Cleaning files

dba083e5 · Nicolas Richart · 7eb2a987 · 7eb2a987 · 7eb2a987 · 7eb2a987
Commit dba083e5 authored 4 months ago by Nicolas Richart
--- a/Dockerfile.desktop
+++ b/Dockerfile.desktop
-# syntax=docker/dockerfile:experimental
-FROM slaclab/x11-desktop:20231115.0
-
-ENV DEBIAN_FRONTEND noninteractive
-
-COPY mozilla.pin /etc/apt/preferences.d/mozilla 
-RUN curl -fsSL https://www.mongodb.org/static/pgp/server-6.0.asc | gpg --dearmor -o /usr/share/keyrings/mongodb-6.0-keyring.gpg \
-  && echo "deb [ arch=amd64,arch64 signed-by=/usr/share/keyrings/mongodb-6.0-keyring.gpg ] https://repo.mongodb.org/apt/ubuntu jammy/mongodb-org/6.0 multiverse" | tee /etc/apt/sources.list.d/mongodb-org-6.0.list \
-  && apt-get update \
-  && wget -q https://packages.mozilla.org/apt/repo-signing-key.gpg -O /usr/share/keyrings/packages.mozilla.org.asc \
-  && echo "deb [ arch=amd64 signed-by=/usr/share/keyrings/packages.mozilla.org.asc ] https://packages.mozilla.org/apt mozilla main" > /etc/apt/sources.list.d/mozilla.list \
-  && apt-get update \
-  && apt-get install -y --no-install-recommends \
-    firefox \
-    zip unzip \
-    python3 python3-dev python3-setuptools python3-pip \
-    libtiff5 \
-    ed jq \
-    sudo \
-    less \
-    netbase iputils-ping net-tools \
-    nodejs \
-    mongodb-mongosh mongodb-database-tools \
-  && apt-get remove chromium \
-  && apt-get clean \
-  && rm -rf /var/lib/apt/lists/* \
-  && ln -s /usr/lib/x86_64-linux-gnu/libtiff.so.5 /usr/lib/x86_64-linux-gnu/libtiff.so.3
-
-ENV CRYOSPARC_ROOT_DIR /app
-RUN mkdir -p ${CRYOSPARC_ROOT_DIR}
-WORKDIR ${CRYOSPARC_ROOT_DIR}
-
-ARG CRYOSPARC_VERSION
-ENV CRYOSPARC_VERSION=${CRYOSPARC_VERSION}
-
-ARG CRYOSPARC_PATCH
-ENV CRYOSPARC_PATCH=${CRYOSPARC_PATCH}
-
-RUN echo "USER=`id -u -n`"
-# install master
-ENV CRYOSPARC_MASTER_DIR ${CRYOSPARC_ROOT_DIR}/cryosparc_master
-RUN --mount=type=secret,id=cryosparc_license_id \
-  curl -L https://get.cryosparc.com/download/master-v${CRYOSPARC_VERSION}/$(cat /run/secrets/cryosparc_license_id) | tar -xz \
-  && cd ${CRYOSPARC_MASTER_DIR} \
-  && sed -i '/^# Other$/ a echo \"CRYOSPARC_FORCE_USER=true\" >> config.sh' ${CRYOSPARC_MASTER_DIR}/install.sh \
-  && bash ./install.sh --license "$(cat /run/secrets/cryosparc_license_id)" --allowroot --yes  \
-  && sed -i 's/^export CRYOSPARC_LICENSE_ID=.*$/export CRYOSPARC_LICENSE_ID=TBD/g' ${CRYOSPARC_MASTER_DIR}/config.sh
-
-# update patches
-RUN if [ "" != "${CRYOSPARC_PATCH}" ]; then wget https://get.cryosparc.com/patch_get/v${CRYOSPARC_VERSION}+${CRYOSPARC_PATCH}/master -O ${CRYOSPARC_ROOT_DIR}/cryosparc_master_patch.tar.gz \
-  && tar -vxzf ${CRYOSPARC_ROOT_DIR}/cryosparc_master_patch.tar.gz --overwrite --strip-components=1 --directory=${CRYOSPARC_MASTER_DIR} \
-  && rm -f ${CRYOSPARC_ROOT_DIR}/cryosparc_master_patch.tar.gz; fi
-
-# patches
-RUN sed -i 's:    disk_has_space=.*:    disk_has_space="true":g'  ${CRYOSPARC_MASTER_DIR}/bin/cryosparcm
-
-# install worker
