Merge pull request #294 from stackhpc/fix/jupyter

Use Python3.9 for jupyter notebook server

Author: sjpb

.github/workflows/stackhpc.yml

@@ -90,11 +90,11 @@ jobs:
           . environments/.stackhpc/activate
           ansible-playbook -vv ansible/adhoc/hpctests.yml
 
-      - name: Run EESSI tests
-        run: |
-          . venv/bin/activate
-          . environments/.stackhpc/activate
-          ansible-playbook -vv ansible/ci/check_eessi.yml
+      # - name: Run EESSI tests
+      #   run: |
+      #     . venv/bin/activate
+      #     . environments/.stackhpc/activate
+      #     ansible-playbook -vv ansible/ci/check_eessi.yml
 
       - name: Confirm Open Ondemand is up (via SOCKS proxy)
         run: |

ansible/ci/check_eessi.yml

@@ -17,18 +17,34 @@
         repo: "https://github.com/eessi/eessi-demo.git"
         dest: "{{ eessi_test_rootdir }}/eessi-demo"
 
-    - name: Run test job
-      ansible.builtin.shell:
-        cmd: |
+    - name: Create batch script
+      copy:
+        dest: "{{ eessi_test_rootdir }}/eessi-demo/TensorFlow/tensorflow.sh"
+        content: |
+          #!/usr/bin/env bash
+          #SBATCH --output=%x.out
+          #SBATCH --error=%x.out
           source /cvmfs/pilot.eessi-hpc.org/latest/init/bash
           srun ./run.sh
+
+    - name: Run test job
+      ansible.builtin.shell:
+        cmd: sbatch --wait tensorflow.sh
         chdir: "{{ eessi_test_rootdir }}/eessi-demo/TensorFlow"
-        executable: /bin/bash
       register: job_output
 
+    - name: Retrieve job output
+      slurp:
+        src: "{{ eessi_test_rootdir }}/eessi-demo/TensorFlow/tensorflow.sh.out"
+      register: _tensorflow_out
+      no_log: true # as its base64 encoded so useless
+
+    - name: Show job output
+      debug:
+        msg: "{{ _tensorflow_out.content | b64decode }}"
+
     - name: Fail if job output contains error
       fail:
         # Note: Job prints live progress bar to terminal, so use regex filter to remove this from stdout
         msg: "Test job using EESSI modules failed. Job output was: {{ job_output.stdout | regex_replace('\b', '') }}"        
-      when: '"Epoch 5/5" not in job_output.stdout'
-      
+      when: '"Epoch 5/5" not in _tensorflow_out.content | b64decode'

