Error updating to v3.1

Install, Configure and Update
1

Hi,

While attempting to update to v3.1, I got the following error:

Update will now be applied to the master installation,
followed by worker installations on other nodes.

Deleting old files…
rm: cannot remove ‘cryosparc_app/nodejs/bin’: Directory not empty
rm: cannot remove ‘cryosparc_app/bundle/programs/server/node_modules/fibers/bin/linux-x64-83-glibc’: Directory not empty
rm: cannot remove ‘cryosparc_app/bundle/programs/server/npm/node_modules/bcrypt/lib/binding/napi-v3’: Directory not empty
rm: cannot remove ‘cryosparc_command/command_core’: Directory not empty
rm: cannot remove ‘cryosparc_liveapp/nodejs/bin’: Directory not empty
rm: cannot remove ‘cryosparc_liveapp/bundle/programs/server/npm/node_modules/bcrypt/lib/binding’: Directory not empty
rm: cannot remove ‘cryosparc_liveapp/bundle/programs/server/node_modules/fibers/bin/linux-x64-57-glibc’: Directory not empty
rm: cannot remove ‘cryosparc_webapp/bundle/programs/server/node_modules/fibers/bin/linux-x64-57’: Directory not empty
rm: cannot remove ‘cryosparc_webapp/bundle/programs/server/npm/node_modules/bcrypt/lib/binding’: Directory not empty
rm: cannot remove ‘cryosparc_webapp/nodejs/bin’: Directory not empty

After trying to restart the instance, I get a database spawn error which cannot be resolved by removing supervisord and mongodb files from /tmp and killing all residual orphan cryosparc processes.

Starting cryoSPARC System master process…
CryoSPARC is not already running.
database: started
command_core: ERROR (spawn error)

Attempting to go back to v3.0.0 suggests that it is already up to date. If I try to downgrade to v2.15.0 I get the following error:

Preparing to install all pip packages…

DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won’t be maintained after that date. A future version of pip will drop support for Python 2.7.
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 “”, line 1, in
File “/tmp/pip-req-build-Ap3cnf/setup.py”, line 77, in
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-Ap3cnf/

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.
Could not find conda environment: cryosparc_master_env
You can list all discoverable environments with conda info --envs.

Warning: Could not activate conda environment; this indicates that a cryoSPARC installation is either incomplete or in progress

===================================================
Successfully updated master to version v2.15.0.

Starting cryoSPARC System master process…
CryoSPARC is not already running.
database: started
Traceback (most recent call last):
File “”, line 1, in
ImportError: No module named pymongo

Any help would be greatly appreciated.

Best wishes,
Andrija

2

Further to my previous message, attempting to update to v3.1 now results in:

CryoSPARC current version v2.15.0
update starting on Fri 29 Jan 14:48:37 GMT 2021

No version specified - updating to latest version.

curl: error while loading shared libraries: libssl.so.1.1: cannot open shared object file: No such file or directory

3

Hi @asente,

It looks like your initial error (Directory not empty) was caused by orphaned cryoSPARC processes running in the background while it was trying to update itself. Please do the following:

  1. Log out of your shell, then log in again (to clear any environment variables set by cryoSPARC)
  2. Then, stop cryoSPARC (cryosparcm stop)
  3. Then, kill any orphaned cryoSPARC processes
    ps -ax | grep “supervisord” (kill only the process that is running from your cryosparc2 install)
ps -ax | grep “cryosparc” (kill all the matching processes related to your cryosparc instance)
ps -ax | grep “mongod” (kill only the process running your cryosparc2 database)

e.g. kill 82681
  4. Update to cryoSPARC v3.1: cryosparcm update
4

Hi @stephan,

Thank you for your reply. I can’t find any orpahed processed running. When I try to update with cryosparcm update I get the following error:

CryoSPARC current version v2.15.0
update starting on Mon 1 Feb 10:16:36 GMT 2021

No version specified - updating to latest version.

curl: error while loading shared libraries: libssl.so.1.1: cannot open shared object file: No such file or directory

Many thanks for your help.

5

Hi @asente,

I think at this point it’s best to re-install the cryoSPARC application. Please note doing this will NOT remove any of your data, but making a backup of your database is imperative.

  1. Make sure cryoSPARC is turned off, and there are no zombie processes.
  2. Backup your database: To find the location of your database, run the command:
    cryosparcm status
    You’ll see an environment variable called CRYOSPARC_DB_PATH that points to the location of your database folder. Make a copy of this folder to a different location (and compress it if you’d like to save a little bit of space e.g. tar -czf <path_to_database>)
  3. Delete the folders cryosparc2_master and cryosparc2_worker (rm -rf cryosparc2_master cryosparc2_worker)
  4. Re-install cryoSPARC by following the guide, but specify the existing path to the database (CRYOSPARC_DB_PATH) to the --dbpath argument when running the ./install.sh command. For example:
    ./install.sh  --license $LICENSE_ID \
              --hostname cryoem.cryosparcserver.edu \
              --dbpath /u/cryosparcuser/cryosparc/cryosparc_database \
              --port 45000

Sorry for the inconvenience- hopefully you can get up and running on the latest version of cryoSPARC quickly!

1 Like
6

Dear @stephan,
Thanks a bunch for your help. Everything is working well after reinstalling.
My best,
Andrija

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