The following scripts are expected to be executed after both SSH'ing into the GitHub self-hosted runner associated with allocation BIO180006_IU and activating the associated python environment.
Scripts were created based of MorphoCloud/MorphoCloudWorkflow@624549e64
For example:
ssh [email protected]
. venv/bin/activate
| #!/usr/bin/env bash | |
| export OS_CLOUD=BIO180006_IU | |
| cd /tmp | |
| git clone https://github.com/MorphoCloud/MorphoCloudWorkflow.git | |
| cd MorphoCloudWorkflow | |
| INSTANCE_NAME="instance-9999" | |
| VOLUME_NAME="My-Data-9999" | |
| INSTANCE_FLAVOR="g3.xl" | |
| # ---------------------------------------------------------------------------- | |
| # Check if instance has a floating IP | |
| # Get instance floating IP | |
| instance_ip=$( | |
| openstack server show $INSTANCE_NAME -c addresses -f json | \ | |
| jq -r '.addresses.auto_allocated_network | if length > 1 then .[1] else "" end' | |
| ) | |
| echo "instance_ip [$instance_ip]" | |
| # Get instance internal IP (also called fixed IP) | |
| instance_internal_ip=$( | |
| openstack server show $INSTANCE_NAME -c addresses -f json | \ | |
| jq -r '.addresses.auto_allocated_network | if length > 0 then .[0] else "" end' | |
| ) | |
| echo "instance_internal_ip [$instance_internal_ip]" | |
| # Determine if instance already has a floating IP assigned | |
| if [[ -n "$instance_ip" ]]; then | |
| has_ip="true" | |
| else | |
| has_ip="false" | |
| fi | |
| echo "has_ip [$has_ip]" | |
| # Check if an unassigned floating IP matches instance IP | |
| has_ip_assigned="false" | |
| if [[ "$has_ip" == "true" ]]; then | |
| json_output=$(openstack floating ip list -f json | jq \ | |
| --arg fixed_ip "$instance_internal_ip" \ | |
| --arg ip "$instance_ip" \ | |
| 'map(select(.Port != null and ."Fixed IP Address" == $fixed_ip and ."Floating IP Address" == $ip))') | |
| floating_ip_address=$(echo "$json_output" | jq -r 'if length > 0 then .[0]["Floating IP Address"] else "" end') | |
| if [[ -n "$floating_ip_address" ]]; then | |
| has_ip_assigned="true" | |
| fi | |
| fi | |
| # If previously assigned IP is not available anymore, discard it. | |
| if [[ "$has_ip_assigned" == "false" ]]; then | |
| instance_ip="" | |
| fi | |
| echo "instance_ip [$instance_ip]" | |
| echo "has_ip_assigned [$has_ip_assigned]" | |
| # ---------------------------------------------------------------------------- | |
| # Retrieve or create floating IP | |
| floating_ip_address="" | |
| floating_ip_uuid="" | |
| if [[ $has_ip_assigned == "false" ]]; then | |
| preferred_ip_address=$instance_ip | |
| echo "preferred_ip_address [$preferred_ip_address]" | |
| # Retrieve unassigned floating IP | |
| json_output=$(openstack floating ip list -f json | jq 'map(select(.Port == null))') | |
| echo "Filtered JSON Output:" | |
| echo "$json_output" | jq | |
| if [[ -n "$preferred_ip_address" ]]; then | |
| floating_ip=$(echo "$json_output" | jq -r --arg ip "$preferred_ip_address" \ | |
| 'map(select(."Floating IP Address" == $ip)) | if length > 0 then .[0] else null end') | |
| else | |
| floating_ip=$(echo "$json_output" | jq -r 'if length > 0 then .[0] else null end') | |
| fi | |
| floating_ip_address=$(echo "$floating_ip" | jq -r '."Floating IP Address" // empty') | |
| floating_ip_uuid=$(echo "$floating_ip" | jq -r '."ID" // empty') | |
