trouble with installing jupyter notebook

[MichelleLiu723]

when i type the command (mila serve notebook) on my local computer, it ask me if i want to pip install jupyter or install it myself. When i choose pip install jupyter i get this long script with error messages:

(experiments) compstaffs-MacBook-Pro:~ mliu$ mila serve notebook
Checking for preferred profile in /home/mila/l/liumiche/.milatools-profile
Using profile: .milatools/profiles/cpdagGFN.bash
==================================================
module load python/3.8 cuda/11.2/cudnn/8.1
source ~/virtualenvs/cpdagGFN/bin/activate
==================================================
? jupyter-notebook is not installed in that environment. Do you want to install it? pip install jupyter
(mila) $ srun pip install jupyter
[=== Module python/3.8 loaded ===]
[=== Module cudatoolkit/11.2 loaded ===]
[=== Module cuda/11.2/cudnn/8.1 loaded ===]
srun: --------------------------------------------------------------------------------------------------
srun: # Using default long-cpu partition (CPU-only)
srun: --------------------------------------------------------------------------------------------------
Collecting jupyter
  Using cached https://files.pythonhosted.org/packages/83/df/0f5dd132200728a86190397e1ea87cd76244e42d39ec5e88efd25b2abd7e/jupyter-1.0.0-py2.py3-none-any.whl
Collecting nbconvert (from jupyter)
  Using cached https://files.pythonhosted.org/packages/37/33/0d339e81b7c6b77020059dd2268c16c4ba63473bdd984991f91ac7ad7ef7/nbconvert-7.2.5-py3-none-any.whl
Collecting jupyter-console (from jupyter)
  Using cached https://files.pythonhosted.org/packages/8b/0c/f9382ca7b7499c8594a5158817a72c95b4c09a6c6f2de10553bfe8905924/jupyter_console-6.4.4-py3-none-any.whl
Collecting notebook (from jupyter)
  Using cached https://files.pythonhosted.org/packages/db/40/2d321ba572dc9a94a090d92c9826291a1dcee1e05bc6c1d641ce419b701d/notebook-6.5.2-py3-none-any.whl
Collecting qtconsole (from jupyter)
  Using cached https://files.pythonhosted.org/packages/cc/00/4133199dc738e7f497385af86e619f5c29592aaa4c1731fbbc3ec7bb7080/qtconsole-5.4.0-py3-none-any.whl
Collecting ipykernel (from jupyter)
  Using cached https://files.pythonhosted.org/packages/c5/91/3740ea00e8bb766742937a781bce18b6d344bfd99c48e5ea89b4681ef089/ipykernel-6.18.0-py3-none-any.whl
Collecting ipywidgets (from jupyter)
  Using cached https://files.pythonhosted.org/packages/e4/56/990c10ca8751182ace2464cb0e4baafb7087a40c185c9142b9cd18683fac/ipywidgets-8.0.2-py3-none-any.whl
Collecting traitlets>=5.0 (from nbconvert->jupyter)
  Using cached https://files.pythonhosted.org/packages/ed/f9/caefd8c90955184e7426ef930e38c185e047169b520b35bdd57d341d03f4/traitlets-5.5.0-py3-none-any.whl
Collecting packaging (from nbconvert->jupyter)
  Using cached https://files.pythonhosted.org/packages/05/8e/8de486cbd03baba4deef4142bd643a3e7bbe954a784dc1bb17142572d127/packaging-21.3-py3-none-any.whl
Collecting jinja2>=3.0 (from nbconvert->jupyter)
  Using cached https://files.pythonhosted.org/packages/bc/c3/f068337a370801f372f2f8f6bad74a5c140f6fda3d9de154052708dd3c65/Jinja2-3.1.2-py3-none-any.whl
Collecting defusedxml (from nbconvert->jupyter)
  Using cached https://files.pythonhosted.org/packages/07/6c/aa3f2f849e01cb6a001cd8554a88d4c77c5c1a31c95bdf1cf9301e6d9ef4/defusedxml-0.7.1-py2.py3-none-any.whl
Collecting pandocfilters>=1.4.1 (from nbconvert->jupyter)
  Using cached https://files.pythonhosted.org/packages/5e/a8/878258cffd53202a6cc1903c226cf09e58ae3df6b09f8ddfa98033286637/pandocfilters-1.5.0-py2.py3-none-any.whl
Collecting beautifulsoup4 (from nbconvert->jupyter)
  Using cached https://files.pythonhosted.org/packages/9c/d8/909c4089dbe4ade9f9705f143c9f13f065049a9d5e7d34c828aefdd0a97c/beautifulsoup4-4.11.1-py3-none-any.whl
Collecting mistune<3,>=2.0.3 (from nbconvert->jupyter)
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Collecting markupsafe>=2.0 (from nbconvert->jupyter)
  Using cached https://files.pythonhosted.org/packages/1d/97/2288fe498044284f39ab8950703e88abbac2abbdf65524d576157af70556/MarkupSafe-2.1.1.tar.gz
Collecting jupyterlab-pygments (from nbconvert->jupyter)
