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goraj/reproduce_segfault.log

Created December 5, 2018 22:11
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reproduce_segfault.log
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reproduce_segfault.log
-bash-4.2$ ./Miniconda3-latest-Linux-x86_64.sh -b -p ~/m3_centos7
PREFIX=/home/username/m3_centos7
installing: python-3.7.0-hc3d631a_0 ...
Python 3.7.0 (default, Jun 28 2018, 13:15:42)
[GCC 7.2.0]
installing: ca-certificates-2018.03.07-0 ...
installing: conda-env-2.6.0-1 ...
installing: libgcc-ng-8.2.0-hdf63c60_1 ...
installing: libstdcxx-ng-8.2.0-hdf63c60_1 ...
installing: libffi-3.2.1-hd88cf55_4 ...
installing: ncurses-6.1-hf484d3e_0 ...
installing: openssl-1.0.2p-h14c3975_0 ...
installing: xz-5.2.4-h14c3975_4 ...
installing: yaml-0.1.7-had09818_2 ...
installing: zlib-1.2.11-ha838bed_2 ...
installing: libedit-3.1.20170329-h6b74fdf_2 ...
installing: readline-7.0-h7b6447c_5 ...
installing: tk-8.6.8-hbc83047_0 ...
installing: sqlite-3.24.0-h84994c4_0 ...
installing: asn1crypto-0.24.0-py37_0 ...
installing: certifi-2018.8.24-py37_1 ...
installing: chardet-3.0.4-py37_1 ...
installing: idna-2.7-py37_0 ...
installing: pycosat-0.6.3-py37h14c3975_0 ...
installing: pycparser-2.18-py37_1 ...
installing: pysocks-1.6.8-py37_0 ...
installing: ruamel_yaml-0.15.46-py37h14c3975_0 ...
installing: six-1.11.0-py37_1 ...
installing: cffi-1.11.5-py37he75722e_1 ...
installing: setuptools-40.2.0-py37_0 ...
installing: cryptography-2.3.1-py37hc365091_0 ...
installing: wheel-0.31.1-py37_0 ...
installing: pip-10.0.1-py37_0 ...
installing: pyopenssl-18.0.0-py37_0 ...
installing: urllib3-1.23-py37_0 ...
installing: requests-2.19.1-py37_0 ...
installing: conda-4.5.11-py37_0 ...
installation finished.
-bash-4.2$
-bash-4.2$
-bash-4.2$ source ~/m3_centos7/bin/activate;conda create -n projectname python=3.6
Solving environment: done
## Package Plan ##
environment location: /home/username/m3_centos7/envs/projectname
added / updated specs:
- python=3.6
The following packages will be downloaded:
package | build
---------------------------|-----------------
ncurses-6.1 | he6710b0_1 958 KB
sqlite-3.25.3 | h7b6447c_0 1.9 MB
openssl-1.1.1a | h7b6447c_0 5.0 MB
zlib-1.2.11 | h7b6447c_3 120 KB
python-3.6.7 | h0371630_0 34.3 MB
certifi-2018.10.15 | py36_0 139 KB
setuptools-40.6.2 | py36_0 604 KB
wheel-0.32.3 | py36_0 35 KB
pip-18.1 | py36_0 1.8 MB
------------------------------------------------------------
Total: 44.8 MB
The following NEW packages will be INSTALLED:
ca-certificates: 2018.03.07-0
certifi: 2018.10.15-py36_0
libedit: 3.1.20170329-h6b74fdf_2
libffi: 3.2.1-hd88cf55_4
libgcc-ng: 8.2.0-hdf63c60_1
libstdcxx-ng: 8.2.0-hdf63c60_1
ncurses: 6.1-he6710b0_1
openssl: 1.1.1a-h7b6447c_0
pip: 18.1-py36_0
python: 3.6.7-h0371630_0
readline: 7.0-h7b6447c_5
setuptools: 40.6.2-py36_0
sqlite: 3.25.3-h7b6447c_0
tk: 8.6.8-hbc83047_0
wheel: 0.32.3-py36_0
xz: 5.2.4-h14c3975_4
zlib: 1.2.11-h7b6447c_3
Proceed ([y]/n)? y
Downloading and Extracting Packages
ncurses-6.1 | 958 KB | ########################################################################## | 100%
sqlite-3.25.3 | 1.9 MB | ########################################################################## | 100%
openssl-1.1.1a | 5.0 MB | ########################################################################## | 100%
zlib-1.2.11 | 120 KB | ########################################################################## | 100%
python-3.6.7 | 34.3 MB | ########################################################################## | 100%
certifi-2018.10.15 | 139 KB | ########################################################################## | 100%
setuptools-40.6.2 | 604 KB | ########################################################################## | 100%
