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Hello, Full error thread: Fatal Python error: Aborted Thread 0x00002b0fd9026700 (most recent call first): Thread 0x00002b0fd8e25700 (most recent call first): Thread 0x00002b0fd8c24700 (most recent call first): Current thread 0x00002b0dc13b1f40 (most recent call first): |
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Replies: 7 comments 5 replies
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Hi HdeV, It's good to read you. I hope you are doing well. From the error message, the error is very likely related to Qt : zygote term seems to be used by Chromium that underlies the Qt widget to display HTML content. There is no simpler way to make our software crash than changing PyQt. I believe that Anatomist still work because it did not try to load the Qt version from PyQt but our compiled version. If you try to use PyQt from Anatomist you will probably have the same kind of funny (because unpredictable) result. The reason for that is that PyQt from Pypi comes with its own Qt. Even if it can have compatible version we provide our own Qt because we do not know any way to compile C++ software using the Qt provided by PyQt. And some of our software is in C++. PyQt's Qt and BrainVISA's Qt are not binary compatible but, to tell it simply, all C++ software that uses Qt must use the same Qt binary. And PyQt is such a software. Since BrainVISA may use some Python modules that are in C++ and are using Qt, everything becomes linked with this binary dependency. So, to use BrainVISA, one must use our Qt and our PyQt. I think you don't have to rebuild your environment. You probably have modified PyQt via Yours sincerely. |
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Sorry, I missed that you still got the error after reinstalling BrainVISA. My solution is probably wrong then. Did you modify the Singularity image or are you using the same home directory (for the two installs) ? We may get in touch directly to find out how to solve this, it would be more efficient. |
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Yes that sounds great. Would you have any time soon for a small videoconference maybe? I just sent you an email in case you don't have my lasting email address... |
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We checked that your installation is clean. There is no custom pip installed package therefore I was not looking towards a good solution. Since it works for someone else in the same condition and after reading the errors again, I suspect something related to a low level system problem. It seems that there are problems with Python threading (both in Qt and in Soma-Workflow). Could it be possible that Python cannot properly run a thread anymore in your environment (you told me that you removed some cluster modules) ? I told you to wait but I changed my mind, it may be a good idea to get in touch with your support team either to ask them if they have an idea or simply to reset your environment. |
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Did you removed your comment ? I received a mail but cannot see it her. Anyway, you can test threading with the following Python code.
```
from __future__ import print_function
import threading
import time
def thread_function(t):
print('here')
time.sleep(t)
print('there')
t = threading.Thread(target=thread_function, args=(2,))
t.start()
t.join()
```
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Yes I did, I felt bad about asking you this question when I could easily find my answer online... Apart from that I reinstalled a new casa-distro and brainvisa image (casa-dev-5.3-17) and when opening brainvisa, I first get the upload/update databases window and then brainvisa crashes, with a much less verbose error message: connect to computing resource: login-e-12 Still zygote being unhappy... |
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I have useful new information: I have just assisted a new colleague in installing the new 5.1.0 release of brainvisa. Everything (bv, anatomist) went well until we tried to open brainvisa: she got this error message: connect to computing resource: login-e-15 So what I have now is:
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Hi, |
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That worked! My brainvisa is up and running again \o/ |
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Then we have to provide a fix for the binary distribution... |
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Ok thanks! |
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I have opened a ticket here: brainvisa/axon#66 |
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Hi,
I don't know what is zygote, but is seems to be in the Qt web browser module: QtWebEngine. This module replaces the older QtWebKit, and has been activated somewhat by mistake in the 5.1.0 release. So we can try using the older one again. This will likely fix the problem for you, but is not a long run solution because Qt6 will not provide QtWebKit any longer. Anyway for now it should fix things. Note that I have no idea why it doesn't work on your system in a container, whereas it works well for us in the same container.
Since you have a developer setup, just run
bv_makerto update and startbrainvisaagain. Let's see if this works before going further...