joonkeekim / mediar-napari Goto Github PK

Hey, you all,
In working on Linux remote cluster
I followed the instructions in the installation part, and then I submitted bsub missions with GPU:

(mediar-napari) [barc@access4 mediar-napari]$ bsub -q gpu-interactive -gpu num=1:j_exclusive=yes:gmem=8G:gmodel=NVIDIAA40 -R rusage[mem=10000] -R affinity[thread*4] -m hgn_2022_hosts -Is -XF "/bin/bash -l"

when in running

(mediar-napari) [barc@hgn22 mediar-napari]$ napari -w mediar

Im getting:

WARNING: Could not load the Qt platform plugin "xcb" in "" even though it was found.
08:56:47 WARNING Could not load the Qt platform plugin "xcb" in "" even though it was found.
WARNING: This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

08:56:47 WARNING This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

Aborted (core dumped)

I tried to reinstall it, but it didn't help.

I had a similar problem in the past in a GUI app that didn't require GPU as a mandatory requirement.
The problem was solved when I installed PyQt5 and QtPy independently but in this case the pip install "napari[all]" install both as you can see in the following pip list:

(mediar-napari) [barc@access4 mediar-napari]$ pip list |grep Py*
Package                       Version      Editable project location
Pint                          0.21.1
Pygments                      2.17.2
PyOpenGL                      3.1.7
PyQt5                         5.15.10
PyQt5-Qt5                     5.15.2
PyQt5-sip                     12.13.0
PyWavelets                    1.4.1
PyYAML                        6.0.1
QtPy                          2.4.1

Please help me with this issue.
Thanks

Hi! My Napari crashed when I clicked run segmentation and the crash report said Napari crashed with a segmentation fault (SIGSEGV). It happens to all 3 cell segmentation tools.
My computer is MacOS with M2 chip, 24G memory.
I saw some old posts that said it might occur because of some memory issues. So I want to check if this is a problem I could try something to solve, or it is some internal conflict between the operation of my system and the package provided by developers?

Hi there. Running mediar on the provided 3D+2Ch cell sample gives me the below error.
I did not have time to go through the code, but I've noticed that it tries to allocate most of the VRAM more than once. I've also noticed that running mediar on a multichannel 2D image provokes a similar behaviour, while a 2D RGB image (conforming to your 2D sample) is segmented w/o any issues.

OutOfMemoryError: CUDA out of memory. Tried to allocate 37.50 GiB. GPU 0 has a total capacity of 44.53 GiB of which 4.67 GiB is free. Process 1818 has 264.07 MiB memory in use. Including non-PyTorch memory, this process has 38.34 GiB memory in use. Of the allocated memory 37.96 GiB is allocated by PyTorch, and 19.14 MiB is reserved by PyTorch but unallocated. If reserved but unallocated memory is large try setting PYTORCH_CUDA_ALLOC_CONF=expandable_segments:True to avoid fragmentation. See documentation for Memory Management (https://pytorch.org/docs/stable/notes/cuda.html#environment-variables)

Works fine immediately after installation but after deactivating conda environment and reactivating I'm receiving this error every time. The model files have not been moved. Any ideas?

Hi!
I followed the installation instructions: create a new environment, download Napari, download the packages from github, download the models and put them in the home directory, and install -r requirements.py.
After completing all the steps and running mediar, I received a warning that I was missing necessary packages such as pytorch, timm, monai, csbdeep, stardist, fastremap, imagecodecs, and cellpose. I installed all of these packages as prompted by the error warning. After each step, I tested mediar separately, and only when I installed imagecodecs and cellpose did my Napari start crashing and force quitting immediately after running mediar.
I was suggested by other technicians that the requirements.py shall contain all the packages required for mediar, but I do receive a warning that the imagecodecs cannot be installed in my computer as following:
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for imagecodecs
Running setup.py clean for imagecodecs
Failed to build imagecodecs
ERROR: Could not build wheels for imagecodecs, which is required to install pyproject.toml-based projects

I think this is why I get other warnings when I try to run mediar after ignoring this error message.
Any idea on how to fix this?

Here is my Napari output info:

napari: 0.4.19.post1
Platform: macOS-12.6-arm64-arm-64bit
System: MacOS 12.6
Python: 3.8.19 | packaged by conda-forge | (default, Mar 20 2024, 12:49:57) [Clang 16.0.6 ]
Qt: 5.15.11
PyQt5: 5.15.10
NumPy: 1.24.4
SciPy: 1.10.1
Dask: 2023.5.0
VisPy: 0.14.2
magicgui: 0.8.2
superqt: 0.6.3
in-n-out: 0.2.0
app-model: 0.2.6
npe2: 0.7.5

OpenGL:

GL version: 2.1 Metal - 76.3
MAX_TEXTURE_SIZE: 16384
Screens:

screen 1: resolution 1470x956, scale 2.0
Settings path:

/Users/lylayu/Library/Application Support/napari/mediar-napari-test-withoutcellpose_00897f8debca681c586e8093dfaf5b95dcf4f211/settings.yaml
Plugins:
mediar: 0.0.1 (6 contributions)
napari: 0.4.19.post1 (77 contributions)
napari-console: 0.0.9 (0 contributions)
napari-svg: 0.1.10 (2 contributions)

I am using macOS system, after successfully installing Napari, I cannot enter the file named mediar-napari through the terminal. Looks like it did not create this directory in my environment? I run into the same issue with the other 3 cell segmentation plugins of Napari as well, any idea how to solve this?