Update vmd

astrocyte-vmd/Dockerfile

 FROM git.biohpc.swmed.edu:5050/astrocyte/container/astrocyte-viz-base:ubuntu-18
 
-ARG ARG_HOME="/home/headless"
-ARG STARTUPDIR="/dockerstartup"
-ARG LOG_FOLDER="/tmp/astrocyte-vmd"
-
-ENV LANG en_US.UTF-8
-ENV HOME=${ARG_HOME:-/home/headless}
-ENV PW=${ARG_PW:-headless}
-ENV STARTUPDIR="/dockerstartup"
-ENV DISPLAY=":6"
-ENV VNC_PORT="5906"
-ENV VNC_RESOLUTION="1280x1024"
-ENV VNC_BLACKLIST_THRESHOLD=-20
-ENV VNC_BLACKLIST_TIMEOUT=-0
-ENV VNC_COL_DEPTH=24
-ENV LOG_FOLDER=${LOG_FOLDER:-"/tmp/astrocyte-vmd"}
-ENV NO_VNC_HOME="/usr/share/usr/local/share/noVNCdim"
-ENV NO_VNC_PORT="6900"
-ENV AUTOSTART_COMMAND="xfce4-terminal -e /usr/local/bin/vmd"
-
 COPY ["./src/vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz", "vmd-1.9.3.tar.gz"]
 COPY ["./src/NAMD_2.14_Linux-x86_64-multicore.tar.gz", "namd-2.14.tar.gz"]
 

astrocyte-vmd/build_singularity.sh

@@ -9,10 +9,6 @@ BIOHPC_REGISTRY="git.biohpc.swmed.edu:5050/astrocyte/container"
 # build docker
 sudo docker build -t ${REGISTRY}/${REPO}:${TAG} .
 
-# # push to registry
-# sudo docker login
-# sudo docker push ${REGISTRY}/${REPO}:${TAG}
-
 # push to BioHPC
 export DOCKER_BUILDKIT=0
 export COMPOSE_DOCKER_CLI_BUILD=0

astrocyte-vmd/run_singularity.sh

@@ -2,32 +2,10 @@
 REPO="astrocyte-vmd"
 TAG="latest"
 
-# Set the DISPLAY
-DISPLAY=":6"
-used_ports=$(lsof -i -P -n | grep TCP | awk -F: '{print $NF}' | awk '{print $1}' | sort -un)
-for i in $(seq 6 99); do
-    if echo $used_ports | grep -w $(expr 5900 + $i) > /dev/null; then
-        continue
-    else
-        DISPLAY=":$i";
-        break
-    fi
-done
-
-# Set novnc http port
-for i in $(seq 0 99); do
-    NO_VNC_PORT=$(expr 6900 + $i)
-    if echo $used_ports | grep -w $NO_VNC_PORT > /dev/null; then
-        continue
-    else
-        break
-    fi
-done
-
 # Prepare log file locations
 calling_username=$(id -un)
 host_name=$(hostname -s)
-logfolder=/tmp/astrocyte-vmd-${host_name}-${calling_username}-$(echo $DISPLAY | tr -d ":")
+logfolder=/tmp/astrocyte-vmd-${host_name}-${calling_username}-$(date +%s)
 rm -fr $logfolder
 mkdir -p $logfolder/$calling_username
 mkdir -p $logfolder/run
@@ -35,7 +13,7 @@ mkdir -p $logfolder/var/log
 chmod -R 777 $logfolder
 chmod 700 $logfolder
 
-AUTOSTART_COMMAND="xfce4-terminal -e /usr/local/bin/vmd"
+AUTOSTART_COMMAND="cd $outputDir; xfce4-terminal -e /usr/local/bin/vmd"
 
 # Prepare the bind string 
 bind_strings="$logfolder/run:/run,$logfolder/var/log:/var/log"
@@ -49,8 +27,7 @@ if [[ $host_str == 'biohpcw' ]] || [[ $host_str == 'Nucleus' ]]; then
 fi
 
 # mount and run
-SINGULARITYENV_DISPLAY="$DISPLAY" \
-SINGULARITYENV_NO_VNC_PORT="$NO_VNC_PORT" \
+SINGULARITYENV_NO_VNC_PORT="${VIZAPP_PORT:-$NO_VNC_PORT}" \
 SINGULARITYENV_AUTOSTART_COMMAND="$AUTOSTART_COMMAND" \
 SINGULARITYENV_LOG_FOLDER="$logfolder" \
 singularity run --nv -e \