-ENV CRYOSPARC_WORKER_DIR ${CRYOSPARC_ROOT_DIR}/cryosparc_worker
-RUN --mount=type=secret,id=cryosparc_license_id \
-  curl -L https://get.cryosparc.com/download/worker-v${CRYOSPARC_VERSION}/$(cat /run/secrets/cryosparc_license_id) | tar -xz \
-  && cd ${CRYOSPARC_WORKER_DIR} \
-  && bash ./install.sh --license "$(cat /run/secrets/cryosparc_license_id)" --yes \
-  && sed -i 's/^export CRYOSPARC_LICENSE_ID=.*$/export CRYOSPARC_LICENSE_ID=TBD/g' ${CRYOSPARC_WORKER_DIR}/config.sh
-
-# update patches
-RUN if [ ! -z "${CRYOSPARC_PATCH}" ]; then wget https://get.cryosparc.com/patch_get/v${CRYOSPARC_VERSION}+${CRYOSPARC_PATCH}/worker -O ${CRYOSPARC_ROOT_DIR}/cryosparc_worker_patch.tar.gz \
-  && tar -vxzf ${CRYOSPARC_ROOT_DIR}/cryosparc_worker_patch.tar.gz --overwrite --strip-components=1 --directory=${CRYOSPARC_WORKER_DIR} \
-  && rm -f ${CRYOSPARC_ROOT_DIR}/cryosparc_worker_patch.tar.gz; fi
-
-# compile libtiff
-RUN ${CRYOSPARC_MASTER_DIR}/deps/anaconda/envs/cryosparc_master_env/bin/python3 ${CRYOSPARC_MASTER_DIR}/cryosparc_compute/blobio/tiff.py \
-  && ${CRYOSPARC_WORKER_DIR}/deps/anaconda/envs/cryosparc_worker_env/bin/python3 ${CRYOSPARC_WORKER_DIR}/cryosparc_compute/blobio/tiff.py
-####
-## install motioncor
-####
-ARG MOTIONCOR2_VERSION=1.4.5
-ENV MOTIONCOR2_VERSION=${MOTIONCOR2_VERSION}
-ENV CUDA_TOOLKIT_VERSION="Cuda100-10-22-2021"
-RUN cd /usr/local/bin \
-  && curl -L 'https://drive.google.com/uc?export=download&id=1-Ub5lBBmel8U8U0uibORiH6wfxp9I1kn' > MotionCor2_${MOTIONCOR2_VERSION}.zip \
-  && unzip MotionCor2_${MOTIONCOR2_VERSION}.zip \
-  && rm -f MotionCor2_${MOTIONCOR2_VERSION}.zip \
-  && ln -sf MotionCor2_${MOTIONCOR2_VERSION}-${CUDA_TOOLKIT_VERSION} MotionCor2
-
-###
-# install topaz
-###
-ARG TOPAZ_VERSION=0.2.5
-ENV TOPAZ_VERSION=${TOPAZ_VERSION}
-ENV TOPAZ_CUDA_TOOLKIT_VERSION=12.2.0
-RUN /app/cryosparc_worker/deps/anaconda/bin/conda install topaz=${TOPAZ_VERSION} cuda-libraries-dev cuda-nvcc cuda-nvtx cuda-cupti -c nvidia/label/cuda-${TOPAZ_CUDA_TOOLKIT_VERSION} -c tbepler -c pytorch
-
-###
-#
-### finish off
-COPY entrypoint.bash /entrypoint.bash
-COPY cryosparc.sh /cryosparc.sh
-COPY cryosparc-server.sh ${CRYOSPARC_MASTER_DIR}/bin/cryosparc-server.sh
-
-# autostart stuff
-COPY cryosparc.desktop /cryosparc.desktop
-RUN rm -f /etc/xdg/autostart/xscreensaver.desktop /etc/xdg/autostart/blueman.desktop /etc/xdg/autostart/mate-screensaver.desktop /etc/xdg/autostart/print-applet.desktop /etc/xdg/autostart/xfce4-power-manager.desktop /etc/xdg/autostart/mate-power-manager.desktop
-
-EXPOSE 39000
-EXPOSE 39001
-EXPOSE 39002
-EXPOSE 39003
-EXPOSE 39004
-EXPOSE 39006
-
-ENTRYPOINT /entrypoint.bash
--- a/Singularity
+++ b/Singularity
-#From: docker://slaclab/cryosparc-docker:2.13.2-0
-From: docker://slaclab/cryosparc-docker:4.0.3-0
--- a/cryosparc-server.sh
+++ b/cryosparc-server.sh
-#!/bin/bash -xe
-
-# ensure we have a cryosparc directory under home
-export CRYOSPARC_DATADIR=${HOME}/cryosparc
-echo "Creating cryosparc datadir ${CRYOSPARC_DATADIR}..."