| echo "floating_ip_address [$floating_ip_address]" | |
| echo "floating_ip_uuid [$floating_ip_uuid]" | |
| fi | |
| if [[ -z "$floating_ip_address" ]]; then | |
| json_output=$(openstack floating ip create public -f json) | |
| echo "Floating IP Creation Output:" | |
| echo "$json_output" | jq | |
| floating_ip_uuid=$( | |
| echo $json_output | | |
| jq -r ".id" | |
| ) | |
| echo "floating_ip_uuid [$floating_ip_uuid]" | |
| floating_ip_address=$( | |
| echo $json_output | | |
| jq -r ".floating_ip_address" | |
| ) | |
| echo "floating_ip_address [$floating_ip_address]" | |
| fi | |
| # ---------------------------------------------------------------------------- | |
| openstack volume create --size 100 "$VOLUME_NAME" | |
| # ---------------------------------------------------------------------------- | |
| # The MorphCloud workflow uses a unique UUID generated with: | |
| # python3 -c "import uuid; print(uuid.uuid4())" | |
| exoClientUuid=b7b75870-ecb5-4aca-ae73-49474a7f531e | |
| # See "currentExoServerVersion" in exosphere/src/Types/Server.elm | |
| exoServerVersion=5 | |
| FLOATING_IP_UUID=$floating_ip_uuid | |
| echo "INSTANCE_FLAVOR [$INSTANCE_FLAVOR]" | |
| echo "FLOATING_IP_UUID [$FLOATING_IP_UUID]" | |
| echo "exoServerVersion [$exoServerVersion]" | |
| echo "exoClientUuid [$exoClientUuid]" | |
| openstack server create "$INSTANCE_NAME" \ | |
| --nic net-id="auto_allocated_network" \ | |
| --security-group "exosphere" \ | |
| --flavor $INSTANCE_FLAVOR \ | |
| --image "Featured-Ubuntu22" \ | |
| --key-name "jcfr" \ | |
| --property "exoGuac={\"v\":1,\"ssh\":true,\"vnc\":true}" \ | |
| --property "exoClientUuid=$exoClientUuid" \ | |
| --property "exoServerVersion=$exoServerVersion" \ | |
| --property "[email protected]" \ | |
| --property "exoFloatingIpOption=useFloatingIp" \ | |
| --property "exoFloatingIpReuseOption=$FLOATING_IP_UUID" \ | |
| --property "exoSetup={\"status\":\"waiting\",\"epoch\":null}" \ | |
| --user-data ./cloud-config \ | |
| --wait \ | |
| --column created \ | |
| --column flavor \ | |
| --column image \ | |
| --column name \ | |
| --column status | |
| # Associate floating IP with created instance | |
| has_ip=$( | |
| openstack server show $INSTANCE_NAME -c addresses -f json | \ | |
| jq -r '.addresses.auto_allocated_network[1] != null' | |
| ) | |
| echo "has_ip [$has_ip]" | |
| if [[ $has_ip != "true" ]]; then | |
| openstack server add floating ip "$INSTANCE_NAME" $FLOATING_IP_ADDRESS | |
| fi | |
| # ---------------------------------------------------------------------------- | |
| # Poll instance setup status | |
| echo Polling "$INSTANCE_NAME" setup status | |
| max_wait_time=1200 # Maximum wait time in seconds (1200s -> 20mins) | |
| wait_interval=5 # Interval between status checks in seconds | |
| total_wait_time=0 | |
| while [ $total_wait_time -lt $max_wait_time ]; do | |
| status=$(openstack console log show $INSTANCE_NAME | \ | |
| grep "^\{\"status\":\"" | \ | |
| tail -1 | \ | |
| jq -r '.status // "pending"') | |
| echo -n "setup status [$status]. " | |
| if [[ "$status" == "complete" ]]; then | |
| echo "Exiting loop." | |
| break | |
| else | |
| echo "Waiting for completion..." | |
| sleep $wait_interval | |
| total_wait_time=$((total_wait_time + wait_interval)) | |
| fi | |
