Dear MRtrix users/experts,
I am running into problems with all of the MRtrix commands, but only under certain conditions.
My pipelines includes a number of MRtrix operations, and they all are working fine when executed locally from a terminal window. However, because some of the operations are very time-consuming (e.g. topup and eddy related), we need to be able to run these in the background.
So, we are attempting to qsub the job, ensuring that we are qsubbing onto a node with plenty of memory (> 100G, although at the moment we are failing with mrconvert which shouldn’t be that memory intensive).
Here is the command used, and the output we’re getting:
qsub -hard -V -cwd -shell n -b y -r y -q all.q@@penguin -l h_vmem=150G -now n ./tempScript.sh
where termpScript.sh contains the following:
module load MRtrix3
/public/apps/MRtrix3/mrtrix3/bin/mrconvert -force /home//PROJECTS/MSPROJ/PROCESSING/subj-016/VISIT_1/DICOM//103_DTI_P_3bVals.dcm /home//PROJECTS/MSPROJ/PROCESSING/subj-016/VISIT_1/MRtrix/103_DTI_P_3bVals.mif 2> ~/tempDirectory/runDTIerror.txt
mrconvert: [WARNING] existing output files will be overwritten
mrconvert: reading DICOM series “103_DTI_P_3bVals”… [=]
mrconvert: [ERROR] memory-mapping failed for file “/home//PROJECTS/MSPROJ/PROCESSING/subj-016/VISIT_1/DICOM/103_DTI_P_3bVals.dcm”: Cannot allocate memory
Thanks for any advice you can provide in solving this issue.