External Email - Use Caution dear all,
is there any progress on this issue? can I send more information to help with debugging? judging from the other entries of the mailing list this is not an issue that concerns only me. thank you for your attention, bests fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1dOZP5j8XdDioY7tViTW7NqEi9mrvvba6PAbK6uv63gP7Q8bNrlLCYFkKfvXXNpcvR7MIg3L5wRfoQWO66UdM1HtJA4W7iKqfq4FhnnE9W2R2KwGDIaI7MjIpsOL5VryAdycFZZismV1CFp4rNE47COVEcaN7m-ypDnjnXobdlMmq5EirIKZSBuBmmU3BrEdMYwD-BFb3nS8AdCafRfCfvjcSJaTNtkXlb52Ab49xmqiAfSbLVpAV32A2F_b5QaItKY0wLlYGCGD0ZC1nbr_gag/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/1C5zQD6S2aQEn7dMGBOKijRrWY8INlUWuanF5g6gCvX_Y1b1F-tAXUd55vvYP2ExpFYOE4G_Gf0Ujo0hS1Y2GnTUxWS4Q-Hw7ryBf9XfzTCb8akQhMElGzETBV9Y9Dx77zF8x-MJ9GUD0FyloeWVletfQc1s8UEKQ3yoaKTFfJ2V8wWshKFJa_JP1qacQoSHNmMiXI_FcftEAwml4E2oNwVLDD4wbGRONmoBUwVEiXo5dl7kMXPeg0RsJWGcPzoL3tA375bU9hNlgebAeMlJOhg/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1R3-Q2awQvkHA7pJ5-Bypzc-0X_unyiumlI9PjumZoPxQt07p2OV6Ic1U3XRYL4eNBJal5v0TRUTOvxYTlIeLC1WTMxI-rtEtG8N77JaaMIF13TDkl5R43K7OsP1ahBNt1eNtB_F2H91UBJElxnZ9OxetTmgwCn-WoMBTZsXBsH7BO7zP_6eZ54cIYpYTvBuEgv1DwLFBLnNlUpt_JuYJSDx4zM-kLZt3qrNjw67fNp5cbpAoaJCV0cCgR2NfJCsLdepyT15Wfal__W5aiZ2SPg/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1R3-Q2awQvkHA7pJ5-Bypzc-0X_unyiumlI9PjumZoPxQt07p2OV6Ic1U3XRYL4eNBJal5v0TRUTOvxYTlIeLC1WTMxI-rtEtG8N77JaaMIF13TDkl5R43K7OsP1ahBNt1eNtB_F2H91UBJElxnZ9OxetTmgwCn-WoMBTZsXBsH7BO7zP_6eZ54cIYpYTvBuEgv1DwLFBLnNlUpt_JuYJSDx4zM-kLZt3qrNjw67fNp5cbpAoaJCV0cCgR2NfJCsLdepyT15Wfal__W5aiZ2SPg/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 ________________________________________ Von: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Bernardoni, Fabio <fabio.bernard...@uniklinikum-dresden.de> Gesendet: Donnerstag, 20. Mai 2021 11:17:05 An: Freesurfer support list Betreff: Re: [Freesurfer] memory allocation error External Email - Use Caution dear Andrew, I was allowing 8, 16, ~36GB of memory in different runs, so I would exclude that this was the problem. bests fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/187My4Jucq7g2iOhroEKk8K8OFGoFoeORTu-mXzokMtuySZfRpdmpBUHAWrZs3PiUgTJQxvI4t7mF19Q65QoVRPm9HIRo1ga6iFYC3emunkTnsx44xyypE8RQ7se9eW1WnrqXrI_Z3OCRQDKjl_O6YrVXw8u2fxs-M2rmDvVwA1c8A6B-TCU2kRIeB7oIt49DW_DM1zE6Vs2u2KvWqA9-ZtIcGYVGPwCKGzShIT5OOvNrJjUldtN0AoNqCDk2gUFd6DjRtozUhmyNbDtaEpIJOQ/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/15nLSigNtaEzdHxIpWerC4ukwoFMkkmjnCaSZHFWvxZoHCXH4XhBy49dgkjt_Vq9EFKvYq9xxQ4wmBIAl28GFHwhUJe7IfUAQkVKEMD5fvpyeYO8Shfw1PZr2zy9p7hm86gBaVav8UarY5wXbQ2FUH7lzmO3kgv-sylrFq8rFfmbsx-WSHLLJyi6zQDOV0A7vxj7uJyZDym-vCiDaPrxTdvo7Tws6y8FnBWgAvc-2BMa-GAAkHZJOPrvFuJw9Nh5WXnTa0wo5mD-Qgvp8aHL22A/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1bhSP0g6m-KCmnhx95IzYxybOAfEOuUmdr5O1AghDUiWJ_SONFEYWrYhfZopDBWkhbc3TWSyW9QsbMRNKTE24SQ_x0a3HOEgV3T4EbIQz1B5mWM6kfZAIiPy36Rhb9HX2U6c3GoyoRPlN7ut_eBPi4d14AvKs_N9pnhWq0dQwrRAHHun-Yqv9qrGkYegJ02POCOw-MnqxRpFSqRpWAOWBZnCq_pGQ2U55zXSRVdQzl3vGgyJxJ3V56k8BwsKP6I8sXGy5TpVmhHFr_P52dATl6A/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1bhSP0g6m-KCmnhx95IzYxybOAfEOuUmdr5O1AghDUiWJ_SONFEYWrYhfZopDBWkhbc3TWSyW9QsbMRNKTE24SQ_x0a3HOEgV3T4EbIQz1B5mWM6kfZAIiPy36Rhb9HX2U6c3GoyoRPlN7ut_eBPi4d14AvKs_N9pnhWq0dQwrRAHHun-Yqv9qrGkYegJ02POCOw-MnqxRpFSqRpWAOWBZnCq_pGQ2U55zXSRVdQzl3vGgyJxJ3V56k8BwsKP6I8sXGy5TpVmhHFr_P52dATl6A/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 ________________________________________ Von: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Hoopes, Andrew <ahoo...@mgh.harvard.edu> Gesendet: Mittwoch, 19. Mai 2021 20:38:45 An: Freesurfer support list Betreff: Re: [Freesurfer] memory allocation error Hi Fabio, How much memory are you allowing for this process? You might want to just try increasing the limit on the slurm job to see if that works. Best Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bernardoni, Fabio <fabio.bernard...@uniklinikum-dresden.de> Date: Tuesday, May 11, 2021 at 4:22 AM To: freesurfer mailing list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] memory allocation error External Email - Use Caution Sorry I forgot the attachment. Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 ________________________________________ Von: Bernardoni, Fabio Gesendet: Dienstag, 11. Mai 2021 10:20:19 An: freesurfer mailing list Betreff: AW: memory allocation error Dear Freesurfers, when running the longitudinal preprocessing on a subject, I get the same error as described here (see recon-all.log attached): https://secure-web.cisco.com/1my6XFSQF3uEj1ZrgriH6ZF1WxWnqfBMBdiuPDNdXZfq_XO9uhiKwZPYEvG3NS0vJSxZM7hcmTWq1hUXJUt2_XigG_UONfGk8UL_5FWLEktb3qrFvDpcgohhnKOb1j6uAWMIE10PVwXrnLZx4Gf441Olp7jcMNX8eLVVNtPMcFPE5OH3N4cODD6Z83hDSq2HPzZH7tQ78HFekvVecIFyNfG7sKdlEVUVjwFGX6pd4c9fRkVgt6eCj-kuSxbdQrF2OBr2Vi1IX-Bz_UzXD9ZcLyw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg57542.html my FS version is: recon-all -version freesurfer-linux-centos7_x86_64-7.1.1-20200714-abaea9e and I did not perform any editing, so there is no control points to remove as suggested in the above post (which also refers to version 6). Therefore, if I understand correctly, my problem is a different one. Any clue what I might be doing wrong? Other possibly useful information: uname -a Linux tauruslogin6.taurus.hrsk.tu-dresden.de 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 11 19:12:04 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux Thanks for any hint/help Fabio Bernardoni Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F; http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/http%3A%2F%2Fwww.uniklinikum-dresden.de Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1o1Y3xlwbME1n3aKNjXzGQSIxc55dHM1BEbl1wrgFkE_TFDPgAysargFL54OYEQkzqQuT-idHfxWrjX9JD9cJxuGnzslSgKIYgXPPW7fFxvIlD5RB5gk7Cl57joRtsztgXL76twyZrGWRlN7OGujuX5JZwxmU8bWmhoDRs_gFnwQdmj7Y6onI8JzeAJ7u8BvK84qFrMitHnFpYAXvMxGhfVbneeDNteLH3OvnROuB-WwaFOwNWOflkp7IGYd0ogdtBV47OlIrA_2kjms08imJag/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