-mkdir -p ${CRYOSPARC_DATADIR}
-mkdir -p ${CRYOSPARC_DATADIR}/run
-mkdir -p ${CRYOSPARC_DATADIR}/cryosparc_database
-
-export PATH=${CRYOSPARC_MASTER_DIR}/bin:${CRYOSPARC_WORKER_DIR}/bin:${CRYOSPARC_MASTER_DIR}/deps/anaconda/bin/:$PATH
-
-export CRYOSPARC_MASTER_HOSTNAME=${CRYOSPARC_MASTER_HOSTNAME:-$(hostname -s)}
-echo "setting CRYOSPARC_MASTER_HOSTNAME=${CRYOSPARC_MASTER_HOSTNAME}"
-
-###
-# master initiation
-###
-CRYOSPARC_LICENSE_ID=${CRYOSPARC_LICENSE_ID:-$1}
-if [ "${CRYOSPARC_LICENSE_ID}" == "" ]; then
-  echo "CRYOSPARC_LICENSE_ID required to continue..."
-  exit 127
-fi
-CRYOSPARC_BASE_PORT=${CRYOSPARC_BASE_PORT:-"39000"}
-
-echo "Starting cryosparc master..."
-cd ${CRYOSPARC_MASTER_DIR}
-# modify configuration
-printf "%s\n" "1,\$s/^export CRYOSPARC_MASTER_HOSTNAME=.*$/export CRYOSPARC_MASTER_HOSTNAME=${CRYOSPARC_MASTER_HOSTNAME}/g" wq | ed -s ${CRYOSPARC_MASTER_DIR}/config.sh
-printf "%s\n" "1,\$s/^export CRYOSPARC_LICENSE_ID=.*$/export CRYOSPARC_LICENSE_ID=${CRYOSPARC_LICENSE_ID}/g" wq | ed -s ${CRYOSPARC_MASTER_DIR}/config.sh
-printf "%s\n" "1,\$s|^export CRYOSPARC_DB_PATH=.*$|export CRYOSPARC_DB_PATH=${CRYOSPARC_DATADIR}/cryosparc_database|g" wq | ed -s ${CRYOSPARC_MASTER_DIR}/config.sh
-printf "%s\n" "1,\$s/^export CRYOSPARC_BASE_PORT=.*$/export CRYOSPARC_BASE_PORT=${CRYOSPARC_BASE_PORT}/g" wq | ed -s ${CRYOSPARC_MASTER_DIR}/config.sh
-echo '====='
-cat ${CRYOSPARC_MASTER_DIR}/config.sh
-echo '====='
-
-# envs
-THIS_USER=$(whoami)
-THIS_USER_SUFFIX=${USER_SUFFIX:-'@slac.stanford.edu'}
-echo "Starting cryoSPARC in ${CRYOSPARC_MASTER_DIR} as ${THIS_USER}${THIS_USER_SUFFIX} with..."
