chrisburr
commented
3 years ago This is an issue for root as well. Getting llvmlite from pip avoids the issue so I suspect it's an issue with how llvmlite is dynamically linking to LLVM.
Closed danschef closed 3 years ago
chrisburr
commented
3 years ago This is an issue for root as well. Getting llvmlite from pip avoids the issue so I suspect it's an issue with how llvmlite is dynamically linking to LLVM.
chrisburr
commented
3 years ago Actually it's not that simple, it's still a problem if I switch to static linking by removing this line:
chrisburr
commented
3 years ago I can get a working binary if I:
--link-static when calling llvm-config hereThe CMake build can be fixed by applying:
diff --git a/ffi/CMakeLists.txt.old b/ffi/CMakeLists.txt
old mode 100644
new mode 100755
index d87735c..59f1b4b
--- a/ffi/CMakeLists.txt.old
+++ b/ffi/CMakeLists.txt
@@ -61,3 +61,4 @@ list(REMOVE_ITEM llvm_libs "OptRemarks")
# Link against LLVM libraries
target_link_libraries(llvmlite ${llvm_libs})
+set_property(TARGET llvmlite APPEND_STRING PROPERTY LINK_FLAGS "-Wl,--exclude-libs,ALL")
xhochy
commented
3 years ago Probably something in the qgis stack is statically linking LLVM and doesn't use a (correct) version script. Probably switching that component to dynamic LLVM linkage should help here.
chrisburr
commented
3 years ago Yup, that was the problem for root (static linking is essential in this case but the symbols weren't being hidden correctly).
Creating the environment and greping for symbols I don't notice anything suspicious. My best guess would be that it's an OpenGL issue on @danschef's machine with the graphics card driver linking to LLVM without hiding the symbols. Similar to the bug being reported here:
IIRC export LIBGL_ALWAYS_INDIRECT=1 can help in some cases as a workaround for the buggy drivers.
danschef
commented
3 years ago @chrisburr Thanks a lot for looking into this! I just installed qgis + numba again on another machine (Kubuntu 17.04) and there is no error when importing numba within the QGIS Python console. So, at least, this does not seem to be a Linux issue in general. Is there anything I can do to make sure it is not an OpenGL issue only on my machine as you guessed?
Here is the output of conda list on that second machine:
I am using a fresh MambaForge:
chrisburr
commented
3 years ago What GPU and driver do you have on the problematic machine?
danschef
commented
3 years ago Does the glxinfo output help?
chrisburr
commented
3 years ago Yup, that was very helpful. Did you try running with export LIBGL_ALWAYS_INDIRECT=1?
danschef
commented
3 years ago Wow, that works!
chrisburr
commented
3 years ago Excellent! In that case it is the mesa bug I that I linked earlier. Upgrading mesa should fix it but you probably don't want to do that unless you're upgrading the entire VM for other reasons. 😄
There is not much that can be done from conda-forge's perspective unfortunately so I'll close this.
danschef
commented
3 years ago I updated all packages on that server and got no error anymore. Thanks a lot for all for your efforts, that was really helpful!
I did:
sudo apt update # 170 packages upgradable
sudo apt upgrade
sudo apt update # all packages up-to-date
sudo add-apt-repository ppa:kisak/kisak-mesa
sudo apt update # 14 packages upgradable
sudo apt upgrade
sudo apt update # all packages up-to-date
sudo apt install mesa # E: Unable to locate package mesa
I am not sure why mesa can´t be located in the last step, however everything seems to work fine now.
Ofloo
commented
1 year ago rolled back to the amdgpu-install and now clinfo works again so both intel gpu and radeon gpu are working with opencl and obs works.
I initially filed this issue in the numba-feedstock (see here). However, @henryiii pointed me to LLVM, so I re-open the issue here:
Issue:
I am currently involved in the development of a QGIS plugin that uses numba under the hood (requires llvmlite) and there seems to be a compatibility issue between numba and QGIS on Linux (at least on my Ubuntu 20.04 machine).
When installing qgis and numba from conda-forge into the same environment, qgis crashes when trying to import numba via the QGIS Python console. Here is a minimal environment that reproduces the issue:
$ conda create -n qgisnumba -c conda-forge qgis numbaThis installs the following environment (
conda list):QGIS can than be started by running
qgison the command line and everything works fine. However, as soon as I open a Python console within QGIS and import numba, QGIS crashes and raises the following error at the command line:Note that when I start a Python console directly on the command line (without QGIS), I can import qgis and numba without any issues. So the error only occurs when numba is imported from the QGIS command line (or by a QGIS plugin which uses numba). We also tested this with the same environment on Windows, without any issues.
Details about
condaand system (conda info):