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mazzalab / pyntacle

A high performance python package for network analysis based on non canonical metrics
http://pyntacle.css-mendel.it
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[cmd] error in Pyntacle test #46

Closed Bioswinger closed 3 years ago

Bioswinger commented 3 years ago

Quick start guide notebook

Hardware features: intel, 8 CPU, RAM 12GB SODIMM DDR4

Command used: pyntacle test

error received: 

Searching the best set(s) of nodes of size 2 that maximizes the group-betweenness using 7 processs
Evaluating 496 possible solutions
Brute-force search of the best group of nodes of size 2 using 7 processes
Terminating: fork() called from a process already using GNU OpenMP, this is unsafe.
Terminating: fork() called from a process already using GNU OpenMP, this is unsafe.
Terminating: fork() called from a process already using GNU OpenMP, this is unsafe.
Terminating: fork() called from a process already using GNU OpenMP, this is unsafe.
Terminating: fork() called from a process already using GNU OpenMP, this is unsafe.
Terminating: fork() called from a process already using GNU OpenMP, this is unsafe.
Terminating: fork() called from a process already using GNU OpenMP, this is unsafe.
[('BM', 'BR'), ('BM', 'BS'), ('BM', 'BS2'), ('BM', 'BS3'), ('BM', 'BW'), ('BM', 'CD'), ('BM', 'CR'), ('BM', 'DB'), ('BM', 'DI'), ('BM', 'EE'), ('BM', 'GM'), ('BM', 'GS'), ('BM', 'HA'), ('BM', 'HB'), ('BM', 'HS'), ('BM', 'JE'), ('BM', 'KA'), ('BM', 'KR'), ('BM', 'LK'), ('BM', 'LR'), ('BM', 'MG'), ('BM', 'MJ'), ('BM', 'NP'), ('BM', 'PH'), ('BM', 'PS'), ('BM', 'SF'), ('BM', 'SR'), ('BM', 'TO'), ('BM', 'WD'), ('BM', 'WL'), ('BM', 'WS'), ('BR', 'BS'), ('BR', 'BS2'), ('BR', 'BS3'), ('BR', 'BW'), ('BR', 'CD'), ('BR', 'CR'), ('BR', 'DB'), ('BR', 'DI'), ('BR', 'EE'), ('BR', 'GM'), ('BR', 'GS'), ('BR', 'HA'), ('BR', 'HB'), ('BR', 'HS'), ('BR', 'JE'), ('BR', 'KA'), ('BR', 'KR'), ('BR', 'LK'), ('BR', 'LR'), ('BR', 'MG'), ('BR', 'MJ'), ('BR', 'NP'), ('BR', 'PH'), ('BR', 'PS'), ('BR', 'SF'), ('BR', 'SR'), ('BR', 'TO'), ('BR', 'WD'), ('BR', 'WL'), ('BR', 'WS'), ('BS', 'BS2'), ('BS', 'BS3'), ('BS', 'BW'), ('BS', 'CD'), ('BS', 'CR'), ('BS', 'DB'), ('BS', 'DI'), ('BS', 'EE'), ('BS', 'GM'), ('BS', 'GS')] generated an exception: A process in the process pool was terminated abruptly while the future was running or pending.
