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Introduce slurm cluster

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Jan Eitzinger 2023-06-23 08:38:15 +02:00
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106
docker-compose.yml
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@ -62,22 +62,22 @@ services:
cap_add: cap_add:
- SYS_NICE - SYS_NICE
mysql: # mysql:
container_name: cc-mysql # container_name: cc-mysql
image: mysql:8.0.22 # image: mysql:8.0.22
command: ["--default-authentication-plugin=mysql_native_password"] # command: ["--default-authentication-plugin=mysql_native_password"]
environment: # environment:
MYSQL_ROOT_PASSWORD: ${MYSQL_ROOT_PASSWORD} # MYSQL_ROOT_PASSWORD: ${MYSQL_ROOT_PASSWORD}
MYSQL_DATABASE: ${MYSQL_DATABASE} # MYSQL_DATABASE: ${MYSQL_DATABASE}
MYSQL_USER: ${MYSQL_USER} # MYSQL_USER: ${MYSQL_USER}
MYSQL_PASSWORD: ${MYSQL_PASSWORD} # MYSQL_PASSWORD: ${MYSQL_PASSWORD}
ports: # ports:
- "127.0.0.1:${MYSQL_PORT}:3306" # - "127.0.0.1:${MYSQL_PORT}:3306"
# volumes: # # volumes:
# - ${DATADIR}/sql-init:/docker-entrypoint-initdb.d # # - ${DATADIR}/sql-init:/docker-entrypoint-initdb.d
# - ${DATADIR}/sqldata:/var/lib/mysql # # - ${DATADIR}/sqldata:/var/lib/mysql
cap_add: # cap_add:
- SYS_NICE # - SYS_NICE
phpmyadmin: phpmyadmin:
container_name: cc-phpmyadmin container_name: cc-phpmyadmin
@ -89,4 +89,76 @@ services:
ports: ports:
- "127.0.0.1:${PHPMYADMIN_PORT}:80" - "127.0.0.1:${PHPMYADMIN_PORT}:80"
depends_on: depends_on:
- db - mariadb
slurm-controller:
container_name: slurm-controller
build:
context: ./slurm/controller
privileged: true
volumes:
- ./home:/home
- ./secret:/.secret
restart: always
environment:
USE_SLURMDBD: 'true'
CLUSTER_NAME: snowflake
CONTROL_MACHINE: controller
SLURMCTLD_PORT: 6817
SLURMD_PORT: 6818
ACCOUNTING_STORAGE_HOST: database
ACCOUNTING_STORAGE_PORT: 6819
COMPUTE_NODES: worker01 worker02
PARTITION_NAME: docker
slurm-database:
container_name: slurm-database
build:
context: ./slurm/database
depends_on:
- slurm-controller
privileged: true
volumes:
- ./home:/home
- ./secret:/.secret
restart: always
environment:
DBD_ADDR: database
DBD_HOST: database
DBD_PORT: 6819
STORAGE_HOST: database.local.dev
STORAGE_PORT: 3306
STORAGE_PASS: password
STORAGE_USER: slurm
slurm-worker01:
container_name: slurm-worker01
build:
context: ./slurm/worker
depends_on:
- slurm-controller
privileged: true
volumes:
- ./home:/home
- ./secret:/.secret
restart: always
environment:
CONTROL_MACHINE: controller
ACCOUNTING_STORAGE_HOST: database
COMPUTE_NODES: worker01 worker02
slurm-worker02:
container_name: slurm-worker02
build:
context: ./slurm/worker
depends_on:
- slurm-controller
privileged: true
volumes:
- ./home:/home
- ./secret:/.secret
restart: always
environment:
CONTROL_MACHINE: controller
ACCOUNTING_STORAGE_HOST: database
COMPUTE_NODES: worker01 worker02