-SOCK_FILE=$(cryosparcm env | grep CRYOSPARC_SUPERVISOR_SOCK_FILE | sed 's/^.*CRYOSPARC_SUPERVISOR_SOCK_FILE=//' | sed 's/"//g')
-rm -f "${SOCK_FILE}" || true
-cryosparcm restart
-
-# always set the password to license
-cryosparcm createuser    --email ${THIS_USER}${THIS_USER_SUFFIX} --password "${CRYOSPARC_LICENSE_ID}" --name "User"
-cryosparcm resetpassword --email ${THIS_USER}${THIS_USER_SUFFIX} --password "${CRYOSPARC_LICENSE_ID}"
-
-# need to restart to get login prompt
-cryosparcm restart
-
-# remove all existing lanes and register standard lanes
-echo "Registering job lanes..."
-/app/cryosparc_master/bin/cryosparcm cli 'get_scheduler_targets()'  | python -c "import sys, ast, json; print( json.dumps(ast.literal_eval(sys.stdin.readline())) )" | jq '.[].name' | sed 's:"::g' | xargs -n1 -I \{\} /app/cryosparc_master/bin/cryosparcm cli 'remove_scheduler_target_node("'{}'")'
-# add slurm lanes
-for i in `ls -1 /app/slurm/`; do
-  cd /app/slurm/$i
-  /app/cryosparc_master/bin/cryosparcm cluster connect
-done
-cd ${CRYOSPARC_MASTER_DIR}
-
-echo "Success starting cryosparc master!"
-
-###
-# worker initiation
-###
-echo "Starting cryosparc worker for ${CRYOSPARC_MASTER_HOSTNAME}..."
-export TMPDIR=${TMPDIR:-"/tmp/${THIS_USER}"}/cryosparc/
-mkdir -p ${TMPDIR}
-
-cd ${CRYOSPARC_WORKER_DIR}
-# assume same config file
-#printf "%s\n" "1,\$s/^export CRYOSPARC_LICENSE_ID=.*$/export CRYOSPARC_LICENSE_ID=${CRYOSPARC_LICENSE_ID}/g" wq | ed -s ${CRYOSPARC_WORKER_DIR}/config.sh
-#printf "%s\n" "1,\$s/^export CRYOSPARC_MASTER_HOSTNAME=.*$/export CRYOSPARC_MASTER_HOSTNAME=${CRYOSPARC_MASTER_HOSTNAME}/g" wq | ed -s ${CRYOSPARC_WORKER_DIR}/config.sh
-
-# start worker
-#/app/cryosparc_worker/bin/cryosparcw connect --worker localhost --master cryosparc-api-$(whoami) --ssdpath $TMPDIR/
-#TODO: delete existing workers first...?
-/app/cryosparc_worker/bin/cryosparcw connect --worker ${CRYOSPARC_MASTER_HOSTNAME} --master ${CRYOSPARC_MASTER_HOSTNAME} --ssdpath $TMPDIR/
-
-###
-# monitor forever
-###
-echo "Success starting cryosparc worker!"
-
-# should probably catch kill to terminate the instance
-while :
-do
-  echo 'heartbeat...'
