almalinux10-x86_64-openchami-slurm

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1 Introduction

This guide presents a simple cluster installation procedure using components from the OpenHPC software stack. OpenHPC represents an aggregation of a number of common ingredients required to deploy and manage an HPC Linux* cluster including provisioning tools, resource management, I/O clients, development tools, and a variety of scientific libraries. These packages have been pre-built with HPC integration in mind while conforming to common Linux distribution standards. The documentation herein is intended to be reasonably generic, but uses the underlying motivation of a small, 4-node stateless cluster installation to define a step-by-step process. Several optional customizations are included and the intent is that these collective instructions can be modified as needed for local site customizations.

Base Linux Edition: this edition of the guide highlights installation without the use of a companion configuration management system and directly uses distro-provided package management tools for component selection. The steps that follow also highlight specific changes to system configuration files that are required as part of the cluster install process.

1.1 Target Audience

This guide is targeted at experienced Linux system administrators for HPC environments. Knowledge of software package management, system networking, and PXE booting is assumed. Command-line input examples are highlighted throughout this guide via the following syntax:

echo "OpenHPC hello world"

Unless specified otherwise, the examples presented are executed with elevated (root) privileges. The examples also presume use of the BASH login shell, though the equivalent commands in other shells can be substituted. In addition to specific command-line instructions called out in this guide, an alternate convention is used to highlight potentially useful tips or optional configuration options. These tips are highlighted via the following format:

1.2 Requirements/Assumptions

This installation recipe assumes the availability of a single head node, and four compute nodes. The head node serves as the overall system management server (SMS) and is provisioned with AlmaLinux 10 and is subsequently configured to provision the remaining compute nodes with openchami in a stateless configuration. For power management, we assume that the compute node baseboard management controllers (BMCs) are available via IPMI from the chosen head node. For file systems, we assume that the chosen head node will host an NFS file system that is made available to the compute nodes.

Installation information is also discussed to optionally mount a parallel file system and in this case, the parallel file system is assumed to exist previously.

An outline of the physical architecture discussed is shown in the figure above and highlights the high-level networking configuration. The head node requires at least two Ethernet interfaces with eth0 connected to the local data center network and eth1 used to provision and manage the cluster backend (note that these interface names are examples and may be different depending on local settings and OS conventions). Two logical IP interfaces are expected to each compute node: the first is the standard Ethernet interface that will be used for provisioning and resource management. The second is used to connect to each host’s BMC and is used for power management and remote console access. Physical connectivity for these two logical IP networks is often accommodated via separate cabling and switching infrastructure; however, an alternate configuration can also be accommodated via the use of a shared NIC, which runs a packet filter to divert management packets between the host and BMC. Independent of the actual networking configuration it is recommended to have additional security boundaries like a firewall to protect the network interfaces from the Internet.

In addition to the IP networking, there is an optional high-speed network (InfiniBand or Omni-Path in this recipe) that is also connected to each of the hosts. This high speed network is used for application message passing and optionally for parallel file system connectivity as well (e.g. to existing Lustre or BeeGFS storage targets).

1.3 Inputs

As this recipe details installing a cluster starting from bare-metal, there is a requirement to define IP addresses and gather hardware MAC addresses in order to support a controlled provisioning process. These values are necessarily unique to the hardware being used, and this document uses variable substitution (${variable}) in the command-line examples that follow to highlight where local site inputs are required. A summary of the required and optional variables used throughout this recipe are presented below. Note that while the example definitions above correspond to a small 4-node compute subsystem, the compute parameters are defined in array format to accommodate logical extension to larger node counts.

1.4 Installation Template

The collection of command-line instructions that follow in this guide, when combined with local site inputs, can be used to implement a bare-metal system installation and configuration. The format of these commands is intended to be usable via direct cut and paste (with variable substitution for site-specific settings). Alternatively, the OpenHPC documentation package (docs-ohpc) includes a template script which includes a summary of all of the commands used herein. This script can be used in conjunction with a simple text file to define the local site variables defined in the previous section (see Requirements/Assumptions) and is provided as a convenience for administrators. For additional information on accessing this script, please see the Automation Appendix.

2 Install Base Operating System

2.1 Install OS

In an external setting, installing the desired Base OS on a head node typically involves booting from a DVD ISO image on a new server. With this approach, insert the AlmaLinux 10 DVD, power cycle the host, and follow the distro provided directions to install the Base OS on your chosen head node. Alternatively, if choosing to use a pre-installed server, please verify that it is provisioned with the required AlmaLinux 10 distribution.

Prior to beginning the installation process of OpenHPC components, several additional considerations are noted here for the head node configuration. First, the installation recipe herein assumes that the head node name is resolvable locally. Depending on the manner in which you installed the Base OS, there may be an adequate entry already defined in /etc/hosts. If not, the following addition can be used to identify your head node.

echo ${sms_ip} ${sms_name} >> /etc/hosts

While it is theoretically possible to enable SELinux on a cluster provisioned with openchami, doing so is beyond the scope of this document. Even the use of permissive mode can be problematic and we therefore recommend disabling SELinux on the head node. If SELinux components are installed locally, the selinuxenabled command can be used to determine if SELinux is currently enabled. If enabled, consult the distro documentation for information on how to disable.

2.2 Configure HTTPS Proxy (Optional)

If your environment requires an HTTPS caching proxy for external network access, configure it here before installing any packages. The placeholder below marks where site-specific proxy setup should be injected by a pre-processing step.

