Numpy installation error


I have the error below during installation. Any hints on what is wrong? I upgraded numpy and several other packages with pip, but so far nothing works.



  Right now, all GPUs will be enabled...
 RuntimeError: module compiled against API version 0xb but this version of numpy is 0xa
terminate called after throwing an instance of 'std::runtime_error'
  what():  numpy failed to initialize
/home/andrzejr/cryosparc/bin/cryosparc: line 91: 12435 Aborted                 (core dumped) python "$script_dir/" "$@"

Traceback (most recent call last):
  File "/home/andrzejr/cryosparc/bin/", line 128, in <module>
    trycall(["cryosparc", "configure", "gpu", "enable", "all"])
  File "/home/andrzejr/cryosparc/bin/", line 8, in trycall
    ret = subprocess.check_output(cmds, **kwargs)
  File "/usr/lib/python2.7/", line 219, in check_output
    raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command '['cryosparc', 'configure', 'gpu', 'enable', 'all']' returned non-zero exit status 134

Hey @andrzej,

Can you do the following:

eval $(cryosparc env)
which python
(should be the cryosparc/anaconda2/bin/python, not system python)
python -c "import numpy; print numpy.__version__;"

If that reports 1.11.2 then that is the correct version. Given that this error is happening during GPU checks, it could be pyCUDA that was compiled with the wrong numpy version. Try this:

cryosparc reinstallpycuda
cryosparc configure initial

I should add that the cryosparc command won’t be available immediately because your initial config didn’t finish, so you’ll need to do:
export PATH=/home/andrzejr/cryosparc/bin:$PATH