[LSST|dm-users 627] Re: Error when Running Chris Walter's: Introduction to the DM AFW packages ipython notebook
Simon Krughoff
simon.krughoff at gmail.com
Thu May 7 17:03:22 PDT 2015
Very strange. It looks like the lsst64def module was not built. It may
work better to solve this in a session where we can share screens, but let
me know what you see with the following.
Do you have a file called lsst64defs.py in
/Users/dawson/lsst/EupsBuildDir/DarwinX86/base-10.0-5-g766159b/base-10.0-5-g766159b/python?
If so, what is in it?
If not, what does the following give you if you run it in the python
directory?
m4 -Dm4_RTLD_GLOBAL=8 -Dm4_RTLD_NOW=2 < lsst64defs.py.m4 >
/Users/dawson/lsst/EupsBuildDir/DarwinX86/base-10.0-5-g766159b/base-10.0-5-g766159b/python/lsst64defs.py
Simon
On Thu, May 7, 2015 at 4:49 PM, Will Dawson <will at dawsonresearch.com> wrote:
> Simon,
>
> Here is the .failed file.
>
> Thanks for your time,
> Will
>
>
>
> On May 7, 2015, at 4:43 PM, Simon Krughoff <simon.krughoff at gmail.com>
> wrote:
>
> Will,
>
> Actually, it looks like a test failed when you were building. The failed
> test log should be in:
>
> /Users/dawson/lsst/EupsBuildDir/DarwinX86/base-10.0-5-g766159b/base-10.0-5-g766159b/tests/.tests
>
> There will be a file with the .failed suffix. In there will be the
> messages about why that test failed.
>
> Can you send that along?
>
> Simon
>
> On Thu, May 7, 2015 at 4:37 PM, Will Dawson <will at dawsonresearch.com>
> wrote:
>
>> Simon,
>>
>> I’ve attached the build.log. apparently the error is related to the CC
>> compiler (note I am running Yosemite).
>>
>> Thanks,
>> Will
>>
>>
>>
>> On May 7, 2015, at 4:29 PM, Simon Krughoff <simon.krughoff at gmail.com>
>> wrote:
>>
>> Hi Will,
>>
>> If you can attach the contents of /Users/dawson/lsst/
>> EupsBuildDir/DarwinX86/base-10.0-5-g766159b/build.log. We might be able
>> to diagnose.
>>
>> Simon
>>
>> On Thu, May 7, 2015 at 4:11 PM, Will Dawson <will at dawsonresearch.com>
>> wrote:
>>
>>> Jim / Dominique,
>>>
>>> Thank you for the suggestions. Apparently the
>>> SingleFrameMeasurementConfig/Task are not in v10.0, as I get the following
>>> error when instantiating it
>>>
>>> AttributeError: 'module' object has no attribute
>>> 'SingleFrameMeasurementConfig'
>>>
>>> I tried installing 10_1_rc3 and got through 23/55 programs before
>>> encountering the following error:
>>>
>>> eups distrib: Failed to build base-10.0-5-g766159b.eupspkg: Command:
>>> source /Users/dawson/lsst/eups/bin/setups.sh; export
>>> EUPS_PATH=/Users/dawson/lsst;
>>> (/Users/dawson/lsst/EupsBuildDir/DarwinX86/base-10.0-5-g766159b/build.sh)
>>> >> /Users/dawson/lsst/EupsBuildDir/DarwinX86/base-10.0-5-g766159b/build.log
>>> 2>&1
>>> 4>/Users/dawson/lsst/EupsBuildDir/DarwinX86/base-10.0-5-g766159b/build.msg
>>> exited with code 252
>>>
>>> I am burnt out on switching between different distributions (in part
>>> motivated by dm stack and galsim I recently switched from macports to
>>> homebrew and canopy to anaconda) and fixing the things that will inevitably
>>> break so I don’t feel like trying the CernVMFS distribution. I will just
>>> wait for v10_1.
