Population_template error libgomp: Thread creation failed: Resource temporarily unavailable

1

I am trying to run population template for FBA analysis.

The script runs for several hours and has been allocated 250GB of memory

mrregister /data/bswift-1/dcallow/CONNECTOME/dwi/fod_input/100307.wmfod.mif linear_template11.mif -type nonlinear -nl_niter 5 -nl_warp_full warps_0/100307.mif -transformed inpu$

mrregister: [WARNING] existing output files will be overwritten

mrregister: preloading data for "/data/bswift-1/dcallow/CONNECTOME/dwi/fod_input/100307.wmfod.mif"... [mrregister: preloading data for "/data/bswift-1/dcallow/CONNECTOME/dwi/f$

mrregister: preloading data for "linear_template11.mif"... [mrregister: preloading data for "linear_template11.mif"... [mrregister: preloading data for "linear_template11.mif$

mrregister: SH series detected, performing FOD registration

=============]

mrregister: running non-linear registration

mrregister: nonlinear stage 1, scale factor 0.29999999999999999, lmax 2


libgomp:

libgomp:

libgomp: Thread creation failed: Resource temporarily unavailable

libgomp:

libgomp:

libgomp:

Thread creation failed: Resource temporarily unavailable

Thread creation failed: Resource temporarily unavailable

libgomp: Thread creation failed: Resource temporarily unavailable

libgomp: Thread creation failed: Resource temporarily unavailable

For reference, this is what has been created in the temporary population folder before the script runs out.

average_header.mif linear_template0.mif linear_template5.mif linear_transforms linear_transforms_4 log.txt warps_12 warps_5
command.txt linear_template1.mif linear_template6.mif linear_transforms_0 linear_transforms_5 masks_transformed warps_13 warps_6
cwd.txt linear_template10.mif linear_template7.mif linear_transforms_1 linear_transforms_6 warps warps_14 warps_7
error.txt linear_template11.mif linear_template8.mif linear_transforms_10 linear_transforms_7 warps_0 warps_15 warps_8
init_nl_template_mask.mif linear_template2.mif linear_template9.mif linear_transforms_11 linear_transforms_8 warps_1 warps_2 warps_9
initial_template.mif linear_template3.mif linear_transform_average.txt linear_transforms_2 linear_transforms_9 warps_10 warps_3
inputs_transformed linear_template4.mif linear_transform_average_inv.txt linear_transforms_3 linear_transforms_initial warps_11 warps_4

2

Hi @CallowBrainProject,

This is a pretty deep error within the libraries utilised by MRtrix3, and isn’t a native MRtrix3 error.

To at least make a start on this we’d need to know:

  1. Precisely which version of MRtrix3 is being used.

  2. What compiler was used to build MRtrix3, and which version of such;

  3. What hardware the script is being executed on, and whether it is shared with other users.

Cheers
Rob

3

Did you use the openmp build option in ./configure? I’d add the content of config to the list of required info and whether mrtrix3 was compiled on the machine where it is used.

4

Thanks for the tip. I realized Ii was using an old download that didn’t have openmp version. I am retrying on the new version. Thank you!