| done | |
| if [ $total_wait_time -ge $max_wait_time ]; then | |
| echo "::error ::Maximum wait time ($max_wait_time seconds) exceeded." | |
| fi | |
| # Explicitly set status to "complete" | |
| exoSetup='{"status":"complete", "epoch": '$(date '+%s')'000}' | |
| openstack server set \ | |
| --property "exoSetup=$exoSetup" \ | |
| $INSTANCE_NAME | |
| echo "status [$status]" | |
| # ---------------------------------------------------------------------------- | |
| # Rename MyData directory to MyData-tmp | |
| INSTANCE_IP=$FLOATING_IP_ADDRESS | |
| ssh \ | |
| -o StrictHostKeyChecking=no \ | |
| -o UserKnownHostsFile=/dev/null \ | |
| -o LogLevel=ERROR \ | |
| exouser@$INSTANCE_IP \ | |
| 'mv /media/volume/MyData /media/volume/MyData-tmp' | |
| # ---------------------------------------------------------------------------- | |
| # Attach volume | |
| instance_id=$(openstack server list -f json | \ | |
| jq \ | |
| --arg instance_name "$INSTANCE_NAME" \ | |
| -c '.[] | select(.Name == $instance_name)' | \ | |
| jq -r '.ID' | tail -1) | |
| echo "instance_id [$instance_id]" | |
| volume_id=$(openstack volume list -f json | \ | |
| jq \ | |
| --arg volume_name "$VOLUME_NAME" \ | |
| -c '.[] | select(.Name == $volume_name)' | \ | |
| jq -r '.ID' | tail -1) | |
| echo "volume_id [$volume_id]" | |
| openstack server set \ | |
| --property "exoVolumes::$volume_id={\"name\":\"MyData\"}" \ | |
| $instance_id | |
| openstack server add volume \ | |
| $instance_id \ | |
| $volume_id | |
| # ---------------------------------------------------------------------------- | |
| # Copy installed files into attached volume | |
| function check_mountpoint_ready { | |
| ssh \ | |
| -o StrictHostKeyChecking=no \ | |
| -o UserKnownHostsFile=/dev/null \ | |
| -o LogLevel=ERROR \ | |
| exouser@$INSTANCE_IP \ | |
| 'mountpoint -q /media/volume/MyData' | |
| } | |
| set +e | |
| max_attempts=5 | |
| for attempt in $(seq 1 $max_attempts); do | |
| echo "Checking if mount point is ready ($attempt/$max_attempts)" | |
| check_mountpoint_ready | |
| if check_mountpoint_ready; then | |
| echo "Mount point /media/volume/MyData is ready." | |
| break | |
| else | |
| echo "Mount point not ready. Retrying in 5 seconds..." | |
| sleep 5 | |
| fi | |
| done | |
| if ! check_mountpoint_ready; then | |
| echo "::error ::Mount point /media/volume/MyData not ready after $((max_attempts * 5)) seconds." | |
| exit 1 | |
| fi | |
| set -e | |
| ssh \ | |
| -o StrictHostKeyChecking=no \ | |
| -o UserKnownHostsFile=/dev/null \ | |
| -o LogLevel=ERROR \ | |
| exouser@$INSTANCE_IP \ | |
| '[ ! -d /media/volume/MyData/Slicer ] && mv /media/volume/MyData-tmp/Slicer /media/volume/MyData/Slicer && rmdir /media/volume/MyData-tmp || rm -rf /media/volume/MyData-tmp' | |
| # ---------------------------------------------------------------------------- | |
| # Create Renviron file | |
| ssh \ | |
| -o StrictHostKeyChecking=no \ | |
| -o UserKnownHostsFile=/dev/null \ | |
| -o LogLevel=ERROR \ | |
| exouser@$INSTANCE_IP \ | |
| 'echo -e "R_LIBS_SITE=/media/share/MorphoCloudCephShare/R/x86_64-pc-linux-gnu-library/4.4/\nR_LIBS_USER=/media/volume/MyData/R/x86_64-pc-linux-gnu-library/4.4/" > /home/exouser/.Renviron && mkdir -p /media/volume/MyData/R/x86_64-pc-linux-gnu-library/4.4/' | |
