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Type:
Task
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Status: Done (View Workflow)
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Priority:
Normal
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Component/s: None
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Labels:None
Reducing data set of GA targets with m-band, flux calibration fails in the middle with the error message below:
INFO 2023-01-16T16:39:45.573-1000 fitPfsFluxReference ({'visit': 83219, 'dateObs': '2022-11-21'})(fitPfsFluxReference.py:290)- Fitting models to spectra (takes some time)...
INFO 2023-01-16T17:18:37.548-1000 fitPfsFluxReference ({'visit': 83219, 'dateObs': '2022-11-21'})(fitPfsFluxReference.py:322)- Making reference spectra by interpolation
WARN 2023-01-16T17:19:56.388-1000 astropy ({'visit': 83219, 'dateObs': '2022-11-21'})(logger.py:211)- VerifyWarning: Keyword name 'MP_ABSENT_FIBER' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created.
WARN 2023-01-16T17:19:56.390-1000 astropy ({'visit': 83219, 'dateObs': '2022-11-21'})(logger.py:211)- VerifyWarning: Keyword name 'MP_BAD_FIBER' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created.
WARN 2023-01-16T17:19:56.390-1000 astropy ({'visit': 83219, 'dateObs': '2022-11-21'})(logger.py:211)- VerifyWarning: Keyword name 'MP_DEFICIENT_BBFLUXES' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created.
WARN 2023-01-16T17:19:56.391-1000 astropy ({'visit': 83219, 'dateObs': '2022-11-21'})(logger.py:211)- VerifyWarning: Keyword name 'MP_FITBBSED_FAILED' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created.
WARN 2023-01-16T17:19:56.392-1000 astropy ({'visit': 83219, 'dateObs': '2022-11-21'})(logger.py:211)- VerifyWarning: Keyword name 'MP_ESTIMATERADIALVELOCITY_FAILED' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created.
WARN 2023-01-16T17:19:56.393-1000 astropy ({'visit': 83219, 'dateObs': '2022-11-21'})(logger.py:211)- VerifyWarning: Keyword name 'MP_FITMODELS_FAILED' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created.
WARN 2023-01-16T17:19:56.394-1000 astropy ({'visit': 83219, 'dateObs': '2022-11-21'})(logger.py:211)- VerifyWarning: Keyword name 'MP_MAKEREFERENCESPECTRA_FAILED' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created.
/work/stack_INFRA-312/stack/miniconda3-py38_4.9.2-3.0.0/Linux64/drp_stella/w.2023.02/python/pfs/drp/stella/fitReference.py:81: IntegrationWarning: The maximum number of subdivisions (100) has been achieved.
If increasing the limit yields no improvement it is advised to analyze
the integrand in order to determine the difficulties. If the position of a
local difficulty can be determined (singularity, discontinuity) one will
probably gain from splitting up the interval and calling the integrator
on the subranges. Perhaps a special-purpose integrator should be used.
return scipy.integrate.quad(function, self.wavelength[0], self.wavelength[-1],
/work/stack_INFRA-312/stack/miniconda3-py38_4.9.2-3.0.0/Linux64/drp_stella/w.2023.02/python/pfs/drp/stella/fitReference.py:81: IntegrationWarning: The maximum number of subdivisions (100) has been achieved.
If increasing the limit yields no improvement it is advised to analyze
the integrand in order to determine the difficulties. If the position of a
local difficulty can be determined (singularity, discontinuity) one will
probably gain from splitting up the interval and calling the integrator
on the subranges. Perhaps a special-purpose integrator should be used.
