External Email - Use Caution That is clarifying, thank you very much!
Brunno M Campos University of Campinas Em dom., 23 de fev. de 2025 às 01:51, fsbuild <fsbu...@contbay.com> escreveu: > External Email - Use Caution > > > If I understand the recon-all script correctly, the default is to run with > -openmp 1 and even if you were to instead specify the available -DoParallel > option, that would set openmp to 4 threads (and itkthreads to 4) to do work > in parallel. I don't run recon-all with options that increase the number > of threads beyond the defaults because it is not cluster friendly. But > even for the default settings, you need ~16G of system RAM to run the > Ubuntu 22 OS, freesurfer 7.4.1 running recon-all and whatever other > processes run on the machine. > > Given that you specified -openmpi 8, i.e., you added 7 more threads with > ~16G of physical RAM to spare, then even with memory management it could be > a memory underrun occurred causing the process to exit with Signal 6, e.g., > memory allocation fails. You could try and profile machine resource usage > by keeping a program like "glances" running on the console and see if > reports critical errors in memory usage, CPU load, etc., while recon-all > runs. Maybe try the DoParallel option instead to see if the machine has > enough resources to run that. > > - R. > > > On 2/21/25 06:10, Brunno M. de Campos (bru...@unicamp.br) wrote: > > External Email - Use Caution > Hi, > I would also like to include here the entire set of lines I am using. > Since there are three different parallel-associated flags for recon-all, I > am also concerned about my choice (OpenMP). > > >> recon-all -i Sub_1_Time_1.nii -subjid Sub_1_Time_1 -qcache -sd > ./OUTPUT_DIR -all -openmp 8 > >> recon-all -i Sub_1_Time_2.nii -subjid Sub_1_Time_2 -qcache -sd > ./OUTPUT_DIR -all -openmp 8 > > >> recon-all -base ./OUTPUT_DIR/Sub_1_base -tp ./OUTPUT_DIR/Sub_1_Time_1 > -tp ./OUTPUT_DIR/Sub_1_Time_2 -sd "./OUTPUT_DIR -all -openmp 8 > > >> recon-all -long ./OUTPUT_DIR/Sub_1_Time_1 ./OUTPUT_DIR/Sub_1_base -sd > ./OUTPUT_DIR -all -openmp 8 > >> recon-all -long ./OUTPUT_DIR/Sub_1_Time_2 ./OUTPUT_DIR/Sub_1_base -sd > ./OUTPUT_DIR -all -openmp 8 > > Thank you very much! > > Brunno M Campos > University of Campinas > > > Em qui., 20 de fev. de 2025 às 08:50, Brunno M. de Campos < > bru...@unicamp.br> escreveu: > >> Hi, thanks. >> >> > version of freersurfer you are running: 7.4.1 >> > OS name and version you are running: Ubuntu 22 >> > amount of RAM on your machine: 32 gb >> >> Best, >> >> Brunno M Campos >> University of Campinas >> >> >> Em qui., 20 de fev. de 2025 às 08:47, fsbuild <fsbu...@contbay.com> >> escreveu: >> >>> External Email - Use Caution >>> >>> Please list: >>> >>> > version of freersurfer you are running >>> > OS name and version you are running >>> > amount of RAM on your machine >>> >>> - R. >>> >>> On Feb 20, 2025, at 05:58, Brunno M. de Campos <bru...