Issue with ports since v5?

Install, Configure and Update
1

Other lab members who I work with have been using ports within the “ephemeral range” in CyroSPARC v4 (all in the 39000 range). When I installed v5.0, I cannot create a port in the ephemeral range: 32768-60999. I tried installing with base ports at various base ports outside of this range (e.g. 31000 and 61000), but I am encountering issues with even starting CryoSPARC. This is an example output of what happens:

cryosparcm changeport 32650

⚠ Unable to access `ip_unprivileged_port_start`. Continuing without `ip_unprivileged_port_start` check.

Requested change base CryoSPARC port from 64080 to 32650. This will perform the following actions:

  1. Stop cryoSPARC

  2. Set the CRYOSPARC_BASE_PORT variable in config.sh to the new port

  3. Reconfigure the database to use the new port

  4. Start cryoSPARC

Please ensure you have a recent database backup before proceeding

Change base port? [y/N]: y

Continuing.

Stopping CryoSPARC ...

database: stopped

Shut down

Wrote changes to config.sh

Starting CryoSPARC database... 

database: started

Warning: Could not get database status (attempt 1/3)

It appears that CryoSPARC gets stuck at trying to start the database.

Could I please get some help on this issue? Thank you!

2

@MetabolicNerd Please can you

  1. run these commands
    head -n 1 /proc/1/cmdline
uname -a
cryosparcm log database | grep -A 11 "MongoDB starting" | tail -n 30
cryosparcm log database | tail -n 30
    (and post their outputs)
  2. perform the multi-step CryoSPARC shutdown procedure
  3. retry the command
    cryosparcm changeport 32650
3

Hi @wtempel appreciate the help a lot. I think I localized this to an issue with our HPC cluster’s installation packages. For now, I temporarily downgraded to v4.7. But I will update this post when I have a working issue or if I figure out more precisely what went wrong. I think it’s because our node is using glibc 2.17 (CentOS 7–era), but CryoSPARC v5.0 might be using a newer version? Thanks.

4

Correct. CryoSPARC v5 requires a newer version of glibc.

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