wheel-0.32.3 | 35 KB | ########################################################################## | 100%
pip-18.1 | 1.8 MB | ########################################################################## | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate projectname
#
# To deactivate an active environment, use
#
# $ conda deactivate
(base) -bash-4.2$ conda activate projectname
(projectname) -bash-4.2$ conda install dask distributed
Solving environment: done
## Package Plan ##
environment location: /home/username/m3_centos7/envs/projectname
added / updated specs:
- dask
- distributed
The following packages will be downloaded:
package | build
---------------------------|-----------------
python-dateutil-2.7.5 | py36_0 275 KB
numpy-base-1.15.4 | py36h81de0dd_0 4.2 MB
sortedcontainers-2.1.0 | py36_0 45 KB
msgpack-python-0.5.6 | py36h6bb024c_1 99 KB
packaging-18.0 | py36_0 33 KB
click-7.0 | py36_0 118 KB
zict-0.1.3 | py36_0 18 KB
pyyaml-3.13 | py36h14c3975_0 178 KB
tblib-1.3.2 | py36_0 16 KB
intel-openmp-2019.1 | 144 885 KB
pandas-0.23.4 | py36h04863e7_0 10.1 MB
pytz-2018.7 | py36_0 250 KB
jpeg-9b | h024ee3a_2 248 KB
partd-0.3.9 | py36_0 32 KB
mkl_fft-1.0.6 | py36h7dd41cf_0 150 KB
cytoolz-0.9.0.1 | py36h14c3975_1 419 KB
heapdict-1.0.0 | py36_2 7 KB
toolz-0.9.0 | py36_0 91 KB
freetype-2.9.1 | h8a8886c_1 822 KB
psutil-5.4.8 | py36h7b6447c_0 311 KB
jinja2-2.10 | py36_0 184 KB
mkl_random-1.0.1 | py36h4414c95_1 373 KB
pyparsing-2.3.0 | py36_0 101 KB
blas-1.0 | mkl 6 KB
dask-1.0.0 | py36_0 4 KB
libgfortran-ng-7.3.0 | hdf63c60_0 1.3 MB
bokeh-1.0.2 | py36_0 5.3 MB
tornado-5.1.1 | py36h7b6447c_0 663 KB
libtiff-4.0.9 | he85c1e1_2 567 KB
six-1.11.0 | py36_1 21 KB
olefile-0.46 | py36_0 48 KB
libpng-1.6.35 | hbc83047_0 335 KB
dask-core-1.0.0 | py36_0 1.2 MB
markupsafe-1.1.0 | py36h7b6447c_0 26 KB
mkl-2018.0.3 | 1 198.7 MB
numpy-1.15.4 | py36h1d66e8a_0 35 KB
cloudpickle-0.6.1 | py36_0 27 KB
pillow-5.3.0 | py36h34e0f95_0 599 KB
locket-0.2.0 | py36_1 8 KB
distributed-1.25.0 | py36_0 817 KB
------------------------------------------------------------
Total: 228.4 MB
The following NEW packages will be INSTALLED:
blas: 1.0-mkl
bokeh: 1.0.2-py36_0
click: 7.0-py36_0
cloudpickle: 0.6.1-py36_0
cytoolz: 0.9.0.1-py36h14c3975_1
dask: 1.0.0-py36_0
dask-core: 1.0.0-py36_0
distributed: 1.25.0-py36_0
freetype: 2.9.1-h8a8886c_1
heapdict: 1.0.0-py36_2
intel-openmp: 2019.1-144
jinja2: 2.10-py36_0
jpeg: 9b-h024ee3a_2
libgfortran-ng: 7.3.0-hdf63c60_0
libpng: 1.6.35-hbc83047_0
libtiff: 4.0.9-he85c1e1_2
locket: 0.2.0-py36_1
markupsafe: 1.1.0-py36h7b6447c_0
mkl: 2018.0.3-1
mkl_fft: 1.0.6-py36h7dd41cf_0
mkl_random: 1.0.1-py36h4414c95_1
msgpack-python: 0.5.6-py36h6bb024c_1
numpy: 1.15.4-py36h1d66e8a_0
numpy-base: 1.15.4-py36h81de0dd_0
olefile: 0.46-py36_0
packaging: 18.0-py36_0
pandas: 0.23.4-py36h04863e7_0
partd: 0.3.9-py36_0
pillow: 5.3.0-py36h34e0f95_0
psutil: 5.4.8-py36h7b6447c_0
pyparsing: 2.3.0-py36_0
python-dateutil: 2.7.5-py36_0
pytz: 2018.7-py36_0
pyyaml: 3.13-py36h14c3975_0
six: 1.11.0-py36_1
sortedcontainers: 2.1.0-py36_0
tblib: 1.3.2-py36_0
toolz: 0.9.0-py36_0
tornado: 5.1.1-py36h7b6447c_0
yaml: 0.1.7-had09818_2
zict: 0.1.3-py36_0
Proceed ([y]/n)? y
Downloading and Extracting Packages
python-dateutil-2.7. | 275 KB | ########################################################################## | 100%
numpy-base-1.15.4 | 4.2 MB | ########################################################################## | 100%
sortedcontainers-2.1 | 45 KB | ########################################################################## | 100%
msgpack-python-0.5.6 | 99 KB | ########################################################################## | 100%
packaging-18.0 | 33 KB | ########################################################################## | 100%