return scipy.integrate.quad(function, self.wavelength[0], self.wavelength[-1],
WARNING: VerifyWarning: Keyword name 'MP_ABSENT_FIBER' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created. [astropy.io.fits.card]
WARNING: VerifyWarning: Keyword name 'MP_BAD_FIBER' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created. [astropy.io.fits.card]
WARNING: VerifyWarning: Keyword name 'MP_DEFICIENT_BBFLUXES' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created. [astropy.io.fits.card]
WARNING: VerifyWarning: Keyword name 'MP_FITBBSED_FAILED' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created. [astropy.io.fits.card]
WARNING: VerifyWarning: Keyword name 'MP_ESTIMATERADIALVELOCITY_FAILED' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created. [astropy.io.fits.card]
WARNING: VerifyWarning: Keyword name 'MP_FITMODELS_FAILED' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created. [astropy.io.fits.card]
WARNING: VerifyWarning: Keyword name 'MP_MAKEREFERENCESPECTRA_FAILED' is greater than 8 characters or contains characters not allowed by the FITS standard; a HIERARCH card will be created. [astropy.io.fits.card]
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/work/stack_INFRA-312/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-3.0.0/lib/python3.8/site-packages/scipy/optimize/_minpack_py.py", line 809, in curve_fit
transform = cholesky(sigma, lower=True)
File "/work/stack_INFRA-312/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-3.0.0/lib/python3.8/site-packages/scipy/linalg/_decomp_cholesky.py", line 88, in cholesky
c, lower = _cholesky(a, lower=lower, overwrite_a=overwrite_a, clean=True,
File "/work/stack_INFRA-312/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-3.0.0/lib/python3.8/site-packages/scipy/linalg/_decomp_cholesky.py", line 37, in _cholesky
raise LinAlgError("%d-th leading minor of the array is not positive "
numpy.linalg.LinAlgError: 16-th leading minor of the array is not positive definiteThe above exception was the direct cause of the following exception:Traceback (most recent call last):
File "/work/stack_INFRA-312/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-3.0.0/lib/python3.8/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/work/stack_INFRA-312/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-3.0.0/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/work/stack_INFRA-312/stack/miniconda3-py38_4.9.2-3.0.0/Linux64/pipe_base/g590c34a36e+5da9528084/python/lsst/pipe/base/cmdLineTask.py", line 433, in __call__
result = self.runTask(task, dataRef, kwargs)
File "/work/stack_INFRA-312/stack/miniconda3-py38_4.9.2-3.0.0/Linux64/pipe_base/g590c34a36e+5da9528084/python/lsst/pipe/base/cmdLineTask.py", line 504, in runTask
return task.runDataRef(dataRef, **kwargs)
File "/work/stack_INFRA-312/stack/miniconda3-py38_4.9.2-3.0.0/Linux64/drp_stella/w.2023.02/python/pfs/drp/stella/fitPfsFluxReference.py", line 174, in runDataRef
reference = self.run(pfsConfig, merged, mergedLsf)
File "/work/stack_INFRA-312/stack/miniconda3-py38_4.9.2-3.0.0/Linux64/drp_stella/w.2023.02/python/pfs/drp/stella/fitPfsFluxReference.py", line 275, in run
radialVelocities = self.getRadialVelocities(pfsConfig, pfsMerged, pfsMergedLsf, bbPdfs)
File "/work/stack_INFRA-312/stack/miniconda3-py38_4.9.2-3.0.0/Linux64/drp_stella/w.2023.02/python/pfs/drp/stella/fitPfsFluxReference.py", line 423, in getRadialVelocities
radialVelocities.append(self.estimateRadialVelocity.run(spectrum, modelSpectrum))
File "/work/stack_INFRA-312/stack/miniconda3-py38_4.9.2-3.0.0/Linux64/drp_stella/w.2023.02/python/pfs/drp/stella/estimateRadialVelocity.py", line 166, in run
pfit, pcov = scipy.optimize.curve_fit(
File "/work/stack_INFRA-312/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-3.0.0/lib/python3.8/site-packages/scipy/optimize/_minpack_py.py", line 811, in curve_fit
raise ValueError("`sigma` must be positive definite.") from e
ValueError: `sigma` must be positive definite.
"""The above exception was the direct cause of the following exception:Traceback (most recent call last):
File "/work/stack_INFRA-312/stack/miniconda3-py38_4.9.2-3.0.0/Linux64/drp_stella/w.2023.02/bin/fitPfsFluxReference.py", line 3, in <module>
FitPfsFluxReferenceTask.parseAndRun()
File "/work/stack_INFRA-312/stack/miniconda3-py38_4.9.2-3.0.0/Linux64/pipe_base/g590c34a36e+5da9528084/python/lsst/pipe/base/cmdLineTask.py", line 688, in parseAndRun
resultList = taskRunner.run(parsedCmd)
File "/work/stack_INFRA-312/stack/miniconda3-py38_4.9.2-3.0.0/Linux64/pipe_base/g590c34a36e+5da9528084/python/lsst/pipe/base/cmdLineTask.py", line 244, in run
resultList = list(mapFunc(self, targetList))
File "/work/stack_INFRA-312/stack/miniconda3-py38_4.9.2-3.0.0/Linux64/pipe_base/g590c34a36e+5da9528084/python/lsst/pipe/base/cmdLineTask.py", line 47, in _runPool
return pool.map_async(function, iterable).get(timeout)
File "/work/stack_INFRA-312/conda/miniconda3-py38_4.9.2/envs/lsst-scipipe-3.0.0/lib/python3.8/multiprocessing/pool.py", line 771, in get
raise self._value
ValueError: `sigma` must be positive definite.
Note that I specified like `--id visit=83219 spectrograph=1`.