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piff failing tests #50
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This is the test that reads in the output of the
in the tests directory? It should make a number of files in the output directory:
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Do |
here you go
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This looks like it's crashing the first time it tries to import galsim. I'm not sure why it would fail when doing so from piffify, but not when running the tests directly. Maybe check that And if you're willing to investigate a bit, maybe try running it within gdb, so you can get a backtrace. Maybe that will give a better clue about the nature of the seg fault. |
I just added some print statements on branch "#50". So could you try checking out this branch and running |
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Here is the tail end of valgrind
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Hm. Not what I expected at all. Maybe the image is getting corrupted somehow. I added some more print statements to investigate. This time could you please run The output might be long, so maybe easier to just redirect to a file and send me that file by email instead of posting here. |
Actually, one quick sanity check first. Was this where you were expecting boost to come from?
You didn't do |
That is what I expected. I'm using the system libraries for everything that I can. I did notice one of your dependencies installed mkl into anaconda however. |
Output of |
Anaconda's going to be the death of me someday probably. I've managed to reproduce this error on my system with Anaconda python3, so I'm investigating. (The same system where I reproduced this error.) |
This is very frustrating. About 1/3 of the time, I even get seg faults doing
in the Piff directory. Here's a run of 5 in a row that seg faulted before the 6th finally worked.
This makes me inclined to believe this is a bug in Anaconda, but I'm still trying to work down to a minimum test case. So far I've determined that when running Maybe Anaconda is garbage collecting in between, so maybe there's some kind of memory leak where memory gets deleted, but GalSim still tries to access it? Trying to keep an open mind that this could be a GalSim or Piff bug, rather than just blame Anaconda. Even though every other system I have, it all works fine... |
I finally tracked it down. Turns out it was a bug in GalSim that apparently has only shown up on this system yet. But a bonda fide bug that is worth fixing. So not Anaconda's fault. :) I think there's probably still some kind of bug in Anaconda causing seg faults, since I still get seg faults randomly at the very start or end of python programs. Even |
FYI for reference, I'm using miniconda and I've not installed numba, so I don't have a stdc++ library in Anaconda /lib. And on this system I don't see the random seg faults in |
Good. I think I'm going to post an issue about gcc 5+ working badly with Anaconda, since it shows up more purely with TreeCorr. Then there's no boost or TMV to connect with, so it's pure python-compiled-with-g++ leading to library errors at run time. Maybe something they'd be willing to consider trying to fix. But I'm glad this isn't an issue with miniconda at least. |
We've been having some trouble with LSST's conda packages recently due to anaconda's reference system being CentOS 5 with (I think) a custom gcc 5. That caused trouble when we built against it with later glibc versions or older gcc versions. I haven't been fully following the discussion, but if you think it may be the same thing, LSST's |
anaconda uses |
@esheldon The bug fix was merged into GalSim master branch. Could you confirm that this fixes things on your system? |
@TallJimbo Thanks for letting us know. I was actually wondering about that, since I know you guys have been moving toward using c++11 features now, and I thought you were using Anaconda. I was wondering whether those two facts were causing trouble for you. |
Here is what went to stderr (I noticed a lot of other info went to stdout)
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PIFF master
latest anaconda on ubuntu 16.04
galsim master
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