36.0pt"> <span lang="EN-US">Vladislav</span><o:p></o:p></p> <div> <div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">Dne středa 24. května 2023 v 9:06:47 UTC+2 uživatel Krack Matthias napsal:<o:p></o:p></span></p> </div> </div> <div> <blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm"> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt">Hi Vladislav</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="DE-CH" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">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.</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">HTH</span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt">Matthias</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> </div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:36.0pt"> <span lang="EN-US" style="font-size:11.0pt"> </span><span style="font-size:11.0pt"><o:p></o:p></span></p> <div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm"> <p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:12.0pt;margin-left:72.0pt"> <b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">cp...@googlegroups.com <cp...@googlegroups.com> on behalf of Vladislav Sláma <sla...@gmail.com><br> <b>Date: </b>Tuesday, 23 May 2023 at 18:36<br> <b>To: </b>cp2k <cp...@googlegroups.com><br> <b>Subject: </b>[CP2K:18833] Dipole moment segmentation fault</span><span style="font-size:11.0pt"><o:p></o:p></span></p> </div> <p style="mso-margin-top-alt:5.0pt;margin-right:0cm;margin-bottom:0cm;margin-left:72.0pt"> Dear all,<o:p></o:p></p> <p style="mso-margin-top-alt:5.0pt;margin-right:0cm;margin-bottom:0cm;margin-left:72.0pt"> 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?<o:p></o:p></p> <p style="mso-margin-top-alt:5.0pt;margin-right:0cm;margin-bottom:0cm;margin-left:72.0pt"> <o:p></o:p></p> <p style="mso-margin-top-alt:5.0pt;margin-right:0cm;margin-bottom:0cm;margin-left:72.0pt"> Thank you. Best wishes,<o:p></o:p></p> <p style="mso-margin-top-alt:5.0pt;margin-right:0cm;margin-bottom:0cm;margin-left:72.0pt"> Vladislav<o:p></o:p></p> </div> </div> <div> <div> <p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;margin-left:72.0pt"> <span style="font-size:11.0pt">-- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+uns...@googlegroups.com.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/f1ad08c5-e388-4e1a-bbbc-fbd46e715bf6n%40googlegroups.com?utm_medium=email&utm_source=footer" target="_blank"> https://groups.google.com/d/msgid/cp2k/f1ad08c5-e388-4e1a-bbbc-fbd46e715bf6n%40googlegroups.com</a>.<o:p></o:p></span></p> </div> </div> </blockquote> </div> </blockquote> </div> <p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:11.0pt">-- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/9b03e074-7bc9-4b4a-be26-54b0dc37f1e8n%40googlegroups.com?utm_medium=email&utm_source=footer"> https://groups.google.com/d/msgid/cp2k/9b03e074-7bc9-4b4a-be26-54b0dc37f1e8n%40googlegroups.com</a>.<o:p></o:p></span></p> </div> </body> </html> <p></p> -- <br /> You received this message because you are subscribed to the Google Groups "cp2k" group.<br /> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+unsubscribe@googlegroups.com">cp2k+unsubscribe@googlegroups.com</a>.<br /> To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/ZRAP278MB0827C27C443B3036FB1173ABF4419%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM?utm_medium=email&utm_source=footer">https://groups.google.com/d/msgid/cp2k/ZRAP278MB0827C27C443B3036FB1173ABF4419%40ZRAP278MB0827.CHEP278.PROD.OUTLOOK.COM</a>.<br />