WiredTiger error while updating

Troubleshooting
1

Hi,

Recently the cryosparc webpage was not displaying and it was showing only the status bar which goes left and right. So Stopped cryosparc and updated to version 2.4.2. Now when I start cryosparc I get

database FATAL Exited too quickly (process log may have details)

error. Im sure no one else has permission to touch the installation director and no others instances were running. I tried to chmod and chown all directories. Also looked if any orphaned supervisord processes etc etc. Also there is no socks file in the /tmp.

I looked in to cryosparcm log database and it pointed to WiredTIger error.

2018-11-26T12:38:28.802+0100 E STORAGE [initandlisten] WiredTiger error (0) [1543232308:802365][29562:0x7f0e3d4f1d40], file:WiredTiger.wt, connection: WiredTiger.turtle: encountered an illegal file format or internal value
2018-11-26T12:38:28.802+0100 E STORAGE [initandlisten] WiredTiger error (-31804) [1543232308:802418][29562:0x7f0e3d4f1d40], file:WiredTiger.wt, connection: the process must exit and restart: WT_PANIC: WiredTiger library panic

It would be great help if the community could help with the following

  1. Is there a way to recover the database ? or is it completely corrupt.

  2. if now way to recover the database is it possible to import them from the Project directories.

  3. In case if I have to start from ( if 1 and 2 is not possible ) , Do I need to completely reinstall or tell the cryosparc to use a new database.

Thanks in advance for your time and help.

best regards
Rajan

2

Hi,

We couldnt fix it, so I tried to install a fresh cryosparc ( after moving the old and made new folder name and started clean). When I do the installation everything is OK but its trying to start, its giving database: ERROR (spawn error).

I checked for any instances of cryosparc running. Also looked in /tmp for sock file. All looked clean ( ps -ef | grep cryosparc was empty).

But when I did cryosparcm log database its complaining that it couldnt lock the file. ERROR is below

Cryosparc/2.45/cryosparc2_database/mongod.lock No locks available. Is a mongod instance already running?

I havd restarted the computer and did a clean fresh installation and the error still persist. Is there any residual sock file somewhere hindering it ?? I am running as a user and checked all possible areas ( /tmp for example).

We are happy to receive any help in this regards.

Thanks

best
Rajan