Crush out the application 3-5 min after start the app

Install, Configure and Update
1

I am a new CryoSPARC user. I recently installed CryoSPARC v5.0.6 on our institutional HPC cluster and was able to start it successfully by connecting from my local machine. However, about 3–5 minutes after launching the application, I could no longer connect from my local machine.

I checked the CryoSPARC status and found that it was no longer running, suggesting that it had crashed. When I examined the log files, I found the following messages (see below). Could this be an issue with the HPC environment, or is it more likely due to a problem with my CryoSPARC installation. I have also attached the log from a successful startup for comparison. Thank you very much for your help.

“2026-07-23 08:59:20,703 WARN received SIGTERM indicating exit request

2026-07-23 08:59:38,174 INFO Creating socket tcp://0.0.0.0:64002

2026-07-23 08:59:38,175 INFO Closing socket tcp://0.0.0.0:64002

2026-07-23 08:59:38,182 INFO RPC interface ‘supervisor’ initialized

2026-07-23 08:59:38,184 INFO daemonizing the supervisord process

2026-07-23 08:59:38,185 INFO supervisord started with pid 2050954

2026-07-23 08:59:43,485 INFO spawned: ‘database’ with pid 2051194

2026-07-23 08:59:44,540 INFO success: database entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)

2026-07-23 08:59:45,268 INFO spawned: ‘cache’ with pid 2051311

2026-07-23 08:59:46,349 INFO success: cache entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)

2026-07-23 08:59:51,239 INFO Creating socket tcp://0.0.0.0:64002“.

$RUNNING_PATH/cryosparcm status

CryoSPARC System master node installed at

/gpfs/data/XX/cryosparc/cryosparc_master

Current CryoSPARC version: v5.0.6

CryoSPARC process status:

api:0 RUNNING pid 2051542, uptime 0:01:28

api:1 RUNNING pid 2051543, uptime 0:01:28

api:2 RUNNING pid 2051544, uptime 0:01:28

app RUNNING pid 2052845, uptime 0:01:06

app_api RUNNING pid 2052940, uptime 0:01:05

cache RUNNING pid 2051311, uptime 0:01:34

command_vis RUNNING pid 2052784, uptime 0:01:09

database RUNNING pid 2051194, uptime 0:01:36

scheduler RUNNING pid 2052727, uptime 0:01:10

──

✓ License is valid

───

global config variables:

export CRYOSPARC_LICENSE_ID=“[redacted]”

export CRYOSPARC_MASTER_HOSTNAME=“XXXX-ln3.cm.cluster”

export CRYOSPARC_DB_PATH=“/gpfs/data/XXXX/cryosparc/cryosparc_database”

export CRYOSPARC_BASE_PORT=64000

export CRYOSPARC_INSECURE=false

export CRYOSPARC_DB_ENABLE_AUTH=true

export CRYOSPARC_CLICK_WRAP=true

2

Welcome to the forum @sk94 .

  1. Is XXXX-ln3.cm.cluster the headnode or a compute node of the cluster?
  2. Do you run CryoSPARC services and cryosparcm inside a shell that is managed by a cluster workload manager, like slurm?
  3. Have you asked your institutional HPC support team for advice about running CryoSPARC on that specific HPC cluster? You may point them to the CryoSPARC guide and encourage them to ask questions on this forum.

Gentle reminder: Please do not post confidential information such as your CryoSPARC license ID (now redacted).

3

After asking here, I solved this problem. As you asked, XXXX-ln3.cm.cluster is a login node. I needed to move into another node to run CryoSPARC continuously. Now, I am running cryosparcm using slurm. Thank you so much your comment.

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