click-7.0 | 118 KB | ########################################################################## | 100%
zict-0.1.3 | 18 KB | ########################################################################## | 100%
pyyaml-3.13 | 178 KB | ########################################################################## | 100%
tblib-1.3.2 | 16 KB | ########################################################################## | 100%
intel-openmp-2019.1 | 885 KB | ########################################################################## | 100%
pandas-0.23.4 | 10.1 MB | ########################################################################## | 100%
pytz-2018.7 | 250 KB | ########################################################################## | 100%
jpeg-9b | 248 KB | ########################################################################## | 100%
partd-0.3.9 | 32 KB | ########################################################################## | 100%
mkl_fft-1.0.6 | 150 KB | ########################################################################## | 100%
cytoolz-0.9.0.1 | 419 KB | ########################################################################## | 100%
heapdict-1.0.0 | 7 KB | ########################################################################## | 100%
toolz-0.9.0 | 91 KB | ########################################################################## | 100%
freetype-2.9.1 | 822 KB | ########################################################################## | 100%
psutil-5.4.8 | 311 KB | ########################################################################## | 100%
jinja2-2.10 | 184 KB | ########################################################################## | 100%
mkl_random-1.0.1 | 373 KB | ########################################################################## | 100%
pyparsing-2.3.0 | 101 KB | ########################################################################## | 100%
blas-1.0 | 6 KB | ########################################################################## | 100%
dask-1.0.0 | 4 KB | ########################################################################## | 100%
libgfortran-ng-7.3.0 | 1.3 MB | ########################################################################## | 100%
bokeh-1.0.2 | 5.3 MB | ########################################################################## | 100%
tornado-5.1.1 | 663 KB | ########################################################################## | 100%
libtiff-4.0.9 | 567 KB | ########################################################################## | 100%
six-1.11.0 | 21 KB | ########################################################################## | 100%
olefile-0.46 | 48 KB | ########################################################################## | 100%
libpng-1.6.35 | 335 KB | ########################################################################## | 100%
dask-core-1.0.0 | 1.2 MB | ########################################################################## | 100%
markupsafe-1.1.0 | 26 KB | ########################################################################## | 100%
mkl-2018.0.3 | 198.7 MB | ########################################################################## | 100%
numpy-1.15.4 | 35 KB | ########################################################################## | 100%
cloudpickle-0.6.1 | 27 KB | ########################################################################## | 100%
pillow-5.3.0 | 599 KB | ########################################################################## | 100%
locket-0.2.0 | 8 KB | ########################################################################## | 100%
distributed-1.25.0 | 817 KB | ########################################################################## | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(projectname) -bash-4.2$ pip install umap-learn