2.3 Enable EL Package Repositories

In addition to the OpenHPC package repository, the head node also requires access to the standard base OS distro repositories in order to resolve necessary dependencies. For AlmaLinux 10, the requirements are to have access to the BaseOS, Appstream, Extras, CRB, and EPEL repositories for which mirrors are freely available online:

Although the public EPEL repository would be enabled automatically upon installation of the ohpc-release package, we install it now. Note that this does depend on the AlmaLinux 10 Extras repository, which is shipped with AlmaLinux 10 and is typically enabled by default. In contrast, the CRB repository is typically disabled in a standard install, but can be enabled from EPEL as follows:

dnf -y install epel-release dnf-plugins-core
dnf config-manager --set-enabled crb

2.4 Configure Firewall

Provisioning services rely on DHCP, TFTP, and HTTP network protocols. Depending on the local Base OS configuration on the head node, default firewall rules may prohibit these services. Consequently, this recipe assumes that the local firewall running on the head node is disabled (it is still recommended to have additional security boundaries like a firewall to protect the cluster from the Internet). If installed, the default firewall service can be disabled as follows:

systemctl disable --now firewalld || true

2.5 Add Hostname

echo "${sms_ip} ${sms_name}" >> /etc/hosts

2.6 Configure NTP

HPC systems rely on synchronized clocks throughout the system and the NTP protocol can be used to facilitate this synchronization. To enable NTP services on the head node with a specific server ${ntp_server}, and allow this server to serve as a local time server for the cluster, issue the following:

dnf -y install chrony
systemctl enable chronyd.service
echo "local stratum 10" >> /etc/chrony.conf
echo "server ${ntp_server}" >> /etc/chrony.conf
echo "allow all" >> /etc/chrony.conf
systemctl restart chronyd

Tip

Note: Note that the “allow all” option specified for the chrony time daemon allows all servers on the local network to be able to synchronize with the head node. Alternatively, you can restrict access to fixed IP ranges and an example config line allowing access to a local class B subnet is as follows:

allow 192.168.0.0/16

2.7 Generate SSH Key Pair

An SSH key pair on the head node enables passwordless access to compute nodes and is useful for automating cluster configuration tasks.

[[ -f ~/.ssh/id_ed25519 ]] || ssh-keygen -t ed25519 -f ~/.ssh/id_ed25519 -N ''

Tip

Note: The key is generated without a passphrase (-N '') to allow unattended use in scripts and automated workflows. Ensure that access to the head node is appropriately restricted.

2.8 Setup NFS Server

Here we set up NFS mounting of a $HOME file system and the public OpenHPC install path (/opt/ohpc/pub) that will be hosted by the head node in this example configuration.

# Install and Start NFS server
dnf -y install nfs-utils
systemctl start nfs-server.service

# Create OpenHPC public packages directory
mkdir -p /opt/ohpc/pub

# Export /home and OpenHPC public packages from head node
echo "/home *(rw,no_subtree_check,fsid=10,no_root_squash)" >> /etc/exports
echo "/opt/ohpc/pub *(ro,no_subtree_check,fsid=11)" >> /etc/exports
exportfs -a

# Restart and enable nfs server
systemctl restart nfs-server
systemctl enable nfs-server

2.9 Optionally add InfiniBand support services on head node

The following command adds OFED and PSM support using base distro-provided drivers to the chosen head node.

dnf -y groupinstall "InfiniBand Support"
# Load IB services
udevadm trigger --type=devices --action=add
systemctl restart rdma-load-modules@infiniband.service

Tip

Note: InfiniBand networks require a subnet management service that can typically be run on either an administrative node, or on the switch itself. The optimal placement and configuration of the subnet manager is beyond the scope of this document, but AlmaLinux 10 provides the opensm package should you choose to run it on the head node.

With the InfiniBand drivers included, you can also enable (optional) IPoIB functionality which provides a mechanism to send IP packets over the IB network. If you plan to mount a Lustre file system over InfiniBand, then having IPoIB enabled is a requirement for the Lustre client. OpenHPC provides a template configuration file to aid in setting up an ib0 interface on the head node. To use, copy the template provided and update the ${sms_ipoib} and ${ipoib_netmask} entries to match local desired settings (alter ib0 naming as appropriate if system contains dual-ported or multiple HCAs).

cp /opt/ohpc/pub/examples/network/centos/ifcfg-ib0 \
    /etc/sysconfig/network-scripts

# Define local IPoIB address and netmask
sed -i "s/master_ipoib/${sms_ipoib}/" \
    /etc/sysconfig/network-scripts/ifcfg-ib0
sed -i "s/ipoib_netmask/${ipoib_netmask}/" \
    /etc/sysconfig/network-scripts/ifcfg-ib0

# configure NetworkManager to *not* override local /etc/resolv.conf
echo "[main]"   >  /etc/NetworkManager/conf.d/90-dns-none.conf
echo "dns=none" >> /etc/NetworkManager/conf.d/90-dns-none.conf
# Start up NetworkManager to initiate ib0
systemctl start NetworkManager

2.10 Optionally add Omni-Path support services on head node

The following command adds Omni-Path support using base distro-provided drivers to the chosen head node.

dnf -y install opa-basic-tools

Tip

Note: OmniPath networks require a subnet management service that can typically be run on either an administrative node, or on the switch itself. The optimal placement and configuration of the subnet manager is beyond the scope of this document, but AlmaLinux 10 provides the opa-fm package should you choose to run it on the head node.

Tip

Note: Many server BIOS configurations have PXE network booting configured as the primary option in the boot order by default. If your compute nodes have a different device as the first in the sequence, the ipmitool utility can be used to enable PXE.

ipmitool -E -I lanplus -H ${bmc_ipaddr} -U root chassis \
    bootdev pxe options=persistent

3 Install OpenHPC Components

3.1 Enable OpenHPC Repository

With the Base OS installed and booted, the next step is to add desired OpenHPC packages onto the head node in order to provide provisioning and resource management services for the rest of the cluster.