| # ---------------------------------------------------------------------------- | |
| # Reboot instance | |
| set +e | |
| ssh \ | |
| -o StrictHostKeyChecking=no \ | |
| -o UserKnownHostsFile=/dev/null \ | |
| -o LogLevel=ERROR \ | |
| exouser@$INSTANCE_IP \ | |
| 'sudo shutdown -r now' | |
| sleep 10 | |
| function check_instance_ready { | |
| ssh \ | |
| -o StrictHostKeyChecking=no \ | |
| -o UserKnownHostsFile=/dev/null \ | |
| -o LogLevel=ERROR \ | |
| exouser@$INSTANCE_IP \ | |
| 'true' | |
| } | |
| max_attempts=3 | |
| instance_ready=false | |
| for attempt in $(seq 1 $max_attempts); do | |
| echo "Checking if instance is ready ($attempt/$max_attempts)" | |
| if check_instance_ready; then | |
| instance_ready=true | |
| echo "Instance '$INSTANCE_NAME' is ready." | |
| break | |
| else | |
| echo "Instance '$INSTANCE_NAME' is not ready. Retrying in 5 seconds..." | |
| sleep 10 | |
| fi | |
| done | |
| if ! $instance_ready; then | |
| echo "::error ::Instance '$INSTANCE_NAME' is not ready after $max_attempts attempts to connect." | |
| fi | |
| set -e | |
| # ---------------------------------------------------------------------------- | |
| # Explicitly set status to complete | |
| exoSetup='{"status":"complete", "epoch": '$(date '+%s')'000}' | |
| openstack server set \ | |
| --property "exoSetup=$exoSetup" \ | |
| $INSTANCE_NAME |
| #!/usr/bin/env bash | |
| export OS_CLOUD=BIO180006_IU | |
| INSTANCE_NAME="instance-9999" | |
| COMMAND_NAME="shelve" | |
| EXPECTED_STATUS="SHELVED_OFFLOADED" | |
| # ---------------------------------------------------------------------------- | |
| # Check if instance has a floating IP | |
| # Get instance floating IP | |
| instance_ip=$( | |
| openstack server show $INSTANCE_NAME -c addresses -f json | \ | |
| jq -r '.addresses.auto_allocated_network | if length > 1 then .[1] else "" end' | |
| ) | |
| echo "instance_ip [$instance_ip]" | |
| # Get instance internal IP (also called fixed IP) | |
| instance_internal_ip=$( | |
| openstack server show $INSTANCE_NAME -c addresses -f json | \ | |
| jq -r '.addresses.auto_allocated_network | if length > 0 then .[0] else "" end' | |
| ) | |
| echo "instance_internal_ip [$instance_internal_ip]" | |
| # Determine if instance already has a floating IP assigned | |
| if [[ -n "$instance_ip" ]]; then | |
| has_ip="true" | |
| else | |
| has_ip="false" | |
| fi | |
| echo "has_ip [$has_ip]" | |
| # Check if an unassigned floating IP matches instance IP | |
| has_ip_assigned="false" | |
| if [[ "$has_ip" == "true" ]]; then | |
| json_output=$(openstack floating ip list -f json | jq \ | |
| --arg fixed_ip "$instance_internal_ip" \ | |
| --arg ip "$instance_ip" \ | |
| 'map(select(.Port != null and ."Fixed IP Address" == $fixed_ip and ."Floating IP Address" == $ip))') | |
| floating_ip_address=$(echo "$json_output" | jq -r 'if length > 0 then .[0]["Floating IP Address"] else "" end') | |
| if [[ -n "$floating_ip_address" ]]; then | |
| has_ip_assigned="true" | |
| fi | |
| fi | |
| # If previously assigned IP is not available anymore, discard it. | |
| if [[ "$has_ip_assigned" == "false" ]]; then | |
| instance_ip="" | |
| fi | |
| echo "instance_ip [$instance_ip]" | |
| echo "has_ip_assigned [$has_ip_assigned]" | |
| FLOATING_IP_ADDRESS=$instance_ip | |
| # ---------------------------------------------------------------------------- | |