806
slurm/README.md Normal file
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@ -0,0 +1,806 @@
# Slurm in Docker
**WORK IN PROGRESS**
Use [Docker](https://www.docker.com/) to explore the various components of [Slurm](https://www.schedmd.com/index.php)
This work represents a small exploratory Slurm cluster using CentOS 7 based Docker images. The intent was to learn the basics of Slurm prior to extending the concept to a more distributed environment.
Images include:
- [Slurm 19.05.1](https://slurm.schedmd.com) - installed from [rpm packages](packages)
- [OpenMPI 3.0.1](https://www.open-mpi.org/doc/current/) - installed from [rpm packages](packages)
- [Lmod 7.7](http://lmod.readthedocs.io/en/latest/index.html) - installed from [distribution files](https://sourceforge.net/projects/lmod/files/)
- [Lmod module packages for CentOS 7](https://github.com/scidas/lmod-modules-centos) - Organized for Slurm-in-Docker use
- [Using Lmod with Slurm-in-Docker](using-lmod-with-slurm-in-docker.md) documentation
## Contents
1. [packages](packages) - Build the RPM packages for running Slurm and OpenMPI on CentOS 7
2. [base](base) - Slurm base image from which other components are derived
3. [controller](controller) - Slurm controller (head-node) definition
4. [database](database) - Slurm database definition (not necessary, but useful for accounting information)
5. [worker](worker) - Slurm worker (compute-node) definition
## Container Overview
An example [docker-compose.yml](docker-compose.yml) file is provided that builds and deploys the diagramed topology
<img width="90%" alt="Slurm cluster" src="https://user-images.githubusercontent.com/5332509/38642211-67a7e1a4-3da7-11e8-85a9-3394ad3c8cb6.png">
Listing of participating containers with FQDNs and their function within the cluster.
Container | Function | FQDN
:-------- | :------- | :---
controller | Slurm Primary Controller | controller.local.dev
database | Slurm Primary Database Daemon | database.local.dev
worker01 | Slurm Worker | worker01.local.dev
worker02 | Slurm Worker | worker02.local.dev
## Configure slurm.conf/slurmdbd.conf
Users may use the default slurm.conf file generated in [docker-entrypoint.sh](https://github.com/SciDAS/slurm-in-docker/blob/master/controller/docker-entrypoint.sh), or preferably create one to better fit their system.
The [Slurm Configuration Tool](https://slurm.schedmd.com/configurator.html) is a useful resource for creating custom slurm.conf files.
Steps to add user profided slurm.conf/slurmdbd.conf:
1. Create ```home/config``` and ```secret``` directories:
```
mkdir -p home/config secret
```
2. Copy configuration files to the ```home/config``` directory:
```
cp <user-provided-slurm.conf> home/config/slurm.conf; cp <user-provided-slurmdbd.conf> home/config/slurmdbd.conf
```
The user can then proceed as normal.
TODO: Have software check validity of custom configuration files.
## Build
Build the slurm RPM files by following the instructions in the [packages](packages) directory.
**Create the base Slurm image**:
Copy the `packages/centos-7/rpms` directory to the `base` directory
```
cd base/
cp -r ../packages/centos-7/rpms .
```
Build the base image
```
docker build -t scidas/slurm.base:19.05.1 .
```
Verify image build
```console
$ docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
scidas/slurm.base 19.05.1 1600621cb483 Less than a second ago 819MB
...
```
All images defined in `docker-compose.yml` will be built from the `scidas/slurm.base:19.05.1` base image
## Usage
An example [docker-compose.yml](docker-compose.yml) file is provided that builds and deploys the diagramed topology (`-d` is used to daemonize the call).
```
docker-compose up -d
```
Four containers should be observed running when completed
```console
$ docker ps
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
995183e9391e scidas/slurm.worker:19.05.1 "/usr/local/bin/tini…" 10 seconds ago Up 30 seconds 22/tcp, 3306/tcp, 6817-6819/tcp, 60001-63000/tcp worker01
bdd7c8daaca2 scidas/slurm.database:19.05.1 "/usr/local/bin/tini…" 10 seconds ago Up 30 seconds 22/tcp, 3306/tcp, 6817-6819/tcp, 60001-63000/tcp database
a8382a486989 scidas/slurm.worker:19.05.1 "/usr/local/bin/tini…" 10 seconds ago Up 30 seconds 22/tcp, 3306/tcp, 6817-6819/tcp, 60001-63000/tcp worker02
24e951854109 scidas/slurm.controller:19.05.1 "/usr/local/bin/tini…" 11 seconds ago Up 31 seconds 22/tcp, 3306/tcp, 6817-6819/tcp, 60001-63000/tcp controller
```
## Examples using Slurm
The examples make use of the following commands.
- `sinfo` - [man page](https://slurm.schedmd.com/sinfo.html)
- `sacctmgr` - [man page](https://slurm.schedmd.com/sacctmgr.html)
- `sacct` - [man page](https://slurm.schedmd.com/sacct.html)
- `srun` - [man page](https://slurm.schedmd.com/srun.html)
- `sbatch` - [man page](https://slurm.schedmd.com/sbatch.html)
- `squeue` - [man page](https://slurm.schedmd.com/squeue.html)
### controller
Use the `docker exec` call to gain a shell on the `controller` container.
```console
$ docker exec -ti controller /bin/bash
[root@controller /]#
```
Issue an `sinfo` call
```console
# sinfo -lN
Wed Apr 11 21:15:35 2018
NODELIST NODES PARTITION STATE CPUS S:C:T MEMORY TMP_DISK WEIGHT AVAIL_FE REASON
worker01 1 docker* idle 1 1:1:1 1998 0 1 (null) none
worker02 1 docker* idle 1 1:1:1 1998 0 1 (null) none
```
Create a `worker` account and `worker` user in Slurm
```console
# sacctmgr -i add account worker description="worker account" Organization=Slurm-in-Docker
Adding Account(s)
worker
Settings
Description = worker account
Organization = slurm-in-docker
Associations
A = worker C = snowflake
Settings
Parent = root
# sacctmgr -i create user worker account=worker adminlevel=None
Adding User(s)
worker
Settings =
Admin Level = None
Associations =
U = worker A = worker C = snowflake
Non Default Settings
```
### database
Use the `docker exec` call to gain a MariaDB/MySQL shell on the `database` container.
```console
$ docker exec -ti database mysql -uslurm -ppassword -hdatabase.local.dev
Welcome to the MariaDB monitor. Commands end with ; or \g.
Your MariaDB connection id is 9
Server version: 5.5.56-MariaDB MariaDB Server
Copyright (c) 2000, 2017, Oracle, MariaDB Corporation Ab and others.
Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.
MariaDB [(none)]>
```
Checkout the `slurm_acct_db` database and it's tables
```console
MariaDB [(none)]> use slurm_acct_db;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A
Database changed
MariaDB [slurm_acct_db]> show tables;
+-----------------------------------+
| Tables_in_slurm_acct_db |
+-----------------------------------+
| acct_coord_table |
| acct_table |
| clus_res_table |
| cluster_table |
| convert_version_table |
| federation_table |
| qos_table |
| res_table |
| snowflake_assoc_table |
| snowflake_assoc_usage_day_table |
| snowflake_assoc_usage_hour_table |
| snowflake_assoc_usage_month_table |
| snowflake_event_table |
| snowflake_job_table |
| snowflake_last_ran_table |
| snowflake_resv_table |
| snowflake_step_table |
| snowflake_suspend_table |
| snowflake_usage_day_table |
| snowflake_usage_hour_table |
| snowflake_usage_month_table |
| snowflake_wckey_table |
| snowflake_wckey_usage_day_table |
| snowflake_wckey_usage_hour_table |
| snowflake_wckey_usage_month_table |
| table_defs_table |
| tres_table |
| txn_table |
| user_table |
+-----------------------------------+
29 rows in set (0.00 sec)
```
Validate that the `worker` user was entered into the database
```console
MariaDB [slurm_acct_db]> select * from user_table;
+---------------+------------+---------+--------+-------------+
| creation_time | mod_time | deleted | name | admin_level |
+---------------+------------+---------+--------+-------------+
| 1523481120 | 1523481120 | 0 | root | 3 |
| 1523481795 | 1523481795 | 0 | worker | 1 |
+---------------+------------+---------+--------+-------------+
2 rows in set (0.00 sec)
```
### worker01 and worker02
Use the `docker exec` call to gain a shell on either the `worker01` or `worker02` container and become the user `worker`.
```console
$ docker exec -ti -u worker worker01 /bin/bash
[worker@worker01 /]$ cd ~
[worker@worker01 ~]$ pwd
/home/worker
```
Test password-less `ssh` between containers
```console
