numpy.dtype size changed, may indicate binary incompatibility

[gavkhar-a]

Summary

Additional details

• QSIPrep version: 1.0.1
• Docker version:
• Singularity version: Apptainer 1.3.6-1.el8

I am trying to run QSIprep on BIDS-formatted dwi data

Every time I try running it, I get this error message

Like this:

<Process Process-2:
Traceback (most recent call last):
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
    self.run()
  File "/opt/conda/envs/qsiprep/lib/python3.10/multiprocessing/process.py", line 108, in run
    self._target(*self._args, **self._kwargs)
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/cli/workflow.py", line 51, in build_workflow
    from ..workflows.base import init_qsiprep_wf
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/workflows/base.py", line 45, in <module>
    from ..interfaces import (
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/interfaces/__init__.py", line 4, in <module>
    from .confounds import DMRISummary, GatherConfounds
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/interfaces/confounds.py", line 29, in <module>
    from .gradients import concatenate_bvals, concatenate_bvecs
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsiprep/interfaces/gradients.py", line 10, in <module>
    from dipy.reconst.dti import decompose_tensor
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/dipy/reconst/dti.py", line 13, in <module>
    from dipy.data import get_sphere
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/dipy/data/__init__.py", line 11, in <module>
    from dipy.core.gradients import GradientTable, gradient_table
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/dipy/core/gradients.py", line 10, in <module>
    from dipy.core.sphere import disperse_charges, HemiSphere
  File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/dipy/core/sphere.py", line 8, in <module>
    from dipy.reconst.recspeed import remove_similar_vertices
  File "recspeed.pyx", line 1, in init dipy.reconst.recspeed
ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject>

I updated the python on server and used the latest version of QSIprep. What could I be doing wrong?
-->
Thanks in advance!

[mattcieslak]

Hi! You shouldn't be using any python outside of the container. This suggests that you are auto-mounting a local python installation when you run apptainer and your local numpy isn't compatible with the one in the container. Can you try running apptainer with --containall?

[gavkhar-a]

Hi Matt, thank you for this! Do you know where in the script I would run the apptainer --containall?
Here is my script for a reference:

#!/bin/bash
#SBATCH --job-name=qsiprep
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=6
#SBATCH --time=50:00:00
#SBATCH --mem=24000
#SBATCH --mail-user=ga2541@umd.edu
#SBATCH --mail-type=ALL
#
Sub=$1
participant=${Sub#sub-}
bids_dir=/scratch/zt1/project/romeo-prj/shared/fact
output_dir=/scratch/zt1/project/romeo-prj/shared/fact_qsiprep_output
work_dir=/scratch/zt1/project/romeo-prj/shared/fact_qsiprep_work
module load apptainer

echo "------------------------------------------------------------------"
echo "started QSIprep"
echo ${Sub}
date
echo "------------------------------------------------------------------"

cd /home/${USER}/scratch

apptainer exec --cleanenv \
    --bind ${bids_dir}:/data:ro \
    --bind ${output_dir}:/out \
    --bind ${work_dir}:/work \
    qsiprep_1.0.1.sif \
    qsiprep /data /out participant \
    --participant-label ${participant} \
    --fs-license-file /home/${USER}/license.txt \
    --separate-all-dwis \
    --output-resolution 1.25 \
    --skip-bids-validation \
    -w /work

echo "------------------------------------------------------------------"
echo "Ended QSIprep"
echo ${Sub}
date
echo "------------------------------------------------------------------"  

[mattcieslak]

right before qsiprep_1.0.1.sif