App: ERROR (spawn error)

Install, Configure and Update
1

Greetings dear community, I was restarting CryoSPARC and an app error occured:

[yuexin@yxtaiyi ~]$ cryosparcm restart
CryoSPARC is running.
Stopping cryoSPARC
command_core: stopped
command_rtp: stopped
command_vis: stopped
database: stopped
Shut down
Starting cryoSPARC System master process..
CryoSPARC is not already running.
configuring database
    configuration complete
database: started
checkdb success
command_core: started
    command_core connection succeeded
    command_core startup successful
command_vis: started
command_rtp: started
    command_rtp connection succeeded
    command_rtp startup successful
app: ERROR (spawn error)

I checked the status and log app, the output is following down, shows an node error:

[yuexin@yxtaiyi ~]$ cryosparcm status | grep -v LICENSE
----------------------------------------------------------------------------
CryoSPARC System master node installed at
/home/yuexin/cryosparc/cryosparc_master
Current cryoSPARC version: v4.3.1
----------------------------------------------------------------------------

CryoSPARC process status:

app                              FATAL     Exited too quickly (process log may have details)
app_api                          STOPPED   Not started
app_api_dev                      STOPPED   Not started
app_legacy                       STOPPED   Not started
app_legacy_dev                   STOPPED   Not started
command_core                     RUNNING   pid 138047, uptime 0:03:12
command_rtp                      RUNNING   pid 138660, uptime 0:03:03
command_vis                      RUNNING   pid 138545, uptime 0:03:04
database                         RUNNING   pid 137694, uptime 0:03:16

----------------------------------------------------------------------------
License is valid
----------------------------------------------------------------------------

global config variables:
export CRYOSPARC_MASTER_HOSTNAME="localhost"
export CRYOSPARC_DB_PATH="/home/yuexin/cryosparc/cryosparc_database"
export CRYOSPARC_BASE_PORT=39000
export CRYOSPARC_DEVELOP=false
export CRYOSPARC_INSECURE=false
export CRYOSPARC_CLICK_WRAP=true
export CRYOSPARC_HEARTBEAT_SECONDS=600

[HPM] Client disconnected
[HPM] Client disconnected
node: error while loading shared libraries: libnode.so.93: cannot open shared object file: No such file or directory
node: error while loading shared libraries: libnode.so.93: cannot open shared object file: No such file or directory
node: error while loading shared libraries: libnode.so.93: cannot open shared object file: No such file or directory

How should I deal with this? Many thanks!

2

I tried to find **libnode.so.93** in our workstation, and it seems cryosparc did have this file:

[root@yxtaiyi yuexin]# sudo find / -type f -name "libnode.so.93"
find: ‘/run/user/1004/doc’: Permission denied
find: ‘/run/user/1004/gvfs’: Permission denied
find: ‘/run/user/1002/doc’: Permission denied
find: ‘/run/user/1002/gvfs’: Permission denied
find: ‘/run/user/1000/doc’: Permission denied
find: ‘/run/user/1000/gvfs’: Permission denied
/home/yuexin/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/libnode.so.93
/gpu_temp/backup_for_SSD/yuexin/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/libnode.so.93

But when i perform

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/yuexin/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib

The error stays the same.

The TCP port seems not all available

[yuexin@yxtaiyi lib]$ netstat -tuplen | grep :3900
(No info could be read for "-p": geteuid()=1000 but you should be root.)
tcp        0      0 0.0.0.0:39001           0.0.0.0:*               LISTEN      1000       2633300805 -
tcp        0      0 0.0.0.0:39002           0.0.0.0:*               LISTEN      1000       2627579628 -
tcp        0      0 0.0.0.0:39003           0.0.0.0:*               LISTEN      1000       2632665881 -
tcp        0      0 0.0.0.0:39005           0.0.0.0:*               LISTEN      1000       2633160510 -

Getting confused

3

I performed this

sudo sh -c 'echo "/home/yuexin/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib" >> /etc/ld.so.conf.d/cryosparc_libnode_so_93.conf'
sudo ldconfig
export LD_LIBRARY_PATH=/home/yuexin/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib:$LD_LIBRARY_PATH

and it seems work well

[yuexin@yxtaiyi ld.so.conf.d]$ cryosparcm restart
CryoSPARC is running.
Stopping cryoSPARC
command_core: stopped
command_rtp: stopped
command_vis: stopped
database: stopped
Shut down
Starting cryoSPARC System master process..
CryoSPARC is not already running.
configuring database
    configuration complete
database: started
checkdb success
command_core: started
    command_core connection succeeded
    command_core startup successful
command_vis: started
command_rtp: started
    command_rtp connection succeeded
    command_rtp startup successful
app: started
app_api: started
-----------------------------------------------------

CryoSPARC master started.
 From this machine, access cryoSPARC and cryoSPARC Live at
    http://localhost:39000

 From other machines on the network, access cryoSPARC and cryoSPARC Live at
    http://localhost:39000


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and refresh until you see the cryoSPARC web interface.