[('BS', 'HA'), ('BS', 'HB'), ('BS', 'HS'), ('BS', 'JE'), ('BS', 'KA'), ('BS', 'KR'), ('BS', 'LK'), ('BS', 'LR'), ('BS', 'MG'), ('BS', 'MJ'), ('BS', 'NP'), ('BS', 'PH'), ('BS', 'PS'), ('BS', 'SF'), ('BS', 'SR'), ('BS', 'TO'), ('BS', 'WD'), ('BS', 'WL'), ('BS', 'WS'), ('BS2', 'BS3'), ('BS2', 'BW'), ('BS2', 'CD'), ('BS2', 'CR'), ('BS2', 'DB'), ('BS2', 'DI'), ('BS2', 'EE'), ('BS2', 'GM'), ('BS2', 'GS'), ('BS2', 'HA'), ('BS2', 'HB'), ('BS2', 'HS'), ('BS2', 'JE'), ('BS2', 'KA'), ('BS2', 'KR'), ('BS2', 'LK'), ('BS2', 'LR'), ('BS2', 'MG'), ('BS2', 'MJ'), ('BS2', 'NP'), ('BS2', 'PH'), ('BS2', 'PS'), ('BS2', 'SF'), ('BS2', 'SR'), ('BS2', 'TO'), ('BS2', 'WD'), ('BS2', 'WL'), ('BS2', 'WS'), ('BS3', 'BW'), ('BS3', 'CD'), ('BS3', 'CR'), ('BS3', 'DB'), ('BS3', 'DI'), ('BS3', 'EE'), ('BS3', 'GM'), ('BS3', 'GS'), ('BS3', 'HA'), ('BS3', 'HB'), ('BS3', 'HS'), ('BS3', 'JE'), ('BS3', 'KA'), ('BS3', 'KR'), ('BS3', 'LK'), ('BS3', 'LR'), ('BS3', 'MG'), ('BS3', 'MJ'), ('BS3', 'NP'), ('BS3', 'PH'), ('BS3', 'PS'), ('BS3', 'SF'), ('BS3', 'SR'), ('BS3', 'TO')] generated an exception: A process in the process pool was terminated abruptly while the future was running or pending.
[('BS3', 'WD'), ('BS3', 'WL'), ('BS3', 'WS'), ('BW', 'CD'), ('BW', 'CR'), ('BW', 'DB'), ('BW', 'DI'), ('BW', 'EE'), ('BW', 'GM'), ('BW', 'GS'), ('BW', 'HA'), ('BW', 'HB'), ('BW', 'HS'), ('BW', 'JE'), ('BW', 'KA'), ('BW', 'KR'), ('BW', 'LK'), ('BW', 'LR'), ('BW', 'MG'), ('BW', 'MJ'), ('BW', 'NP'), ('BW', 'PH'), ('BW', 'PS'), ('BW', 'SF'), ('BW', 'SR'), ('BW', 'TO'), ('BW', 'WD'), ('BW', 'WL'), ('BW', 'WS'), ('CD', 'CR'), ('CD', 'DB'), ('CD', 'DI'), ('CD', 'EE'), ('CD', 'GM'), ('CD', 'GS'), ('CD', 'HA'), ('CD', 'HB'), ('CD', 'HS'), ('CD', 'JE'), ('CD', 'KA'), ('CD', 'KR'), ('CD', 'LK'), ('CD', 'LR'), ('CD', 'MG'), ('CD', 'MJ'), ('CD', 'NP'), ('CD', 'PH'), ('CD', 'PS'), ('CD', 'SF'), ('CD', 'SR'), ('CD', 'TO'), ('CD', 'WD'), ('CD', 'WL'), ('CD', 'WS'), ('CR', 'DB'), ('CR', 'DI'), ('CR', 'EE'), ('CR', 'GM'), ('CR', 'GS'), ('CR', 'HA'), ('CR', 'HB'), ('CR', 'HS'), ('CR', 'JE'), ('CR', 'KA'), ('CR', 'KR'), ('CR', 'LK'), ('CR', 'LR'), ('CR', 'MG'), ('CR', 'MJ'), ('CR', 'NP'), ('CR', 'PH')] generated an exception: A process in the process pool was terminated abruptly while the future was running or pending.
[('CR', 'PS'), ('CR', 'SF'), ('CR', 'SR'), ('CR', 'TO'), ('CR', 'WD'), ('CR', 'WL'), ('CR', 'WS'), ('DB', 'DI'), ('DB', 'EE'), ('DB', 'GM'), ('DB', 'GS'), ('DB', 'HA'), ('DB', 'HB'), ('DB', 'HS'), ('DB', 'JE'), ('DB', 'KA'), ('DB', 'KR'), ('DB', 'LK'), ('DB', 'LR'), ('DB', 'MG'), ('DB', 'MJ'), ('DB', 'NP'), ('DB', 'PH'), ('DB', 'PS'), ('DB', 'SF'), ('DB', 'SR'), ('DB', 'TO'), ('DB', 'WD'), ('DB', 'WL'), ('DB', 'WS'), ('DI', 'EE'), ('DI', 'GM'), ('DI', 'GS'), ('DI', 'HA'), ('DI', 'HB'), ('DI', 'HS'), ('DI', 'JE'), ('DI', 'KA'), ('DI', 'KR'), ('DI', 'LK'), ('DI', 'LR'), ('DI', 'MG'), ('DI', 'MJ'), ('DI', 'NP'), ('DI', 'PH'), ('DI', 'PS'), ('DI', 'SF'), ('DI', 'SR'), ('DI', 'TO'), ('DI', 'WD'), ('DI', 'WL'), ('DI', 'WS'), ('EE', 'GM'), ('EE', 'GS'), ('EE', 'HA'), ('EE', 'HB'), ('EE', 'HS'), ('EE', 'JE'), ('EE', 'KA'), ('EE', 'KR'), ('EE', 'LK'), ('EE', 'LR'), ('EE', 'MG'), ('EE', 'MJ'), ('EE', 'NP'), ('EE', 'PH'), ('EE', 'PS'), ('EE', 'SF'), ('EE', 'SR'), ('EE', 'TO'), ('EE', 'WD')] generated an exception: A process in the process pool was terminated abruptly while the future was running or pending.
[('EE', 'WL'), ('EE', 'WS'), ('GM', 'GS'), ('GM', 'HA'), ('GM', 'HB'), ('GM', 'HS'), ('GM', 'JE'), ('GM', 'KA'), ('GM', 'KR'), ('GM', 'LK'), ('GM', 'LR'), ('GM', 'MG'), ('GM', 'MJ'), ('GM', 'NP'), ('GM', 'PH'), ('GM', 'PS'), ('GM', 'SF'), ('GM', 'SR'), ('GM', 'TO'), ('GM', 'WD'), ('GM', 'WL'), ('GM', 'WS'), ('GS', 'HA'), ('GS', 'HB'), ('GS', 'HS'), ('GS', 'JE'), ('GS', 'KA'), ('GS', 'KR'), ('GS', 'LK'), ('GS', 'LR'), ('GS', 'MG'), ('GS', 'MJ'), ('GS', 'NP'), ('GS', 'PH'), ('GS', 'PS'), ('GS', 'SF'), ('GS', 'SR'), ('GS', 'TO'), ('GS', 'WD'), ('GS', 'WL'), ('GS', 'WS'), ('HA', 'HB'), ('HA', 'HS'), ('HA', 'JE'), ('HA', 'KA'), ('HA', 'KR'), ('HA', 'LK'), ('HA', 'LR'), ('HA', 'MG'), ('HA', 'MJ'), ('HA', 'NP'), ('HA', 'PH'), ('HA', 'PS'), ('HA', 'SF'), ('HA', 'SR'), ('HA', 'TO'), ('HA', 'WD'), ('HA', 'WL'), ('HA', 'WS'), ('HB', 'HS'), ('HB', 'JE'), ('HB', 'KA'), ('HB', 'KR'), ('HB', 'LK'), ('HB', 'LR'), ('HB', 'MG'), ('HB', 'MJ'), ('HB', 'NP'), ('HB', 'PH'), ('HB', 'PS'), ('HB', 'SF')] generated an exception: A process in the process pool was terminated abruptly while the future was running or pending.
[('HB', 'SR'), ('HB', 'TO'), ('HB', 'WD'), ('HB', 'WL'), ('HB', 'WS'), ('HS', 'JE'), ('HS', 'KA'), ('HS', 'KR'), ('HS', 'LK'), ('HS', 'LR'), ('HS', 'MG'), ('HS', 'MJ'), ('HS', 'NP'), ('HS', 'PH'), ('HS', 'PS'), ('HS', 'SF'), ('HS', 'SR'), ('HS', 'TO'), ('HS', 'WD'), ('HS', 'WL'), ('HS', 'WS'), ('JE', 'KA'), ('JE', 'KR'), ('JE', 'LK'), ('JE', 'LR'), ('JE', 'MG'), ('JE', 'MJ'), ('JE', 'NP'), ('JE', 'PH'), ('JE', 'PS'), ('JE', 'SF'), ('JE', 'SR'), ('JE', 'TO'), ('JE', 'WD'), ('JE', 'WL'), ('JE', 'WS'), ('KA', 'KR'), ('KA', 'LK'), ('KA', 'LR'), ('KA', 'MG'), ('KA', 'MJ'), ('KA', 'NP'), ('KA', 'PH'), ('KA', 'PS'), ('KA', 'SF'), ('KA', 'SR'), ('KA', 'TO'), ('KA', 'WD'), ('KA', 'WL'), ('KA', 'WS'), ('KR', 'LK'), ('KR', 'LR'), ('KR', 'MG'), ('KR', 'MJ'), ('KR', 'NP'), ('KR', 'PH'), ('KR', 'PS'), ('KR', 'SF'), ('KR', 'SR'), ('KR', 'TO'), ('KR', 'WD'), ('KR', 'WL'), ('KR', 'WS'), ('LK', 'LR'), ('LK', 'MG'), ('LK', 'MJ'), ('LK', 'NP'), ('LK', 'PH'), ('LK', 'PS'), ('LK', 'SF'), ('LK', 'SR')] generated an exception: A process in the process pool was terminated abruptly while the future was running or pending.
[('LK', 'TO'), ('LK', 'WD'), ('LK', 'WL'), ('LK', 'WS'), ('LR', 'MG'), ('LR', 'MJ'), ('LR', 'NP'), ('LR', 'PH'), ('LR', 'PS'), ('LR', 'SF'), ('LR', 'SR'), ('LR', 'TO'), ('LR', 'WD'), ('LR', 'WL'), ('LR', 'WS'), ('MG', 'MJ'), ('MG', 'NP'), ('MG', 'PH'), ('MG', 'PS'), ('MG', 'SF'), ('MG', 'SR'), ('MG', 'TO'), ('MG', 'WD'), ('MG', 'WL'), ('MG', 'WS'), ('MJ', 'NP'), ('MJ', 'PH'), ('MJ', 'PS'), ('MJ', 'SF'), ('MJ', 'SR'), ('MJ', 'TO'), ('MJ', 'WD'), ('MJ', 'WL'), ('MJ', 'WS'), ('NP', 'PH'), ('NP', 'PS'), ('NP', 'SF'), ('NP', 'SR'), ('NP', 'TO'), ('NP', 'WD'), ('NP', 'WL'), ('NP', 'WS'), ('PH', 'PS'), ('PH', 'SF'), ('PH', 'SR'), ('PH', 'TO'), ('PH', 'WD'), ('PH', 'WL'), ('PH', 'WS'), ('PS', 'SF'), ('PS', 'SR'), ('PS', 'TO'), ('PS', 'WD'), ('PS', 'WL'), ('PS', 'WS'), ('SF', 'SR'), ('SF', 'TO'), ('SF', 'WD'), ('SF', 'WL'), ('SF', 'WS'), ('SR', 'TO'), ('SR', 'WD'), ('SR', 'WL'), ('SR', 'WS'), ('TO', 'WD'), ('TO', 'WL'), ('TO', 'WS'), ('WD', 'WL'), ('WD', 'WS'), ('WL', 'WS')] generated an exception: A process in the process pool was terminated abruptly while the future was running or pending.
ETesting gr-finder sgd with 7 cpus
mazzalab commented 3 years ago

This should be related to the way your system handles multi-threading through OpenMP. I cannot reproduce your error. Open another issue with more specific details if this error comes up again, also outside the test suite.