Merge pull request #4607 from sgibson91/higher-dev-shm-limits

Enable higher limits for `/dev/shm` for all users
2i2c-org · Aug 12, 2024 · 61c711e · 61c711e
2 parents d41012c + 800d55a
commit 61c711e
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diff --git a/config/clusters/2i2c-aws-us/itcoocean.values.yaml b/config/clusters/2i2c-aws-us/itcoocean.values.yaml
@@ -59,6 +59,8 @@ jupyterhub:
           mountPath: /home/jovyan/shared-public
           subPath: _shared-public
           readOnly: false
+        - name: dev-shm
+          mountPath: /dev/shm
     initContainers:
       - name: volume-mount-ownership-fix
         image: busybox:1.36.1

diff --git a/config/clusters/2i2c/climatematch.values.yaml b/config/clusters/2i2c/climatematch.values.yaml
@@ -16,6 +16,8 @@ jupyterhub:
           mountPath: /home/jovyan/shared
           subPath: _shared
           readOnly: true
+        - name: dev-shm
+          mountPath: /dev/shm
     initContainers:
       - name: volume-mount-ownership-fix
         image: busybox:1.36.1

diff --git a/config/clusters/hhmi/daskhub-common.values.yaml b/config/clusters/hhmi/daskhub-common.values.yaml
@@ -68,6 +68,8 @@ basehub:
             mountPath: /home/jovyan/shared-readonly
             subPath: _shared
             readOnly: true
+          - name: dev-shm
+            mountPath: /dev/shm
       initContainers:
         - name: volume-mount-ownership-fix
           image: busybox:1.36.1

diff --git a/config/clusters/hhmi/spyglass.values.yaml b/config/clusters/hhmi/spyglass.values.yaml
@@ -62,11 +62,16 @@ jupyterhub:
         - name: shared-dir-pv
           persistentVolumeClaim:
             claimName: home-nfs
+        - name: dev-shm
+          emptyDir:
+            medium: Memory
       extraVolumeMounts:
         - name: shared-dir-pv
           mountPath: /home/jovyan/shared-readonly
           subPath: _shared
           readOnly: true
+        - name: dev-shm
+          mountPath: /dev/shm
     defaultUrl: /git-pull?repo=https%3A%2F%2Fgithub.com%2FLorenFrankLab%2Fspyglass-demo&urlpath=lab%2Ftree%2Fspyglass-demo%2Fnotebooks%2F00_HubQuickStart.ipynb&branch=main
     image:
       name: quay.io/lorenlab/hhmi-spyglass-image

diff --git a/config/clusters/nasa-veda/common.values.yaml b/config/clusters/nasa-veda/common.values.yaml
@@ -121,6 +121,8 @@ basehub:
             mountPath: /home/jovyan/shared
             subPath: _shared
             readOnly: true
+          - name: dev-shm
+            mountPath: /dev/shm
       profileList:
         - display_name: Choose your environment and resources
           default: true

diff --git a/config/clusters/pchub/common.values.yaml b/config/clusters/pchub/common.values.yaml
@@ -98,6 +98,8 @@ basehub:
             mountPath: /home/jovyan/shared
             subPath: _shared
             readOnly: true
+          - name: dev-shm
+            mountPath: /dev/shm
       profileList:
         - display_name: "Pangeo Notebook"
           slug: pangeo

diff --git a/docs/howto/features/ephemeral.md b/docs/howto/features/ephemeral.md
@@ -123,11 +123,18 @@ ephemeral hub's users.
          # We still don't want to have per-user storage
          type: none
          extraVolumes:
+           # We include the dev-shm extraVolume as the list of extraVolumes from base hub will be overwritten
+           - name: dev-shm
+             emptyDir:
+               medium: Memory
            - name: shared-dir-pvc
              persistentVolumeClaim:
                # The name of the PVC setup by nfs.yaml for the ephemeral hub to use
                claimName: home-nfs
          extraVolumeMounts:
+           # We include the dev-shm extraVolumeMount as the list of extraVolumeMounts from base hub will be overwritten
+           - name: dev-shm
+             mountPath: /dev/shm
            - name: shared-dir-pvc
              mountPath: /home/jovyan/shared
              subPath: _shared

diff --git a/docs/howto/features/per-user-db.md b/docs/howto/features/per-user-db.md
@@ -81,11 +81,18 @@ jupyterhub:
             subPath: data
     storage:
       extraVolumes:
+           # We include the dev-shm extraVolume as the list of extraVolumes from base hub will be overwritten
+           - name: dev-shm
+             emptyDir:
+               medium: Memory
         - name: postgres-db
           persistentVolumeClaim:
             # This should match what is set as `name` in the earlier step under `custom.singleuser.extraPVCs`
             claimName: 'postgres-{username}'
       extraVolumeMounts:
+           # We include the dev-shm extraVolumeMount as the list of extraVolumeMounts from base hub will be overwritten
+           - name: dev-shm
+             mountPath: /dev/shm
         - name: postgres-db
           mountPath: /var/lib/postgresql/data
           # postgres recommends against mounting a volume directly here

diff --git a/docs/topic/infrastructure/storage-layer.md b/docs/topic/infrastructure/storage-layer.md
@@ -96,6 +96,8 @@ jupyterhub:
         # mounts below are copied from basehub's values that we override by
         # specifying extraVolumeMounts (lists get overridden when helm values
         # are combined)
+        - name: dev-shm
+          mountPath: /dev/shm
         - name: home
           mountPath: /home/jovyan/shared-readwrite
           subPath: _shared

diff --git a/helm-charts/basehub/values.yaml b/helm-charts/basehub/values.yaml
@@ -773,11 +773,17 @@ jupyterhub:
       static:
         pvcName: home-nfs
         subPath: "{username}"
+      extraVolumes:
+        - name: dev-shm
+          emptyDir:
+            medium: Memory
       extraVolumeMounts:
         - name: home
           mountPath: /home/jovyan/shared
           subPath: _shared
           readOnly: true
+        - name: dev-shm
+          mountPath: /dev/shm
 
         # For all pods, mount home in both /home/jovyan (done via singleuser.storage.static)
         # as well as /home/rstudio. This allows rocker images (which use the