>>>
>>> Will
>>>
>>> On May 7, 2015, at 2:33 PM, Dominique Boutigny <boutigny at in2p3.fr>
>>> wrote:
>>>
>>> Hi Will,
>>>
>>> As far as I know, v10_1 will be released in a couple of days so I don't
>>> think that you should invest too much time in v10_0. In the mean time you
>>> can use v10_1_rc3 which is very close to v10_1, either by installing it
>>> directly (
>>> https://confluence.lsstcorp.org/display/LSWUG/LSST+Software+User+Guide)
>>> or even simpler using the CernVMFS distrib : see
>>> https://github.com/airnandez/lsst-cvmfs
>>> With the later, once CernVMFS is installed you have nothing to build,
>>> the packages are loaded on demand from the network, so this takes a little
>>> bit of time the first time, but then it is cached on your local disk and it
>>> is as fast as a local install.
>>>
>>> Dominique
>>>
>>> On 05/07/2015 01:35 PM, Will Dawson wrote:
>>>
>>> Dominique,
>>>
>>> Thank you for translating the error. The problem then seems to be with
>>> an inconsistent DM functions default parameter settings. From the notebook
>>> the schema and measurement configuration is set by
>>>
>>> schema = lsst.afw.table.SourceTable.makeMinimalSchema()
>>> measureSourcesConfig = lsst.meas.algorithms.SourceMeasurementConfig()
>>>
>>> So it appears that makeMinimialSchema() and SourceMeasurementConfig()
>>> need to be made compatible (perhaps is has been in v10_1). Should I be
>>> using v10_1 instead of v10_0?
>>>
>>> Thank you for the very helpful CFHTLS references.
>>>
>>> Regards,
>>> Will
>>>
>>> On May 7, 2015, at 12:09 PM, Dominique Boutigny <boutigny at in2p3.fr>
>>> wrote:
>>>
>>> Hi Will,
>>>
>>> Yes, the schema has changed in the latest stack versions and
>>> "flux.sinc_flux" is not any more in the source table schema. Something
>>> directly replacing sinc_flux was present in the v10_0 but this has been
>>> completely replaced in the latest stack_v10_1. There are now 10 Aperture
>>> flux corresponding to 10 different radii.
>>>
>>> You can have a look to
>>> http://nbviewer.ipython.org/github/DarkEnergyScienceCollaboration/CFHTLS-Reprocess/tree/master/notebooks/
>>> to get notebook examples with the most recent stack.
>>>
>>> I can have a look to Chris' notebooks if you wish.
>>>
>>> Best,
>>>
>>> Dominique
>>>
>>> On 05/07/2015 11:52 AM, Will Dawson wrote:
>>>
>>> I encountered an error when running Chris Walter’s Introduction to the
>>> DM AFW packages
>>> <http://nbviewer.ipython.org/github/DarkEnergyScienceCollaboration/DataManagementWorkbook/blob/master/Basic%20DM%20AFW%20Introduction.ipynb> ipython
>>> notebook. In the second to last step when I run the command:
>>>
>>> # Apply the measurement routines to the exposure using the sources as
>>> input
>>> measure.run(exposure, sources)
>>>
>>> I get the following error:
>>>
>>> ---------------------------------------------------------------------------NotFoundError Traceback (most recent call last)<ipython-input-19-77c6eca8bda0> in <module>() 16 17 # Apply the measurement routines to the exposure using the sources as input---> 18 measure.run(exposure, sources) 19 20 # Now let's look at the output from some of the measurment algorithms.
