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License: MIT License
repository for collaborating with sherlock users to create containers
License: MIT License
Hi, thanks for the help in getting pytorch running in python 2.7 using your Dockerfile at https://github.com/researchapps/sherlock/blob/master/pytorch-dev/Dockerfile.py2. I did have to make some changes to get it to work however:
+++ Dockerfile.new 2018-08-14 09:44:08.542990180 +1000
@@ -20,17 +20,19 @@
/opt/conda/bin/conda config --add channels conda-forge && \
/opt/conda/bin/conda install -y numpy pyyaml scipy ipython mkl && \
/opt/conda/bin/conda install -y matplotlib scikit-learn scikit-image && \
+ /opt/conda/bin/conda install -y typing && \
/opt/conda/bin/conda install -c intel mkl-include && \
/opt/conda/bin/conda install -c pytorch magma-cuda90 && \
/opt/conda/bin/conda clean -ya
-RUN /opt/conda/bin/conda update -y base conda
+RUN /opt/conda/bin/conda update -y conda
ENV PATH /opt/conda/bin:$PATH
# This must be done before pip so that requirements.txt is available
RUN git clone https://github.com/pytorch/pytorch /opt/pytorch && \
cd /opt/pytorch && \
git submodule update --init
RUN pip install --upgrade pip
-RUN TORCH_CUDA_ARCH_LIST="3.5 5.2 6.0 6.1 7.0+PTX" TORCH_NVCC_FLAGS="-Xfatbin -compress-all" \
+RUN cd /opt/pytorch && \
+ TORCH_CUDA_ARCH_LIST="3.5 5.2 6.0 6.1 7.0+PTX" TORCH_NVCC_FLAGS="-Xfatbin -compress-all" \
CMAKE_PREFIX_PATH="$(dirname $(which conda))/../" \
pip install -v .
RUN git clone https://github.com/pytorch/vision.git && cd vision && pip install -v .
I hope this is useful if this problem is reproducible for other people.
From discussion in an email thread, moved here for documentation and preservation:
So it seems that pvacseq may work using:
singularity exec --bind $PWD:/scif/data/pvacseq --app pvacseq pvacseq.simg pvacseq -h
I will test that with real data ASAP.
I thought that similarly VEP should work with
singularity exec --bind $PWD:/scif/data/VEP --app VEP pvacseq.simg VEP
/.singularity.d/actions/exec: 9: exec: VEP: not found
or
singularity run --bind $PWD:/scif/data/VEP --app VEP pvacseq.simg
No Singularity runscript for contained app: VEP
Hello,
I am trying to use the python3 installed in the container (which python
gives opt/conda/bin/python
) to show up as a kernel in jupyter.
To do so, in the location ${HOME}/.local/share/jupyter/kernels
, I specify a new directory called mykernel
and added a kernel.json
file of the following description:
{
"language": "python",
"argv": ["home/lalit/singularity",
"exec",
"-w",
"/home/lalit/singularity/test.simg",
"/opt/conda/bin/python",
"-m",
"ipykernel",
"-f",
"{connection_file}"
],
"display_name": "Python 3 (Singularity)"
}
But this gives a kernel not found error (shown below) upon starting a jupyter notebook. I think the paths to the singularity
and test.simg
are correct and this error stems from some permissions issue. Any clue on how to solve this? Thanks.
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist-packages/tornado/web.py", line 1699, in _execute
result = await result
File "/usr/lib/python3.5/asyncio/futures.py", line 363, in __iter__
return self.result() # May raise too.
File "/usr/lib/python3.5/asyncio/futures.py", line 274, in result
raise self._exception
File "/usr/local/lib/python3.5/dist-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/usr/local/lib/python3.5/dist-packages/notebook/services/sessions/handlers.py", line 72, in post
type=mtype))
File "/usr/local/lib/python3.5/dist-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/usr/lib/python3.5/asyncio/futures.py", line 274, in result
raise self._exception
File "/usr/local/lib/python3.5/dist-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/usr/local/lib/python3.5/dist-packages/notebook/services/sessions/sessionmanager.py", line 88, in create_session
kernel_id = yield self.start_kernel_for_session(session_id, path, name, type, kernel_name)
File "/usr/local/lib/python3.5/dist-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/usr/lib/python3.5/asyncio/futures.py", line 274, in result
raise self._exception
File "/usr/local/lib/python3.5/dist-packages/tornado/gen.py", line 742, in run
yielded = self.gen.throw(*exc_info) # type: ignore
File "/usr/local/lib/python3.5/dist-packages/notebook/services/sessions/sessionmanager.py", line 101, in start_kernel_for_session
self.kernel_manager.start_kernel(path=kernel_path, kernel_name=kernel_name)
File "/usr/local/lib/python3.5/dist-packages/tornado/gen.py", line 735, in run
value = future.result()
File "/usr/lib/python3.5/asyncio/futures.py", line 274, in result
raise self._exception
File "/usr/local/lib/python3.5/dist-packages/tornado/gen.py", line 209, in wrapper
yielded = next(result)
File "/usr/local/lib/python3.5/dist-packages/notebook/services/kernels/kernelmanager.py", line 168, in start_kernel
super(MappingKernelManager, self).start_kernel(**kwargs)
File "/usr/local/lib/python3.5/dist-packages/jupyter_client/multikernelmanager.py", line 110, in start_kernel
km.start_kernel(**kwargs)
File "/usr/local/lib/python3.5/dist-packages/jupyter_client/manager.py", line 259, in start_kernel
**kw)
File "/usr/local/lib/python3.5/dist-packages/jupyter_client/manager.py", line 204, in _launch_kernel
return launch_kernel(kernel_cmd, **kw)
File "/usr/local/lib/python3.5/dist-packages/jupyter_client/launcher.py", line 138, in launch_kernel
proc = Popen(cmd, **kwargs)
File "/usr/lib/python3.5/subprocess.py", line 947, in __init__
restore_signals, start_new_session)
File "/usr/lib/python3.5/subprocess.py", line 1551, in _execute_child
raise child_exception_type(errno_num, err_msg)
PermissionError: [Errno 13] Permission denied
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