I started getting the following error when running classification and ab initial reconstruction jobs.
2D classification:
Traceback (most recent call last): File “/home/greg/cryosparc/cryosparc-compute/sparcjob.py”, line 542, in cuda_devs = current_experiment_params[‘cuda_devs’])
File “/home/greg/cryosparc/cryosparc-compute/class2D.py”, line 244, in abinit sigma_init_mean = n.sqrt(n.mean(sigproc.rotational_average(sigma2_init)[:radwn_max])) TypeError: slice indices must be integers or None or have an index method
ab initial reconstruction:
Traceback (most recent call last):
File “/home/greg/cryosparc/cryosparc-compute/sparcjob.py”, line 533, in
cuda_devs = current_experiment_params[‘cuda_devs’])
File “/home/greg/cryosparc/cryosparc-compute/abinit_fast.py”, line 387, in abinit
eps = 1.0/sigproc.rotational_average(H, n.round(radwn))[1:].max()
File “/home/greg/cryosparc/cryosparc-compute/sigproc.py”, line 282, in rotational_average
raps = n.bincount(ir, weights=(1-f)*M, minlength=maxRadius) +
TypeError: ‘numpy.float64’ object cannot be interpreted as an index
jobs that worked before now fail, now it didn’t work .This error start after the start of Iteration 0.
a. I checked the numpy version that cryoSPARC with
eval $(cryosparc env)
python -c “import numpy; print numpy.version”
It is 1.14.3.
the numpy version in the cryosparc installation has been updated
eval $(cryosparc env)
conda install numpy=1.11.2
Solving environment: done
RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa
b. check with which python from the cryosparc installation
eval $(cryosparc env)
python -c “import numpy; print numpy.file”
It is /home/greg/.local/lib/python2.7/site-packages/numpy/init.pyc
check system’s PYTHONPATH variable
python -c “import sys; print(’\n’.join(sys.path))”
/usr/lib/python2.7
/usr/lib/python2.7/plat-x86_64-linux-gnu
/usr/lib/python2.7/lib-tk
/usr/lib/python2.7/lib-old
/usr/lib/python2.7/lib-dynload
/home/greg/.local/lib/python2.7/site-packages
/usr/local/lib/python2.7/dist-packages
/usr/lib/python2.7/dist-packages
/usr/lib/python2.7/dist-packages/PILcompat
/usr/lib/python2.7/dist-packages/gtk-2.0
Any suggestions on what to try ?