-  sleep 300
-done
--- a/cryosparc.desktop
+++ b/cryosparc.desktop
-[Desktop Entry]
-Type=Application
-Exec=sh ./cryosparc_launcher.sh
-Hidden=false
-X-GNOME-Autostart-enabled=true
-Name=CryoSPARC Web App
--- a/firefox.autostart
+++ b/firefox.autostart
-[Desktop Entry]
-Type=Application
-Exec=sh /tmp/cryosparc_launcher.sh
-Hidden=false
-X-GNOME-Autostart-enabled=true
-Name=CryoSPARC Launcher
--- a/kubernetes/PROD
+++ b/kubernetes/PROD
-namespace=cryosparc-prod
-nodeSelectors="storage/cryoem=true group/cryoem=true accelerator=nvidia"
-cryosparc_image=slaclab/cryosparc-live
-cryosparc_version=2.9.1-0
--- a/kubernetes/deployment.yaml
+++ b/kubernetes/deployment.yaml
-apiVersion: apps/v1
-kind: Deployment
-metadata:
-  name: cryosparc-${USER}
-  labels:
-    app: cryosparc-${USER}
-spec:
-  selector:
-    matchLabels:
-      app: cryosparc-${USER}
-  template:
-    metadata:
-      labels:
-        app: cryosparc-${USER}
-    spec:
-      nodeSelector:
-$(list=(${nodeSelectors// / }); for k in "${!list[@]}"; do kv=(${list[k]//\=/ }); echo "        ${kv[0]}: ${kv[1]}"; done)
-      containers:
-      - image: ${cryosparc_image}:${cryosparc_version}
-        name: cryosparc
-        env:
-        - name: CRYOSPARC_LICENSE_ID
-          value: ${CRYOSPARC_LICENSE_ID}
-        - name: JUPYTERHUB_USER
-          value: ${USER}
-        - name: EXTERNAL_UID
-          value: ${EXTERNAL_UID}
-        - name: EXTERNAL_GROUPS
-          value: ${EXTERNAL_GROUPS}
-        - name: HOMEDIRS
-          value: /gpfs/slac/cryo/fs1/u/
-        ports:
-        - containerPort: 39000
-        - containerPort: 39001
-        - containerPort: 39002
-        - containerPort: 39003
-        - containerPort: 39004
-        - containerPort: 39005
-        - containerPort: 39006
-        volumeMounts:
-        - name: gpfs-home
-          mountPath: /gpfs/slac/cryo/fs1/u/
-        - name: gpfs-exp
-          mountPath: /gpfs/slac/cryo/fs1/exp/
-        - name: gpfs-g
-          mountPath: /gpfs/slac/cryo/fs1/g/
-        - name: scratch
-          mountPath: /scratch/
-        - name: tmp
-          mountPath: /tmp/
-      volumes:
-      - name: gpfs
-        persistentVolumeClaim:
-          claimName: ${namespace}--gpfs-home
-      - name: gpfs
-        persistentVolumeClaim:
-          claimName: ${namespace}--gpfs-exp
-      - name: gpfs
-        persistentVolumeClaim:
-          claimName: ${namespace}--gpfs-g
-      - name: scratch
-        persistentVolumeClaim:
-          claimName: ${namespace}--scratch
-      - name: tmp
-        persistentVolumeClaim:
-          claimName: ${namespace}--tmp
-
--- a/kubernetes/endpoint.yaml
+++ b/kubernetes/endpoint.yaml
---
-
-apiVersion: v1
-kind: Service
-metadata:
-  name: cryosparc-${USER}
-  labels:
-    name: cryosparc-${USER}
-spec:
-  type: ClusterIP
-  ports:
-  - name: http
-    port: 39000
-    protocol: TCP
-  selector:
-    name: cryosparc-${USER}
-
---
-apiVersion: extensions/v1beta1
-kind: Ingress
-metadata:
-  name: cryosparc-${USER}
-  annotations:
-    nginx.ingress.kubernetes.io/proxy-connect-timeout: "30s"
-    nginx.ingress.kubernetes.io/proxy-read-timeout: "20s"
-    nginx.ingress.kubernetes.io/client-max-body-size: "50m"
-    nginx.ingress.kubernetes.io/proxy-body-size: "50m"
-spec:
-  tls:
-    - hosts:
-      - cryosparc.slac.stanford.edu
-      secretName: tls-certificate
-  rules:
-    - host: cryosparc.slac.stanford.edu
-      http:
-        paths:
-        - path: /${USER}
