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benedictpaten / jobTree

Python based pipeline management software for clusters (but checkout toil: https://github.com/BD2KGenomics/toil, its successor)
MIT License
24 stars 18 forks source link

errors in "make test" #2

Closed thirtyeggs closed 10 years ago

thirtyeggs commented 13 years ago

Hi Benedict,

I got some error messages when I ran "make test"


Starting to create the job tree setup for the first time
Traceback (most recent call last):
  File "/projects/gec/tool/assemblathon1/jobTree/bin/scriptTreeTest_Sort.py", line 119, in <module>
    main()
  File "/gpfs2/projects/gec/tool/assemblathon1/jobTree/test/sort/scriptTreeTest_Sort.py", line 112, in main
    i = Stack(Setup(options.fileToSort, int(options.N))).startJobTree(options)
  File "/gpfs2/projects/gec/tool/assemblathon1/jobTree/scriptTree/stack.py", line 112, in startJobTree
    config, batchSystem = createJobTree(options)
  File "/gpfs2/projects/gec/tool/assemblathon1/jobTree/src/jobTreeRun.py", line 221, in createJobTree
    batchSystem = loadTheBatchSystem(config)
  File "/gpfs2/projects/gec/tool/assemblathon1/jobTree/src/jobTreeRun.py", line 157, in loadTheBatchSystem
    batchSystem = GridengineBatchSystem(config)
  File "/gpfs2/projects/gec/tool/assemblathon1/jobTree/batchSystems/gridengine.py", line 136, in __init__
    self.obtainSystemConstants()
  File "/gpfs2/projects/gec/tool/assemblathon1/jobTree/batchSystems/gridengine.py", line 267, in obtainSystemConstants
    p = subprocess.Popen(["qhost"], stdout = subprocess.PIPE,stderr = subprocess.STDOUT)
  File "/usr/lib64/python2.6/subprocess.py", line 595, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.6/subprocess.py", line 1106, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory
E
======================================================================
ERROR: Uses the jobTreeTest code to test the scriptTree Target wrapper.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/gpfs2/projects/gec/tool/assemblathon1/jobTree/test/scriptTree/scriptTreeTest.py", line 31, in testScriptTree_Example
    system(command)
  File "/gpfs2/projects/gec/tool/assemblathon1/sonLib/bioio.py", line 160, in system
    raise RuntimeError("Command: %s exited with non-zero status %i" % (command, i))
RuntimeError: Command: scriptTreeTest_Wrapper.py --jobTree /gpfs2/projects/gec/tool/assemblathon1/jobTree/tmp_KEwg5sdOhb/jobTree --logLevel=INFO --retryCount=10 exited with non-zero status 256

======================================================================
ERROR: Tests that the global and local temp dirs of a job behave as expected.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/gpfs2/projects/gec/tool/assemblathon1/jobTree/test/scriptTree/scriptTreeTest.py", line 39, in testScriptTree_Example2
    system(command)
  File "/gpfs2/projects/gec/tool/assemblathon1/sonLib/bioio.py", line 160, in system
    raise RuntimeError("Command: %s exited with non-zero status %i" % (command, i))
RuntimeError: Command: scriptTreeTest_Wrapper2.py --jobTree /gpfs2/projects/gec/tool/assemblathon1/jobTree/tmp_GKficygzKn/jobTree --logLevel=INFO --retryCount=0 exited with non-zero status 256

======================================================================
ERROR: Tests the jobTreeStats utility using the scriptTree_sort example.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/gpfs2/projects/gec/tool/assemblathon1/jobTree/test/utilities/statsTest.py", line 35, in testJobTreeStats_SortSimple
    system(command)
  File "/gpfs2/projects/gec/tool/assemblathon1/sonLib/bioio.py", line 160, in system
    raise RuntimeError("Command: %s exited with non-zero status %i" % (command, i))
RuntimeError: Command: scriptTreeTest_Sort.py --jobTree /gpfs2/projects/gec/tool/assemblathon1/jobTree/tmp_rZqK92206Q/jobTree --logLevel=DEBUG --fileToSort=/gpfs2/projects/gec/tool/assemblathon1/jobTree/tmp_rZqK922
06Q/tmp_wj73HRVMZx --N 1000 --stats --jobTime 0.5 exited with non-zero status 256

----------------------------------------------------------------------
Ran 14 tests in 318.742s

FAILED (errors=3)

Could I ask what it happened? Thank you.

Regards,

Yun

benedictpaten commented 13 years ago

Hi Yun, Can you please post a fuller log output of the tests.. as this is not sufficient to tell me why they failed. I think it's because grid engine is installed on your system, but non-functional, but I could be wrong.