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Cleaning, stabilizing and testing

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This commit is contained in:
Aditya Ujeniya
2025-07-04 11:22:03 +02:00
parent 60a346dec1
commit 1ec3c7d80f
12 changed files with 28 additions and 202 deletions
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20
README.md
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@@ -10,13 +10,11 @@ It includes the following containers:
|Slurm Database service|slurmdbd|6817|
|Slurm Rest service with JWT authentication|slurmrestd|6820|
|Slurm Worker|node01|6818|
|MariaDB service|mariadb|3306|
|InfluxDB serice|influxdb|8086|
|NATS service|nats|4222, 6222, 8222|
|cc-metric-store service|cc-metric-store|8084|
|OpenLDAP|openldap|389, 636|
The setup comes with fixture data for a Job archive, cc-metric-store checkpoints, InfluxDB, MariaDB, and a LDAP user directory.
The setup comes with fixture data for a Job archive, cc-metric-store checkpoints, and a LDAP user directory.
## Prerequisites
@@ -44,11 +42,11 @@ Note: You can install all these dependencies via predefined installation steps i
If you are using different linux flavors, you will have to adapt `prerequisite_installation_script.sh` as well as `setupDev.sh`.
## Setup
## Setup Procedure
1. Clone `cc-backend` repository in chosen base folder: `$> git clone https://github.com/ClusterCockpit/cc-backend.git`
2. Run `$ ./setupDev.sh`: **NOTICE** The script will download files of a total size of 338MB (mostly for the cc-metric-store data).
2. Run the setup bash file: `$> ./setupDev.sh`: **NOTICE** The script will download files of a total size of 338MB (mostly for the cc-metric-store data).
3. The setup-script launches the supporting container stack in the background automatically if everything went well. Run `$> ./cc-backend/cc-backend -server -dev` to start `cc-backend`.
@@ -72,9 +70,9 @@ You can also login as regular user using any credential in the LDAP user directo
When you are done cloning the cc-backend repo and once you execute `setupDev.sh` file, it will copy a preconfigured `config.json` from `misc/config.json` and replace the `cc-backend/config.json`, which will be used by cc-backend, once you start the server.
The preconfigured config.json attaches to:
#### 1. MariaDB docker service on port 3306 (database: ccbackend)
#### 2. OpenLDAP docker service on port 389
#### 3. cc-metric-store docker service on port 8084
#### 1. OpenLDAP docker service on port 389
#### 2. cc-metric-store docker service on port 8084
#### 3. cc-slurm-adapter is running on slurmctld docker service.
cc-metric-store also has a preconfigured `config.json` in `cc-metric-store/config.json` which attaches to NATS docker service on port 4222 and subscribes to topic 'hpc-nats'.
@@ -94,7 +92,7 @@ Now that you can see the docker services, and if you want to manually access the
> **`Example`**: You want to run slurm commands like `sinfo` or `squeue` or `scontrol` on slurm controller, you cannot directly access it.
You need to **`bash`** into the running service by using the following command:
You need to open a **`bash`** session in the running service by using the following command:
```
$ docker exec -it <docker service name> bash
@@ -103,7 +101,7 @@ $ docker exec -it <docker service name> bash
$ docker exec -it slurmctld bash
#or
$ docker exec -it mariadb bash
$ docker exec -it cc-metric-store bash
```
Once you start a **`bash`** on any docker service, then you may execute any service related commands in that **`bash`**.
@@ -147,7 +145,7 @@ You may also use the never expiring token directly from the file for any of your
## Known Issues
* `docker-compose` installed on Ubuntu (18.04, 20.04) via `apt-get` can not correctly parse `docker-compose.yml` due to version differences. Install latest version of `docker-compose` from https://docs.docker.com/compose/install/ instead.
* You need to ensure that no other web server is running on ports 8080 (cc-backend), 8082 (cc-metric-store), 8086 (InfluxDB), 4222 and 8222 (Nats), or 3306 (MariaDB). If one or more ports are already in use, you have to adapt the related config accordingly.
* You need to ensure that no other web server is running on ports 8080 (cc-backend), 8084 (cc-metric-store), 4222 and 8222 (Nats). If one or more ports are already in use, you have to adapt the related config accordingly.
* Existing VPN connections sometimes cause problems with docker. If `docker-compose` does not start up correctly, try disabling any active VPN connection. Refer to https://stackoverflow.com/questions/45692255/how-make-openvpn-work-with-docker for further information.
## Docker services and restarting the services

