On 18/01/15 at 23:50 +1100, Stuart Prescott wrote: > Control: tag -1 unreproducible > > The actual failure is: > > test_raxml_tool ... FAIL > > […] > > ====================================================================== > ERROR: test_raxml (test_raxml_tool.AppTests) > Run RAxML using the wrapper. > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/«BUILDDIR»/python- > biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Tests/test_raxml_tool.py", > line 45, in test_raxml > out, err = cmd() > File "/«BUILDDIR»/python- > biopython-1.64+dfsg/.pybuild/pythonX.Y_2.7/build/Bio/Application/__init__.py", > > line 513, in __call__ > stdout_str, stderr_str) > ApplicationError: Non-zero return code 255 from 'raxmlHPC -m PROTCATWAG -n > test -p 10000 -s Phylip/interlaced2.phy' > > ---------------------------------------------------------------------- > > I cannot reproduce this failure in a jessie chroot. I'm unable to cause > raxmlHPC to exit(-1) here when I try (although it certainly has plenty of > places where it can do that in its code).
Trying to run raxml manually, I get: (jessie-amd64-sbuild)user@ip-172-31-5-2:/tmp/python-biopython-1.64+dfsg/Tests$ raxmlHPC -m PROTCATWAG -n test -p 10000 -s Phylip/interlaced2.phy Use raxml with SSE3 support (1 cpus) The number of threads is currently set to 1 Specify the number of threads to run via -T numberOfThreads NumberOfThreads must be set to an integer value greater than 1 (jessie-amd64-sbuild)user@ip-172-31-5-2:/tmp/python-biopython-1.64+dfsg/Tests$ echo $? 255 However on my laptop, I get: *** lucas@grr:/tmp/python-biopython-1.64+dfsg/Tests$ raxmlHPC -m PROTCATWAG -n test -p 10000 -s Phylip/interlaced2.phy Use raxml with AVX support (2 cpus) This is the RAxML Master Pthread This is RAxML Worker Pthread Number: 1 So it seems that raxml tries to guess the fastest possible implementation based on CPU capabilities. /proc/cpuinfo on EC2 does not include AVX, so it fallbacks to a SSE3 implementation, that requires specifying the number of threads. (it works if I add -T 2) Ideally, there would be a sane default for each RAxML implementation. It can easily be argued that this is not RC, given that it should be possible to build the package on a machine where SSE3 is not the default raxml implementation. Another option could be to add '-T 2' to the raxml command-line, but I haven't checked what happens if -T is specified on an implementation that does not support threads. Or just switch to using raxmlHPC-PTHREADS, but then it defeats the purpose of the test... Lucas -- To UNSUBSCRIBE, email to debian-bugs-rc-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org