[worker@worker01 ~]$ hostname
worker01.local.dev
[worker@worker01 ~]$ ssh worker02
[worker@worker02 ~]$ hostname
worker02.local.dev
[worker@worker02 ~]$ ssh controller
[worker@controller ~]$ hostname
controller.local.dev
```
### Slurm commands
All commands are issued as the user `worker` from the `controller` node
```console
$ docker exec -ti -u worker controller /bin/bash
[worker@controller /]$ cd ~
[worker@controller ~]$ pwd
/home/worker
```
- For the rest of this section the `[worker@controller ~]$` prompt will be shortend to simply `$`
Test the `sacct` and `srun` calls
```console
$ sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
$ srun -N 2 hostname
worker01.local.dev
worker02.local.dev
$ sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
2 hostname docker worker 2 COMPLETED 0:0
```
Test the `sbatch` call
Make a job file named: `slurm_test.job`
```bash
#!/bin/bash
#SBATCH --job-name=SLURM_TEST
#SBATCH --output=SLURM_TEST.out
#SBATCH --error=SLURM_TEST.err
#SBATCH --partition=docker
srun hostname | sort
```
Run the job using `sbatch`
```console
$ sbatch -N 2 slurm_test.job
Submitted batch job 3
```
Check the `sacct` output
```console
$ sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
2 hostname docker worker 2 COMPLETED 0:0
3 SLURM_TEST docker worker 2 COMPLETED 0:0
3.batch batch worker 1 COMPLETED 0:0
3.0 hostname worker 2 COMPLETED 0:0
```
Check the output files
```console
$ ls -1
SLURM_TEST.err
SLURM_TEST.out
slurm_test.job
$ cat SLURM_TEST.out
worker01.local.dev
worker02.local.dev
```
Test the `sbatch --array` and `squeue` calls
Make a job file named `array_test.job`:
```bash
#!/bin/bash
#SBATCH -N 1
#SBATCH -c 1
#SBATCH -t 24:00:00
###################
## %A == SLURM_ARRAY_JOB_ID
## %a == SLURM_ARRAY_TASK_ID (or index)
## %N == SLURMD_NODENAME (directories made ahead of time)
#SBATCH -o %N/%A_%a_out.txt
#SBATCH -e %N/%A_%a_err.txt
snooze=$(( ( RANDOM % 10 ) + 1 ))
echo "$(hostname) is snoozing for ${snooze} seconds..."
sleep $snooze
```
This job defines output directories as being `%N` which reflect the `SLURMD_NODENAME` variable. The output directories will need to exist ahead of time in this particular case, and can be determined by finding all available nodes in the `NODELIST` and creating the directories.
```console
$ sinfo -N
NODELIST NODES PARTITION STATE
worker01 1 docker* idle
worker02 1 docker* idle
$ mkdir worker01 worker02
```
The job when run will direct it's output files to the directory defined by the node on which it is running. Each iteration will sleep from 1 to 10 seconds randomly before moving onto the next run in the array.
We will run an array of 20 jobs, 2 at a time, until the array is completed. The status can be found using the `squeue` command.
```console
$ sbatch --array=1-20%2 array_test.job
Submitted batch job 4
$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
4_[3-20%2] docker array_te worker PD 0:00 1 (JobArrayTaskLimit)
4_1 docker array_te worker R 0:01 1 worker01
4_2 docker array_te worker R 0:01 1 worker02
...
$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
4_[20%2] docker array_te worker PD 0:00 1 (JobArrayTaskLimit)
4_19 docker array_te worker R 0:04 1 worker02
4_18 docker array_te worker R 0:10 1 worker01
$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
```
Looking into each of the `worker01` and `worker02` directories we can see which jobs were run on each node.
```console
$ ls
SLURM_TEST.err array_test.job worker01
SLURM_TEST.out slurm_test.job worker02
$ ls worker01
4_11_err.txt 4_16_err.txt 4_1_err.txt 4_3_err.txt 4_7_err.txt
4_11_out.txt 4_16_out.txt 4_1_out.txt 4_3_out.txt 4_7_out.txt
4_14_err.txt 4_18_err.txt 4_20_err.txt 4_5_err.txt 4_9_err.txt
4_14_out.txt 4_18_out.txt 4_20_out.txt 4_5_out.txt 4_9_out.txt
$ ls worker02
4_10_err.txt 4_13_err.txt 4_17_err.txt 4_2_err.txt 4_6_err.txt
4_10_out.txt 4_13_out.txt 4_17_out.txt 4_2_out.txt 4_6_out.txt
4_12_err.txt 4_15_err.txt 4_19_err.txt 4_4_err.txt 4_8_err.txt
4_12_out.txt 4_15_out.txt 4_19_out.txt 4_4_out.txt 4_8_out.txt
```
And looking at each `*_out.txt` file view the output
```console
$ cat worker01/4_14_out.txt
worker01.local.dev is snoozing for 10 seconds...
$ cat worker02/4_6_out.txt
worker02.local.dev is snoozing for 7 seconds...
```
Using the `sacct` call we can see when each job in the array was executed
```console
$ sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
2 hostname docker worker 2 COMPLETED 0:0
3 SLURM_TEST docker worker 2 COMPLETED 0:0
3.batch batch worker 1 COMPLETED 0:0
3.0 hostname worker 2 COMPLETED 0:0
4_20 array_tes+ docker worker 1 COMPLETED 0:0
4_20.batch batch worker 1 COMPLETED 0:0
4_1 array_tes+ docker worker 1 COMPLETED 0:0
4_1.batch batch worker 1 COMPLETED 0:0
4_2 array_tes+ docker worker 1 COMPLETED 0:0
4_2.batch batch worker 1 COMPLETED 0:0
4_3 array_tes+ docker worker 1 COMPLETED 0:0
4_3.batch batch worker 1 COMPLETED 0:0
4_4 array_tes+ docker worker 1 COMPLETED 0:0
4_4.batch batch worker 1 COMPLETED 0:0
4_5 array_tes+ docker worker 1 COMPLETED 0:0
4_5.batch batch worker 1 COMPLETED 0:0
4_6 array_tes+ docker worker 1 COMPLETED 0:0
4_6.batch batch worker 1 COMPLETED 0:0
4_7 array_tes+ docker worker 1 COMPLETED 0:0
4_7.batch batch worker 1 COMPLETED 0:0
4_8 array_tes+ docker worker 1 COMPLETED 0:0
4_8.batch batch worker 1 COMPLETED 0:0
4_9 array_tes+ docker worker 1 COMPLETED 0:0
4_9.batch batch worker 1 COMPLETED 0:0
4_10 array_tes+ docker worker 1 COMPLETED 0:0
4_10.batch batch worker 1 COMPLETED 0:0
4_11 array_tes+ docker worker 1 COMPLETED 0:0
4_11.batch batch worker 1 COMPLETED 0:0
4_12 array_tes+ docker worker 1 COMPLETED 0:0
4_12.batch batch worker 1 COMPLETED 0:0
4_13 array_tes+ docker worker 1 COMPLETED 0:0
4_13.batch batch worker 1 COMPLETED 0:0
4_14 array_tes+ docker worker 1 COMPLETED 0:0
4_14.batch batch worker 1 COMPLETED 0:0
4_15 array_tes+ docker worker 1 COMPLETED 0:0
4_15.batch batch worker 1 COMPLETED 0:0
4_16 array_tes+ docker worker 1 COMPLETED 0:0
4_16.batch batch worker 1 COMPLETED 0:0
4_17 array_tes+ docker worker 1 COMPLETED 0:0
4_17.batch batch worker 1 COMPLETED 0:0
4_18 array_tes+ docker worker 1 COMPLETED 0:0
4_18.batch batch worker 1 COMPLETED 0:0
4_19 array_tes+ docker worker 1 COMPLETED 0:0
4_19.batch batch worker 1 COMPLETED 0:0
```
## Examples using MPI
The examples make use of the following commands.
- `ompi_info` - [man page](https://www.open-mpi.org/doc/v3.0/man1/ompi_info.1.php)
- `mpicc` - [man page](https://www.open-mpi.org/doc/v3.0/man1/mpicc.1.php)
- `srun` - [man page](https://slurm.schedmd.com/srun.html)
- `sbatch` - [man page](https://slurm.schedmd.com/sbatch.html)
- `squeue` - [man page](https://slurm.schedmd.com/squeue.html)
- `sacct` - [man page](https://slurm.schedmd.com/sacct.html)
### controller
All commands are issued as the user `worker` from the `controller` node
```console
$ docker exec -ti -u worker controller /bin/bash
[worker@controller /]$ cd ~
[worker@controller ~]$ pwd
/home/worker
```
Available implementions of MPI
```console
$ srun --mpi=list
srun: MPI types are...
srun: none
srun: pmi2
srun: openmpi
```
About Open MPI
```console
$ ompi_info
Package: Open MPI root@a6fd2549e449 Distribution
Open MPI: 3.0.1
Open MPI repo revision: v3.0.1
Open MPI release date: Mar 29, 2018
Open RTE: 3.0.1
Open RTE repo revision: v3.0.1
Open RTE release date: Mar 29, 2018
OPAL: 3.0.1
OPAL repo revision: v3.0.1
OPAL release date: Mar 29, 2018
MPI API: 3.1.0
Ident string: 3.0.1
Prefix: /usr
Configured architecture: x86_64-redhat-linux-gnu
Configure host: a6fd2549e449
Configured by: root
Configured on: Fri Apr 13 02:32:11 UTC 2018
Configure host: a6fd2549e449
Configure command line: '--build=x86_64-redhat-linux-gnu'
'--host=x86_64-redhat-linux-gnu'
'--program-prefix=' '--disable-dependency-tracking'
'--prefix=/usr' '--exec-prefix=/usr'
'--bindir=/usr/bin' '--sbindir=/usr/sbin'
'--sysconfdir=/etc' '--datadir=/usr/share'
'--includedir=/usr/include' '--libdir=/usr/lib64'
'--libexecdir=/usr/libexec' '--localstatedir=/var'
'--sharedstatedir=/var/lib'
'--mandir=/usr/share/man'
'--infodir=/usr/share/info' '--with-slurm'
'--with-pmi' '--with-libfabric='
'LDFLAGS=-Wl,--build-id -Wl,-rpath -Wl,/lib64
-Wl,--enable-new-dtags'
...
```
Hello world using `mpi_hello.out`
