Webapp tends to stop working while running heavy 3DVA jobs?

Troubleshooting
1

Hi,

Is it possible that running a heavy 3DVA job (> 30 components, millions of particles (128 pix), up to 4 angstrom) slows down or even stops (temporarily) the webapp? I have experiencing this several times.

Thanks,
Kotaro

2

Hi @kttn,

Thanks for the post. Are you running cryoSPARC in a single workstation configuration, meaning both the master components (web application, database, etc.) are running on the same machine as the jobs? If so, it may be possible that high CPU/memory or network load could cause the web application (and any other process running on the machine) to slow down or become unresponsive.

If you have a utility such as htop installed it can provide more insight into the various processes running on the machine and CPU/memory usage.

- Suhail

3

Hi @sdawood,

Thank you for the comment. We are running in cluster mode. The master node also serves as a worker. All the machines have a plenty of free CPU and RAM while running 3DVA jobs. So it may be a network issue. I’ll look for any bottleneck in out network, and if any, will replace the bottleneck device to see if it changes this situation.

Thanks,
Kotaro

4

Hi @kttn,

We made some changes in cryoSPARC v3.3 that speed up performance of the web application when working in large projects. When you get a chance, try upgrading and let me know if it solves the issue.

Thanks,
Suhail

2 Likes
5

Hi @kttn,

Did you get a chance to upgrade to v3.3? I’m interested to hear whether it helps the issue you were running into with unresponsiveness.

- Suhail

6

Hi @sdawood,

Thank you for the performance updates.

I have already upgraded to v3.3 and also switched our network from 1GbE to 10GbE, but haven’t tested 3DVAs yet.

I’ll soon test heavy 3DVA calculations and let you know the results. (in both 1GbE and 10GbE.)

Thanks,
Kotaro

7

Hi @sdawood,

I started a heavy 3DVA job with > 30 components, millions of particles (128 pix), up to 4 angstrom, and now the webapp is not responding, even with 10GbE network.

As before, the 3DVA process is still running on a worker node, the master node’s CPU and RAM have a plenty of free resources, and cryosparcm status shows no problem…

Kotaro

8

Hi @kttn,

Is it just that cryoSPARC is slow when you’re running this 3DVA job or the entire master node? For example, if you try running some command line programs or filesystem commands (ls) from the master node, do you still experience a delay? Additionally, please reply with the output of the following logs:

cryosparcm log command_core | tail -n 100

cryosparcm log database | tail -n 100

- Suhail