2
dataGenerationScript.sh
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@@ -1,4 +1,6 @@
#!/bin/bash
set -euo pipefail
echo ""
echo "|--------------------------------------------------------------------------------------|"
echo "| This is Data generation script for docker services |"

4
docker-compose.yml
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@@ -91,8 +91,8 @@ services:
- "6819:6819"
node01:
container_name: node01
hostname: node01
container_name: f0101
hostname: f0101
build:
context: ./slurm/worker
depends_on:

5
misc/config.json
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@@ -8,8 +8,9 @@
"jwts": {
"max-age": "2000h"
},
"db-driver": "mysql",
"db": "root:root@tcp(0.0.0.0:3306)/ccbackend",
"apiAllowedIPs": [
"*"
],
"ldap": {
"url": "ldap://0.0.0.0",
"user_base": "ou=users,dc=example,dc=com",

2
scripts/checkModules.sh
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@@ -1,5 +1,7 @@
#!/bin/bash
set -euo pipefail
cd scripts
# Check if required perl modules are installed

100
scripts/checkpointsToInflux.pl
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@@ -1,100 +0,0 @@
#!/usr/bin/env perl
use strict;
use warnings;
use utf8;
use File::Path qw( make_path rmtree );
use Cpanel::JSON::XS qw( decode_json encode_json );
use File::Slurp;
use Data::Dumper;
use Time::Piece;
use Sort::Versions;
use REST::Client;
### INFLUXDB
my $newCheckpoints = './data/cc-metric-store/checkpoints';
my @CheckpClusters;
my $verbose = 1;
my $restClient = REST::Client->new();
$restClient->setHost('http://localhost:8086'); # Adapt port here!
$restClient->addHeader('Authorization', "Token 74008ea2a8dad5e6f856838a90c6392e"); # compare .env file
$restClient->addHeader('Content-Type', 'text/plain; charset=utf-8');
$restClient->addHeader('Accept', 'application/json');
$restClient->getUseragent()->ssl_opts(SSL_verify_mode => 0); # Temporary: Disable Cert Check
$restClient->getUseragent()->ssl_opts(verify_hostname => 0); # Temporary: Disable Cert Check
# Get clusters by cc-metric-store/$subfolder
opendir my $dhc, $newCheckpoints or die "can't open directory: $!";
while ( readdir $dhc ) {
chomp; next if $_ eq '.' or $_ eq '..' or $_ eq 'job-archive';
my $cluster = $_;
push @CheckpClusters, $cluster;
}
# start to read checkpoints for influx
foreach my $cluster ( @CheckpClusters ) {
print "Starting to read updated checkpoint-files into influx for $cluster\n";
opendir my $dhLevel1, "$newCheckpoints/$cluster" or die "can't open directory: $!";
while ( readdir $dhLevel1 ) {
chomp; next if $_ eq '.' or $_ eq '..';
my $level1 = $_;
if ( -d "$newCheckpoints/$cluster/$level1" ) {
my $nodeSource = "$newCheckpoints/$cluster/$level1/";
my @files = read_dir($nodeSource);
my $length = @files;
if (!@files || $length != 14) { # needs 14 files == 7 days worth of data
next;
}
my @sortedFiles = sort { versioncmp($a,$b) } @files; # sort alphanumerically: _Really_ start with index == 0 == 1609459200.json
my $nodeMeasurement;
foreach my $file (@sortedFiles) {
# print "$file\n";
my $rawstr = read_file("$nodeSource/$file");
my $json = decode_json($rawstr);
my $fileMeasurement;
foreach my $metric (keys %{$json->{metrics}}) {
my $start = $json->{metrics}->{$metric}->{start};
my $timestep = $json->{metrics}->{$metric}->{frequency};
my $data = $json->{metrics}->{$metric}->{data};
my $length = @$data;
my $measurement;
while (my ($index, $value) = each(@$data)) {
if ($value) {
my $timestamp = $start + ($timestep * $index);
$measurement .= "$metric,cluster=$cluster,hostname=$level1,type=node value=".$value." $timestamp"."\n";
}
}
# Use v2 API for Influx2
if ($measurement) {
# print "Adding: #VALUES $length KEY $metric"."\n";
$fileMeasurement .= $measurement;
}
}
if ($fileMeasurement) {
$nodeMeasurement .= $fileMeasurement;
}
}
$restClient->POST("/api/v2/write?org=ClusterCockpit&bucket=ClusterCockpit&precision=s", "$nodeMeasurement"); # compare .env for bucket and org
my $responseCode = $restClient->responseCode();
if ( $responseCode eq '204') {
if ( $verbose ) {
print "INFLUX API WRITE: CLUSTER $cluster HOST $level1"."\n";
};
} else {
if ( $responseCode ne '422' ) { # Exclude High Frequency Error 422 - Temporary!
my $response = $restClient->responseContent();
print "INFLUX API WRITE ERROR CODE ".$responseCode.": ".$response."\n";
};
};
}
}
}
print "Done for influx\n";