Create a new file called `mpi_hello.c` in `/home/worker` and compile it:
```c
/******************************************************************************
* * FILE: mpi_hello.c
* * DESCRIPTION:
* * MPI tutorial example code: Simple hello world program
* * AUTHOR: Blaise Barney
* * LAST REVISED: 03/05/10
* ******************************************************************************/
#include <mpi.h>
#include <stdio.h>
#include <stdlib.h>
#define MASTER 0
int main (int argc, char *argv[]) {
int numtasks, taskid, len;
char hostname[MPI_MAX_PROCESSOR_NAME];
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &numtasks);
MPI_Comm_rank(MPI_COMM_WORLD,&taskid);
MPI_Get_processor_name(hostname, &len);
printf ("Hello from task %d on %s!\n", taskid, hostname);
if (taskid == MASTER)
printf("MASTER: Number of MPI tasks is: %d\n",numtasks);
//while(1) {}
MPI_Finalize();
}
```
```console
$ mpicc mpi_hello.c -o mpi_hello.out
$ ls | grep mpi
mpi_hello.c
mpi_hello.out
```
Test `mpi_hello.out` using the MPI versions avalaible on the system with `srun`
- single node using **openmpi**
```console
$ srun --mpi=openmpi mpi_hello.out
Hello from task 0 on worker01.local.dev!
MASTER: Number of MPI tasks is: 1
$ sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
2 mpi_hello+ docker worker 1 COMPLETED 0:0
```
- two nodes using **openmpi**
```console
$ srun -N 2 --mpi=openmpi mpi_hello.out
Hello from task 0 on worker01.local.dev!
MASTER: Number of MPI tasks is: 2
Hello from task 1 on worker02.local.dev!
$ sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
2 mpi_hello+ docker worker 1 COMPLETED 0:0
3 mpi_hello+ docker worker 2 COMPLETED 0:0
```
- two nodes using **pmi2**
```console
$ srun -N 2 --mpi=pmi2 mpi_hello.out
Hello from task 0 on worker01.local.dev!
MASTER: Number of MPI tasks is: 2
Hello from task 1 on worker02.local.dev!
$ sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
2 mpi_hello+ docker worker 1 COMPLETED 0:0
3 mpi_hello+ docker worker 2 COMPLETED 0:0
4 mpi_hello+ docker worker 2 COMPLETED 0:0
```
Run a batch array with a sleep to observe the queue
Create a file named `mpi_batch.job` in `/home/worker` (similar to the script used for the `sbatch --array` example from above, and make an output directory named `mpi_out`)
file `mpi_batch.job`:
```bash
#!/bin/bash
#SBATCH -N 1
#SBATCH -c 1
#SBATCH -t 24:00:00
###################
## %A == SLURM_ARRAY_JOB_ID
## %a == SLURM_ARRAY_TASK_ID (or index)
#SBATCH -o mpi_out/%A_%a_out.txt
#SBATCH -e mpi_out/%A_%a_err.txt
snooze=$(( ( RANDOM % 10 ) + 1 ))
sleep $snooze
srun -N 2 --mpi=openmpi mpi_hello.out
```
Make directory `mpi_out`
```console
$ mkdir mpi_out
```
Run an `sbatch` array of 5 jobs, one at a time, using both nodes.
```console
$ sbatch -N 2 --array=1-5%1 mpi_batch.job
Submitted batch job 10
$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
10_[2-5%1] docker mpi_batc worker PD 0:00 2 (JobArrayTaskLimit)
10_1 docker mpi_batc worker R 0:03 2 worker[01-02]
$ sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
...
10_[2-5%1] mpi_batch+ docker worker 2 PENDING 0:0
10_1 mpi_batch+ docker worker 2 COMPLETED 0:0
10_1.batch batch worker 1 COMPLETED 0:0
10_1.0 mpi_hello+ worker 2 COMPLETED 0:0
```
...
```console
$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
10_[4-5%1] docker mpi_batc worker PD 0:00 2 (JobArrayTaskLimit)
10_3 docker mpi_batc worker R 0:05 2 worker[01-02]
$ sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
...
10_[4-5%1] mpi_batch+ docker worker 2 PENDING 0:0
10_1 mpi_batch+ docker worker 2 COMPLETED 0:0
10_1.batch batch worker 1 COMPLETED 0:0
10_1.0 mpi_hello+ worker 2 COMPLETED 0:0
10_2 mpi_batch+ docker worker 2 COMPLETED 0:0
10_2.batch batch worker 1 COMPLETED 0:0
10_2.0 mpi_hello+ worker 2 COMPLETED 0:0
10_3 mpi_batch+ docker worker 2 COMPLETED 0:0
10_3.batch batch worker 1 COMPLETED 0:0
10_3.0 mpi_hello+ worker 2 COMPLETED 0:0
```
...
```console
$ squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
$ sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
...
10_5 mpi_batch+ docker worker 2 COMPLETED 0:0
10_5.batch batch worker 1 COMPLETED 0:0
10_5.0 mpi_hello+ worker 2 COMPLETED 0:0
10_1 mpi_batch+ docker worker 2 COMPLETED 0:0
10_1.batch batch worker 1 COMPLETED 0:0
10_1.0 mpi_hello+ worker 2 COMPLETED 0:0
10_2 mpi_batch+ docker worker 2 COMPLETED 0:0
10_2.batch batch worker 1 COMPLETED 0:0
10_2.0 mpi_hello+ worker 2 COMPLETED 0:0
10_3 mpi_batch+ docker worker 2 COMPLETED 0:0
10_3.batch batch worker 1 COMPLETED 0:0
10_3.0 mpi_hello+ worker 2 COMPLETED 0:0
10_4 mpi_batch+ docker worker 2 COMPLETED 0:0
10_4.batch batch worker 1 COMPLETED 0:0
10_4.0 mpi_hello+ worker 2 COMPLETED 0:0
```
Check the `mpi_out` output directory
```console
$ ls mpi_out/
10_1_err.txt 10_2_err.txt 10_3_err.txt 10_4_err.txt 10_5_err.txt
10_1_out.txt 10_2_out.txt 10_3_out.txt 10_4_out.txt 10_5_out.txt
$ cat mpi_out/10_3_out.txt
Hello from task 1 on worker02.local.dev!
Hello from task 0 on worker01.local.dev!
MASTER: Number of MPI tasks is: 2
```
## Tear down
The containers, networks, and volumes associated with the cluster can be torn down by simply running:
```
./teardown.sh
```
Each step of this teardown may also be run individually:
The containers can be stopped and removed using `docker-compose`
```console
$ docker-compose stop
Stopping worker01 ... done
Stopping database ... done
Stopping worker02 ... done
Stopping controller ... done
$ docker-compose rm -f
Going to remove worker01, database, worker02, controller
Removing worker01 ... done
Removing database ... done
Removing worker02 ... done
Removing controller ... done
```
The network and volumes can be removed using their representative `docker` commands
- Volumes
```console
$ docker volume list
DRIVER VOLUME NAME
...
local slurmindocker_home
local slurmindocker_secret
$ docker volume rm slurmindocker_home slurmindocker_secret
slurmindocker_home
slurmindocker_secret
```
- Network
```console
$ docker network list
NETWORK ID NAME DRIVER SCOPE
...
a94c168fb653 slurmindocker_slurm bridge local
$ docker network rm slurmindocker_slurm
slurmindocker_slurm
```
## References
Slurm workload manager: [https://www.schedmd.com/index.php](https://www.schedmd.com/index.php)
- Slurm is a highly configurable open-source workload manager. In its simplest configuration, it can be installed and configured in a few minutes (see [Caos NSA and Perceus: All-in-one Cluster Software Stack](http://www.linux-mag.com/id/7239/1/) by Jeffrey B. Layton). Use of optional plugins provides the functionality needed to satisfy the needs of demanding HPC centers. More complex configurations rely upon a database for archiving accounting records, managing resource limits by user or bank account, and supporting sophisticated scheduling algorithms.
Docker: [https://www.docker.com](https://www.docker.com)
- Docker is the company driving the container movement and the only container platform provider to address every application across the hybrid cloud. Today’s businesses are under pressure to digitally transform but are constrained by existing applications and infrastructure while rationalizing an increasingly diverse portfolio of clouds, datacenters and application architectures. Docker enables true independence between applications and infrastructure and developers and IT ops to unlock their potential and creates a model for better collaboration and innovation.
OpenMPI: [https://www.open-mpi.org](https://www.open-mpi.org)
- The Open MPI Project is an open source [Message Passing Interface](http://www.mpi-forum.org/) implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Open MPI offers advantages for system and software vendors, application developers and computer science researchers.
Lmod: [http://lmod.readthedocs.io/en/latest/index.html](http://lmod.readthedocs.io/en/latest/index.html)
- Lmod is a Lua based module system that easily handles the MODULEPATH Hierarchical problem. Environment Modules provide a convenient way to dynamically change the users’ environment through modulefiles. This includes easily adding or removing directories to the PATH environment variable. Modulefiles for Library packages provide environment variables that specify where the library and header files can be found.

