HPC: CryoSPARC ports in use by other CryoSPARC users

1

I am the “system admin” for CryoSPARC on our HPC where we have RedHat 8.4 and SLURM. CryoSPARC version is 4.6.

Each CryoSPARC user has their own copy. Recently, we have been facing an issue where say when one user B starts CryoSPARC, their database connects to another user’s (A) command core.

Example:

# lsof -i :39222
COMMAND     PID     USER   FD   TYPE     DEVICE SIZE/OFF NODE NAME
mongod  1801784 user_B  122u  IPv4 4191339709      0t0  TCP localhost:39231->localhost:39222 (ESTABLISHED)
python  1802027 user_B   13u  IPv4 4191103296      0t0  TCP localhost:39222->localhost:39231 (ESTABLISHED)

where: 39220-39229 are left for user A’s CryoSPARC, where 39220 is the base port, and 39230-39239 are left for user B’s CryoSPARC, where 39230 is the base port.

Is there a way to fix this? Since CryoSPARC is accessing the other user’s ports, I am not sure what we can do from the system end. We have reserved certain ports for CryoSPARC, so non-CryoSPARC users’ processes do not access these ports.

Thanks!

2

@himi If the python process is shown in the lsof output is still running, please can you post the output of the command

ps -o user:12,pid,ppid,command -p 1801784,1802027

Also, what is the ephemeral port range on that computer:

cat /proc/sys/net/ipv4/ip_local_port_range

?