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December 5, 2018 22:11
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reproduce_segfault.log
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| -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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