@unicamp.br> >>> wrote: >>> >>> External Email - Use Caution >>> >>> Dear all, >>> >>> I run my script for longitudinal processing based on: individual >>> processing (recon-all -i) + base image creation (recon-all -base) and >>> longitudinal processing (recon-all -long). >>> >>> In some cases (not always), the process terminates with errors, >>> apparently at the same stage. The log states, among other things, "Reading >>> texture...*** buffer overflow detected ***: terminated Command terminated >>> by signal 6". >>> >>> 1 - I assume that I have exceeded my memory capacity. Am I correct? >>> I have, in fact, written a script that parallelizes these processes, but >>> I might be distributing the workload poorly if that is the case. >>> >>> 2 - If this is indeed the issue, do you know the peak memory required >>> for such a process? >>> >>> Thank you! >>> Brunno M Campos >>> University of Campinas >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/1ENsUO3GommiGkEzUw-Bc5gUYYwwcEDNZKeVmhnFXfgw4xPIxCLzYLMRry4YRILp2Ds22I7fWwyATL-80rWCvWIgeGeWgVZ5inz3KVqgK28KdSlh79JdX4qBeHdxXb2oTyA2xcMkj8WZAP6_DO7fjJXwPJpIaTD-et3smkxZKR0HU0Ywdlla8_F5NOArOIj9CjUIsqyX6pUNq4PzO9-VxRJUEoAdG0DoCTONLnYuR_JnmsI-3xjLe1HC7c8Jz9CQusrgoWqxJROqWgj4kY8GiZWbF2Fk6N7K_WLgBEwuJ6bqs0lqed5dvalWGlL1Qx6i34N1_Mw7YSS_esYnfF8kN8g/https%3A%2F%2Fmail.nmr.mgh.harvard..edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> <https://secure-web.cisco.com/1sjikz6yK0UpP7uwVL4Jmd0-iE28t-gDUPiP3Ui7ckoAZ7evEKKVoaELXUeoJYNxh6LPVM9cK-x3imtf9ylilr21PWMnYwpuNUFrAeqJYRU1E9bqJzscCswXO6sly7-HLAfXdnysWuLhsihdVVqkLpJ8tpS8vdRCy0fWe3I2G5zi6PAxkWsyq5v_jr6an09nLgmZgFe9OvlAnBuDOWWeawp3_Tdxt-0FcRf8Nd0cW3kafm4tN4D1oH-rzPxDQrO9td01hGsBuB3rtVD9lAeWkKDgTQQpZ66uke1j3PaMQHJSNSSmea3mwZSQCvYOcRbvSab3aniYpzHkJxoS_j0zc1g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/1ENsUO3GommiGkEzUw-Bc5gUYYwwcEDNZKeVmhnFXfgw4xPIxCLzYLMRry4YRILp2Ds22I7fWwyATL-80rWCvWIgeGeWgVZ5inz3KVqgK28KdSlh79JdX4qBeHdxXb2oTyA2xcMkj8WZAP6_DO7fjJXwPJpIaTD-et3smkxZKR0HU0Ywdlla8_F5NOArOIj9CjUIsqyX6pUNq4PzO9-VxRJUEoAdG0DoCTONLnYuR_JnmsI-3xjLe1HC7c8Jz9CQusrgoWqxJROqWgj4kY8GiZWbF2Fk6N7K_WLgBEwuJ6bqs0lqed5dvalWGlL1Qx6i34N1_Mw7YSS_esYnfF8kN8g/https%3A%2F%2Fmail.nmr.mgh.harvard..edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> <https://secure-web.cisco.com/1sjikz6yK0UpP7uwVL4Jmd0-iE28t-gDUPiP3Ui7ckoAZ7evEKKVoaELXUeoJYNxh6LPVM9cK-x3imtf9ylilr21PWMnYwpuNUFrAeqJYRU1E9bqJzscCswXO6sly7-HLAfXdnysWuLhsihdVVqkLpJ8tpS8vdRCy0fWe3I2G5zi6PAxkWsyq5v_jr6an09nLgmZgFe9OvlAnBuDOWWeawp3_Tdxt-0FcRf8Nd0cW3kafm4tN4D1oH-rzPxDQrO9td01hGsBuB3rtVD9lAeWkKDgTQQpZ66uke1j3PaMQHJSNSSmea3mwZSQCvYOcRbvSab3aniYpzHkJxoS_j0zc1g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>> The information in this e-mail is intended only for the person to whom >>> it is addressed. 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