Merge pull request #3 from ClusterCockpit/dev

Check for all installed modules before starting docker services.

docker-compose.yml

@@ -21,24 +21,6 @@ services:
     depends_on:
       - nats
 
-  influxdb:
-    container_name: influxdb
-    image: influxdb:latest
-    command: ["--reporting-disabled", "--log-level=debug"]
-    environment:
-      DOCKER_INFLUXDB_INIT_MODE: setup
-      DOCKER_INFLUXDB_INIT_USERNAME: devel
-      DOCKER_INFLUXDB_INIT_PASSWORD: ${INFLUXDB_PASSWORD}
-      DOCKER_INFLUXDB_INIT_ORG: ${INFLUXDB_ORG}
-      DOCKER_INFLUXDB_INIT_BUCKET: ${INFLUXDB_BUCKET}
-      DOCKER_INFLUXDB_INIT_RETENTION: 100w
-      DOCKER_INFLUXDB_INIT_ADMIN_TOKEN: ${INFLUXDB_ADMIN_TOKEN}
-    ports:
-      - "0.0.0.0:8086:8086"
-    volumes:
-      - ${DATADIR}/influxdb/data:/var/lib/influxdb2
-      - ${DATADIR}/influxdb/config:/etc/influxdb2
-
   openldap:
     container_name: ldap
     image: osixia/openldap:1.5.0
@@ -144,3 +126,21 @@ services:
       - /etc/localtime:/etc/localtime:ro
     ports:
       - "6820:6820"
+
+  # influxdb:
+  #   container_name: influxdb
+  #   image: influxdb:latest
+  #   command: ["--reporting-disabled", "--log-level=debug"]
+  #   environment:
+  #     DOCKER_INFLUXDB_INIT_MODE: setup
+  #     DOCKER_INFLUXDB_INIT_USERNAME: devel
+  #     DOCKER_INFLUXDB_INIT_PASSWORD: ${INFLUXDB_PASSWORD}
+  #     DOCKER_INFLUXDB_INIT_ORG: ${INFLUXDB_ORG}
+  #     DOCKER_INFLUXDB_INIT_BUCKET: ${INFLUXDB_BUCKET}
+  #     DOCKER_INFLUXDB_INIT_RETENTION: 100w
+  #     DOCKER_INFLUXDB_INIT_ADMIN_TOKEN: ${INFLUXDB_ADMIN_TOKEN}
+  #   ports:
+  #     - "0.0.0.0:8086:8086"
+  #   volumes:
+  #     - ${DATADIR}/influxdb/data:/var/lib/influxdb2
+  #     - ${DATADIR}/influxdb/config:/etc/influxdb2

scripts/checkModules.sh

@@ -0,0 +1,68 @@
+#!/bin/bash
+
+cd scripts
+
+# Check if required perl modules are installed
+if ./checkPerlModules.pl ../migrateTimestamps.pl | grep "couldn't load"; then
+  echo "Perl Modules missing!"
+  echo -n "Stopped."
+  exit
+else
+  echo "Perl Modules loaded."
+fi
+
+# check if golang is installed and available
+if ! go version; then
+  echo "Golang not installed!"
+  echo -n "Stopped."
+  exit
+else
+  echo "Golang installed."
+fi
+
+# check if docker is installed and available
+if ! docker --version; then
+  echo "Docker not installed!"
+  echo -n "Stopped."
+  exit
+else
+  echo "Docker installed."
+fi
+
+# check if docker-compose is installed and available
+if ! docker-compose --version; then
+  echo "Docker-compose not installed!"
+  echo -n "Stopped."
+  exit
+else
+  echo "Docker-compose installed."
+fi
+
+# check if npm is installed and available
+if ! npm --version; then
+  echo "NPM not installed!"
+  echo -n "Stopped."
+  exit
+else
+  echo "NPM installed."
+fi
+
+# check if make is installed and available
+if ! make --version; then
+  echo "Make not installed!"
+  echo -n "Stopped."
+  exit
+else
+  echo "Make installed."
+fi
+
+# check if gcc is installed and available
+if ! gcc --version; then
+  echo "GCC not installed!"
+  echo -n "Stopped."
+  exit
+else
+  echo "GCC installed."
+fi
+
+cd ..

