Ilastik: Problems Running Ilastik on Fedora 30

Dear All

I am brand new to ilastik! This is probably a relatively basic dependencies issue but I can’t make heads or tails of the output I am getting on attempting to run run_ilastik.sh on my Fedora 30 machine. The terminal output I get is as follows:

Warning: Ignoring your non-empty LD_LIBRARY_PATH
Warning: Ignoring your non-empty PYTHONPATH/PYTHONHOME
Starting ilastik from “/data/fiscal/wilsenac/ilastik-1.3.2post1-Linux”.
Fatal Python error: Segmentation fault

Thread 0x00007f0de9df1700 (most recent call first):
File “/data/fiscal/wilsenac/ilastik-1.3.2post1-Linux/lib/python3.6/threading.py”, line 299 in wait
File “/data/fiscal/wilsenac/ilastik-1.3.2post1-Linux/lib/python3.6/threading.py”, line 551 in wait
File “/data/fiscal/wilsenac/ilastik-1.3.2post1-Linux/lib/python3.6/threading.py”, line 1180 in run
File “/data/fiscal/wilsenac/ilastik-1.3.2post1-Linux/lib/python3.6/threading.py”, line 916 in _bootstrap_inner
File “/data/fiscal/wilsenac/ilastik-1.3.2post1-Linux/lib/python3.6/threading.py”, line 884 in _bootstrap

Current thread 0x00007f0e02b20740 (most recent call first):
File “/data/fiscal/wilsenac/ilastik-1.3.2post1-Linux/ilastik-meta/ilastik/ilastik/shell/gui/startShellGui.py”, line 56 in startShellGui
File “/data/fiscal/wilsenac/ilastik-1.3.2post1-Linux/ilastik-meta/ilastik/ilastik_main.py”, line 143 in main
File “/data/fiscal/wilsenac/ilastik-1.3.2post1-Linux/ilastik-meta/ilastik/ilastik.py”, line 108 in main
File “/data/fiscal/wilsenac/ilastik-1.3.2post1-Linux/ilastik-meta/ilastik/ilastik.py”, line 123 in
./run_ilastik.sh: line 68: 11982 Segmentation fault (core dumped) “{PREFIX}/bin/python" "{PREFIX}/ilastik-meta/ilastik/ilastik.py” “$@”

Any help would be really appreciated.

Thanks in advance
James

a simple thing you could try is using the latest beta version, as it is a bit more isolated from the system environment. Please let us know if you still have the same problem!

Hello there,

I am also experiencing Segmentation fault error while running blockwise obj classification. I made sure that all RAM claimed in LAZYFLOW_TOTAL_RAM_MB were available, but that didn’t help. Is there anything else I should check further?

PS: I am using 1.3.3b2

Many thx!
Tong

Hi @BioinfoTongLI,

I see that the link in this topic points to this version… which is outdated now. I edited the link to point to our latest beta on our webpage. Could you try 1.4.0b8?

Hi Dominik,

Thx for your fast reply!
Isn’t it 1.4.0 the version with NN included?
I didn’t want to bump the version too fast, as ilastik is part of our pipeline. But if that’s the way to fix it, I am more than happy to test the latest. :slight_smile:

Honestly @BioinfoTongLI,

I have no clue if it will fix it. If you’re conservative, you can try 1.3.3post3 (the latest stable)… Segfaults are usually related to some dependency clash and I’d say we got a little better with this over time (of course also thanks to conda-forge :bowing_man: ) :slight_smile:

Unfortunately, I am getting a new error with 1.4.0b8 - Will create an issue on GH repo if that hasn’t been reported yet.
Yeah, I will go with the latest stable maybe. Many thx for your kind advice! :grinning:

uncool that it doesn’t work (same problem?) but cool that you’ll open an issue :)!