To begin, enable use of the OpenHPC repository by adding it to the local list of available package repositories. Note that this requires network access from your head node to the OpenHPC repository, or alternatively, that the OpenHPC repository be mirrored locally. In cases where network external connectivity is available, OpenHPC provides an ohpc-release package that includes GPG keys for package signing and enabling the repository. The example which follows illustrates installation of the ohpc-release package directly from the OpenHPC build server.

dnf -y install http://repos.openhpc.community/OpenHPC/4/EL_10/x86_64/\
ohpc-release-4-1.el10.x86_64.rpm

Tip

Note: Many sites may find it useful or necessary to maintain a local copy of the OpenHPC repositories. To facilitate this need, standalone tar archives are provided – one containing a repository of binary packages as well as any available updates, and one containing a repository of source RPMS. The tar files also contain a simple bash script to configure the package manager to use the local repository after download. To use, simply unpack the tarball where you would like to host the local repository and execute the make_repo.sh script. Tar files for this release can be found at http://repos.openhpc.community/dist/4.1

3.2 Install OpenHPC Base Packages

Now OpenHPC packages can be installed. To add the base package on the head node issue the following:

dnf -y install ohpc-base

4 Install Slurm

4.1 Add Slurm on Head Node

The following command adds the Slurm workload manager server components to the chosen head node. Note that client-side components will be added to the corresponding compute image in a subsequent step. Note that Slurm leverages the use of the munge library to provide authentication services and this daemon also needs to be running on all hosts within the resource management pool.

# Install slurm server meta-package
dnf -y install ohpc-slurm-server

# Use ohpc-provided file for starting SLURM configuration
cp /etc/slurm/slurm.conf.ohpc /etc/slurm/slurm.conf
# Setup default cgroups file
cp /etc/slurm/cgroup.conf.example /etc/slurm/cgroup.conf

# Identify resource manager hostname on head node
sed -i "s/SlurmctldHost=\S\+/SlurmctldHost=${sms_name}/" \
    /etc/slurm/slurm.conf

There are a wide variety of configuration options and plugins available for Slurm and the example config file illustrated above targets a fairly basic installation. In particular, job completion data will be stored in a text file (/var/log/slurm_jobcomp.log) that can be used to log simple accounting information. Sites who desire more detailed information, or want to aggregate accounting data from multiple clusters, will likely want to enable the database accounting back-end. This requires a number of additional local modifications (on top of installing slurm-slurmdbd-ohpc), and users are advised to consult the online documentation for more detailed information on setting up a database configuration for Slurm.

Tip

Note: SLURM requires enumeration of the physical hardware characteristics for compute nodes under its control. In particular, three configuration parameters combine to define consumable compute resources: Sockets, CoresPerSocket, and ThreadsPerCore. The default configuration file provided via OpenHPC assumes the nodes are named c1-c4 and are dual-socket, 8 cores per socket, and two threads per core for this 4-node example. If this does not reflect your local hardware, please update the configuration file at /etc/slurm/slurm.conf accordingly to match your nodes names and particular hardware. Be sure to run scontrol reconfigure to notify SLURM of the changes. Note that the SLURM project provides an easy-to-use online configuration tool that can be accessed here.

5 Install OpenCHAMI Provisioner

Installation is completed in a few parts. First we build the images that the compute nodes will boot off of. Then we configure the cloud-init steps to add a local account, mount remote file systems, and inject the munge key into the OS. OpenHPC components will be added to both the head node and compute nodes. The head node will get the components during install, and compute nodes will get them during image builds.

OpenCHAMI uses an Infrastructure as Code tool called image-builder to translate YAML files to system images in layers to build out reusable file system layers like container images. This enables the rapid rebuild of images in smaller more usable and readable layers. OpenCHAMI uses SquashFS images over S3 to serve to nodes, and Container images through OCI.

5.1 Install OpenCHAMI

To begin we need to add the OpenCHAMI RPM to the head node, by adding it to the list of available packages locally. This requires network access from the head node to the internet. We then source /etc/profile.d/openchami.sh to update the shell.

dnf -y install podman buildah ansible-core nfs-utils tcpdump tftp curl yq jq
rpm --import \
    https://github.com/OpenCHAMI/release/releases/download/\
v0.1.4/repo_public.asc
dnf -y install \
    https://github.com/OpenCHAMI/release/releases/download/\
v0.1.4/openchami-0.1.4.rpm

source /etc/profile.d/openchami.sh

5.2 Certificate Creation

With OpenCHAMI a minimal open source certificate authority from smallstep is needed. The included automation initializes the CA on first startup. We can immediately download a certificate into the system trust bundle on the host for trusting all subsequent OpenCHAMI certificates. Notably, the certificate authority features ACME for automatic certificate rotation.

openchami-certificate-update update ${sms_name}

5.3 Setting no proxy

OpenCHAMI runs its own internal proxy for services which may not interact well if you run another httpd server. Here we set the no proxy variable to prevent lookups.

export additonal_no_proxy="${sms_name},opaal,opaal-idp,smd,smd-init,\
hydra,cloud-init,acme-deploy,bss,haproxy,postgres,step-ca,configurator"
if [ -z "$no_proxy" ]; then
    export no_proxy="$additonal_no_proxy"
else
    export no_proxy="$no_proxy,$additonal_no_proxy"
fi
if [ -z "$NO_PROXY" ]; then
    export NO_PROXY="$additonal_no_proxy"
else
    export NO_PROXY="$NO_PROXY,$additonal_no_proxy"
fi

5.4 Setup DHCP

OpenCHAMI uses CoreDHCP as the DHCP service to provide IP addresses to nodes. There is a default configuration in place that we need to overwrite.