ansible/roles/openondemand/files/jupyter_requirements.txt

@@ -0,0 +1,101 @@
+# Python3.9, pip 23.2.1
+anyio==3.7.1
+argon2-cffi==21.3.0
+argon2-cffi-bindings==21.2.0
+arrow==1.2.3
+asttokens==2.2.1
+async-lru==2.0.4
+attrs==23.1.0
+Babel==2.12.1
+backcall==0.2.0
+beautifulsoup4==4.12.2
+bleach==6.0.0
+certifi==2023.7.22
+cffi==1.15.1
+charset-normalizer==3.2.0
+comm==0.1.3
+debugpy==1.6.7
+decorator==5.1.1
+defusedxml==0.7.1
+exceptiongroup==1.1.2
+executing==1.2.0
+fastjsonschema==2.18.0
+fqdn==1.5.1
+idna==3.4
+importlib-metadata==6.8.0
+ipykernel==6.25.0
+ipython==8.14.0
+ipython-genutils==0.2.0
+ipywidgets==8.1.0
+isoduration==20.11.0
+jedi==0.19.0
+Jinja2==3.1.2
+json5==0.9.14
+jsonpointer==2.4
+jsonschema==4.18.4
+jsonschema-specifications==2023.7.1
+jupyter==1.0.0
+jupyter-console==6.6.3
+jupyter-events==0.7.0
+jupyter-lsp==2.2.0
+jupyter_client==8.3.0
+jupyter_core==5.3.1
+jupyter_server==2.7.0
+jupyter_server_terminals==0.4.4
+jupyterlab==4.0.3
+jupyterlab-pygments==0.2.2
+jupyterlab-widgets==3.0.8
+jupyterlab_server==2.24.0
+MarkupSafe==2.1.3
+matplotlib-inline==0.1.6
+mistune==3.0.1
+nbclient==0.8.0
+nbconvert==7.7.3
+nbformat==5.9.2
+nest-asyncio==1.5.7
+notebook==7.0.1
+notebook_shim==0.2.3
+overrides==7.3.1
+packaging==23.1
+pandocfilters==1.5.0
+parso==0.8.3
+pexpect==4.8.0
+pickleshare==0.7.5
+platformdirs==3.10.0
+prometheus-client==0.17.1
+prompt-toolkit==3.0.39
+psutil==5.9.5
+ptyprocess==0.7.0
+pure-eval==0.2.2
+pycparser==2.21
+Pygments==2.15.1
+python-dateutil==2.8.2
+python-json-logger==2.0.7
+PyYAML==6.0.1
+pyzmq==25.1.0
+qtconsole==5.4.3
+QtPy==2.3.1
+referencing==0.30.0
+requests==2.31.0
+rfc3339-validator==0.1.4
+rfc3986-validator==0.1.1
+rpds-py==0.9.2
+Send2Trash==1.8.2
+six==1.16.0
+sniffio==1.3.0
+soupsieve==2.4.1
+stack-data==0.6.2
+terminado==0.17.1
+tinycss2==1.2.1
+tomli==2.0.1
+tornado==6.3.2
+traitlets==5.9.0
+typing_extensions==4.7.1
+uri-template==1.3.0
+urllib3==2.0.4
+wcwidth==0.2.6
+webcolors==1.13
+webencodings==0.5.1
+websocket-client==1.6.1
+widgetsnbextension==4.0.8
+zipp==3.16.2

ansible/roles/openondemand/tasks/jupyter_compute.yml

@@ -2,20 +2,31 @@
 # See https://osc.github.io/ood-documentation/latest/app-development/tutorials-interactive-apps/add-jupyter/software-requirements.html
 # - Will already have openssl and lmod
 
+- name: Ensure python3.9 installed
+  dnf:
+    name: python39
+  tags: install
+
 - name: Install jupyter venv
   # Requires separate step so that the upgraded pip is used to install packages
   pip:
     name: pip
     state: latest
-    virtualenv: /opt/jupyter
-    virtualenv_command: python3 -m venv
+    virtualenv: /opt/jupyter-py39
+    virtualenv_command: python3.9 -m venv
+  tags: install
+
+- name: Copy jupyter requirements file
+  copy:
+    src: jupyter_requirements.txt
+    dest: /opt/jupyter-py39/jupyter_requirements.txt
   tags: install
 
 - name: Install jupyter package in venv
   pip:
-    name: jupyter
-    virtualenv: /opt/jupyter
-    virtualenv_command: python3 -m venv
+    virtualenv: /opt/jupyter-py39
+    virtualenv_command: python3.9 -m venv
+    requirements: /opt/jupyter-py39/jupyter_requirements.txt
   tags: install
 
 

environments/.stackhpc/ansible.cfg

@@ -11,5 +11,5 @@ roles_path = ../../ansible/roles
 filter_plugins = ../../ansible/filter_plugins
 
 [ssh_connection]
-ssh_args = -o ControlMaster=auto -o ControlPersist=240s -o PreferredAuthentications=publickey -o UserKnownHostsFile=/dev/null
+ssh_args = -o ControlMaster=auto -o ControlPath=~/.ssh/%r@%h-%p -o ControlPersist=240s -o PreferredAuthentications=publickey -o UserKnownHostsFile=/dev/null
 pipelining = True

environments/common/inventory/group_vars/all/openondemand.yml

@@ -37,7 +37,7 @@ openondemand_clusters:
         basic:
           script_wrapper: |
             module purge
-            export PATH=/opt/jupyter/bin/:$PATH
+            export PATH=/opt/jupyter-py39/bin/:$PATH
             %s
           set_host: host=$(hostname -s)
         vnc: