Running PyTorch models using uWSGI can result in the app hanging due to issues lib libgomp. The issue and possible workarounds are discussed in this PyTorch issue:
I spent a couple of days trying to understand why my app was hanging then timing out and eventually tracked it down to the above known issue.
Hopefully, this example will be of use to others running into the same issue.
classify.py uses huggingface transformers with the google/vit-base-patch16-224 model to perform classification on a single image.
A Dockerfile is provided with the failing environment.
When classify.py is run from the command line a result is returned and it exits as expected. When classify.py is run through uwsgi behind nginx pytorch hangs when torch.tensor(...) is called trying to convert the image to a tensor. The gdb backtrace shows that pytorch is stuck somewhere inside libgomp.
The image has remote_pdb and gdb installed.
To build the docker image:
DOCKER_BUILDKIT=1 docker build -t classify .
To launch the container: (This assumes that ports 8888, 8443 and 8080 are not being used on your host)
docker run --privileged -d -p 8888:80 -p 8443:443 -p 8080:8080 classify
To see that the script passes when not run under uwsgi:
docker exec -it <container_name> /app/classify/classify.py
Which should output something like the following:
['street sign', 'book jacket, dust cover, dust jacket, dust wrapper', 'traffic light, traffic signal, stoplight']
To reproduce the failure:
docker exec -it <container_name> tail -f /var/log/uwsgi/uwsgi.log
You may need to wait a little bit to be sure uwsgi is running and try the tail again.
In your browser goto localhost:8888. You should see a white page that is waiting to load.
Run the gdb command shown in the log file above. It should show that things are stuck in libgomp...
docker exec -it <container_name> gdb -p <pid> -ex bt --batch
The backtrace should show things are stuck in libgomp similar to the following:
(gdb) bt -frame-arguments none 10
#0 0x00007f3d587c8cab in ?? () from /usr/local/lib/python3.9/dist-packages/torch/lib/libgomp-a34b3233.so.1
#1 0x00007f3d587c77e9 in ?? () from /usr/local/lib/python3.9/dist-packages/torch/lib/libgomp-a34b3233.so.1
#2 0x00007f3d414ae471 in at::TensorIteratorBase::for_each(c10::function_ref<void (char**, long const*, long, long)>, long) ()
from /usr/local/lib/python3.9/dist-packages/torch/lib/libtorch_cpu.so
#3 0x00007f3d44585bde in at::native::(anonymous namespace)::copy_same_dtype(at::TensorIteratorBase&, bool, bool) ()
from /usr/local/lib/python3.9/dist-packages/torch/lib/libtorch_cpu.so
#4 0x00007f3d4458630f in at::native::(anonymous namespace)::copy_kernel(at::TensorIterator&, bool) ()
from /usr/local/lib/python3.9/dist-packages/torch/lib/libtorch_cpu.so
#5 0x00007f3d416ce4e3 in at::native::copy_impl(at::Tensor&, at::Tensor const&, bool) ()
from /usr/local/lib/python3.9/dist-packages/torch/lib/libtorch_cpu.so
#6 0x00007f3d416cf331 in at::native::copy_(at::Tensor&, at::Tensor const&, bool) ()
from /usr/local/lib/python3.9/dist-packages/torch/lib/libtorch_cpu.so
#7 0x00007f3d41f933ad in at::_ops::copy_::call(at::Tensor&, at::Tensor const&, bool) ()
from /usr/local/lib/python3.9/dist-packages/torch/lib/libtorch_cpu.so
#8 0x00007f3d41941fd8 in at::native::_to_copy(at::Tensor const&, c10::optional<c10::ScalarType>, c10::optional<c10::Layout>, c10::optional<c10::Device>, c10::optional<bool>, bool, c10::optional<c10::MemoryFormat>) () from /usr/local/lib/python3.9/dist-packages/torch/lib/libtorch_cpu.so
#9 0x00007f3d421c3d5a in c10::impl::wrap_kernel_functor_unboxed_<c10::impl::detail::WrapFunctionIntoFunctor_<c10::CompileTimeFunctionPointer<at::Tensor (at::Tensor const&, c10::optional<c10::ScalarType>, c10::optional<c10::Layout>, c10::optional<c10::Device>, c10::optional<bool>, bool, c10::optional<c10::MemoryFormat>), &at::(anonymous namespace)::(anonymous namespace)::wrapper___to_copy>, at::Tensor, c10::guts::typelist::typelist<at::Tensor const&, c10::optional<c10::ScalarType>, c10::optional<c10::Layout>, c10::optional<c10::Device>, c10::optional<bool>, bool, c10::optional<c10::MemoryFormat> > >, at::Tensor (at::Tensor const&, c10::optional<c10::ScalarType>, c10::optional<c10::Layout>, c10::optional<c10::Device>, c10::optional<bool>, bool, c10::optional<c10::MemoryFormat>)>::call(c10::OperatorKernel*, c10::DispatchKeySet, at::Tensor const&, c10::optional<c10::ScalarType>, c10::optional<c10::Layout>, c10::optional<c10::Device>, c10::optional<bool>, bool, c10::optional<c10::MemoryFormat>) ()
from /usr/local/lib/python3.9/dist-packages/torch/lib/libtorch_cpu.so
...
If you want to break in python before the feature extractor call edit classify.py and modify the call to process_image() in the application() function to pass dbg=True then after loading the page in your browser run:
docker exec -it <container_name> telnet localhost 4444
That will leave you at the pdb prompt just before the failing extractor call. The hang occurs inside feature_extractor in the huggingface model when calling torch.tensor(value) on the image numpy array.
Edit entrypoint.sh to comment out the uwsgi call after the # Fails line and uncomment the uwsgi call after the # Workaround line.
Then rebuild the container and run it again. Opening localhost:8888 should now return the expected results.
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