Database error after v4.1.0 update

Install, Configure and Update
17

If CryoSPARC failed to start with a pymongo error after an update to CryoSPARC v4.1.0 or v4.1.1, you may try the following:

  1. ensure that cryosparc_master software is at either v4.1.0 or v4.1.1
  2. download cryosparc_master_patch.tar.gz
  3. confirm file integrity. Output of
    md5sum cryosparc_master_patch.tar.gz
    should match: 8df9953103829632756b809f3c637d2f
  4. cryosparcm stop
  5. confirm no more CryoSPARC processes:
    ps xww | grep -e cryosparc -e mongod
  6. kill, but not kill -9, any CryoSPARC-related processes that may still exist
  7. # substitute correct paths
mv cryosparc_master_patch.tar.gz /path/to/cryosparc_master
cd /path/to/cryosparc_master
tar -xzf cryosparc_master_patch.tar.gz --overwrite --strip-components=1 --directory ./
  8. if cryosparcm start
    still fails, please post error messages on the forum. Otherwise:
  9. update worker(s)
    # substitute correct paths
cp /path/to/cryosparc_master/cryosparc_worker.tar.gz /path/to/cryosparc_worker/
cd /path/to/cryosparc_worker/
./bin/cryosparcw update