When streaming 2D is restarted after more than 100k particles extracted, only the first 100k are processed (Live, bug?)

Hi,

I restarted a 2D streaming job after more than 100k particles had been extracted (see screenshot), but only the first 100k are used, and after finishing the first 100k, the job goes to “completed” status, rather than adding in the rest of the particles. This seems like a bug?

Cheers
Oli

Hi @olibclarke,

When it starts from scratch, the Streaming 2D Classification job uses at most Number of classes × 1000 particles to compute the 2D classes. For example, with 50 classes you would see 50000 particles in use.

After processing and classifying all these particles the job does not make any updates to the classes until a sufficient number of particles are available. Instead, is simply assigns new particles to a class, including the remaining particles not yet classified.

Hope that helps,

Nick

I understand that - but it went to completed status, not waiting.

Ah I see what you mean; we’ve never seen this in our tests and I can’t tell from the code why this would happen - could you post the last few hundred lines at the end of the Streaming 2D Class job to see if there are be any clues there?

Hi @nfrasser, here is the end of the log of the completed job - it seems to have gone to completed status while it was trying to transfer the additional particles to the ssd?

Oli

Hi @olibclarke, to clarify, this is what you see when you open the 2D Class job log and scroll all the way to the bottom? Do you see something else if you click “Follow Latest”?

This is from follow latest. It is the same - it is the last thing in the log

Gotcha, last thing can you also send me the job log from the command line? Use this command (substituting PXX and JXX for the project ID and job ID, respectively):

cryosparcm joblog PXX JXX

Here you go:

========= sending heartbeat
/home/user/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/matplotlib/axes/_axes.py:6571: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.
  warnings.warn("The 'normed' kwarg is deprecated, and has been "
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
/home/user/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py:522: 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`).
  max_open_warning, RuntimeWarning)
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
cryosparc2_compute/util/logsumexp.py:40: RuntimeWarning: divide by zero encountered in log
  return n.log(wa * n.exp(a - vmax) + wb * n.exp(b - vmax) ) + vmax
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
/home/user/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/matplotlib/axes/_axes.py:6571: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.
  warnings.warn("The 'normed' kwarg is deprecated, and has been "
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
/home/user/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py:522: 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`).
  max_open_warning, RuntimeWarning)
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
"tmp.txt" 200L, 6432C                                                                                                                                               1,1           Top
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
/home/user/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/matplotlib/axes/_axes.py:6571: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.
  warnings.warn("The 'normed' kwarg is deprecated, and has been "
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
/home/user/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py:522: 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`).
  max_open_warning, RuntimeWarning)
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
/home/user/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/matplotlib/axes/_axes.py:6571: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.
  warnings.warn("The 'normed' kwarg is deprecated, and has been "
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
/home/user/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py:522: 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`).
  max_open_warning, RuntimeWarning)
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
                                                                                                                                                                    1,1           Top
========= sending heartbeat
/home/user/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/matplotlib/axes/_axes.py:6571: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg.
  warnings.warn("The 'normed' kwarg is deprecated, and has been "
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
/home/user/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/matplotlib/pyplot.py:522: 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`).
  max_open_warning, RuntimeWarning)
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
cryosparc2_compute/util/logsumexp.py:40: RuntimeWarning: divide by zero encountered in log
  return n.log(wa * n.exp(a - vmax) + wb * n.exp(b - vmax) ) + vmax
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
/home/user/software/cryosparc/cryosparc2_worker/bin/cryosparcw: line 68: 44991 Terminated              python -c "import cryosparc2_compute.run as run; run.run()" "$@"

Perfect thanks, based on this I can share some details about what’s happening under the hood.

It’s common for Live to stop Streaming 2D Classification Jobs and/or mark them as “Completed” at its discretion. This could happen when some of the following conditions are met:

  • The job is idle, waiting on more particles
  • You press “Resume/Restart” or “Stop” button under the “2D Classes” tab in Live
  • You change job parameters
  • You kill the job from the Resources panel in cryoSPARC
  • The operating system kills the job’s process for whatever reason

In the last two cases, Live may collect computed or partially-computed classes and mark the job as “Completed” immediately.

I can’t say the exact reason for what you’re seeing without knowing what the system was doing at the time the job restarted. I also can’t immediately see in our Live implementation why the job would stop in your scenario unless something else changed in the system. We’re currently working on making the reason for these state changes more transparent in Live.

The next time the job is completed unexpectedly, could you please DM me the command_rtp.log file from the cryosparc2_master/run directory?

thanks - based on the last part of the job log, it would seem that it died in the middle of transferring the new set of particles. Perhaps the idle timeout is too short, so if there is a particularly large tranche of particles to transfer, the job dies before it can transfer them all to the SSD?