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Collecting tinycss2 (from nbconvert->jupyter)
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Collecting nbclient>=0.5.0 (from nbconvert->jupyter)
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Collecting nbformat>=5.1 (from nbconvert->jupyter)
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Collecting pygments>=2.4.1 (from nbconvert->jupyter)
  Using cached https://files.pythonhosted.org/packages/4f/82/672cd382e5b39ab1cd422a672382f08a1fb3d08d9e0c0f3707f33a52063b/Pygments-2.13.0-py3-none-any.whl
Collecting jupyter-core>=4.7 (from nbconvert->jupyter)
  Using cached https://files.pythonhosted.org/packages/a3/60/63e9e1e18ae427cd925eb970dd452a5b322060207e7f5243ca4620ee0507/jupyter_core-5.0.0-py3-none-any.whl
Collecting importlib-metadata>=3.6; python_version < "3.10" (from nbconvert->jupyter)
  Using cached https://files.pythonhosted.org/packages/b5/64/ef29a63cf08f047bb7fb22ab0f1f774b87eed0bb46d067a5a524798a4af8/importlib_metadata-5.0.0-py3-none-any.whl
Collecting bleach (from nbconvert->jupyter)
  Using cached https://files.pythonhosted.org/packages/d4/87/508104336a2bc0c4cfdbdceedc0f44dc72da3abc0460c57e323ddd1b3257/bleach-5.0.1-py3-none-any.whl
Collecting ipython (from jupyter-console->jupyter)
  Using cached https://files.pythonhosted.org/packages/c7/53/072d677a16fd61f5806d80218c65202cc0ee77b831088af8f79ef59efcf2/ipython-8.6.0-py3-none-any.whl
Collecting jupyter-client>=7.0.0 (from jupyter-console->jupyter)
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Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 (from jupyter-console->jupyter)
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Collecting nest-asyncio>=1.5 (from notebook->jupyter)
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Collecting argon2-cffi (from notebook->jupyter)
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Collecting nbclassic>=0.4.7 (from notebook->jupyter)
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Collecting pyzmq>=17 (from notebook->jupyter)
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Collecting Send2Trash>=1.8.0 (from notebook->jupyter)
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Collecting tornado>=6.1 (from notebook->jupyter)
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Collecting terminado>=0.8.3 (from notebook->jupyter)
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Collecting prometheus-client (from notebook->jupyter)
  Using cached https://files.pythonhosted.org/packages/2e/5e/4225463cdac1098aac718b1d8adf8f9dc3d6aaea55f4f85a2f7d572b4f7c/prometheus_client-0.15.0-py3-none-any.whl
Collecting ipython-genutils (from notebook->jupyter)
  Using cached https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl
Collecting qtpy>=2.0.1 (from qtconsole->jupyter)
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Collecting psutil (from ipykernel->jupyter)
  Using cached https://files.pythonhosted.org/packages/6e/c8/784968329c1c67c28cce91991ef9af8a8913aa5a3399a6a8954b1380572f/psutil-5.9.4-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Collecting matplotlib-inline>=0.1 (from ipykernel->jupyter)
  Using cached https://files.pythonhosted.org/packages/f2/51/c34d7a1d528efaae3d8ddb18ef45a41f284eacf9e514523b191b7d0872cc/matplotlib_inline-0.1.6-py3-none-any.whl
Collecting debugpy>=1.0 (from ipykernel->jupyter)
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Collecting comm>=0.1 (from ipykernel->jupyter)
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Collecting widgetsnbextension~=4.0 (from ipywidgets->jupyter)
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Collecting jupyterlab-widgets~=3.0 (from ipywidgets->jupyter)
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Collecting pyparsing!=3.0.5,>=2.0.2 (from packaging->nbconvert->jupyter)
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Collecting soupsieve>1.2 (from beautifulsoup4->nbconvert->jupyter)
  Downloading https://files.pythonhosted.org/packages/16/e3/4ad79882b92617e3a4a0df1960d6bce08edfb637737ac5c3f3ba29022e25/soupsieve-2.3.2.post1-py3-none-any.whl
Collecting webencodings>=0.4 (from tinycss2->nbconvert->jupyter)
