Patch Motion fails

Motion Correction
1

Hi,
I am new to this forum and also new to CryoEM in general.
I am an experiencened X-Ray crystallographyer and normally manage our IT for that software suits. However, as one of our PhD students is trying some CryoEM now, I am also responsible for CryoSparc.
I set up CryoSparc on our AlphaFold computer, in a Master / Cluster configuration, because I hope that we can acquire more hardware soon. Currently, we have the following setup: NVIDIA® GeForce RTX™ 3090 24GB / Intel® Core™ i9 11900KF / 64GB RAM 3466Mhz / 4TB SSD.
We are running Nvidia 510.54 with Cuda 11.6 (because of AlphaFold) and are queuing all the GPU jobs (AF & CryoSparc) via Slurm. We are running the latest patch 220315.
The Tutorial dataset worked beautifully, however, the first real dataset make trouble. We collected over 15TB of data at the ESRF and regardless how we try to run the patch motion job, these jobs very often fail.

I find a couple of errors in the JobLogs, but cannot really interpret them. Maybe, someone can help?
I’ll often find a couple of these:

LZWDecode: Wrong length of decoded string: data probably corrupted at scanline 1023.
I guess this means, some images are broken?

Although these do occur often:

HOST ALLOCATION FUNCTION: using cudrv.pagelocked_empty
exception in cufft.Plan.del:
I don’t think my memory is running out Htop/ GPUstat and glances, all seem relatively fine.

Finally it breaks like this:

/home/cryosparcuser/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/multiprocessing/process.py:99: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (matplotlib.pyplot.figure) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam figure.max_open_warning).
self._target(*self._args, **self._kwargs)
Traceback (most recent call last):
File “/home/cryosparcuser/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/multiprocessing/queues.py”, line 242, in _feed
send_bytes(obj)
File “/home/cryosparcuser/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/multiprocessing/connection.py”, line 200, in send_bytes
self._send_bytes(m[offset:offset + size])
File “/home/cryosparcuser/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/multiprocessing/connection.py”, line 404, in _send_bytes
self._send(header + buf)
File “/home/cryosparcuser/cryosparc_worker/deps/anaconda/envs/cryosparc_worker_env/lib/python3.7/multiprocessing/connection.py”, line 368, in _send
n = write(self._handle, buf)
BrokenPipeError: [Errno 32] Broken pipe

Any hints?

Best & thanks
Jan

2

Hi,

after more tries - I have the feeling that the “LZWDecode: Wrong length of decoded string: data probably corrupted at scanline” might be the serious problem.
How does CryoSparc handles corrupted files? Is there a way to exclude them during data import?

Best
Jan

3

Hi,

okay after checking all files with “tiffinfo -D” I identified ~ 25/400 images, having an decompression artefact (nearly every 14th image). I guess this is a problem during data collection or data transfer.
Still would be great if CryoSparc could ignore these images (based on a setting?) so that we do not have to manually sort theses images out. (I have thousands more images, I now have to scan through…)
After getting rid of these 25 images, patch motion correction went though smoothly…

Best
Jan

4

@gebauer Gracefully skipping over these images is the expected behavior in cryoSPARC. We are interested in reproducing the behavior you observed and will reach out to you in a direct message.

5

This issue has been addressed in a software patch.

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