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[Bug]: segmentation fault MC3 package after running light curves #628
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@evamariaa, can you see if Kevin's tweak in PR #609 for the file |
Ok, just installed from PR #609 and running through Stage 5 now, so far I didn't get a segmentation fault yet so I'm cautiously optimistic and will let you know if it stays like this! Thanks! |
Same problem, but using MacOS. |
Can one or both of you please try the code in PR #609 and confirm that the problem is resolved for you if you use that version of the code? We'll hopefully have this bug patched ASAP |
Nothing changed since my previous comment, as in it seems to run fine with the PR #609 you mentioned, no segmentation faults so far. But I haven't run Stage 5 much since then because of maintenance on our server. I should be able to run more by the end of the week and let you know! |
I just merged #609 into the Main branch. Try updating your version of Eureka! and let me know if you still have problems. |
Reinstalled Eureka! from the main branch and getting an error now when importing Eureka:
Problem is our cluster was under maintenance for a couple of days and they did lots of updates and there are still some bugs so I'm not sure if it's even a Eureka! issue or not. I will keep you posted. |
Did your installation of mc3 succeed? It looks to me like you might've been missing a C compiler or something which meant mc3 didn't finish installing or something |
@evamariaa, can you confirm whether this issue is resolved now? |
I wish, but no I can't confirm either way. Our cluster here still has issues, particularly with the file and storage system and is completely unusable right now. An external company has been brought in this week to fix it so hopefully I can give you an update sometime next week. |
I just updated to the latest version of Eureka! on my Linux machine and I'm getting a similar error.
I can confirm that I have a valid C compiler, so maybe this is a Linux issue. |
Interesting, I'm running Ubuntu on Windows Subsystem for Linux which should be sufficiently similar to have encountered such an issue on my end if it were a Linux-based issue. I can try reproducing this with a Docker build though to reduce the number of unknowns. |
@taylorbell57 I'm also getting this now, on Ubuntu/WSL, identically to Kevin's error message.
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I pushed a workaround to Main, so updating Eureka! should "fix" the problem until we find a more permanent solution. |
The error is on import. If it fails, you'll get a warning message that states MC3 failed to import. |
I just created a new conda environment and performed a fresh install using Python 3.10 and had no issues importing MC3. Perhaps MC3 has compatibility issues with Python 3.9. |
I know that @jbrande and @evamariaa, could you please see if this is still an issue for you when starting from a fresh install of the main branch version (using |
Sorry for the delay on this, this got a little bit lost in my to-do list. |
Alright, since two of you who previously had issues with this no longer do after creating a new conda environment, I'm going to close this issue as it seems not to be reproducible anymore. If anyone re-encounters this issue, feel free to leave a comment and we can re-open this issue |
FAQ check
Instrument
Light curve fitting (Stages 4-6)
What happened?
I get a segmentation fault after running light curve fits (same for dynesty and emcee, and not on all light curves) and I traced down to MC3 package.
It's the function from MC3
from mc3.stats import time_avg
that causes it, previous Allan plot looks fine so I'm not sure what the issue is that MC3 crashes - is it a Eureka! or a MC3 problem? Either way it's flagged this way.I created a new conda environment and new installation and it still pops up.
Error traceback output
When running with gdb:
EMCEE RESULTS:
rp: 0.09314383900504214 (+0.00023746832716464716, -0.00024390231091873937)
t0: 60336.16629344476 (+0.0001366072174278088, -0.00014108874165685847)
inc: 86.14041037419365 (+0.03564806637537288, -0.03959720206140105)
a: 7.5178380816512576 (+0.012216578350765062, -0.012060384627009313)
u2: 0.0596876616903001 (+0.01720078126260373, -0.016858445839115672)
c0: 1.0037328901325697 (+3.041406496073762e-05, -2.8784564057193762e-05)
c1: -0.00018125230315689576 (+0.00021138404946226995, -0.00022132731635158144)
scatter_mult: 4.604809762772209 (+0.1430173800715835, -0.12412840317554785); 489.802873463214 (+15.212425121351847, -13.203248708624503) ppm
Program received signal SIGSEGV, Segmentation fault.
0x00007ffe987d7c1e in invgamma ()
from /home/ahrer/.conda/envs/eureka-dev/lib/python3.9/site-packages/mc3/lib/_time_averaging.cpython-39-x86_64-linux-gnu.so
What operating system are you using?
Linux
What version of Python are you running?
Python 3.9.7
What Python packages do you have installed?
No response
Code of Conduct
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