| openstack server $COMMAND_NAME "$INSTANCE_NAME" | |
| # ---------------------------------------------------------------------------- | |
| max_wait_time=300 # Maximum wait time in seconds (300s -> 5mins) | |
| if [[ "$EXPECTED_STATUS" == "SHELVED_OFFLOADED" ]]; then | |
| max_wait_time=600 # Maximum wait time in seconds (600s -> 10mins) | |
| fi | |
| echo "Polling '$INSTANCE_NAME' status [max_wait_time=${max_wait_time}s]" | |
| wait_interval=5 # Interval between status checks in seconds | |
| total_wait_time=0 | |
| while [ $total_wait_time -lt $max_wait_time ]; do | |
| status=$(openstack server show $INSTANCE_NAME -f json -c status | \ | |
| jq -r '.status // "PENDING"') | |
| echo -n "status [$status]. " | |
| if [[ "$status" == "$EXPECTED_STATUS" ]]; then | |
| echo "Exiting loop." | |
| break | |
| else | |
| echo "Waiting for completion..." | |
| sleep $wait_interval | |
| total_wait_time=$((total_wait_time + wait_interval)) | |
| fi | |
| done | |
| if [ $total_wait_time -ge $max_wait_time ]; then | |
| echo "::error ::Maximum wait time ($max_wait_time seconds) exceeded." | |
| fi | |
| echo "status [$status]" | |
| # ---------------------------------------------------------------------------- | |
| openstack server remove floating ip "$INSTANCE_NAME" "$FLOATING_IP_ADDRESS" |
| #!/usr/bin/env bash | |
| export OS_CLOUD=BIO180006_IU | |
| INSTANCE_NAME="instance-9999" | |
| COMMAND_NAME="unshelve" | |
| EXPECTED_STATUS="ACTIVE" | |
| # ---------------------------------------------------------------------------- | |
| # Check if instance has a floating IP | |
| # Get instance floating IP | |
| instance_ip=$( | |
| openstack server show $INSTANCE_NAME -c addresses -f json | \ | |
| jq -r '.addresses.auto_allocated_network | if length > 1 then .[1] else "" end' | |
| ) | |
| echo "instance_ip [$instance_ip]" | |
| # Get instance internal IP (also called fixed IP) | |
| instance_internal_ip=$( | |
| openstack server show $INSTANCE_NAME -c addresses -f json | \ | |
| jq -r '.addresses.auto_allocated_network | if length > 0 then .[0] else "" end' | |
| ) | |
| echo "instance_internal_ip [$instance_internal_ip]" | |
| # Determine if instance already has a floating IP assigned | |
| if [[ -n "$instance_ip" ]]; then | |
| has_ip="true" | |
| else | |
| has_ip="false" | |
| fi | |
| echo "has_ip [$has_ip]" | |
| # Check if an unassigned floating IP matches instance IP | |
| has_ip_assigned="false" | |
| if [[ "$has_ip" == "true" ]]; then | |
| json_output=$(openstack floating ip list -f json | jq \ | |
| --arg fixed_ip "$instance_internal_ip" \ | |
| --arg ip "$instance_ip" \ | |
| 'map(select(.Port != null and ."Fixed IP Address" == $fixed_ip and ."Floating IP Address" == $ip))') | |
| floating_ip_address=$(echo "$json_output" | jq -r 'if length > 0 then .[0]["Floating IP Address"] else "" end') | |
| if [[ -n "$floating_ip_address" ]]; then | |
| has_ip_assigned="true" | |
| fi | |
| fi | |
| # If previously assigned IP is not available anymore, discard it. | |
| if [[ "$has_ip" == "true" && "$has_ip_assigned" == "false" ]]; then | |
| json_output=$(openstack floating ip list -f json | jq \ | |
| --arg fixed_ip "$instance_internal_ip" \ | |
| --arg ip "$instance_ip" \ | |