If your router address is different than the internal network address .254 you will need to change this file on your own. CoreDHCP has been configured to only provide addresses to nodes it knows. There are some extra configuration changes you can make to change that.

cat > /etc/openchami/configs/coredhcp.yaml <<EOF
server4:
 plugins:
    - server_id: ${sms_ip}
    - router: ${ipv4_gateway}
    - dns: ${dns_servers}
    - netmask: ${internal_netmask}
    - coresmd: https://${sms_name}:8443 http://${sms_ip}:8081 \
/root_ca/root_ca.crt 30s 1h false
EOF

5.5 Complete basic OpenCHAMI setup for head node

At this point, all of the packages necessary to use OpenCHAMI on the head node should be installed. Next, we create and enable the Container Registry and S3 Object store. These are optional if you have an existing S3 or Container Registry available for use at your local site.

Tip

The S3 and registry containers are configured as Podman Quadlets, which interface with systemd allowing you to perform normal systemd operations on them like:

systemctl status registry
systemctl restart minio-server
journalctl -u registry

mkdir -p /opt/ohpc/admin/data/oci
mkdir -p /opt/ohpc/admin/data/s3

cat > /etc/containers/systemd/registry.container <<EOF
# registry.container
[Unit]
Description=Image OCI Registry
After=network-online.target
Requires=network-online.target

[Container]
ContainerName=registry
HostName=registry
Image=docker.io/library/registry:latest
Volume=/opt/ohpc/admin/data/oci:/var/lib/registry:Z
PublishPort=5000:5000

[Service]
TimeoutStartSec=0
Restart=always

[Install]
WantedBy=multi-user.target
EOF

cat > /etc/containers/systemd/minio.container <<EOF
[Unit]
Description=Minio S3
After=local-fs.target network-online.target
Wants=local-fs.target network-online.target

[Container]
ContainerName=minio-server
Image=docker.io/minio/minio:latest
# Volumes
Volume=/opt/ohpc/admin/data/s3:/data:Z

# Ports
PublishPort=9000:9000
PublishPort=9091:9001

# Environment Variables
Environment=MINIO_ROOT_USER=admin
Environment=MINIO_ROOT_PASSWORD=password1234

# Command to run in container
Exec=server /data --console-address :9001

[Service]
Restart=always

[Install]
WantedBy=multi-user.target
EOF

We need to reload the system daemon, and to allow the MinIO, and OCI Registry containers to start.

systemctl daemon-reload
systemctl start minio.service
systemctl start registry.service

# Handle SSH to compute nodes
echo -e "Host ${compute_prefix}*\n\tStrictHostKeyChecking=no" \
    >> /etc/ssh/ssh_config.d/40-ohpc.conf

5.6 s3cmd Setup

In this recipe OpenCHAMI uses S3 to store and serve images and we need to add configuration files that allow us to access and manage the S3 storage layer for EFI and boot image storage.

dnf -y install s3cmd

cat > ~/.s3cfg <<EOF
# Setup endpoint
host_base = ${sms_name}:9000
host_bucket = ${sms_name}:9000
bucket_location = us-east-1
use_https = False

# Setup access keys
access_key = admin
secret_key = password1234

# Enable S3 v4 signature APIs
signature_v2 = False
EOF

Now we can use the tool to create the buckets we’ll need and set ACLs to public.

s3cmd mb s3://efi
s3cmd setacl s3://efi --acl-public
s3cmd mb s3://boot-images
s3cmd setacl s3://boot-images --acl-public

The nodes need to be able to read from the S3 bucket without authentication so we need to create some read policies.

mkdir -p /opt/ohpc/admin/images
cat > /opt/ohpc/admin/images/public-read-boot.json <<EOF
{
  "Version":"2012-10-17",
  "Statement":[
    {
      "Effect":"Allow",
     "Principal":"*",
      "Action":["s3:GetObject"],
      "Resource":["arn:aws:s3:::boot-images/*"]
    }
  ]
}
EOF
cat > /opt/ohpc/admin/images/public-read-efi.json <<EOF
{
  "Version":"2012-10-17",
  "Statement":[
    {
      "Effect":"Allow",
      "Principal":"*",
      "Action":["s3:GetObject"],
      "Resource":["arn:aws:s3:::efi/*"]
    }
  ]
}
EOF

Lastly we can now apply these policies. Objects stored in the buckets should be publicly available.

s3cmd setpolicy /opt/ohpc/admin/images/public-read-boot.json \
    s3://boot-images \
    --host=${sms_ip}:9000 --host-bucket=${sms_ip}:9000
s3cmd setpolicy /opt/ohpc/admin/images/public-read-efi.json \
    s3://efi \
    --host=${sms_ip}:9000 --host-bucket=${sms_ip}:9000

5.7 OpenCHAMI Client Install

OpenCHAMI is very configurable, and it has a client that allows you to do most of the configuration via the command line, so installing that client makes management much easier.

dnf -y install \
    https://github.com/OpenCHAMI/ochami/releases/download/\
v0.7.2/ochami_0.7.2_linux_amd64.rpm
mkdir -p /etc/ochami && touch /etc/ochami/config.yaml
ochami config cluster set --system --default \
    cluster cluster.uri https://${sms_name}:8443

5.8 Starting OpenCHAMI

Starting OpenCHAMI can take a while especially when the node images are being downloaded for the first time. The status of all OpenCHAMI services can be checked with:

systemctl list-dependencies openchami.target

systemctl start openchami.target

5.9 Compute Image Configuration

# Create compute image configuration directory
mkdir -v -p /opt/ohpc/admin/images/data

5.10 Configure Slurm Client

# Register Slurm server with computes (using "configless" option)
echo SLURMD_OPTIONS="--conf-server ${sms_ip}" \
    > /opt/ohpc/admin/images/data/slurmd

5.11 Building the Base OS Image

The Image Builder is designed to use layered building of system images, as shown below to enable the use of different layers which can be modified and added to build out different capabilities into image layers so a change of one layer does not require a change and rebuild of all other layers.