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Collecting fastjsonschema (from nbformat>=5.1->nbconvert->jupyter)
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Collecting jsonschema>=2.6 (from nbformat>=5.1->nbconvert->jupyter)
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Collecting platformdirs (from jupyter-core>=4.7->nbconvert->jupyter)
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Collecting zipp>=0.5 (from importlib-metadata>=3.6; python_version < "3.10"->nbconvert->jupyter)
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Requirement already satisfied: six>=1.9.0 in /cvmfs/ai.mila.quebec/apps/x86_64/debian/python/3.8/lib/python3.8/site-packages (from bleach->nbconvert->jupyter) (1.14.0)
Collecting decorator (from ipython->jupyter-console->jupyter)
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Collecting stack-data (from ipython->jupyter-console->jupyter)
  Using cached https://files.pythonhosted.org/packages/e7/f1/a1f2fd4a75d371412650b3ddc16741e0de383fe701953566c9288f678a5b/stack_data-0.6.1-py3-none-any.whl
Collecting jedi>=0.16 (from ipython->jupyter-console->jupyter)
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Collecting pickleshare (from ipython->jupyter-console->jupyter)
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Collecting pexpect>4.3; sys_platform != "win32" (from ipython->jupyter-console->jupyter)
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Collecting backcall (from ipython->jupyter-console->jupyter)
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Collecting entrypoints (from jupyter-client>=7.0.0->jupyter-console->jupyter)
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Collecting python-dateutil>=2.8.2 (from jupyter-client>=7.0.0->jupyter-console->jupyter)
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Collecting wcwidth (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->jupyter-console->jupyter)
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Collecting argon2-cffi-bindings (from argon2-cffi->notebook->jupyter)
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  Installing build dependencies: started
  Installing build dependencies: finished with status 'error'
  ERROR: Command errored out with exit status 1:
   command: /home/mila/l/liumiche/virtualenvs/cpdagGFN/bin/python /home/mila/l/liumiche/virtualenvs/cpdagGFN/lib/python3.8/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-4qpqdizx/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=45' 'setuptools_scm>=6.2' wheel 'cffi>=1.0.1'
       cwd: None
  Complete output (85 lines):
  Collecting setuptools>=45
    Using cached https://files.pythonhosted.org/packages/1f/97/c03668380f278f1f8b0486d820c142cf224bba1bd78416e1797b52e0e81c/setuptools-65.6.0-py3-none-any.whl
  Collecting setuptools_scm>=6.2
    Using cached https://files.pythonhosted.org/packages/01/ed/75a20e7b075e8ecb1f84e8debf833917905d8790b78008915bd68dddd5c4/setuptools_scm-7.0.5-py3-none-any.whl
  Collecting wheel
    Using cached https://files.pythonhosted.org/packages/bd/7c/d38a0b30ce22fc26ed7dbc087c6d00851fb3395e9d0dac40bec1f905030c/wheel-0.38.4-py3-none-any.whl
  Collecting cffi>=1.0.1
    Using cached https://files.pythonhosted.org/packages/2b/a8/050ab4f0c3d4c1b8aaa805f70e26e84d0e27004907c5b8ecc1d31815f92a/cffi-1.15.1.tar.gz
  Collecting packaging>=20.0 (from setuptools_scm>=6.2)
    Using cached https://files.pythonhosted.org/packages/05/8e/8de486cbd03baba4deef4142bd643a3e7bbe954a784dc1bb17142572d127/packaging-21.3-py3-none-any.whl
  Collecting tomli>=1.0.0 (from setuptools_scm>=6.2)
    Using cached https://files.pythonhosted.org/packages/97/75/10a9ebee3fd790d20926a90a2547f0bf78f371b2f13aa822c759680ca7b9/tomli-2.0.1-py3-none-any.whl
  Collecting typing-extensions (from setuptools_scm>=6.2)
    Using cached https://files.pythonhosted.org/packages/0b/8e/f1a0a5a76cfef77e1eb6004cb49e5f8d72634da638420b9ea492ce8305e8/typing_extensions-4.4.0-py3-none-any.whl
  Collecting pycparser (from cffi>=1.0.1)
    Using cached https://files.pythonhosted.org/packages/62/d5/5f610ebe421e85889f2e55e33b7f9a6795bd982198517d912eb1c76e1a53/pycparser-2.21-py2.py3-none-any.whl
  Collecting pyparsing!=3.0.5,>=2.0.2 (from packaging>=20.0->setuptools_scm>=6.2)
