Running to the below error when trying to install v2.12.4.
I don’t want to install as root, which this post seems to suggest is a possible solution:
Processing ./deps_bundle/python/python_packages/pip_packages/Flask-JSONRPC-0.3.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/Flask-PyMongo-0.5.1.tar.gz
Processing ./deps_bundle/python/python_packages/pip_packages/libtiff-0.4.2.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-req-build-xttJbL/setup.py", line 77, in <module>
from numpy.distutils.core import setup, Extension
ImportError: No module named numpy.distutils.core
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-req-build-xttJbL/
------------------------------------------------------------------------
Done.
pip packages installation successful.
------------------------------------------------------------------------
Main dependency installation completed. Continuing...
------------------------------------------------------------------------
Completed.
Currently checking hash for mongodb
Dependencies for mongodb have changed - reinstalling...
------------------------------------------------------------------------
mongodb 3.4.10 installation successful.
------------------------------------------------------------------------
Completed.
Completed dependency check.
************ CRYOSPARC MASTER INSTALLATION COMPLETE **************
CryoSPARC System master has now been installed.
Add bin directory to your ~/.bashrc ?
1) Yes
2) No
#? 2
To run cryosparc, be sure to add "/opt/packages/cryosparc_v2/cryosparc2_master/bin" to your path
or add a symlink to "/opt/packages/cryosparc_v2/cryosparc2_master/bin/cryosparcm" to your path.
************ CRYOSPARC SYSTEM: STANDALONE INSTALLER **************
The installer will now download, install and connect the worker
package on this machine. The worker package will allow cryoSPARC
to run compute jobs.
******************************************************************
Starting cryoSPARC...
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: ERROR (spawn error)
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: No module named pymongo
I agree, installing as root is not the ideal option. Can you post your full system specs (OS, CUDA, CPU, RAM, GPUs, etc)? Can you also confirm you tried the force override option?
Tried cryosparcm update --override and got this error:
Successfully installed Flask-JSONRPC-0.3.1 Flask-PyMongo-0.5.1 libtiff-0.4.2
You are using pip version 9.0.1, however version 19.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
------------------------------------------------------------------------
Done.
pip packages installation successful.
------------------------------------------------------------------------
Main dependency installation completed. Continuing...
------------------------------------------------------------------------
Completed.
Currently checking hash for mongodb
Forcing reinstall for dependency mongodb...
------------------------------------------------------------------------
mongodb 3.4.10 installation successful.
------------------------------------------------------------------------
Completed.
Completed dependency check.
===================================================
Successfully updated master from version v2.12.4 to version v2.12.4.
===================================================
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: ERROR (spawn error)
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/opt/packages/cryosparc_v2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 1149, in database_names
"listDatabases")["databases"]]
File "/opt/packages/cryosparc_v2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/database.py", line 491, in command
with client._socket_for_reads(read_preference) as (sock_info, slave_ok):
File "/opt/packages/cryosparc_v2/cryosparc2_master/deps/anaconda/lib/python2.7/contextlib.py", line 17, in __enter__
return self.gen.next()
File "/opt/packages/cryosparc_v2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 859, in _socket_for_reads
with self._get_socket(read_preference) as sock_info:
File "/opt/packages/cryosparc_v2/cryosparc2_master/deps/anaconda/lib/python2.7/contextlib.py", line 17, in __enter__
return self.gen.next()
File "/opt/packages/cryosparc_v2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/mongo_client.py", line 823, in _get_socket
server = self._get_topology().select_server(selector)
File "/opt/packages/cryosparc_v2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 214, in select_server
address))
File "/opt/packages/cryosparc_v2/cryosparc2_master/deps/anaconda/lib/python2.7/site-packages/pymongo/topology.py", line 189, in select_servers
self._error_message(selector))
pymongo.errors.ServerSelectionTimeoutError: localhost:39001: [Errno 111] Connection refused