First let’s define the lowest layer of the image which disables the installation of documentation files to reduce the size of the image:

echo -e "%_excludedocs 1" >> /opt/ohpc/admin/images/data/rpmmacros
cat > /opt/ohpc/admin/images/nodocs.yaml <<EOF
options:
  layer_type: 'base'
  name: 'almalinux10-nodocs'
  publish_tags: '10'
  pkg_manager: 'dnf'
  parent: 'scratch'
  publish_registry: '${sms_name}:5000/${compute_prefix}'
  registry_opts_push:
    - '--tls-verify=false'
repos:
  - alias: 'almalinux10_BaseOS'
    url: 'https://repo.almalinux.org/almalinux/10/BaseOS/x86_64/os/'
    gpg: 'https://repo.almalinux.org/almalinux/RPM-GPG-KEY-AlmaLinux-10'
  - alias: 'almalinux10_AppStream'
    url: 'https://repo.almalinux.org/almalinux/10/AppStream/x86_64/os/'
    gpg: 'https://repo.almalinux.org/almalinux/RPM-GPG-KEY-AlmaLinux-10'
packages:
  - bash
  - dnf
  - dnf-plugins-core
copyfiles:
  - src: '/data/rpmmacros'
    dest: '/root/.rpmmacros'
EOF

podman run \
    --rm \
    --device /dev/fuse \
    --network host \
    -v /opt/ohpc/admin/images/data:/data \
    -v /opt/ohpc/admin/images/nodocs.yaml:/home/builder/config.yaml \
    ghcr.io/openchami/image-build:latest image-build \
        --config config.yaml \
        --log-level INFO

Now let’s define a base layer we can use to build on. This base layer will install common packages and also create our initramfs. In this recipe it’s created to build an initramfs that supports liveOS so the image will boot into memory.

cat > /opt/ohpc/admin/images/base.yaml <<EOF
options:
  layer_type: 'base'
  name: 'almalinux10-base'
  publish_tags: '10'
  pkg_manager: 'dnf'
  parent: '${sms_name}:5000/${compute_prefix}/almalinux10-nodocs:10'
  publish_registry: '${sms_name}:5000/${compute_prefix}'
  registry_opts_pull:
    - '--tls-verify=false'
  registry_opts_push:
    - '--tls-verify=false'
repos:
  - alias: 'almalinux10_BaseOS'
    url: 'https://repo.almalinux.org/almalinux/10/BaseOS/x86_64/os/'
    gpg: 'https://repo.almalinux.org/almalinux/RPM-GPG-KEY-AlmaLinux-10'
  - alias: 'almalinux10_AppStream'
    url: 'https://repo.almalinux.org/almalinux/10/AppStream/x86_64/os/'
    gpg: 'https://repo.almalinux.org/almalinux/RPM-GPG-KEY-AlmaLinux-10'
package_groups:
  - 'Minimal Install'
  - 'Development Tools'
packages:
  - kernel
  - wget
  - dracut-live
  - cloud-init
  - chrony
  - rsyslog
  - sudo
cmds:
  - cmd: >
      DRACUT_NO_XATTR=1 dracut --add "dmsquash-live livenet network-manager"
      --kver "\$(basename /lib/modules/*)"
      -N -f --logfile /tmp/dracut.log 2>/dev/null
    loglevel: INFO
  - cmd: 'echo DRACUT LOG:; cat /tmp/dracut.log'
    loglevel: INFO
EOF

Now let’s build this base layer. This will take about 5 minutes but we should not have to rebuild it very often.

podman run \
    --rm \
    --device /dev/fuse \
    --network host \
    -v /opt/ohpc/admin/images/base.yaml:/home/builder/config.yaml \
    ghcr.io/openchami/image-build:latest image-build \
        --config config.yaml \
        --log-level DEBUG

Now we can build on top of the base layer by setting it to be the parent of the compute-base layer.

cat > /opt/ohpc/admin/images/compute-base.yaml << EOF
options:
  layer_type: 'base'
  name: 'compute-base'
  publish_tags:
    - '10'
  pkg_manager: 'dnf'
  parent: '${sms_name}:5000/${compute_prefix}/almalinux10-base:10'
  publish_registry: '${sms_name}:5000/${compute_prefix}'
  registry_opts_pull:
    - '--tls-verify=false'
  registry_opts_push:
    - '--tls-verify=false'
repos:
  - alias: 'almalinux10_CRB'
    url: 'https://repo.almalinux.org/almalinux/10/CRB/x86_64/os/'
    gpg: 'https://repo.almalinux.org/almalinux/RPM-GPG-KEY-AlmaLinux-10'
  - alias: 'Epel10'
    url: 'https://dl.fedoraproject.org/pub/epel/10z/Everything/x86_64/'
    gpg: 'https://dl.fedoraproject.org/pub/epel/RPM-GPG-KEY-EPEL-10'
package_groups:
  - 'InfiniBand Support'
packages:
  - vim
  - nfs-utils
  - tcpdump
  - traceroute
  - git
  - http://repos.openhpc.community/OpenHPC/4/EL_10/x86_64/\
ohpc-release-4-1.el10.x86_64.rpm
EOF

Then we can build it. Any modifications to the above configuration will only require a rebuild of this layer.