Collecting umap-learn
Collecting scikit-learn>=0.16 (from umap-learn)
Using cached https://files.pythonhosted.org/packages/10/26/d04320c3edf2d59b1fcd0720b46753d4d603a76e68d8ad10a9b92ab06db2/scikit_learn-0.20.1-cp36-cp36m-manylinux1_x86_64.whl
Requirement already satisfied: numpy>=1.13 in ./m3_centos7/envs/projectname/lib/python3.6/site-packages (from umap-learn) (1.15.4)
Collecting numba>=0.37 (from umap-learn)
Using cached https://files.pythonhosted.org/packages/31/55/938f0023a4f37fe24460d46846670aba8170a6b736f1693293e710d4a6d0/numba-0.41.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting scipy>=0.19 (from umap-learn)
Using cached https://files.pythonhosted.org/packages/a8/0b/f163da98d3a01b3e0ef1cab8dd2123c34aee2bafbb1c5bffa354cc8a1730/scipy-1.1.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting llvmlite>=0.26.0dev0 (from numba>=0.37->umap-learn)
Using cached https://files.pythonhosted.org/packages/a2/60/d22966c97a47687ac1cc57c2e756380897c264f1ce40780105d7dbcd9564/llvmlite-0.26.0-cp36-cp36m-manylinux1_x86_64.whl
Installing collected packages: scipy, scikit-learn, llvmlite, numba, umap-learn
Successfully installed llvmlite-0.26.0 numba-0.41.0 scikit-learn-0.20.1 scipy-1.1.0 umap-learn-0.3.7
(projectname) -bash-4.2$
(projectname) -bash-4.2$
(projectname) -bash-4.2$ python ~/reproduce.py
distributed.nanny - WARNING - Worker process 1815 was killed by unknown signal
/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/semaphore_tracker.py:143: UserWarning: semaphore_tracker: There appear to be 1 leaked semaphores to clean up at shutdown
len(cache))
/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/semaphore_tracker.py:143: UserWarning: semaphore_tracker: There appear to be 1 leaked semaphores to clean up at shutdown
len(cache))
/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/semaphore_tracker.py:143: UserWarning: semaphore_tracker: There appear to be 1 leaked semaphores to clean up at shutdown
len(cache))
distributed.nanny - WARNING - Worker process 1775 was killed by unknown signal
/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/semaphore_tracker.py:143: UserWarning: semaphore_tracker: There appear to be 1 leaked semaphores to clean up at shutdown
len(cache))
distributed.nanny - WARNING - Worker process 1783 was killed by unknown signal
/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/semaphore_tracker.py:143: UserWarning: semaphore_tracker: There appear to be 1 leaked semaphores to clean up at shutdown
len(cache))
distributed.nanny - WARNING - Worker process 1773 was killed by unknown signal
distributed.nanny - WARNING - Worker process 1808 was killed by unknown signal
distributed.nanny - WARNING - Restarting worker
distributed.nanny - WARNING - Restarting worker
distributed.nanny - WARNING - Restarting worker
distributed.nanny - WARNING - Restarting worker
distributed.nanny - WARNING - Restarting worker
distributed.nanny - WARNING - Worker process 1786 was killed by unknown signal
/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/semaphore_tracker.py:143: UserWarning: semaphore_tracker: There appear to be 1 leaked semaphores to clean up at shutdown
len(cache))
distributed.nanny - WARNING - Restarting worker
distributed.nanny - WARNING - Worker process 1791 was killed by unknown signal
/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/semaphore_tracker.py:143: UserWarning: semaphore_tracker: There appear to be 1 leaked semaphores to clean up at shutdown
len(cache))
distributed.nanny - WARNING - Worker process 1795 was killed by unknown signal
/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/semaphore_tracker.py:143: UserWarning: semaphore_tracker: There appear to be 1 leaked semaphores to clean up at shutdown
len(cache))