65
scripts/checkpointsToInflux.sh
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@@ -1,65 +0,0 @@
#!/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"

4
scripts/prerequisite_installation_script.sh
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@@ -1,5 +1,7 @@
#!/bin/bash -l
set -euo pipefail
sudo apt-get update
sudo apt-get upgrade -f -y
@@ -33,7 +35,7 @@ sudo cpan Time::Piece
sudo cpan Sort::Versions
sudo groupadd docker
sudo usermod -aG docker ubuntu
sudo usermod -aG docker $USER
sudo shutdown -r -t 0

12
scripts/sqliteToMariadb.sh
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@@ -1,12 +0,0 @@
#!/bin/bash
echo "Will run prerequisites 'apt install python3-pip' and 'pip install sqlite3-to-mysql'"
sudo apt install python3-pip
pip install sqlite3-to-mysql
echo "'sqlite3mysql' requires running DB container, will fail otherwise."
# -f FILE -d DBNAME -u USER -h HOST -P PORT
~/.local/bin/sqlite3mysql -f job.db -d ClusterCockpit -u root --mysql-password root -h localhost -P 3306

6
setupDev.sh
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@@ -1,5 +1,5 @@
#!/bin/bash
set -eu
set -euo pipefail
echo ""
echo "|--------------------------------------------------------------------------------------|"
echo "| Welcome to cc-docker automatic deployment script. |"
@@ -41,15 +41,13 @@ chmod u+x dataGenerationScript.sh
cd cc-backend
rm -rf var
if [ ! -d var ]; then
wget https://hpc-mover.rrze.uni-erlangen.de/HPC-Data/0x7b58aefb/eig7ahyo6fo2bais0ephuf2aitohv1ai/job-archive-demo.tar
tar xf job-archive-demo.tar
rm ./job-archive-demo.tar
cp ./configs/env-template.txt .env
cp ./configs/config-demo.json config.json
cp ../misc/config.json config.json
sed -i 's/"addr": *"127\.0\.0\.1:8080"/"addr": "0.0.0.0:8080"/' config.json

2
slurm/controller/docker-entrypoint.sh
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@@ -208,7 +208,7 @@ _slurmctld() {
sleep 2
done
sacctmgr -i add cluster name=linux
sacctmgr -i add cluster name=fritz
sleep 2s
echo "Starting slurmctld"
cp -f /etc/slurm/slurm.conf /.secret/

8
slurm/controller/slurm.conf
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@@ -2,7 +2,7 @@
#
# See the slurm.conf man page for more information.
#
ClusterName=linux
ClusterName=fritz
ControlMachine=slurmctld
ControlAddr=slurmctld
#BackupController=
@@ -94,12 +94,12 @@ AccountingStoragePort=6819
#
# COMPUTE NODES
PartitionName=DEFAULT Nodes=node01
PartitionName=debug Nodes=node01 Default=YES MaxTime=INFINITE State=UP
# PartitionName=DEFAULT Nodes=f0101
PartitionName=main Nodes=f0101 Default=YES MaxTime=INFINITE State=UP
# # COMPUTE NODES
# NodeName=c[1-2] RealMemory=1000 State=UNKNOWN
NodeName=node01 CPUs=1 Boards=1 SocketsPerBoard=1 CoresPerSocket=1 ThreadsPerCore=1
NodeName=f0101 CPUs=1 Boards=1 SocketsPerBoard=1 CoresPerSocket=1 ThreadsPerCore=1
# #
# # PARTITIONS