podman run \
    --rm \
    --device /dev/fuse \
    --network host \
    -v /opt/ohpc/admin/images/compute-base.yaml:/home/builder/config.yaml \
    ghcr.io/openchami/image-build:latest image-build \
        --config config.yaml \
        --log-level DEBUG

You can keep adding layers as you see fit, and branch off if so desired. We will use the next layer to add additional packages later on so no need to build it just yet.

cp /etc/hosts /opt/ohpc/admin/images/data
cat > /opt/ohpc/admin/images/compute-prod.yaml << EOF
options:
  layer_type: 'base'
  name: 'compute-prod'
  publish_tags:
    - '10'
  pkg_manager: 'dnf'
  parent: '${sms_name}:5000/${compute_prefix}/compute-base:10'
  publish_registry: '${sms_name}:5000/${compute_prefix}'
  registry_opts_pull:
    - '--tls-verify=false'
  registry_opts_push:
    - '--tls-verify=false'
  # Publish SquashFS image to local S3
  publish_s3: 'http://${sms_name}:9000'
  s3_prefix: 'compute/base/'
  s3_bucket: 'boot-images'
repos:
  - alias: 'OpenHPC'
    url: 'http://repos.openhpc.community/OpenHPC/4/EL_10'
    gpg: 'file:///etc/pki/rpm-gpg/RPM-GPG-KEY-OpenHPC-4'
copyfiles:
  - src: '/data/hosts'
    dest: '/etc/hosts'
  - src: '/data/slurmd'
    dest: '/etc/sysconfig/slurmd'
packages:
  - ohpc-base-compute
  - ohpc-slurm-client
  - pdsh-ohpc
  - lmod-ohpc
cmds:
  - cmd: systemctl disable firewalld
    loglevel: INFO
  - cmd: >-
      echo '${sms_ip}:/home /home nfs nfsvers=3,nodev,nosuid 0 0'
      >> /etc/fstab
    loglevel: INFO
  - cmd: >-
      echo '${sms_ip}:/opt/ohpc/pub /opt/ohpc/pub nfs nfsvers=3,nodev,nosuid 0 0'
      >> /etc/fstab
    loglevel: INFO
  - cmd: mkdir -p /opt/ohpc/pub
    loglevel: INFO
  - cmd: echo "account required pam_slurm.so" >> /etc/pam.d/sshd
    loglevel: INFO
  - cmd: systemctl enable munge slurmd
    loglevel: INFO
  - cmd: ln -sf ../usr/share/zoneinfo/UTC /etc/localtime
    loglevel: INFO
EOF

6 Additional Customization

This chapter highlights common additional customizations that can optionally be applied to the local cluster environment. Details on the steps required for each of these customizations are discussed further in the following sections.

6.1 Enable InfiniBand drivers

If your compute resources support InfiniBand, the following commands add OFED and PSM support using base distro-provided drivers to the compute image.

# Add IB support and enable
dnf -y --installroot="$CHROOT" groupinstall "InfiniBand Support"

6.2 Enable Omni-Path drivers

If your compute resources support Omni-Path, the following commands add OPA support using base distro-provided drivers to the compute image.

# Add OPA support and enable
dnf -y --installroot="$CHROOT" install opa-basic-tools
dnf -y --installroot="$CHROOT" install libpsm2

6.3 Increase locked memory limits

In order to utilize InfiniBand or Omni-Path as the underlying high speed interconnect, it is generally necessary to increase the locked memory settings for system users. This can be accomplished by adding the /etc/security/limits.d/40-ohpc-limits.conf file and this should be performed on all job submission hosts. In this recipe, jobs are submitted from the head node, and the following commands can be used to update the maximum locked memory settings on both the head node and compute nodes:

# Update memlock settings on head node
echo '* soft memlock unlimited' >> \
  /etc/security/limits.d/40-ohpc-limits.conf
echo '* hard memlock unlimited' >> \
  /etc/security/limits.d/40-ohpc-limits.conf
# Update memlock settings on compute
C="echo '* soft memlock unlimited' >> /etc/security/limits.d/40-ohpc-limits.conf" \
  yq -i '.cmds += [{"cmd": strenv(C)}]' /opt/ohpc/admin/images/compute-prod.yaml
C="echo '* hard memlock unlimited' >> /etc/security/limits.d/40-ohpc-limits.conf" \
  yq -i '.cmds += [{"cmd": strenv(C)}]' /opt/ohpc/admin/images/compute-prod.yaml

6.4 Enable ssh control via resource manager

An additional optional customization that is recommended is to restrict ssh access on compute nodes to only allow access by users who have an active job associated with the node. This can be enabled via the use of a pluggable authentication module (PAM) provided as part of the Slurm package installs. To enable this feature on compute nodes, issue the following:

C="echo 'account    required     pam_slurm.so' >> /etc/pam.d/sshd" \
  yq -i '.cmds += [{"cmd": strenv(C)}]' /opt/ohpc/admin/images/compute-prod.yaml

6.5 GPU Drivers

To add the optional NVIDIA GPU driver to the compute nodes, an additional external dnf repository provided by NVIDIA must be configured. Once the repository is configured, the GPU driver needs to be installed on the compute image and the corresponding toolkit installed on the SMS node.

OpenHPC provides a convenience package to enable the NVIDIA repository locally along with compatibility packages that integrate the NVIDIA HPC SDK within the standard OpenHPC user environment.