>>> /Users/dawson/lsst/DarwinX86/pipe_base/10.0+2/python/lsst/pipe/base/timer.pyc in wrapper(self, *args, **keyArgs) 116 logInfo(obj = self, prefix = func.__name__ + "Start") 117 try:--> 118 res = func(self, *args, **keyArgs) 119 finally: 120 logInfo(obj = self, prefix = func.__name__ + "End")
>>> /Users/dawson/lsst/DarwinX86/meas_algorithms/10.0+2/python/lsst/meas/algorithms/measurement.pyc in measure(self, exposure, sources, noiseImage, noiseMeanVar, references, refWcs) 422 423 self.log.info("Measuring %d sources" % len(sources))--> 424 self.config.slots.setupTable(sources.table, prefix=self.config.prefix) 425 426 self.preMeasureHook(exposure, sources)
>>> /Users/dawson/lsst/DarwinX86/meas_algorithms/10.0+2/python/lsst/meas/algorithms/measurement.pyc in setupTable(self, table, prefix) 57 if self.centroid is not None: table.defineCentroid(prefix + self.centroid) 58 if self.shape is not None: table.defineShape(prefix + self.shape)---> 59 if self.apFlux is not None: table.defineApFlux(prefix + self.apFlux) 60 if self.modelFlux is not None: table.defineModelFlux(prefix + self.modelFlux) 61 if self.psfFlux is not None: table.definePsfFlux(prefix + self.psfFlux)
>>> /Users/dawson/lsst/DarwinX86/afw/10.0+3/python/lsst/afw/table/tableLib.pyc in defineApFlux(self, *args) 9869 def defineApFlux(self, *args): 9870 """defineApFlux(SourceTable self, std::string const & name)"""-> 9871 return _tableLib.SourceTable_defineApFlux(self, *args) 9872 9873 def getApFluxDefinition(self):
>>> NotFoundError:
>>> File "src/table/Schema.cc <http://schema.cc/>", line 239, in SchemaItem<T> lsst::afw::table::detail::SchemaImpl::find(const std::string &) const [T = double]
>>> Field or subfield withname 'flux.sinc_flux' not found with type 'D'. {0}
>>> lsst::pex::exceptions::NotFoundError: 'Field or subfield withname 'flux.sinc_flux' not found with type 'D'.'
>>>
>>>
>>> Perhaps this is related to the fact that the notebook was written in
>>> 2013 and I am using v10.0 of the stack. As I am new to the stack, and given
>>> the surprisingly complex error message for such a seemingly simple command,
>>> I am hoping that the experts can shed some light on the matter.
>>>
>>> Thanks,
>>> Will Dawson
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> dm-users mailing listdm-users at lists.lsst.orghttps://lists.lsst.org/mailman/listinfo/dm-users
>>>
>>>
>>> --
>>> Dominique Boutigny - CNRS / CC-IN2P3
>>> Now at SLAC National Accelerator Laboratory
>>>
>>> Kavli Building - Room 221
>>> Mail : boutigny at in2p3.fr - boutigny at slac.stanford.edu
>>> Office : +1 650-926-5759 - Cellular : +1 774-232-0912
>>>
>>> _______________________________________________
>>> dm-users mailing list
>>> dm-users at lists.lsst.org
>>> https://lists.lsst.org/mailman/listinfo/dm-users
>>>
>>>
>>>
>>> --
>>> Dominique Boutigny - CNRS / CC-IN2P3
>>> Now at SLAC National Accelerator Laboratory
>>>
>>> Kavli Building - Room 221
>>> Mail : boutigny at in2p3.fr - boutigny at slac.stanford.edu
>>> Office : +1 650-926-5759 - Cellular : +1 774-232-0912
>>>
>>> _______________________________________________
>>> dm-users mailing list
>>> dm-users at lists.lsst.org
>>> https://lists.lsst.org/mailman/listinfo/dm-users
>>>
>>>
>>>
>>> _______________________________________________
>>> dm-users mailing list
>>> dm-users at lists.lsst.org
>>> https://lists.lsst.org/mailman/listinfo/dm-users
>>>
>>
>>
>>
>> --
>> K. Simon Krughoff
>> University of Washington
>> Department of Astronomy
>>
>> Physics-Astronomy Bldg.
>> 3910 15th Ave NE
>> Room C319
>> Seattle WA 98195-0002
>> USA
>>
>> (206)543-9487
>>
>>
>>
>>
>
>
> --
> K. Simon Krughoff
> University of Washington
> Department of Astronomy
>
> Physics-Astronomy Bldg.
> 3910 15th Ave NE
> Room C319
> Seattle WA 98195-0002
> USA
>
> (206)543-9487
>
>
>
>
--
K. Simon Krughoff
University of Washington
Department of Astronomy
Physics-Astronomy Bldg.
3910 15th Ave NE
Room C319
Seattle WA 98195-0002
USA
(206)543-9487
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