-          backend:
-            serviceName: cryosparc-${USER}
-            servicePort: 39000
-
-
--- a/kubernetes/gen_template.sh
+++ b/kubernetes/gen_template.sh
-#!/bin/bash
-
-# set -x
-
-CONFIG_FILE="ENVIRONMENT"
-if [ -n "${1}" ]; then
-    CONFIG_FILE="${1}"
-fi
-
-# import key value pairs
-source ./${CONFIG_FILE}
-
-# stolen from https://starkandwayne.com/blog/bashing-your-yaml/
-function gen_template() {
-    rm -f final.yaml temp.yaml  
-    ( echo "cat <<EOF >final.yaml";
-      cat $1;
-      echo "EOF";
-    ) >temp.yaml
-    . temp.yaml
-    cat final.yaml
-    rm -f final.yaml temp.yaml  
-}
-
-gen_template "${2}"
--- a/kubernetes/init.sh
+++ b/kubernetes/init.sh
-#!/bin/sh
-
-source ./PROD
-kubectl create namespace ${namespace}
-./gen_template.sh PROD storage.yaml |  kubectl -n ${namespace} create -f -
--- a/kubernetes/storage.yaml
+++ b/kubernetes/storage.yaml
---
-
-kind: PersistentVolume
-apiVersion: v1
-metadata:
-  name: ${namespace}--gpfs-home
-  labels:
-    type: local
-spec:
-  storageClassName: ${namespace}--gpfs-home
-  capacity:
-    storage: 10000Gi
-  accessModes:
-    - ReadWriteMany
-  hostPath:
-    path: /gpfs/slac/cryo/fs1/u/
-
---
-
-kind: PersistentVolumeClaim
-apiVersion: v1
-metadata:
-  name: gpfs-home
-spec:
-  storageClassName: ${namespace}--gpfs-home
-  accessModes:
-    - "ReadWriteMany"
-  resources:
-    requests:
-      storage: 100Gi
-
---
-
-kind: PersistentVolume
-apiVersion: v1
-metadata:
-  name: ${namespace}--gpfs-exp
-  labels:
-    type: local
-spec:
-  storageClassName: ${namespace}--gpfs-exp
-  capacity:
-    storage: 10000Gi
-  accessModes:
-    - ReadWriteMany
-  hostPath:
-    path: /gpfs/slac/cryo/fs1/exp/
-
---
-
-kind: PersistentVolumeClaim
-apiVersion: v1
-metadata:
-  name: gpfs-exp
-spec:
-  storageClassName: ${namespace}--gpfs-exp
-  accessModes:
-    - "ReadWriteMany"
-  resources:
-    requests:
-      storage: 100Gi
-
---
-
-kind: PersistentVolume
-apiVersion: v1
-metadata:
-  name: ${namespace}--gpfs-g
-  labels:
-    type: local
-spec:
-  storageClassName: ${namespace}--gpfs-g
-  capacity:
-    storage: 10000Gi
-  accessModes:
-    - ReadWriteMany
-  hostPath:
-    path: /gpfs/slac/cryo/fs1/g/
-
---
-
-kind: PersistentVolumeClaim
-apiVersion: v1
-metadata:
-  name: gpfs-g
-spec:
-  storageClassName: ${namespace}--gpfs-g
-  accessModes:
-    - "ReadWriteMany"
-  resources:
-    requests:
-      storage: 100Gi
-
-
---
-
-kind: PersistentVolume
-apiVersion: v1
-metadata:
-  name: ${namespace}--scratch
-  labels:
-    type: local
-spec:
-  storageClassName: ${namespace}--scratch
-  capacity:
-    storage: 10000Gi
-  accessModes:
-    - ReadWriteMany
-  hostPath:
-    path: /scratch/
-
---
-
-kind: PersistentVolumeClaim
-apiVersion: v1
-metadata:
-  name: scratch
-spec:
-  storageClassName: ${namespace}--scratch
-  accessModes:
-    - "ReadWriteMany"
-  resources:
-    requests:
-      storage: 100Gi
-
---
-
-kind: PersistentVolume
-apiVersion: v1
-metadata:
-  name: ${namespace}--tmp
-  labels:
-    type: local
-spec:
-  storageClassName: ${namespace}--tmp
-  capacity:
-    storage: 10000Gi
-  accessModes:
-    - ReadWriteMany
-  hostPath:
-    path: /tmp/
-
---
-
-kind: PersistentVolumeClaim
-apiVersion: v1
-metadata:
-  name: tmp
-spec:
-  storageClassName: ${namespace}--tmp
-  accessModes:
-    - "ReadWriteMany"
-  resources:
-    requests:
-      storage: 100Gi
--- a/mozilla.pin
+++ b/mozilla.pin
-Package: *
-Pin: origin packages.mozilla.org
-Pin-Priority: 1000