# Add NVIDIA GPU driver repository to the head node
dnf -y install cuda-repo-ohpc

# Add NVIDIA GPU driver repository to the compute nodes
yq -i '.packages += ["cuda-repo-ohpc"]' \
    /opt/ohpc/admin/images/compute-prod.yaml

# Install the GPU driver on the compute nodes
yq -i '.packages += ["nvidia-driver:latest-dkms"]' \
    /opt/ohpc/admin/images/compute-prod.yaml

# Enable DKMS service to automatically rebuild driver
C="systemctl enable dkms" \
  yq -i '.cmds += [{"cmd": strenv(C)}]' /opt/ohpc/admin/images/compute-prod.yaml

# Install the toolkit on the head node
yq -i '.packages += ["cuda-devel-ohpc", "nvidia-driver-cuda"]' \
    /opt/ohpc/admin/images/compute-prod.yaml

6.6 Enable System Log Forwarding

It is often desirable to consolidate system logging information for the cluster in a central location, both to provide easy access to the data, and to reduce the impact of storing data inside the compute node’s memory footprint if it is stateless. The following commands highlight the steps necessary to configure compute nodes to forward their logs to the head node, and to allow the head node to accept these log requests.

# Configure head node to receive messages and reload rsyslog configuration
echo 'module(load="imudp")' >> /etc/rsyslog.d/ohpc.conf
echo 'input(type="imudp" port="514")' >> /etc/rsyslog.d/ohpc.conf
systemctl restart rsyslog

# Define compute node forwarding destination
C="echo '*.* @${sms_ip}:514' > /etc/rsyslog.d/ohpc-forward.conf" \
  yq -i '.cmds += [{"cmd": strenv(C)}]' /opt/ohpc/admin/images/compute-prod.yaml

# Disable most local logging on computes.
# Emergency and boot logs will remain on the compute nodes
C="sed -i 's/^\*\.info/#\*\.info/' /etc/rsyslog.conf" \
  yq -i '.cmds += [{"cmd": strenv(C)}]' /opt/ohpc/admin/images/compute-prod.yaml
C="sed -i 's/^authpriv/#authpriv/' /etc/rsyslog.conf" \
  yq -i '.cmds += [{"cmd": strenv(C)}]' /opt/ohpc/admin/images/compute-prod.yaml
C="sed -i 's/^mail/#mail/' /etc/rsyslog.conf" \
  yq -i '.cmds += [{"cmd": strenv(C)}]' /opt/ohpc/admin/images/compute-prod.yaml
C="sed -i 's/^cron/#cron/' /etc/rsyslog.conf" \
  yq -i '.cmds += [{"cmd": strenv(C)}]' /opt/ohpc/admin/images/compute-prod.yaml
C="sed -i 's/^uucp/#uucp/' /etc/rsyslog.conf" \
  yq -i '.cmds += [{"cmd": strenv(C)}]' /opt/ohpc/admin/images/compute-prod.yaml

6.7 Intel oneAPI Compiler Runtime

If planning to install the Intel® oneAPI compiler runtime (see Optional Development Tool Builds), register the following additional path (/opt/intel) to share with computes:

# (Optional) Setup NFS mount for /opt/intel if planning to install oneAPI packages
mkdir -v /opt/intel
echo "/opt/intel *(ro,no_subtree_check,fsid=12)" >> /etc/exports
C="echo '${sms_ip}:/opt/intel /opt/intel nfs nfsvers=4,nodev 0 0' >> /etc/fstab" \
  yq -i '.cmds += [{"cmd": strenv(C)}]' /opt/ohpc/admin/images/compute-prod.yaml

6.8 Cluster Admin Tools

6.8.1 Add ClusterShell

ClusterShell is an event-based Python library to execute commands in parallel across cluster nodes. Installation and basic configuration defining three node groups (adm, compute, and all) is as follows:

# Install ClusterShell
dnf -y install clustershell

# Setup node definitions
mv /etc/clustershell/groups.d/local.cfg \
   /etc/clustershell/groups.d/local.cfg.orig
echo "adm: ${sms_name}" > \
  /etc/clustershell/groups.d/local.cfg
echo "compute: ${compute_prefix}[1-${num_computes}]" >> \
  /etc/clustershell/groups.d/local.cfg
echo "all: @adm,@compute" >> \
  /etc/clustershell/groups.d/local.cfg

6.8.2 Add genders

genders is a static cluster configuration database or node typing database used for cluster configuration management. Other tools and users can access the genders database in order to make decisions about where an action, or even what action, is appropriate based on associated types or “genders”. Values may also be assigned to and retrieved from a gender to provide further granularity. The following example highlights installation and configuration of two genders: compute and bmc.

# Install genders
dnf -y install genders-ohpc

# Generate a sample genders file
echo -e "${sms_name}\tsms" > /etc/genders
for ((i=0; i<num_computes; i++)) ; do
          echo -e "${c_name[$i]}\tcompute,bmc=${c_bmc[$i]}"
    done >> /etc/genders

6.8.3 Add ConMan

conman is a serial console management program designed to support a large number of console devices and simultaneous users. It supports logging console device output and connecting to compute node consoles via IPMI serial-over-lan. Installation and example configuration is outlined below.

# Install conman to provide a front-end to compute consoles and log output
dnf -y install conman-ohpc

# Configure conman for computes
# (note your IPMI password is required for console access)
for ((i=0; i<num_computes; i++)) ; do
    echo -n 'CONSOLE name="'"${c_name[$i]}"'" dev="ipmi:'"${c_bmc[$i]}"'" '
    echo -n 'ipmiopts="'U:"${bmc_username}",P:
    echo "${IPMI_PASSWORD:-undefined}",W:solpayloadsize'"'
    done >> /etc/conman.conf

# Enable and start conman
systemctl enable conman
systemctl start conman

6.8.4 Add NHC

Resource managers often provide for a periodic “node health check” to be performed on each compute node to verify that the node is working properly. Nodes which are determined to be “unhealthy” can be marked as down or offline so as to prevent jobs from being scheduled or run on them. This helps increase the reliability and throughput of a cluster by reducing preventable job failures due to misconfiguration, hardware failure, etc. OpenHPC distributes nhc to fulfill this requirement.