    Using cached https://files.pythonhosted.org/packages/6c/10/a7d0fa5baea8fe7b50f448ab742f26f52b80bfca85ac2be9d35cdd9a3246/pyparsing-3.0.9-py3-none-any.whl
  Installing collected packages: setuptools, pyparsing, packaging, tomli, typing-extensions, setuptools-scm, wheel, pycparser, cffi
    Running setup.py install for cffi: started
      Running setup.py install for cffi: finished with status 'error'
      ERROR: Command errored out with exit status 1:
       command: /home/mila/l/liumiche/virtualenvs/cpdagGFN/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-a5obestd/cffi/setup.py'"'"'; __file__='"'"'/tmp/pip-install-a5obestd/cffi/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-gs9rsn3v/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-4qpqdizx/overlay --compile --install-headers /home/mila/l/liumiche/virtualenvs/cpdagGFN/include/site/python3.8/cffi
           cwd: /tmp/pip-install-a5obestd/cffi/
      Complete output (56 lines):
      Package libffi was not found in the pkg-config search path.
      Perhaps you should add the directory containing `libffi.pc'
      to the PKG_CONFIG_PATH environment variable
      No package 'libffi' found
      Package libffi was not found in the pkg-config search path.
      Perhaps you should add the directory containing `libffi.pc'
      to the PKG_CONFIG_PATH environment variable
      No package 'libffi' found
      Package libffi was not found in the pkg-config search path.
      Perhaps you should add the directory containing `libffi.pc'
      to the PKG_CONFIG_PATH environment variable
      No package 'libffi' found
      Package libffi was not found in the pkg-config search path.
      Perhaps you should add the directory containing `libffi.pc'
      to the PKG_CONFIG_PATH environment variable
      No package 'libffi' found
      Package libffi was not found in the pkg-config search path.
      Perhaps you should add the directory containing `libffi.pc'
      to the PKG_CONFIG_PATH environment variable
      No package 'libffi' found
      running install
      running build
      running build_py
      creating build
      creating build/lib.linux-x86_64-3.8
      creating build/lib.linux-x86_64-3.8/cffi
      copying cffi/lock.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/error.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/vengine_cpy.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/recompiler.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/model.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/vengine_gen.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/cparser.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/cffi_opcode.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/ffiplatform.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/commontypes.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/api.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/setuptools_ext.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/pkgconfig.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/backend_ctypes.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/verifier.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/__init__.py -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/_cffi_include.h -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/parse_c_type.h -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/_embedding.h -> build/lib.linux-x86_64-3.8/cffi
      copying cffi/_cffi_errors.h -> build/lib.linux-x86_64-3.8/cffi
      running build_ext
      building '_cffi_backend' extension
      creating build/temp.linux-x86_64-3.8
      creating build/temp.linux-x86_64-3.8/c
      gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -DFFI_BUILDING=1 -DUSE__THREAD -DHAVE_SYNC_SYNCHRONIZE -I/usr/include/ffi -I/usr/include/libffi -I/home/mila/l/liumiche/virtualenvs/cpdagGFN/include -I/cvmfs/ai.mila.quebec/apps/arch/distro/python/3.8/include/python3.8 -c c/_cffi_backend.c -o build/temp.linux-x86_64-3.8/c/_cffi_backend.o
      c/_cffi_backend.c:15:10: fatal error: ffi.h: No such file or directory
       #include <ffi.h>