/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/semaphore_tracker.py:143: UserWarning: semaphore_tracker: There appear to be 1 leaked semaphores to clean up at shutdown
len(cache))
distributed.nanny - WARNING - Worker process 1787 was killed by unknown signal
distributed.nanny - WARNING - Restarting worker
distributed.nanny - WARNING - Restarting worker
distributed.nanny - WARNING - Restarting worker
distributed.nanny - WARNING - Worker process 1774 was killed by unknown signal
/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/semaphore_tracker.py:143: UserWarning: semaphore_tracker: There appear to be 1 leaked semaphores to clean up at shutdown
len(cache))
distributed.nanny - WARNING - Restarting worker
^CTraceback (most recent call last):
File "/home/username/reproduce.py", line 46, in <module>
result = client.gather(pool)
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/site-packages/distributed/client.py", line 1652, in gather
asynchronous=asynchronous)
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/site-packages/distributed/client.py", line 670, in sync
return sync(self.loop, func, *args, **kwargs)
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/site-packages/distributed/utils.py", line 275, in sync
e.wait(10)
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/threading.py", line 551, in wait
signaled = self._cond.wait(timeout)
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/threading.py", line 299, in wait
gotit = waiter.acquire(True, timeout)
KeyboardInterrupt
distributed.nanny - WARNING - Worker process 2251 was killed by unknown signal
distributed.nanny - WARNING - Worker process 2214 was killed by unknown signal
distributed.nanny - WARNING - Worker process 2213 was killed by unknown signal
distributed.nanny - WARNING - Worker process 2212 was killed by unknown signal
distributed.nanny - WARNING - Worker process 2075 was killed by unknown signal
distributed.nanny - WARNING - Worker process 2065 was killed by unknown signal
distributed.nanny - WARNING - Worker process 2170 was killed by unknown signal
distributed.nanny - WARNING - Worker process 2070 was killed by unknown signal
distributed.nanny - WARNING - Worker process 2064 was killed by unknown signal
Traceback (most recent call last):
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/queues.py", line 240, in _feed
send_bytes(obj)
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/connection.py", line 200, in send_bytes
self._send_bytes(m[offset:offset + size])
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/connection.py", line 404, in _send_bytes
self._send(header + buf)
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/connection.py", line 368, in _send
n = write(self._handle, buf)
BrokenPipeError: [Errno 32] Broken pipe
Traceback (most recent call last):
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/queues.py", line 240, in _feed
send_bytes(obj)
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/connection.py", line 200, in send_bytes
self._send_bytes(m[offset:offset + size])
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/connection.py", line 404, in _send_bytes
self._send(header + buf)
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/multiprocessing/connection.py", line 368, in _send
n = write(self._handle, buf)
BrokenPipeError: [Errno 32] Broken pipe
distributed.nanny - WARNING - Worker process 2073 was killed by unknown signal
tornado.application - ERROR - Exception in Future <Future cancelled> after timeout
Traceback (most recent call last):
File "/home/username/m3_centos7/envs/projectname/lib/python3.6/site-packages/tornado/gen.py", line 970, in error_callback
future.result()
concurrent.futures._base.CancelledError
(projectname) -bash-4.2$
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