Troubles after update to 2.13.2

Troubleshooting
1

Hi I just updated to 2.13.2

and now it doesnt quite work anymore. >I only get white pages when connecting to the webapp but also the output of the update didn’t look promising from the start
Update will now be applied to the master installation,
followed by worker installations on other node.

  Deleting old files...
  Extracting...
  Done.
  Updating dependencies...
  Checking dependencies... 
  Dependencies for python have not changed.
  Currently checking hash for mongodb
  Dependencies for mongodb have not changed.
  Completed dependency check. 
 
===================================================
Successfully updated master from version v2.13.0 to version v2.13.2.
===================================================
 
Starting cryoSPARC System master process..
CryoSPARC is not already running.
database: ERROR (spawn error)
command_core: ERROR (spawn error)
  cryosparc command core startup complete.
command_vis: started
command_proxy: ERROR (spawn error)
webapp: started

What could be the issue?

here is the database log:
2020-01-31T11:37:31.129+0100 I CONTROL [initandlisten] MongoDB starting : pid=29236 port=39001 dbpath=/home/david.haselbach/software/cryosparc2/cryosparc2_database 64-bit host=pcl-imp-20.imp.ac.at
2020-01-31T11:37:31.129+0100 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2020-01-31T11:37:31.129+0100 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2020-01-31T11:37:31.129+0100 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2020-01-31T11:37:31.129+0100 I CONTROL [initandlisten] allocator: tcmalloc
2020-01-31T11:37:31.129+0100 I CONTROL [initandlisten] modules: none
2020-01-31T11:37:31.129+0100 I CONTROL [initandlisten] build environment:
2020-01-31T11:37:31.129+0100 I CONTROL [initandlisten] distarch: x86_64
2020-01-31T11:37:31.129+0100 I CONTROL [initandlisten] target_arch: x86_64
2020-01-31T11:37:31.129+0100 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/home/david.haselbach/software/cryosparc2/cryosparc2_database”, journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2020-01-31T11:37:31.149+0100 E NETWORK [initandlisten] listen(): bind() failed Address already in use for socket: 0.0.0.0:39001
2020-01-31T11:37:31.149+0100 E NETWORK [initandlisten] addr already in use
2020-01-31T11:37:31.149+0100 E NETWORK [initandlisten] Failed to set up sockets during startup.
2020-01-31T11:37:31.149+0100 E STORAGE [initandlisten] Failed to set up listener: InternalError: Failed to set up sockets
2020-01-31T11:37:31.149+0100 I NETWORK [initandlisten] shutdown: going to close listening sockets…
2020-01-31T11:37:31.149+0100 I NETWORK [initandlisten] shutdown: going to flush diaglog…
2020-01-31T11:37:31.149+0100 I CONTROL [initandlisten] now exiting
2020-01-31T11:37:31.149+0100 I CONTROL [initandlisten] shutting down with code:48
2020-01-31T11:37:32.195+0100 I CONTROL [initandlisten] MongoDB starting : pid=29239 port=39001 dbpath=/home/david.haselbach/software/cryosparc2/cryosparc2_database 64-bit host=pcl-imp-20.imp.ac.at
2020-01-31T11:37:32.195+0100 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2020-01-31T11:37:32.195+0100 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2020-01-31T11:37:32.195+0100 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2020-01-31T11:37:32.195+0100 I CONTROL [initandlisten] allocator: tcmalloc
2020-01-31T11:37:32.195+0100 I CONTROL [initandlisten] modules: none
2020-01-31T11:37:32.195+0100 I CONTROL [initandlisten] build environment:
2020-01-31T11:37:32.195+0100 I CONTROL [initandlisten] distarch: x86_64
2020-01-31T11:37:32.195+0100 I CONTROL [initandlisten] target_arch: x86_64
2020-01-31T11:37:32.195+0100 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/home/david.haselbach/software/cryosparc2/cryosparc2_database”, journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2020-01-31T11:37:32.231+0100 E NETWORK [initandlisten] listen(): bind() failed Address already in use for socket: 0.0.0.0:39001
2020-01-31T11:37:32.231+0100 E NETWORK [initandlisten] addr already in use
2020-01-31T11:37:32.231+0100 E NETWORK [initandlisten] Failed to set up sockets during startup.
2020-01-31T11:37:32.231+0100 E STORAGE [initandlisten] Failed to set up listener: InternalError: Failed to set up sockets
2020-01-31T11:37:32.231+0100 I NETWORK [initandlisten] shutdown: going to close listening sockets…