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FROM krallin/centos-tini:7
MAINTAINER Michael J. Stealey <stealey@renci.org>
ENV SLURM_VERSION=19.05.1 \
MUNGE_UID=981 \
SLURM_UID=982 \
WORKER_UID=1000
RUN groupadd -g $MUNGE_UID munge \
&& useradd -m -c "MUNGE Uid 'N' Gid Emporium" -d /var/lib/munge -u $MUNGE_UID -g munge -s /sbin/nologin munge \
&& groupadd -g $SLURM_UID slurm \
&& useradd -m -c "Slurm workload manager" -d /var/lib/slurm -u $SLURM_UID -g slurm -s /bin/bash slurm \
&& groupadd -g $WORKER_UID worker \
&& useradd -m -c "Workflow user" -d /home/worker -u $WORKER_UID -g worker -s /bin/bash worker
# install packages for general functionality
RUN yum -y install \
epel-release \
&& yum -y install \
sudo \
wget \
which \
tree \
mariadb-server \
mariadb-devel \
munge \
munge-libs \
munge-devel \
openssh-server \
openssh-clients
# install slurm 19.05.1
COPY rpms /packages
# /usr/bin/mpiexec from slurm-torque conflicts with openmpi install
WORKDIR /packages
RUN yum -y localinstall $(ls | grep -v -e 'torque' -e 'openmpi')
WORKDIR /
VOLUME ["/home", "/.secret"]
# 22: SSH
# 3306: MariaDB
# 6817: Slurm Ctl D
# 6818: Slurm D
# 6819: Slurm DBD
EXPOSE 22 3306 6817 6818 6819

