Details
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Type:
Story
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Status: Done
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Resolution: Done
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Fix Version/s: None
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Component/s: qa_explorer
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:AP S19-3
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Team:Alert Production
Description
When I try to run writeObjectTable.py on lsst-dev, it fails with a segfault & long backtrace, starting like:
[tmorton@lsst-dev01 DM-14289]$ bash writeTables_test.sh
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Caught signal 11, backtrace follows:
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/ssd/lsstsw/stack3_20171021/stack/miniconda3-4.3.21-10a4fa6/Linux64/utils/16.0-6-g3610b4f/lib/libutils.so(+0x15214) [0x7f078a865214]
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/usr/lib64/libc.so.6(+0x362f0) [0x7f080a5892f0]
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/ssd/lsstsw/stack3_20171021/python/miniconda3-4.3.21/bin/../lib/libstdc++.so.6(std::basic_string<char, std::char_traits<char>, std::allocator<char> >::basic_string(std::string const&)+0xb) [0x7f08032b640b]
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/ssd/lsstsw/stack3_20171021/python/miniconda3-4.3.21/lib/python3.6/site-packages/pyarrow/../../../libparquet.so.1(+0x177ddc) [0x7f071bcb6ddc]
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/ssd/lsstsw/stack3_20171021/python/miniconda3-4.3.21/lib/python3.6/site-packages/pyarrow/../../../libparquet.so.1(+0x1696c3) [0x7f071bca86c3]
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/ssd/lsstsw/stack3_20171021/python/miniconda3-4.3.21/lib/python3.6/site-packages/pyarrow/../../../libparquet.so.1(+0x175e8b) [0x7f071bcb4e8b]
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/ssd/lsstsw/stack3_20171021/python/miniconda3-4.3.21/lib/python3.6/site-packages/pyarrow/../../../libparquet.so.1(parquet::ApplicationVersion::ApplicationVersion(std::string const&)+0x6d) [0x7f071bc4aa5d]
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/ssd/lsstsw/stack3_20171021/python/miniconda3-4.3.21/lib/python3.6/site-packages/pyarrow/../../../libparquet.so.1(+0x83590) [0x7f071bbc2590]
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/lib64/ld-linux-x86-64.so.2(+0xfb03) [0x7f080b964b03]
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/lib64/ld-linux-x86-64.so.2(+0x146de) [0x7f080b9696de]
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/lib64/ld-linux-x86-64.so.2(+0xf914) [0x7f080b964914]
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/lib64/ld-linux-x86-64.so.2(+0x13ccb) [0x7f080b968ccb]
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/usr/lib64/libdl.so.2(+0xfbb) [0x7f080b02dfbb]
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...etc
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The script I am running is the following:
RERUN1=/datasets/hsc/repo/rerun/RC/w_2018_28/DM-14988/
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OUTPUT1=/project/tmorton/DM-14289/w28
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RERUN2=/datasets/hsc/repo/rerun/RC/w_2018_26/DM-14689/
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OUTPUT2=/project/tmorton/DM-14289/w26
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TRACT=9615
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PATCH=4,4
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FILTERS=HSC-G^HSC-R^HSC-I
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writeObjectTable.py $RERUN1 --output $OUTPUT1 --id tract=$TRACT patch=$PATCH filter=$FILTERS --no-versions -j 20
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writeObjectTable.py $RERUN2 --output $OUTPUT2 --id tract=$TRACT patch=$PATCH filter=$FILTERS --no-versions -j 20
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writeQATable.py $OUTPUT1 --output $OUTPUT1 --id tract=$TRACT patch=$PATCH --no-versions -j 20 --clobber-config
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writeQATable.py $OUTPUT2 --output $OUTPUT2 --id tract=$TRACT patch=$PATCH --no-versions -j 20 --clobber-config
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I can run the identical script in the jupyterlab environment container and everything is great.
I think this is related to the fact that I can run the qa_explorer tests on the JL env but not lsst-dev, where it hangs with a segfault as well (DM-14224). It is making testing of DM-14289 difficult, since I can't do it on lsst-dev.
Attachments
Issue Links
Activity
John Swinbank Can we try again in /software/lsstsw/stack_20181012/stack/miniconda3-4.5.4-fcd27eb?
Tim Morton [X] we can look into that. Last time I installed pyviz, it did not install everything I expected, but I didn't try very hard.
$ echo $EUPS_PATH
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/software/lsstsw/stack_20181012/stack/miniconda3-4.5.4-fcd27eb
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$ python -c'import pyarrow; print(pyarrow.__version__); import pandas; print(pandas.__version__)'
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0.9.0
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0.23.1
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$ python tests/testParquet.py
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tests/testParquet.py:50: ResourceWarning: unclosed file <_io.BufferedReader name='/scratch/swinbank/qa_explorer/tests/multilevel_test.parq'>
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self.df = pq.read_table(os.path.join(ROOT, self.testFilename)).to_pandas()
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tests/testParquet.py:58: ResourceWarning: unclosed file <_io.BufferedReader name='testParquet_setUp-z1jcykz2*.parq'>
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del self.parq
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.tests/testParquet.py:58: ResourceWarning: unclosed file <_io.BufferedReader name='testParquet_setUp-9drf9xba*.parq'>
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del self.parq
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.tests/testParquet.py:58: ResourceWarning: unclosed file <_io.BufferedReader name='testParquet_setUp-uy26sjr8*.parq'>
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del self.parq
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.tests/testParquet.py:50: ResourceWarning: unclosed file <_io.BufferedReader name='/scratch/swinbank/qa_explorer/tests/simple_test.parq'>
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self.df = pq.read_table(os.path.join(ROOT, self.testFilename)).to_pandas()
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tests/testParquet.py:58: ResourceWarning: unclosed file <_io.BufferedReader name='testParquet_setUp-c3my1abk*.parq'>
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del self.parq
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.tests/testParquet.py:58: ResourceWarning: unclosed file <_io.BufferedReader name='testParquet_setUp-0uq2w8kk*.parq'>
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del self.parq
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.
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----------------------------------------------------------------------
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Ran 5 tests in 7.903s
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OK
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This is now working as far as I can tell.
Simon Krughoff and Adam Thornton: there's probably a better place to suggest this, but it's probably better to have the JLab environment (and by extension, the shared stack) to install pyviz rather than the individual components (bokeh/holoviews/datashader/etc.) individually from the bleeding edge.