Error encountered meas_base using -t sims (sims_2_3_1)

Support
#1

Hi,
I’m working to support upcoming DESC Twinkles runs (at SLAC) with an updated DMstack installation (lsst_apps and lsst_sims). This is using a RH6 machine with gcc 4.9.2. We required a new tag of lsst_sims, and @danielsf kindly set us up last night. I started from scratch and decided to do a “eups distrib install lsst_apps -t sims --nolocks” It went along happily for quite awhile, but ended here:

 [ 58/70 ]  meas_base 12.1+3 ... 

***** error: from /nfs/farm/g/lsst/u1/software/redhat6-x86_64-64bit-gcc44/DMstack/w.2016.40/EupsBuildDir/Linux64/meas_base-12.1+3/build.log:

tests/testApertureFlux.py

tests/testMeasureSources.py

tests/testSincPhotSums.py

tests/testScaledApertureFlux.py

The following tests failed:
/nfs/farm/g/lsst/u1/software/redhat6-x86_64-64bit-gcc44/DMstack/w.2016.40/EupsBuildDir/Linux64/meas_base-12.1+3/meas_base-12.1+3/tests/.tests/testClassification.py.failed
/nfs/farm/g/lsst/u1/software/redhat6-x86_64-64bit-gcc44/DMstack/w.2016.40/EupsBuildDir/Linux64/meas_base-12.1+3/meas_base-12.1+3/tests/.tests/testJacobian.py.failed
/nfs/farm/g/lsst/u1/software/redhat6-x86_64-64bit-gcc44/DMstack/w.2016.40/EupsBuildDir/Linux64/meas_base-12.1+3/meas_base-12.1+3/tests/.tests/testApertureFlux.py.failed
/nfs/farm/g/lsst/u1/software/redhat6-x86_64-64bit-gcc44/DMstack/w.2016.40/EupsBuildDir/Linux64/meas_base-12.1+3/meas_base-12.1+3/tests/.tests/testMeasureSources.py.failed
/nfs/farm/g/lsst/u1/software/redhat6-x86_64-64bit-gcc44/DMstack/w.2016.40/EupsBuildDir/Linux64/meas_base-12.1+3/meas_base-12.1+3/tests/.tests/testSincPhotSums.py.failed
/nfs/farm/g/lsst/u1/software/redhat6-x86_64-64bit-gcc44/DMstack/w.2016.40/EupsBuildDir/Linux64/meas_base-12.1+3/meas_base-12.1+3/tests/.tests/testScaledApertureFlux.py.failed
6 tests failed
scons: *** [checkTestStatus] Error 1
scons: building terminated because of errors.
+ exit -4
eups distrib: Failed to build meas_base-12.1+3.eupspkg: Command:
	source /nfs/farm/g/lsst/u1/software/redhat6-x86_64-64bit-gcc44/DMstack/w.2016.40/eups/bin/setups.sh; export EUPS_PATH=/nfs/farm/g/lsst/u1/software/redhat6-x86_64-64bit-gcc44/DMstack/w.2016.40; (/nfs/farm/g/lsst/u1/software/redhat6-x86_64-64bit-gcc44/DMstack/w.2016.40/EupsBuildDir/Linux64/meas_base-12.1+3/build.sh) >> /nfs/farm/g/lsst/u1/software/redhat6-x86_64-64bit-gcc44/DMstack/w.2016.40/EupsBuildDir/Linux64/meas_base-12.1+3/build.log 2>&1 4>/nfs/farm/g/lsst/u1/software/redhat6-x86_64-64bit-gcc44/DMstack/w.2016.40/EupsBuildDir/Linux64/meas_base-12.1+3/build.msg 
exited with code 252

Any suggestions or known recent issues with meas_base?
Thanks,
Heather

#2

The fact that the lines above this one indicate no test output suggest that the tests are crashing straight away. Can you confirm that the listed .failed files contain no useful output?

You might have to go into the meas_base build directory, set it up and run the tests manually.

#3

Thanks, @timj. Yes, sadly the *.failed files are all empty.
I might need some guidance on how to setup meas_build so I can run the tests manually… I’m poking around the build.sh script.

#4 
git clone git@github.com:LSST/meas_base.git
cd meas_base
setup -r .
scons
1 Like
#5

and just to close out this issue… I realized I was using an older python installation :slight_smile: Once I fixed that, I have no longer encountered any problems with meas_base. Sorry for the trouble.

#6

Thanks. newinstall.sh is meant to check your python version and the EUPS python package is also meant to check. Did you somehow switch the python in your path between doing the install of the EUPS python validation package and the rest of the eups distrib install?

#7

No, there was no change in the version of python during the installation process. This was an older anaconda installation (2.5.0) - one I probably updated a few times, but python itself was at 2.7.11. I am still a little surprised it caused trouble, but once I saw that I could do a full install just fine when using the vanilla python that newinstall offered, I was left to assume my trouble was due to my python installation.
Attempting to re-run the unit tests by hand, I got as far as receiving a “Segmentation fault” with little else to go on, short of debugging, Then I realized I was pointing to a python install that I had not intended to use. Once I fixed that and re-installed, things went just fine.

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#8

I realize this is old, but for the record, an anaconda install on Linux with numpy /scipy etc installed without no-mkl produces this exact error from meas_base (at least in the v12 version of meas_base). The miniconda install from LSST uses the no-mkl versions so would not produce the segfault errors.

1 Like