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SLURM_VERSION = 19.05.1
IMAGE = scidas/slurm.base
DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
.PHONY: all build clean test
all: build
build:
cp -r "$(DIR)/../packages/centos-7/rpms" .
docker build -t $(IMAGE):$(SLURM_VERSION) .
clean:
@[ -z $(docker images -q $(IMAGE):$(SLURM_VERSION)) ] || docker rmi $(IMAGE):$(SLURM_VERSION)
rm -rf rpms

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# Slurm Base Image
TODO

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FROM scidas/slurm.base:19.05.1
MAINTAINER Michael J. Stealey <stealey@renci.org>
# install openmpi 3.0.1
RUN yum -y install \
gcc-c++ \
gcc-gfortran \
&& yum -y localinstall \
/packages/openmpi-*.rpm
# install Lmod 7.7
RUN yum -y install \
lua-posix \
lua \
lua-filesystem \
lua-devel \
wget \
bzip2 \
expectk \
make \
&& wget https://sourceforge.net/projects/lmod/files/Lmod-7.7.tar.bz2 \
&& tar -xjvf Lmod-7.7.tar.bz2
WORKDIR /Lmod-7.7
RUN ./configure --prefix=/opt/apps \
&& make install \
&& ln -s /opt/apps/lmod/lmod/init/profile /etc/profile.d/z00_lmod.sh \
&& ln -s /opt/apps/lmod/lmod/init/cshrc /etc/profile.d/z00_lmod.csh
WORKDIR /
ENV USE_SLURMDBD=true \
CLUSTER_NAME=snowflake \
CONTROL_MACHINE=controller \
SLURMCTLD_PORT=6817 \
SLURMD_PORT=6818 \
ACCOUNTING_STORAGE_HOST=database \
ACCOUNTING_STORAGE_PORT=6819 \
PARTITION_NAME=docker
# clean up
RUN rm -f /packages/slurm-*.rpm /packages/openmpi-*.rpm \
&& yum clean all \
&& rm -rf /var/cache/yum \
&& rm -f /Lmod-7.7.tar.bz2
COPY docker-entrypoint.sh /docker-entrypoint.sh
ENTRYPOINT ["/usr/local/bin/tini", "--", "/docker-entrypoint.sh"]

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SLURM_VERSION = 19.05.1
IMAGE = scidas/slurm.controller
.PHONY: all build clean test
all: build
build:
docker build -t $(IMAGE):$(SLURM_VERSION) .
clean:
@[ -z $(docker images -q $(IMAGE):$(SLURM_VERSION)) ] || docker rmi $(IMAGE):$(SLURM_VERSION)

