Added docs for HPC on K8s. #17
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docs/docs/hpc-on-k8s/genome.md
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| spec: | ||
| containers: | ||
| - name: dummy-job | ||
| image: shubhamdang/fastqc_python_image:latest |
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Is this still the image repository or has the openflight one been created now?
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updated and image is present in openflighthpc dockerhub account.
docs/docs/hpc-on-k8s/genome.md
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| - name: MINIO_AKEY | ||
| value: "Mq6wmeNk0NOc0vD9Efut" | ||
| - name: MINIO_SKEY | ||
| value: "Z3ETBqC3GuIiU9PomjBbmmC5h8I5I7WgN1wNWlCG" |
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Not sure if these are sensitive secret keys or example ones but may be worth noting in the documentation what these keys should be set to (and maybe where to find them?)
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Added doc in minio to create access key added the the link of minio in workload notes.
docs/docs/hpc-on-k8s/tensorflow.md
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| spec: | ||
| containers: | ||
| - name: dummy-job | ||
| image: shubhamdang/custom_tensorflow:1.15.5 |
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Is this still the image repository or has the openflight one been created now?
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updated and image is prsent in openflighthpc dockerhub account.
docs/docs/hpc-on-k8s/hadoop.md
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| - name: MINIO_AKEY | ||
| value: "Mq6wmeNk0NOc0vD9Efut" | ||
| - name: MINIO_SKEY | ||
| value: "Z3ETBqC3GuIiU9PomjBbmmC5h8I5I7WgN1wNWlCG" |
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Not sure if these are sensitive secret keys or example ones but may be worth noting in the documentation what these keys should be set to (and maybe where to find them?)
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Added doc in minio to create access key added the the link of minio in workload notes.
docs/docs/hpc-on-k8s/pytorch.md
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| - name: MINIO_AKEY | ||
| value: "Mq6wmeNk0NOc0vD9Efut" | ||
| - name: MINIO_SKEY | ||
| value: "Z3ETBqC3GuIiU9PomjBbmmC5h8I5I7WgN1wNWlCG" |
There was a problem hiding this comment.
Not sure if these are sensitive secret keys or example ones but may be worth noting in the documentation what these keys should be set to (and maybe where to find them?)
There was a problem hiding this comment.
Added doc in minio to create access key added the the link of minio in workload notes.
docs/docs/hpc-on-k8s/simpy.md
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| - name: MINIO_AKEY | ||
| value: "Mq6wmeNk0NOc0vD9Efut" | ||
| - name: MINIO_SKEY | ||
| value: "Z3ETBqC3GuIiU9PomjBbmmC5h8I5I7WgN1wNWlCG" |
There was a problem hiding this comment.
Not sure if these are sensitive secret keys or example ones but may be worth noting in the documentation what these keys should be set to (and maybe where to find them?)
There was a problem hiding this comment.
Added doc in minio to create access key added the the link of minio in workload notes.
docs/docs/hpc-on-k8s/tensorflow.md
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| - name: MINIO_AKEY | ||
| value: "Mq6wmeNk0NOc0vD9Efut" | ||
| - name: MINIO_SKEY | ||
| value: "Z3ETBqC3GuIiU9PomjBbmmC5h8I5I7WgN1wNWlCG" |
There was a problem hiding this comment.
Not sure if these are sensitive secret keys or example ones but may be worth noting in the documentation what these keys should be set to (and maybe where to find them?)
There was a problem hiding this comment.
Added doc in minio to create access key added the the link of minio in workload notes.
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docs/docs/hpc-on-k8s/minio.md
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| - storageClass: | ||
| - Minio rootUser | ||
| - Minio rootPassword | ||
| - Minio ServiceType | ||
| - Minio API port | ||
| - Minio console port |
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I think it's worth doing something with this section, either:
- Explaining what these configurations are
- Removing it entirely (as I don't see why we need to mention them here?)
Regardless, using the CLI arg names (e.g. rootUser is what flags spellcheck errors however these can also be alleviated by wrapping them in backticks to make them in-line code). This'll also address removing these from codespell.
| ```bash | ||
| helm repo add bitnami https://charts.bitnami.com/bitnami | ||
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| helm install -n default --set global.storageClass=longhorn --set auth.rootUser=admin --set auth.rootPassword=test123456 --set service.type=NodePort --set service.nodePorts.api=31100 --set service.nodePorts.console=31101 --set persistence.size=2Gi my-minio bitnami/minio --version 12.9.4 |
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I know that there were some issues in testing where the previous 8Gi persistent size was an issue but just changing it to 2 could also bring up issues with file storage.
Perhaps there should be a note or some information about considerations and constraints for the storage size.
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| # Steps to create bio-user in bio namespace | |||
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I think this file needs some explanation of:
- What the users are for
- What the users have access to
docs/docs/hpc-on-k8s/user.md
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| kubectl config use-context bio-context | ||
| ``` | ||
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| ## Steps to create physics-user in bio namespace |
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This step being a H2 puts it at the same level as the rest of the docs. I have tripped up trying to add this user because I've followed the doc in order and switched to the bio-context and then received errors.
Fixing the formatting and probably noting the differences between the different contexts (as mentioned in the comment earlier in this file) should clear this up
docs/docs/hpc-on-k8s/genome.md
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| kind: Job | ||
| metadata: | ||
| generateName: fastqc- | ||
| namespace: default |
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As discussed IRL I think it's worth this job using the bio-context otherwise the users section isn't being put to any use
docs/docs/hpc-on-k8s/hadoop.md
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| value: <minio ip like "10.151.15.78"> | ||
| - name: MINIO_PORT | ||
| value: <minio port like "31100"> | ||
| # Minio Access Key | ||
| - name: MINIO_AKEY | ||
| value: <minio-access-key> | ||
| # Minio Secret Key | ||
| - name: MINIO_SKEY | ||
| value: <minio-secret-key> | ||
| - name: BUCKET_NAME | ||
| value: <minio bucket name like "hadoop"> |
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Some issues experienced IRL with not quoting strings, perhaps putting the entire <> section in quotes would make this a little clearer (especially as the access key and secret key don't have any indication of this being needed)
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| - Docker must be installed on all nodes of the Kubernetes cluster. | ||
| - Password-less SSH access must be set up from the rke node to all Kubernetes nodes. | ||
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Experienced issues with bringing up rke before having firewall disabled (or appropriate rules setup for internal network communication) which were only fixed after making firewall correct and then restarting docker.
It seems sensible then to make one of the prerequisites be firewall related
docs/docs/hpc-on-k8s/genome.md
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| - name: MINIO_IP | ||
| value: <minio ip like "10.151.15.78"> | ||
| - name: MINIO_PORT | ||
| value: <minio port like "31100"> | ||
| # Minio Access Key | ||
| - name: MINIO_AKEY | ||
| value: <minio-access-key> | ||
| # Minio Secret Key | ||
| - name: MINIO_SKEY | ||
| value: <minio-secret-key> | ||
| - name: BUCKET_NAME | ||
| value: <minio bucket name like "genome"> |
There was a problem hiding this comment.
Some issues experienced IRL with not quoting strings, perhaps putting the entire <> section in quotes would make this a little clearer (especially as the access key and secret key don't have any indication of this being needed)
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