something goes wrong. It seems a python script crashes and cactus goes idle. Thread activity from that moment on is zero: (Please note on the bold thread, a python script crashed?)
Cactus does not return any error and just goes idle forever. I use a single machine with 64 threads and 250gb ram, all software and hardware requirements are met. I hope that you will be able to help me. Thank you! The log file contains the following:
_Process Process-18:
Traceback (most recent call last):
File "/data/sag/tvw/tools/cactus/progressiveCactus/submodules/cactus/bin/cactus_progressive.py", line 239, in
Process Process-12:
Process Process-15:
Process Process-3:
Traceback (most recent call last):
Traceback (most recent call last):
Process Process-4:
Traceback (most recent call last):
Process Process-5:
Traceback (most recent call last):
Process Process-14:
Traceback (most recent call last):echo
Process Process-6:
Process Process-19:
Process Process-13:
Traceback (most recent call last):
Process Process-16:
Process Process-2:
Traceback (most recent call last):
Process Process-11:
Process Process-20:
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
Process Process-8:
Traceback (most recent call last):
Process Process-9:
Traceback (most recent call last):
Process Process-7:
Traceback (most recent call last):
Process Process-10:
Process Process-17:
main()
File "/data/sag/tvw/tools/cactus/progressiveCactus/submodules/cactus/progressive/cactus_progressive.py", line 235, in main
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
Traceback (most recent call last):
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
Traceback (most recent call last):
self.run()
File "/usr/lib64/python2.6/multiprocessing/process.py", line 88, in run
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in bootstrap
Traceback (most recent call last):
Hello,
I successfully managed to install progressive cactus and load the python vm. However, when i try to build an alignment using the following command:
(python)[tvw@cl3node038 progressiveCactus]$ bin/runProgressiveCactus.sh examples/blanchette00.txt ../workDir ../outputfiles/test.hal --maxThreads 20 --overwrite
something goes wrong. It seems a python script crashes and cactus goes idle. Thread activity from that moment on is zero: (Please note on the bold thread, a python script crashed?)
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 43637 tvw 20 0 26988 2476 1068 R 2.0 0.0 0:21.12 top 43311 tvw 20 0 108m 2092 1140 S 0.0 0.0 0:00.17 sshd 43312 tvw 20 0 116m 2108 1572 S 0.0 0.0 0:00.26 bash 43546 tvw 20 0 108m 2104 1140 S 0.0 0.0 0:00.09 sshd 43547 tvw 20 0 116m 2020 1544 S 0.0 0.0 0:00.05 bash 43869 tvw 20 0 103m 1344 1116 S 0.0 0.0 0:00.00 runProgressiveC 43875 tvw 20 0 293m 19m 3540 S 0.0 0.0 0:00.76 python 43900 tvw 20 0 103m 1332 1100 S 0.0 0.0 0:00.00 sh 43905 tvw 20 0 297m 20m 3516 S 0.0 0.0 0:00.70 python 43910 tvw 20 0 0 0 0 Z 0.0 0.0 0:00.01 python < defunct> 43911 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43912 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43913 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43914 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43915 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43916 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43917 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43918 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43919 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43920 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43921 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43922 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43923 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43924 tvw 20 0 223m 17m 892 S 0.0 0.0 0:00.00 python 43925 tvw 20 0 223m 17m 896 S 0.0 0.0 0:00.00 python 43926 tvw 20 0 223m 17m 896 S 0.0 0.0 0:00.00 python 43927 tvw 20 0 223m 17m 896 S 0.0 0.0 0:00.00 python 43928 tvw 20 0 223m 17m 896 S 0.0 0.0 0:00.00 python 43929 tvw 20 0 223m 17m 896 S 0.0 0.0 0:00.00 python
Cactus does not return any error and just goes idle forever. I use a single machine with 64 threads and 250gb ram, all software and hardware requirements are met. I hope that you will be able to help me. Thank you! The log file contains the following:
2015-01-19 13:54:22.411757: Beginning Progressive Cactus Alignment
_Process Process-18: Traceback (most recent call last): File "/data/sag/tvw/tools/cactus/progressiveCactus/submodules/cactus/bin/cactus_progressive.py", line 239, in
Process Process-12:
Process Process-15:
Process Process-3:
Traceback (most recent call last):
Traceback (most recent call last):
Process Process-4:
Traceback (most recent call last):
Process Process-5:
Traceback (most recent call last):
Process Process-14:
Traceback (most recent call last):echo
Process Process-6:
Process Process-19:
Process Process-13:
Traceback (most recent call last):
Process Process-16:
Process Process-2:
Traceback (most recent call last):
Process Process-11:
Process Process-20:
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
Process Process-8:
Traceback (most recent call last):
Process Process-9:
Traceback (most recent call last):
Process Process-7:
Traceback (most recent call last):
Process Process-10:
Process Process-17:
main()
File "/data/sag/tvw/tools/cactus/progressiveCactus/submodules/cactus/progressive/cactus_progressive.py", line 235, in main
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
Traceback (most recent call last):
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
Traceback (most recent call last):
self.run()
File "/usr/lib64/python2.6/multiprocessing/process.py", line 88, in run
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in bootstrap
Traceback (most recent call last):