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# Slurm Controller
TODO

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#!/usr/bin/env bash
set -e
# start sshd server
_sshd_host() {
if [ ! -d /var/run/sshd ]; then
mkdir /var/run/sshd
ssh-keygen -t rsa -f /etc/ssh/ssh_host_rsa_key -N ''
fi
/usr/sbin/sshd
}
# setup worker ssh to be passwordless
_ssh_worker() {
if [[ ! -d /home/worker ]]; then
mkdir -p /home/worker
chown -R worker:worker /home/worker
fi
cat > /home/worker/setup-worker-ssh.sh <<'EOF2'
mkdir -p ~/.ssh
chmod 0700 ~/.ssh
ssh-keygen -b 2048 -t rsa -f ~/.ssh/id_rsa -q -N "" -C "$(whoami)@$(hostname)-$(date -I)"
cat ~/.ssh/id_rsa.pub > ~/.ssh/authorized_keys
chmod 0640 ~/.ssh/authorized_keys
cat >> ~/.ssh/config <<EOF
Host *
StrictHostKeyChecking no
UserKnownHostsFile /dev/null
LogLevel QUIET
EOF
chmod 0644 ~/.ssh/config
cd ~/
tar -czvf ~/worker-secret.tar.gz .ssh
cd -
EOF2
chmod +x /home/worker/setup-worker-ssh.sh
chown worker: /home/worker/setup-worker-ssh.sh
sudo -u worker /home/worker/setup-worker-ssh.sh
}
# start munge and generate key
_munge_start() {
chown -R munge: /etc/munge /var/lib/munge /var/log/munge /var/run/munge
chmod 0700 /etc/munge
chmod 0711 /var/lib/munge
chmod 0700 /var/log/munge
chmod 0755 /var/run/munge
/sbin/create-munge-key -f
sudo -u munge /sbin/munged
munge -n
munge -n | unmunge
remunge
}
# copy secrets to /.secret directory for other nodes
_copy_secrets() {
cp /home/worker/worker-secret.tar.gz /.secret/worker-secret.tar.gz
cp /home/worker/setup-worker-ssh.sh /.secret/setup-worker-ssh.sh
cp /etc/munge/munge.key /.secret/munge.key
rm -f /home/worker/worker-secret.tar.gz
rm -f /home/worker/setup-worker-ssh.sh
}
# generate slurm.conf
_generate_slurm_conf() {
cat > /etc/slurm/slurm.conf <<EOF
#
# Example slurm.conf file. Please run configurator.html
# (in doc/html) to build a configuration file customized
# for your environment.
#
#
# slurm.conf file generated by configurator.html.
#
# See the slurm.conf man page for more information.
#
ClusterName=$CLUSTER_NAME
SlurmctldHost=$CONTROL_MACHINE
#SlurmctldHostr=
#
SlurmUser=slurm
#SlurmdUser=root
SlurmctldPort=$SLURMCTLD_PORT
SlurmdPort=$SLURMD_PORT
AuthType=auth/munge
#JobCredentialPrivateKey=
#JobCredentialPublicCertificate=
StateSaveLocation=/var/spool/slurm/ctld
SlurmdSpoolDir=/var/spool/slurm/d
SwitchType=switch/none
MpiDefault=none
SlurmctldPidFile=/var/run/slurmctld.pid
SlurmdPidFile=/var/run/slurmd.pid
ProctrackType=proctrack/pgid
#PluginDir=
#FirstJobId=
ReturnToService=0
#MaxJobCount=
#PlugStackConfig=
#PropagatePrioProcess=
#PropagateResourceLimits=
#PropagateResourceLimitsExcept=
#Prolog=
#Epilog=
#SrunProlog=
#SrunEpilog=
#TaskProlog=
#TaskEpilog=
#TaskPlugin=
#TrackWCKey=no
#TreeWidth=50
#TmpFS=
#UsePAM=
#
# TIMERS
SlurmctldTimeout=300
SlurmdTimeout=300
InactiveLimit=0
MinJobAge=300
KillWait=30
Waittime=0
#
# SCHEDULING
SchedulerType=sched/backfill
#SchedulerAuth=
#SelectType=select/linear
FastSchedule=1
#PriorityType=priority/multifactor
#PriorityDecayHalfLife=14-0
#PriorityUsageResetPeriod=14-0
#PriorityWeightFairshare=100000
#PriorityWeightAge=1000
#PriorityWeightPartition=10000
#PriorityWeightJobSize=1000
#PriorityMaxAge=1-0
#
# LOGGING
SlurmctldDebug=3
SlurmctldLogFile=/var/log/slurmctld.log
SlurmdDebug=3
SlurmdLogFile=/var/log/slurmd.log
JobCompType=jobcomp/none
#JobCompLoc=
#
# ACCOUNTING
JobAcctGatherType=jobacct_gather/linux
#JobAcctGatherFrequency=30
#
AccountingStorageType=accounting_storage/slurmdbd
AccountingStorageHost=$ACCOUNTING_STORAGE_HOST
AccountingStoragePort=$ACCOUNTING_STORAGE_PORT
#AccountingStorageLoc=
#AccountingStoragePass=
#AccountingStorageUser=
#
# COMPUTE NODES
NodeName=worker[01-02] RealMemory=1800 CPUs=1 State=UNKNOWN
PartitionName=$PARTITION_NAME Nodes=ALL Default=YES MaxTime=INFINITE State=UP
EOF
}
# run slurmctld
_slurmctld() {
if $USE_SLURMDBD; then
echo -n "cheking for slurmdbd.conf"
while [ ! -f /.secret/slurmdbd.conf ]; do
echo -n "."
sleep 1
done
echo ""
fi
mkdir -p /var/spool/slurm/ctld \
/var/spool/slurm/d \
/var/log/slurm
chown -R slurm: /var/spool/slurm/ctld \
/var/spool/slurm/d \
/var/log/slurm
touch /var/log/slurmctld.log
chown slurm: /var/log/slurmctld.log
if [[ ! -f /home/config/slurm.conf ]]; then
echo "### generate slurm.conf ###"
_generate_slurm_conf
else
echo "### use provided slurm.conf ###"
cp /home/config/slurm.conf /etc/slurm/slurm.conf
fi
sacctmgr -i add cluster "${CLUSTER_NAME}"
sleep 2s
/usr/sbin/slurmctld
cp -f /etc/slurm/slurm.conf /.secret/
}
### main ###
_sshd_host
_ssh_worker
_munge_start
_copy_secrets
_slurmctld
tail -f /dev/null

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FROM scidas/slurm.base:19.05.1
MAINTAINER Michael J. Stealey <stealey@renci.org>
ENV DBD_ADDR=database \
DBD_HOST=database \
DBD_PORT=6819 \
STORAGE_HOST=database.local.dev \
STORAGE_PORT=3306 \
STORAGE_PASS=password \
STORAGE_USER=slurm
# clean up
RUN rm -f /packages/slurm-*.rpm /packages/openmpi-*.rpm \
&& yum clean all \
&& rm -rf /var/cache/yum
COPY docker-entrypoint.sh /docker-entrypoint.sh
ENTRYPOINT ["/usr/local/bin/tini", "--", "/docker-entrypoint.sh"]

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SLURM_VERSION = 19.05.1
IMAGE = scidas/slurm.database
.PHONY: all build clean test
all: build
build:
docker build -t $(IMAGE):$(SLURM_VERSION) .
clean:
@[ -z $(docker images -q $(IMAGE):$(SLURM_VERSION)) ] || docker rmi $(IMAGE):$(SLURM_VERSION)

