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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 (brunno@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 <brunno@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 <fsbuild@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 <brunno@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
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That is clarifying, thank you very much!
Brunno M Campos University of Campinas
Em dom., 23 de fev. de 2025 às 01:51, fsbuild fsbuild@contbay.com escreveu:
External Email - Use CautionIf 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 (brunno@unicamp.br) wrote:
External Email - Use CautionHi, 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 < brunno@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 fsbuild@contbay.com escreveu:
External Email - Use CautionPlease 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 brunno@unicamp.br wrote:
External Email - Use CautionDear 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
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