cryoSPARC update on Cluster

Install, Configure and Update
1

Dear cryoSPARC community,

I was trying to update the cryosparc from v4.3.1 to v4.4.1. But I have the error message shown below. Please advise if you have any suggestions on how to solve this issue. Thanks!

$cryosparcm update --version=v4.4.1

CryoSPARC current version v4.3.1
update starting on Fri Jan 12 12:51:19 PST 2024

=============================
Updating to version v4.4.1.

Removing previous downloads…
Downloading master update…
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:–:-- --:–:-- --:–:-- 0
100 604M 100 604M 0 0 18.1M 0 0:00:33 0:00:33 --:–:-- 16.1M
Downloading worker update…
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:–:-- --:–:-- --:–:-- 0
100 3897M 100 3897M 0 0 21.1M 0 0:03:04 0:03:04 --:–:-- 20.8M
Done.

Update will now be applied to the master installation,
followed by worker installations on other nodes.

CryoSPARC is running.
Stopping cryoSPARC
app: stopped
app_api: stopped
command_core: stopped
command_rtp: stopped
command_vis: stopped
database: stopped
Shut down
Deleting old files…
Extracting…
Done.

===================================================
Installing latest master dependencies.

Checking dependencies…
Dependencies for python have changed - reinstalling…

rm: cannot remove ‘/xxx/xxx/xxx/xxx/cryosparc/4.2.1/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib’: Directory not empty
check_install_deps.sh: 66: ERROR: installing python failed.

2

@Nier-Cryo Is it possible that some old CryoSPARC processes have not been terminated?
Under the Linux account that you used to run
cryosparcm update, please can you run these commands and post their outputs:

whoami
ps -eo user,pid,ppid,start,cmd | grep -e cryosparc_[cm] -e mongo
1 Like
3

If you are running a mounted filesystem, such as NFS, sometimes there’s a file lock that I have never been able to figure out how to get rid of, even with CryoSPARC shutdown. If you can’t find a rogue CryoSPARC process (like I can’t), you can either:

  1. Restart the OS
  2. Rename the folder to “lib_old” or something, and update again.
4

Thanks for your reply!

As our solution, we finaly installed the latest version of cryosparc from downloaded master and worker packages. Everything runs well now. I will try your command next time!

5

Thanks!

I will try your suggestions next time!