scripts/checkPerlModules.pl

@@ -0,0 +1,45 @@
+#!/usr/bin/env perl
+use warnings;
+use strict;
+
+my $filename =
+  shift || &help;    # command line argument is perl script to evaluate
+my @modules;         # array of 'use' statements from code we are checking
+
+open( IN, $filename ) or die "couldn't open $filename for processing: $!
++\n";
+
+while (<IN>) {
+  chomp;
+  if ( (/^use/) and not( /strict/ || /warnings/ ) ) {
+    push @modules, $_;
+  }
+}
+close IN;
+for my $code (@modules) {
+  my ( undef, $library ) = split( / /, $code );    # get the module name
+  $library =~ s/;//;                               # clean up the name
+  eval $code;
+  if ($@) {
+    warn "couldn't load $library: $@", "\n";
+  } else {
+    print "$library looks ok\n";
+  }
+}
+
+sub help
+{
+  print <<"END";
+
+checkPerlModules.pl
+
+This script finds all the "use" statements loading modules in the targ
++et perl
+file (specified as a command line argument) and attempts to load them.
+If there are problems loading the module, the error mesage returned is
++ printed.
+
+END
+  exit;
+}
+

scripts/checkpointsToInflux.sh

@@ -0,0 +1,65 @@
+#!/bin/bash
+
+set -euo pipefail
+
+NEW_CHECKPOINTS='../data/cc-metric-store/checkpoints'
+VERBOSE=1
+INFLUX_HOST='http://0.0.0.0:8181'
+
+HEADERS=(
+    -H "Content-Type: text/plain; charset=utf-8"
+    -H "Accept: application/json"
+)
+
+checkp_clusters=()
+while IFS= read -r -d '' dir; do
+    checkp_clusters+=("$(basename "$dir")")
+done < <(find "$NEW_CHECKPOINTS" -mindepth 1 -maxdepth 1 -type d \! -name 'job-archive' -print0)
+
+for cluster in "${checkp_clusters[@]}"; do
+    echo "Starting to read updated checkpoint-files into influx for $cluster"
+
+    while IFS= read -r -d '' level1_dir; do
+        level1=$(basename "$level1_dir")
+        node_source="$NEW_CHECKPOINTS/$cluster/$level1"
+
+        mapfile -t files < <(find "$node_source" -type f -name '*.json' | sort -V)
+        # if [[ ${#files[@]} -ne 14 ]]; then
+        #     continue
+        # fi
+
+        node_measurement=""
+        for file in "${files[@]}"; do
+            rawstr=$(<"$file")
+
+            while IFS= read -r metric; do
+                start=$(jq -r ".metrics[\"$metric\"].start" <<<"$rawstr")
+                timestep=$(jq -r ".metrics[\"$metric\"].frequency" <<<"$rawstr")
+
+                while IFS= read -r index_value; do
+                    index=$(awk -F: '{print $1}' <<<"$index_value")
+                    value=$(awk -F: '{print $2}' <<<"$index_value")
+
+                    if [[ -n "$value" && "$value" != "null" ]]; then
+                        timestamp=$((start + (timestep * index)))
+                        node_measurement+="$metric,cluster=$cluster,hostname=$level1,type=node value=$value $timestamp\n"
+                    fi
+                done < <(jq -r ".metrics[\"$metric\"].data | to_entries | map(\"\(.key):\(.value // \"null\")\") | .[]" <<<"$rawstr")
+            done < <(jq -r '.metrics | keys[]' <<<"$rawstr")
+        done
+
+        if [[ -n "$node_measurement" ]]; then
+            while IFS= read -r  chunk; do
+                response_code=$(curl -s -o /dev/null -w "%{http_code}" "${HEADERS[@]}" --data-binary "$chunk" "$INFLUX_HOST/api/v2/write?bucket=mydb&precision=s")
+                if [[ "$response_code" == "204" ]]; then
+                    [[ "$VERBOSE" -eq 1 ]] && echo "INFLUX API WRITE: CLUSTER $cluster HOST $level1"
+                elif [[ "$response_code" != "422" ]]; then
+                    echo "INFLUX API WRITE ERROR CODE $response_code"
+                fi
+            done < <(echo -e "$node_measurement" | split -l 1000 --filter='cat')
+        fi
+        echo "Done for : "$node_source
+    done < <(find "$NEW_CHECKPOINTS/$cluster" -mindepth 1 -maxdepth 1 -type d -print0)
+done
+
+echo "Done for influx"

setupDev.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+set -eu
 echo ""
 echo "|--------------------------------------------------------------------------------------|"
 echo "| Welcome to cc-docker automatic deployment script.                                    |"
@@ -23,6 +24,9 @@ if [ ! -d cc-backend ]; then
   exit
 fi
 
+chmod u+x scripts/checkModules.sh
+./scripts/checkModules.sh
+
 # Creates data directory if it does not exists.
 # Contains all the mount points required by all the docker services
 # and their static files.