2020-01-31T11:37:32.231+0100 I NETWORK [initandlisten] shutdown: going to flush diaglog…
2020-01-31T11:37:32.231+0100 I CONTROL [initandlisten] now exiting
2020-01-31T11:37:32.231+0100 I CONTROL [initandlisten] shutting down with code:48
2020-01-31T11:37:34.711+0100 I CONTROL [initandlisten] MongoDB starting : pid=29269 port=39001 dbpath=/home/david.haselbach/software/cryosparc2/cryosparc2_database 64-bit host=pcl-imp-20.imp.ac.at
2020-01-31T11:37:34.711+0100 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2020-01-31T11:37:34.711+0100 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2020-01-31T11:37:34.711+0100 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2020-01-31T11:37:34.711+0100 I CONTROL [initandlisten] allocator: tcmalloc
2020-01-31T11:37:34.711+0100 I CONTROL [initandlisten] modules: none
2020-01-31T11:37:34.711+0100 I CONTROL [initandlisten] build environment:
2020-01-31T11:37:34.711+0100 I CONTROL [initandlisten] distarch: x86_64
2020-01-31T11:37:34.711+0100 I CONTROL [initandlisten] target_arch: x86_64
2020-01-31T11:37:34.711+0100 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/home/david.haselbach/software/cryosparc2/cryosparc2_database”, journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2020-01-31T11:37:34.732+0100 E NETWORK [initandlisten] listen(): bind() failed Address already in use for socket: 0.0.0.0:39001
2020-01-31T11:37:34.732+0100 E NETWORK [initandlisten] addr already in use
2020-01-31T11:37:34.732+0100 E NETWORK [initandlisten] Failed to set up sockets during startup.
2020-01-31T11:37:34.732+0100 E STORAGE [initandlisten] Failed to set up listener: InternalError: Failed to set up sockets
2020-01-31T11:37:34.732+0100 I NETWORK [initandlisten] shutdown: going to close listening sockets…
2020-01-31T11:37:34.732+0100 I NETWORK [initandlisten] shutdown: going to flush diaglog…
2020-01-31T11:37:34.732+0100 I CONTROL [initandlisten] now exiting
2020-01-31T11:37:34.732+0100 I CONTROL [initandlisten] shutting down with code:48
2020-01-31T11:37:38.555+0100 I CONTROL [initandlisten] MongoDB starting : pid=29446 port=39001 dbpath=/home/david.haselbach/software/cryosparc2/cryosparc2_database 64-bit host=pcl-imp-20.imp.ac.at
2020-01-31T11:37:38.555+0100 I CONTROL [initandlisten] db version v3.4.10-4-g67ee356c6b
2020-01-31T11:37:38.555+0100 I CONTROL [initandlisten] git version: 67ee356c6be377cda547d16423daef5beb4e8377
2020-01-31T11:37:38.555+0100 I CONTROL [initandlisten] OpenSSL version: OpenSSL 1.0.2p 14 Aug 2018
2020-01-31T11:37:38.555+0100 I CONTROL [initandlisten] allocator: tcmalloc
2020-01-31T11:37:38.555+0100 I CONTROL [initandlisten] modules: none
2020-01-31T11:37:38.555+0100 I CONTROL [initandlisten] build environment:
2020-01-31T11:37:38.555+0100 I CONTROL [initandlisten] distarch: x86_64
2020-01-31T11:37:38.555+0100 I CONTROL [initandlisten] target_arch: x86_64
2020-01-31T11:37:38.555+0100 I CONTROL [initandlisten] options: { net: { port: 39001 }, replication: { oplogSizeMB: 64, replSet: “meteor” }, storage: { dbPath: “/home/david.haselbach/software/cryosparc2/cryosparc2_database”, journal: { enabled: false }, wiredTiger: { engineConfig: { cacheSizeGB: 4.0 } } } }
2020-01-31T11:37:38.585+0100 E NETWORK [initandlisten] listen(): bind() failed Address already in use for socket: 0.0.0.0:39001
2020-01-31T11:37:38.585+0100 E NETWORK [initandlisten] addr already in use
2020-01-31T11:37:38.585+0100 E NETWORK [initandlisten] Failed to set up sockets during startup.
2020-01-31T11:37:38.585+0100 E STORAGE [initandlisten] Failed to set up listener: InternalError: Failed to set up sockets
2020-01-31T11:37:38.585+0100 I NETWORK [initandlisten] shutdown: going to close listening sockets…
2020-01-31T11:37:38.585+0100 I NETWORK [initandlisten] shutdown: going to flush diaglog…
2020-01-31T11:37:38.585+0100 I CONTROL [initandlisten] now exiting
2020-01-31T11:37:38.585+0100 I CONTROL [initandlisten] shutting down with code:48

the command_corelog just contains successful export jobs

2

Hi @david.haselbach,

Did you have an orphaned cryoSPARC process running in the background during the update?

cryosparcm stop

ps -ax | grep “supervisord” (kill only the process that is running from your cryosparc2 install)
ps -ax | grep “cryosparc2_command” (kill all the matching processes related to your cryosparc2 instance)
ps -ax | grep “mongod” (kill only the process running your cryosparc2 database)

e.g. kill 82681 

cryosparcm update --override