5.0.6: ab-initio reconstruction loop

3D Reconstruction
21

EMail is now also out of the outbox -.-

310GB. I can also share it with “my” service

22

Got it. Thanks.

Perfect. Please let me know the details via email or personal message.

23

Some feedback:

I find that changing the minibatch size helps, probably because the algorithm cannot assign initial particles enough.

Jobs on the older 2080 GPUs are more stable then on the newer 4090 GPUs

24

In our testing, reconstructions based on particles from J13 in the project you shared gave virtually identical, plausible volumes between runs on an rtx4090 and quadro-gp100, respectively.

25

Are you testing with RockyLinux 9 or with another distro?

Thanks

26

The GP100 job ran on ubuntu-26.04 (Note that CryoSPARC v5.0.6 is not currently compatible with the default v7 Linux kernel on ubuntu-26.04).
The RTX4090 job ran on ubuntu-22.04.

27

Any chance to check with RockyLinux 9?

28

I have confirmed the same issue on my PC with at least two datasets.

System Environment:

  • CS Version: 5.0.6
  • OS: Rocky Linux
  • GPU: RTX 4000 Ada x4

Note: The issue is sometimes resolved when stopping other jobs running in parallel.

29

Welcome to the forum @kishi .

Interesting. Please can you post the outputs of these commands

uname -a
cat /sys/kernel/mm/transparent_hugepage/enabled
free -h
30

@wtempel Thank you for reply.

Outputs are below.

uname -a
Linux strbioeng01 5.14.0-687.17.1.el9_8.x86_64 #1 SMP PREEMPT_DYNAMIC Wed Jun 24 13:43:37 UTC 2026 x86_64 x86_64 x86_64 GNU/Linux

cat /sys/kernel/mm/transparent_hugepage/enabled
always madvise [never]

free -h
total used free shared buff/cache available

Mem: 125Gi 21Gi 8.6Gi 3.6Gi 100Gi 104Gi
Swap: 4.0Gi 33Mi 4.0Gi

Best,

31

Thanks @kishi. Did you also observe “blank” volume slices for some classes as @biocit showed in the first post?