                ^~~~~~~
      compilation terminated.
      error: command 'gcc' failed with exit status 1
      ----------------------------------------
  ERROR: Command errored out with exit status 1: /home/mila/l/liumiche/virtualenvs/cpdagGFN/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-a5obestd/cffi/setup.py'"'"'; __file__='"'"'/tmp/pip-install-a5obestd/cffi/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-gs9rsn3v/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-4qpqdizx/overlay --compile --install-headers /home/mila/l/liumiche/virtualenvs/cpdagGFN/include/site/python3.8/cffi Check the logs for full command output.
  WARNING: You are using pip version 19.2.3, however version 22.3.1 is available.
  You should consider upgrading via the 'pip install --upgrade pip' command.
  ----------------------------------------
ERROR: Command errored out with exit status 1: /home/mila/l/liumiche/virtualenvs/cpdagGFN/bin/python /home/mila/l/liumiche/virtualenvs/cpdagGFN/lib/python3.8/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-4qpqdizx/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=45' 'setuptools_scm>=6.2' wheel 'cffi>=1.0.1' Check the logs for full command output.
WARNING: You are using pip version 19.2.3, however version 22.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
srun: error: cn-f001: task 0: Exited with exit code 1
srun: launch/slurm: _step_signal: Terminating StepId=2492788.0
Traceback (most recent call last):
  File "/anaconda3/envs/experiments/bin/mila", line 8, in <module>
    sys.exit(main())
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/milatools/cli/__main__.py", line 39, in main
    auto_cli(milatools)
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/coleo/cli.py", line 656, in auto_cli
    result = run_cli(entry, args, **kwargs)
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/coleo/cli.py", line 628, in run_cli
    return call(opts=opts, args=args)
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/coleo/cli.py", line 587, in thunk
    result = fn(*args)
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/milatools/cli/__main__.py", line 447, in notebook
    _standard_server(
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/milatools/cli/__main__.py", line 584, in _standard_server
    if not ensure_program(
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/milatools/cli/profile.py", line 307, in ensure_program
    remote.run(f"srun {install}")
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/milatools/cli/utils.py", line 259, in run
    return self._run(cmd, hide=hide, **kwargs)
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/milatools/cli/utils.py", line 243, in _run
    return self.connection.run(cmd, **kwargs)
  File "<decorator-gen-3>", line 2, in run
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/fabric/connection.py", line 30, in opens
    return method(self, *args, **kwargs)
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/fabric/connection.py", line 725, in run
    return self._run(self._remote_runner(), command, **kwargs)
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/invoke/context.py", line 102, in _run
    return runner.run(command, **kwargs)
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/fabric/runners.py", line 72, in run
    return super(Remote, self).run(command, **kwargs)
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/invoke/runners.py", line 380, in run
    return self._run_body(command, **kwargs)
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/invoke/runners.py", line 442, in _run_body
    return self.make_promise() if self._asynchronous else self._finish()
  File "/anaconda3/envs/experiments/lib/python3.10/site-packages/invoke/runners.py", line 509, in _finish
    raise UnexpectedExit(result)
invoke.exceptions.UnexpectedExit: Encountered a bad command exit code!

Command: 'source .milatools/profiles/cpdagGFN.bash && srun pip install jupyter'

Exit code: 1

Stdout: already printed

Stderr: already printed


(experiments) compstaffs-MacBook-Pro:~ mliu$ mila serve notebook

[lebrice]

Solved: Solution was to add a module load libffi in the profile.