| 'map(select(.Port != null and ."Fixed IP Address" != $fixed_ip and ."Floating IP Address" == $ip))') | |
| has_ip_reassigned=$(echo "$json_output" | jq -r 'if length > 0 then "true" else "false" end') | |
| echo "has_ip_reassigned [$has_ip_reassigned]" | |
| if [[ $has_ip_reassigned == "true" ]]; then | |
| instance_ip="" | |
| fi | |
| fi | |
| echo "instance_ip [$instance_ip]" | |
| echo "has_ip_assigned [$has_ip_assigned]" | |
| # ---------------------------------------------------------------------------- | |
| # Retrieve or create floating IP | |
| floating_ip_address="" | |
| floating_ip_uuid="" | |
| if [[ $has_ip_assigned == "false" ]]; then | |
| preferred_ip_address=$instance_ip | |
| echo "preferred_ip_address [$preferred_ip_address]" | |
| # Retrieve unassigned floating IP | |
| json_output=$(openstack floating ip list -f json | jq 'map(select(.Port == null))') | |
| echo "Filtered JSON Output:" | |
| echo "$json_output" | jq | |
| if [[ -n "$preferred_ip_address" ]]; then | |
| floating_ip=$(echo "$json_output" | jq -r --arg ip "$preferred_ip_address" \ | |
| 'map(select(."Floating IP Address" == $ip)) | if length > 0 then .[0] else null end') | |
| else | |
| floating_ip=$(echo "$json_output" | jq -r 'if length > 0 then .[0] else null end') | |
| fi | |
| floating_ip_address=$(echo "$floating_ip" | jq -r '."Floating IP Address" // empty') | |
| floating_ip_uuid=$(echo "$floating_ip" | jq -r '."ID" // empty') | |
| echo "floating_ip_address [$floating_ip_address]" | |
| echo "floating_ip_uuid [$floating_ip_uuid]" | |
| fi | |
| if [[ -z "$floating_ip_address" ]]; then | |
| json_output=$(openstack floating ip create public -f json) | |
| echo "Floating IP Creation Output:" | |
| echo "$json_output" | jq | |
| floating_ip_uuid=$( | |
| echo $json_output | | |
| jq -r ".id" | |
| ) | |
| echo "floating_ip_uuid [$floating_ip_uuid]" | |
| floating_ip_address=$( | |
| echo $json_output | | |
| jq -r ".floating_ip_address" | |
| ) | |
| echo "floating_ip_address [$floating_ip_address]" | |
| fi | |
| # ---------------------------------------------------------------------------- | |
| openstack server add floating ip "$INSTANCE_NAME" "$floating_ip_address" | |
| # ---------------------------------------------------------------------------- | |
| openstack server $COMMAND_NAME "$INSTANCE_NAME" | |
| max_wait_time=300 # Maximum wait time in seconds (300s -> 5mins) | |
| if [[ "$EXPECTED_STATUS" == "SHELVED_OFFLOADED" ]]; then | |
| max_wait_time=600 # Maximum wait time in seconds (600s -> 10mins) | |
| fi | |
| echo "Polling '$INSTANCE_NAME' status [max_wait_time=${max_wait_time}s]" | |
| wait_interval=5 # Interval between status checks in seconds | |
| total_wait_time=0 | |
| while [ $total_wait_time -lt $max_wait_time ]; do | |
| status=$(openstack server show $INSTANCE_NAME -f json -c status | \ | |
| jq -r '.status // "PENDING"') | |
| echo -n "status [$status]. " | |
| if [[ "$status" == "$EXPECTED_STATUS" ]]; then | |
| echo "Exiting loop." | |
| break | |
| else | |
| echo "Waiting for completion..." | |
| sleep $wait_interval | |
| total_wait_time=$((total_wait_time + wait_interval)) | |
| fi | |
| done | |
| if [ $total_wait_time -ge $max_wait_time ]; then | |
| echo "::error ::Maximum wait time ($max_wait_time seconds) exceeded." | |
| fi | |
| echo "status [$status]" |