Problem installing version 2.8

Troubleshooting
1

Hi
I installed the new version of cryosparc as a fresh installation. It seemed to go fine but when I tried to run programs I got this series of error messages.

john@Var2CSA:~$ cryosparcm start
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
john@Var2CSA:~$ cryosparcm status

CryoSPARC System master node installed at
/srv/home/john/software/cryosparc/cryosparc2_master
Current cryoSPARC version: v2.8.0

cryosparcm process status:

command_core STOPPED Not started
command_proxy STOPPED Not started
command_vis STOPPED Not started
database RUNNING pid 84808, uptime 0:00:20
watchdog_dev STOPPED Not started
webapp STOPPED Not started
webapp_dev STOPPED Not started

global config variables:

export CRYOSPARC_LICENSE_ID=""
export CRYOSPARC_MASTER_HOSTNAME=“Var2CSA”
export CRYOSPARC_DB_PATH="/srv/home/john/software/cryosparc/cryosparc2_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false

john@Var2CSA:~$ cryosparcm lohd
Unknown command lohd
john@Var2CSA:~$ cryosparcm lohs
Unknown command lohs
john@Var2CSA:~$ cryosparcm logs
Unknown command logs
john@Var2CSA:~$ cryosparcm log
tail: cannot open ‘run/.log’ for reading: No such file or directory
tail: no files remaining
john@Var2CSA:~$ cryosparcm help
cryosparcm help

cryosparcm start
  finds open ports
  sets environment vars for supervisord
  launches all processes via supervisord

cryosparcm stop
  shut down all child processes
  shut down supervisord

cryosparcm env
  call as 'eval $(cryosparcm env)'
  prints export statements for all CRYOSPARC_* environment variables

cryosparcm status [--json]
  gives json or plain text including
      current version
      current master running or not
      current port numbers if running
      current root dir

cryosparcm url [--command|--mongodb]
   gives url of where webapp is currently running (or webapp or command)

cryosparcm backup
   Backup cryoSPARC database to a specified file.
        Options:
              --dir=<path>         path to output directory
                                   (run/db_backups/ by default)
              --file=<name>        name of output file
                                   (current datetime by default)

john@Var2CSA:~$ cryosparcm url
Unknown command url
john@Var2CSA:~$ cryosparcm status

CryoSPARC System master node installed at
/srv/home/john/software/cryosparc/cryosparc2_master
Current cryoSPARC version: v2.8.0

cryosparcm process status:

command_core STOPPED Not started
command_proxy STOPPED Not started
command_vis STOPPED Not started
database RUNNING pid 84808, uptime 0:03:20
watchdog_dev STOPPED Not started
webapp STOPPED Not started
webapp_dev STOPPED Not started

global config variables:

export CRYOSPARC_LICENSE_ID=“6ab47de4-86da-11e9-a57b-53c3bf3942c3”
export CRYOSPARC_MASTER_HOSTNAME=“Var2CSA”
export CRYOSPARC_DB_PATH="/srv/home/john/software/cryosparc/cryosparc2_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false

john@Var2CSA:~$ cryosparc env
cryosparc: command not found
john@Var2CSA:~$ cryosparcm env
export “CRYOSPARC_INSECURE=false”
export “CRYOSPARC_LICENSE_ID=6ab47de4-86da-11e9-a57b-53c3bf3942c3”
export “CRYOSPARC_LD_LIBRARY_PATH=”
export “CRYOSPARC_MONGO_PORT=39001”
export “CRYOSPARC_MONGO_CACHE_GB=4”
export “CRYOSPARC_ROOT_DIR=/srv/home/john/software/cryosparc/cryosparc2_master”
export “CRYOSPARC_PATH=/srv/home/john/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin”
export “CRYOSPARC_DEVELOP=false”
export “CRYOSPARC_BASE_PORT=39000”
export “CRYOSPARC_HTTP_PORT=39000”
export “CRYOSPARC_COMMAND_VIS_PORT=39003”
export “CRYOSPARC_DB_PATH=/srv/home/john/software/cryosparc/cryosparc2_database”
export “CRYOSPARC_COMMAND_PROXY_PORT=39004”
export “CRYOSPARC_HEARTBEAT_SECONDS=60”
export “CRYOSPARC_COMMAND_CORE_PORT=39002”
export “CRYOSPARC_MASTER_HOSTNAME=Var2CSA”
export “CRYOSPARC_SUPERVISOR_SOCK_FILE=/tmp/cryosparc-supervisor-f9df7413016646d1ee273b01b13821c4.sock”
export “PATH=/srv/home/john/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/cryosparc2/cryosparc2_master/bin:/srv/home/john/cryosparc2/cryosparc2_master/deps/external/mongodb/bin:/srv/home/john/cryosparc2/cryosparc2_master/deps/anaconda/bin:/srv/home/john/cryosparc2/cryosparc2_master/bin:/srv/home/john/cryosparc2/cryosparc2_master/deps/anaconda/bin:/srv/home/john/cryosparc2/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/external/mongodb/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/srv/home/john/software/cryosparc/cryosparc2_master/deps/anaconda/bin:/srv/home/john/software/cryosparc/cryosparc2_master/bin:/usr/local/scipion:/srv/home/john/cryosparc/bin:/srv/home/john/bin:/srv/home/john/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/Situs_2.8/bin/:/usr/local/bin/EMAN2/bin:/usr/local/bin/EMAN2/lib:/usr/local/bin/cistem-1.0.0-beta:/usr/local/Situs_2.8/bin/:/usr/local/bin/EMAN2/bin:/usr/local/bin/EMAN2/lib:/usr/local/bin/cistem-1.0.0-beta”
export “LD_LIBRARY_PATH=:”
export “LD_PRELOAD=/srv/home/john/software/cryosparc/cryosparc2_master/deps/anaconda/lib/libpython2.7.so.1.0”
export “PYTHONPATH=”
export “PYTHONNOUSERSITE=true”

2

Hi
I have since cleaned up the bashrc file removing the excess instances of cryosparc thereby cleaning the $PATH variable. I then re-installed a standalone work station. I could then initiate cryosparcm and started a project and workspace to use the test data. So far so good, however, when trying to read in the movie files they would queue but not run. At this point I looked at the computational resources and there were none. On the queue request there were no lanes designated or any to be checked (this may be because its a standalone workstation?? I then tried to find out how many GPUs were available using bin/cryosparcw gpulist in cryosparc2_worker directory and it did not find a config.sh file, although there is one in the master (again is this to do with this being a standalone workstation). I tried to use cryosparcw connect to force and update but again this did not work (again it may be due to the standalone workstation issue) but at this point its not clear what direction to go. Any thoughts?

3

Hi @jflanagan01,

It seems like your installation didn’t work properly. Do you happen to be using CentOS? If so, please take a look at this thread: Can't start after update to 2.8