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# Slurm Database
TODO

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#!/usr/bin/env bash
set -e
SLURM_ACCT_DB_SQL=/slurm_acct_db.sql
# start sshd server
_sshd_host() {
if [ ! -d /var/run/sshd ]; then
mkdir /var/run/sshd
ssh-keygen -t rsa -f /etc/ssh/ssh_host_rsa_key -N ''
fi
/usr/sbin/sshd
}
# slurm database user settings
_slurm_acct_db() {
{
echo "create database slurm_acct_db;"
echo "create user '${STORAGE_USER}'@'${STORAGE_HOST}';"
echo "set password for '${STORAGE_USER}'@'${STORAGE_HOST}' = password('${STORAGE_PASS}');"
echo "grant usage on *.* to '${STORAGE_USER}'@'${STORAGE_HOST}';"
echo "grant all privileges on slurm_acct_db.* to '${STORAGE_USER}'@'${STORAGE_HOST}';"
echo "flush privileges;"
} >> $SLURM_ACCT_DB_SQL
}
# start database
_mariadb_start() {
# mariadb somehow expects `resolveip` to be found under this path; see https://github.com/SciDAS/slurm-in-docker/issues/26
ln -s /usr/bin/resolveip /usr/libexec/resolveip
mysql_install_db
chown -R mysql: /var/lib/mysql/ /var/log/mariadb/ /var/run/mariadb
cd /var/lib/mysql
mysqld_safe --user=mysql &
cd /
_slurm_acct_db
sleep 5s
mysql -uroot < $SLURM_ACCT_DB_SQL
}
# start munge using existing key
_munge_start_using_key() {
if [ ! -f /.secret/munge.key ]; then
echo -n "cheking for munge.key"
while [ ! -f /.secret/munge.key ]; do
echo -n "."
sleep 1
done
echo ""
fi
cp /.secret/munge.key /etc/munge/munge.key
chown -R munge: /etc/munge /var/lib/munge /var/log/munge /var/run/munge
chmod 0700 /etc/munge
chmod 0711 /var/lib/munge
chmod 0700 /var/log/munge
chmod 0755 /var/run/munge
sudo -u munge /sbin/munged
munge -n
munge -n | unmunge
remunge
}
# wait for worker user in shared /home volume
_wait_for_worker() {
if [ ! -f /home/worker/.ssh/id_rsa.pub ]; then
echo -n "cheking for id_rsa.pub"
while [ ! -f /home/worker/.ssh/id_rsa.pub ]; do
echo -n "."
sleep 1
done
echo ""
fi
}
# generate slurmdbd.conf
_generate_slurmdbd_conf() {
cat > /etc/slurm/slurmdbd.conf <<EOF
#
# Example slurmdbd.conf file.
#
# See the slurmdbd.conf man page for more information.
#
# Archive info
#ArchiveJobs=yes
#ArchiveDir="/tmp"
#ArchiveSteps=yes
#ArchiveScript=
#JobPurge=12
#StepPurge=1
#
# Authentication info
AuthType=auth/munge
AuthInfo=/var/run/munge/munge.socket.2
#
# slurmDBD info
DbdAddr=$DBD_ADDR
DbdHost=$DBD_HOST
DbdPort=$DBD_PORT
SlurmUser=slurm
#MessageTimeout=300
DebugLevel=4
#DefaultQOS=normal,standby
LogFile=/var/log/slurm/slurmdbd.log
PidFile=/var/run/slurmdbd.pid
#PluginDir=/usr/lib/slurm
#PrivateData=accounts,users,usage,jobs
#TrackWCKey=yes
#
# Database info
StorageType=accounting_storage/mysql
StorageHost=$STORAGE_HOST
StoragePort=$STORAGE_PORT
StoragePass=$STORAGE_PASS
StorageUser=$STORAGE_USER
StorageLoc=slurm_acct_db
EOF
}
# run slurmdbd
_slurmdbd() {
mkdir -p /var/spool/slurm/d \
/var/log/slurm
chown slurm: /var/spool/slurm/d \
/var/log/slurm
if [[ ! -f /home/config/slurmdbd.conf ]]; then
echo "### generate slurmdbd.conf ###"
_generate_slurmdbd_conf
else
echo "### use provided slurmdbd.conf ###"
cp /home/config/slurmdbd.conf /etc/slurm/slurmdbd.conf
fi
/usr/sbin/slurmdbd
cp /etc/slurm/slurmdbd.conf /.secret/slurmdbd.conf
}
### main ###
_sshd_host
_mariadb_start
_munge_start_using_key
_wait_for_worker
_slurmdbd
tail -f /dev/null

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FROM scidas/slurm.base:19.05.1
MAINTAINER Michael J. Stealey <stealey@renci.org>
# install openmpi 3.0.1
RUN yum -y install \
gcc-c++ \
gcc-gfortran \
&& yum -y localinstall \
/packages/openmpi-*.rpm
# install Lmod 7.7
RUN yum -y install \
lua-posix \
lua \
lua-filesystem \
lua-devel \
wget \
bzip2 \
expectk \
make \
&& wget https://sourceforge.net/projects/lmod/files/Lmod-7.7.tar.bz2 \
&& tar -xjvf Lmod-7.7.tar.bz2
WORKDIR /Lmod-7.7
RUN ./configure --prefix=/opt/apps \
&& make install \
&& ln -s /opt/apps/lmod/lmod/init/profile /etc/profile.d/z00_lmod.sh \
&& ln -s /opt/apps/lmod/lmod/init/cshrc /etc/profile.d/z00_lmod.csh
WORKDIR /home/worker
# clean up
RUN rm -f /packages/slurm-*.rpm /packages/openmpi-*.rpm \
&& yum clean all \
&& rm -rf /var/cache/yum \
&& rm -f /Lmod-7.7.tar.bz2
COPY docker-entrypoint.sh /docker-entrypoint.sh
ENTRYPOINT ["/usr/local/bin/tini", "--", "/docker-entrypoint.sh"]

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slurm/worker/Makefile Normal file
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SLURM_VERSION = 19.05.1
IMAGE = scidas/slurm.worker
.PHONY: all build clean test
all: build
build:
docker build -t $(IMAGE):$(SLURM_VERSION) .
clean:
@[ -z $(docker images -q $(IMAGE):$(SLURM_VERSION)) ] || docker rmi $(IMAGE):$(SLURM_VERSION)

3
slurm/worker/README.md Normal file
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# Slurm Worker
TODO

69
slurm/worker/docker-entrypoint.sh Executable file
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#!/usr/bin/env bash
set -e
# start sshd server
_sshd_host() {
if [ ! -d /var/run/sshd ]; then
mkdir /var/run/sshd
ssh-keygen -t rsa -f /etc/ssh/ssh_host_rsa_key -N ''
fi
/usr/sbin/sshd
}
# start munge using existing key
_munge_start_using_key() {
echo -n "cheking for munge.key"
while [ ! -f /.secret/munge.key ]; do
echo -n "."
sleep 1
done
echo ""
cp /.secret/munge.key /etc/munge/munge.key
chown -R munge: /etc/munge /var/lib/munge /var/log/munge /var/run/munge
chmod 0700 /etc/munge
chmod 0711 /var/lib/munge
chmod 0700 /var/log/munge
chmod 0755 /var/run/munge
sudo -u munge /sbin/munged
munge -n
munge -n | unmunge
remunge
}
# wait for worker user in shared /home volume
_wait_for_worker() {
if [ ! -f /home/worker/.ssh/id_rsa.pub ]; then
echo -n "cheking for id_rsa.pub"
while [ ! -f /home/worker/.ssh/id_rsa.pub ]; do
echo -n "."
sleep 1
done
echo ""
fi
}
# run slurmd
_slurmd() {
if [ ! -f /.secret/slurm.conf ]; then
echo -n "cheking for slurm.conf"
while [ ! -f /.secret/slurm.conf ]; do
echo -n "."
sleep 1
done
echo ""
fi
mkdir -p /var/spool/slurm/d
chown slurm: /var/spool/slurm/d
cp /.secret/slurm.conf /etc/slurm/slurm.conf
touch /var/log/slurmd.log
chown slurm: /var/log/slurmd.log
/usr/sbin/slurmd
}
### main ###
_sshd_host
_munge_start_using_key
_wait_for_worker
_slurmd
tail -f /dev/null