The cryoSPARC version is v4.1.1
2D classification ends with the following error
log content shows
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
========= sending heartbeat
uid: invalid handle 562949953454080, wrong generation counter (given 1, expected 14) (errno 1: Operation not permitted)
add column: invalid handle 562949953454080, wrong generation counter (given 1, expected 14) (errno 1: Operation not permitted)
**** handle exception rc
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/plotutil.py:1509: 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).
fig = plt.figure(figsize=figsize)
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_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
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_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
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_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
/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/sigproc.py:894: RuntimeWarning: invalid value encountered in true_divide
frc[k, :copylen] = (AB / n.sqrt(AA*BB))[:copylen]Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 93, in cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/class2D/run.py”, line 512, in cryosparc_compute.jobs.class2D.run.run_class_2D
File “/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/geometry.py”, line 1022, in remove_duplicate_particles
keep_psets.append(pset.mask(keep_mask))
File “/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/dataset.py”, line 1265, in mask
return type(self)([(f, self[f][mask]) for f in self])
File “/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_compute/particles.py”, line 61, in init
super().init(allocate, row_class=Particle)
File “/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/dataset.py”, line 638, in init
self.add_fields([entry[0] for entry in populate])
File “/home/cryosparc/EMsoft/cryosparc/cryosparc_worker/cryosparc_tools/cryosparc/dataset.py”, line 931, in add_fields
assert self._data.addcol_scalar(
AssertionError: Could not add (‘uid’, ‘<u8’) with dtype uint64
set status to failed
========= main process now complete.
========= monitor process now complete.