Update to v2.8.2 causes command_vis and other jobs to fail

Troubleshooting
1

Hi,
I am running V2.8.2 and having problems with template_picker_gpu. I am new to cryosparc and working my through the T20S tutorial.

When I try to run template_picker_gpu I get the following error message below.

Can anyone help with this?
Matt

Launching job on lane default target larapinta …

License is valid.

Running job on master node hostname larapinta

Project P1 Job J18 Started

Master running v2.8.2, worker running v2.8.2

Running on lane default

Resources allocated:

Worker: larapinta

CPU : [0, 1, 2, 3]

GPU : [0]

RAM : [0]

SSD : False

Importing job module for job type template_picker_gpu…

Traceback (most recent call last): File “cryosparc2_worker/cryosparc2_compute/run.py”, line 69, in cryosparc2_compute.run.main (/home/installtest/deps_manage/cryosparc2_package/deploy/stage/cryosparc2_worker/cryosparc2_compute/run.c:3768) File “cryosparc2_compute/jobs/jobregister.py”, line 284, in get_run_function runmod = importlib.import_module("…"+modname, name) File “/usr/local/programs/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/importlib/init.py”, line 37, in import_module import(name) File “cryosparc2_worker/cryosparc2_compute/jobs/template_picker_gpu/run.py”, line 21, in init cryosparc2_compute.jobs.template_picker_gpu.run (/home/installtest/deps_manage/cryosparc2_package/deploy/stage/cryosparc2_worker/cryosparc2_compute/jobs/template_picker_gpu/run.c:15883) File “/usr/local/programs/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/skimage/init.py”, line 158, in <module> from .util.dtype import * File “/usr/local/programs/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/skimage/util/init.py”, line 5, in <module> from .apply_parallel import apply_parallel File “/usr/local/programs/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/skimage/util/apply_parallel.py”, line 8, in <module> import dask.array as da File “/usr/local/programs/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/dask/array/init.py”, line 5, in <module> from .core import (Array, block, concatenate, stack, from_array, store, File “/usr/local/programs/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/dask/array/core.py”, line 29, in <module> from . import chunk File “/usr/local/programs/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/dask/array/chunk.py”, line 73, in <module> nancumprod = npcompat.nancumprod AttributeError: ‘module’ object has no attribute ‘nancumprod’

2

Hi @mwilce,
just curious, when you start cryosparc do all modules run properly? Ever since updating to 2.8.2 command_vis fails to start, and the log file implicates the same module that you’re having trouble with. I can still run jobs in cryosparc, but there are some issues.

Starting cryoSPARC System master process…
CryoSPARC is not already running.
database: started
command_core: started
cryosparc command core startup complete.
command_vis: ERROR (spawn error)
command_proxy: started
webapp: started

cryosparcm log command_vis

Traceback (most recent call last):
File “<string>”, line 1, in <module>
File “cryosparc2_command/command_vis/init.py”, line 24, in <module>
from skimage import measure, transform
File “/home/behrouzi/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/skimage/init.py”, line 158, in <module>
from .util.dtype import *
File “/home/behrouzi/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/skimage/util/init.py”, line 5, in <module>
from .apply_parallel import apply_parallel
File “/home/behrouzi/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/skimage/util/apply_parallel.py”, line 8, in <module>
import dask.array as da
File “/home/behrouzi/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/dask/array/init.py”, line 5, in <module>
from .core import (Array, block, concatenate, stack, from_array, store,
File “/home/behrouzi/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/dask/array/core.py”, line 29, in <module>
from . import chunk
File “/home/behrouzi/cryosparc2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/dask/array/chunk.py”, line 73, in <module>
nancumprod = npcompat.nancumprod
AttributeError: ‘module’ object has no attribute ‘nancumprod’

3

Hi,
Yes I do see the ‘command_vis: ERROR (spawn error)’. Do you have a suggestion as to how to fix this?
Matt

4

Not really, for now I just reverted to 2.8.0 which works.
cryosparcm update --version=2.8.0

5

Having the same issue, but “fixed” by rolling back to 2.8.0…

6

Thanks for the suggestion of rolling back CryoSPARC to 2.8.0. For some reason when I try cryosparcm update --version=2.8.0, the program is unable to download the master and worker tar.gz files - both fail to download???

7

Updating to V2.8.3 fixed my problems!

8

Hi @mwilce, @rbehrouzi,

This issue has indeed been fixed in v2.8.3. It turns out it had to do with one of cryoSPARC’s dependencies. Thank you for reporting this so quickly!