fast data path (SSD) for HDF5 files

configuration.sh

@@ -36,6 +36,7 @@ IMS_BUFFER_PATH=/data/_buffer
 BACKUP_PATH=/data/backup
 ALGO_PATH=/data/algo/
 RETRIEVAL_PATH=/data/thumb
+FAST_DATA_PATH=/data
 
 #middlewares
 RETRIEVAL_PASSWD='retrieval_default'
@@ -80,11 +81,11 @@ DEV_CORE=false
 DEV_IMS=false
 # Complete the keys by running, for example $(cat /proc/sys/kernel/random/uuid) for each.
 # For a production deployment, these keys are automatically generated !
-IMS_PUB_KEY=
-IMS_PRIV_KEY=
-ADMIN_PUB_KEY=
-ADMIN_PRIV_KEY=
-SUPERADMIN_PUB_KEY=
-SUPERADMIN_PRIV_KEY=
-RABBITMQ_PUB_KEY=
-RABBITMQ_PRIV_KEY=
+IMS_PUB_KEY=XXX
+IMS_PRIV_KEY=XXX
+ADMIN_PUB_KEY=XXX
+ADMIN_PRIV_KEY=XXX
+SUPERADMIN_PUB_KEY=XXX
+SUPERADMIN_PRIV_KEY=XXX
+RABBITMQ_PUB_KEY=XXX
+RABBITMQ_PRIV_KEY=XXX

core/deploy.sh

@@ -39,6 +39,7 @@ IMS_URLS="$IMS_URLS]"
 echo "grails.serverURL='http://$CORE_URL'" >> cytomineconfig.groovy
 echo "storage_buffer='$IMS_BUFFER_PATH'" >> cytomineconfig.groovy
 echo "storage_path='$IMS_STORAGE_PATH'" >> cytomineconfig.groovy
+echo "fast_data_path='$FAST_DATA_PATH'" >> cytomineconfig.groovy
 
 echo "grails.imageServerURL=$IMS_URLS" >> cytomineconfig.groovy
 echo "grails.retrievalServerURL =['http://$RETRIEVAL_URL']" >> cytomineconfig.groovy

ims/deploy.sh

@@ -35,6 +35,7 @@ fi
 
 
 chown -R tomcat7:tomcat7 $IMS_STORAGE_PATH
+chown -R tomcat7:tomcat7 $FAST_DATA_PATH
 
 export LD_LIBRARY_PATH=/usr/local/lib/openslide-java
 

start_deploy.sh

@@ -137,13 +137,15 @@ IMS_PRIV_KEY=$(cat /proc/sys/kernel/random/uuid)
 
 # create IMS docker
 #-e IIP_OFF_URL=$IIP_OFF_URL \
-docker run -p 22 -v $IMS_STORAGE_PATH:$IMS_STORAGE_PATH -m 8g -d --name ims --restart=unless-stopped \
+docker run -p 22 -v $IMS_STORAGE_PATH:$IMS_STORAGE_PATH -v $FAST_DATA_PATH:$FAST_DATA_PATH \
+-m 8g -d --name ims --restart=unless-stopped \
 -v /tmp/uploaded/ \
 -e IIP_CYTO_URL=$IIP_CYTO_URL \
 -e IIP_JP2_URL=$IIP_JP2_URL \
 -e IMS_URLS=$IMS_URLS \
 -e IMS_STORAGE_PATH=$IMS_STORAGE_PATH \
 -e IMS_BUFFER_PATH=$IMS_BUFFER_PATH \
+-e FAST_DATA_PATH=$FAST_DATA_PATH \
 -e IS_LOCAL=$IS_LOCAL \
 -e CORE_URL=$CORE_URL \
 -e IMS_PUB_KEY=$IMS_PUB_KEY \
@@ -178,6 +180,7 @@ docker run -m 8g -d -p 22 --name core --link rabbitmq:rabbitmq --link db:db --li
 -e UPLOAD_URL=$UPLOAD_URL \
 -e IMS_STORAGE_PATH=$IMS_STORAGE_PATH \
 -e IMS_BUFFER_PATH=$IMS_BUFFER_PATH \
+-e FAST_DATA_PATH=$FAST_DATA_PATH \
 -e IS_LOCAL=$IS_LOCAL \
 -e ADMIN_PWD=$admin_pwd \
 -e ADMIN_PUB_KEY=$ADMIN_PUB_KEY \

start_dev.sh

@@ -114,13 +114,15 @@ then
     fi
 else
     # create IMS docker
-    docker run -p 22 -v $IMS_STORAGE_PATH:$IMS_STORAGE_PATH -m 8g -d --name ims --restart=unless-stopped \
+    docker run -p 22 -v $IMS_STORAGE_PATH:$IMS_STORAGE_PATH -v $FAST_DATA_PATH:$FAST_DATA_PATH \
+    -m 8g -d --name ims --restart=unless-stopped \
     -v /tmp/uploaded/:/tmp/uploaded/ \
     -e IIP_CYTO_URL=$IIP_CYTO_URL \
     -e IIP_JP2_URL=$IIP_JP2_URL \
     -e IMS_URLS=$IMS_URLS \
     -e IMS_STORAGE_PATH=$IMS_STORAGE_PATH \
     -e IMS_BUFFER_PATH=$IMS_BUFFER_PATH \
+    -e FAST_DATA_PATH=$FAST_DATA_PATH \
     -e IS_LOCAL=$IS_LOCAL \
     -e CORE_URL=$CORE_URL \
     -e IMS_PUB_KEY=$IMS_PUB_KEY \
@@ -151,6 +153,7 @@ then
     -e UPLOAD_URL=$UPLOAD_URL \
     -e IMS_STORAGE_PATH=$IMS_STORAGE_PATH \
     -e IMS_BUFFER_PATH=$IMS_BUFFER_PATH \
+    -e FAST_DATA_PATH=$FAST_DATA_PATH \
     -e IS_LOCAL=$IS_LOCAL \
     -e ADMIN_PWD="admin" \
     -e ADMIN_PUB_KEY=$ADMIN_PUB_KEY \