In a typical scenario, the nhc driver script is run periodically on each compute node by the resource manager client daemon. It loads its configuration file to determine which checks are to be run on the current node (based on its hostname). Each matching check is run, and if a failure is encountered, nhc will exit with an error message describing the problem. It can also be configured to mark nodes offline so that the scheduler will not assign jobs to bad nodes, reducing the risk of system-induced job failures.

# Install NHC on head and compute nodes
dnf -y install nhc-ohpc
yq -i '.packages += ["nhc-ohpc"]' \
    /opt/ohpc/admin/images/compute-prod.yaml

# Register as SLURM's health check program
echo "HealthCheckProgram=/usr/sbin/nhc" >> /etc/slurm/slurm.conf
# execute every five minutes
echo "HealthCheckInterval=300" >> /etc/slurm/slurm.conf

6.9 Add Magpie

Magpie contains a number of scripts to aid in running a variety of big data software frameworks within HPC queuing environments. Examples include Hadoop, Spark, Hbase, Storm, Pig, Mahout, Phoenix, Kafka, Zeppelin, and Zookeeper. Consult the online repository for more information on using these scripts; basic installation is outlined as follows:

# Install magpie
dnf -y install magpie-ohpc

6.10 Charliecloud

Typical Charliecloud workflows are based around Docker containers, but it is not strictly necessary to install Docker itself on the HPC resource. A common pattern is to build the Docker container on a laptop or VM and upload the result to the cluster for use with Charliecloud. More information can be found at https://hpc.github.io/charliecloud/

7 Deploy Cluster

CLUSTER_ACCESS_TOKEN=$(gen_access_token)
export CLUSTER_ACCESS_TOKEN

7.1 Rebuild Image

podman run \
    --rm \
    --device /dev/fuse \
    --network host \
    -e S3_ACCESS=admin \
    -e S3_SECRET=password1234 \
    -v /opt/ohpc/admin/images/data:/data \
    -v /opt/ohpc/admin/images/compute-prod.yaml:/home/builder/config.yaml:z \
    ghcr.io/openchami/image-build:latest \
        image-build \
        --config config.yaml

7.2 Setting Boot Parameters

Boot Script Service (BSS) is what provides the path to vmlinuz and the initrd, and provides the kernel parameters to the node during iPXE.

s3cmd ls -Hr s3://boot-images/

export s3Output=$(s3cmd ls -Hr s3://boot-images/)
export os=$(echo "$s3Output" | awk '{print $4}' | grep 'boot-images/compute')
export ramfs=$(echo "$s3Output" | awk '{print $4}' | grep 'initram')
export hdrs=$(echo "$s3Output" | awk '{print $4}' | grep 'vmlinuz')
export params="ds=nocloud-net;s=http://${sms_ip}:8081/cloud-init/ \
nomodeset ro root=live:http://${sms_ip}:9000/${os:5} ip=dhcp \
overlayroot=tmpfs overlayroot_cfgdisk=disabled apparmor=0 selinux=0 \
console=ttyS0,115200 ip6=off cloud-init=enabled"

mkdir -p /opt/ohpc/admin/nodes
cat > /opt/ohpc/admin/nodes/compute-boot.yaml <<EOF
kernel: 'http://${sms_ip}:9000/${hdrs:5}'
initrd: 'http://${sms_ip}:9000/${ramfs:5}'
params: '${params}'
macs:
EOF
for((i=0; i < $num_computes; i++)); do
    echo "  - ${c_mac[$i]}" >> \
        /opt/ohpc/admin/nodes/compute-boot.yaml
done

ochami -k bss boot params set \
    -f yaml -d @/opt/ohpc/admin/nodes/compute-boot.yaml

7.3 Building cloud-init Image

OpenCHAMI uses cloud-init for post-boot node configuration. We will establish some basic cloud-init configurations here.

7.3.1 Create Default Configuration

Let’s create a directory to hold our default cloud-init configuration and create an SSH key pair that we can use for SSH access later.

mkdir -p /opt/ohpc/admin/cloud-init
ssh-keygen -t ed25519 -q -f "$HOME/.ssh/id_openchami" -N ""
cat >> "$HOME/.ssh/config" <<EOF

Host ${compute_prefix}*
    IdentityFile ~/.ssh/id_openchami
    StrictHostKeyChecking no
    UserKnownHostsFile /dev/null
EOF

cat > /opt/ohpc/admin/cloud-init/defaults.yaml <<EOF
base-url: "http://${sms_ip}:8081/cloud-init"
cluster-name: "CLUSTER"
nid-length: 1
public-keys: []
short-name: "${compute_prefix}"
EOF
for i in /root/.ssh/id*pub; do
    key=$(cat "$i") yq '.public-keys += [strenv(key)]' \
        -i /opt/ohpc/admin/cloud-init/defaults.yaml
done

ochami -k cloud-init defaults set \
    -f yaml -d @/opt/ohpc/admin/cloud-init/defaults.yaml

7.3.2 Configure Munge

OpenCHAMI provides a cloud-init server that can be used, in conjunction with the cloud-init client, to provide post-boot configurations. The configuration below is a minimal configuration that should at least let the root user login using the public key and distribute the munge key file to all compute nodes.

munge_key=$(cat /etc/munge/munge.key | base64 -w 0)
export munge_key
cat > /opt/ohpc/admin/cloud-init/compute.yaml <<EOF
- name: compute
  description: "compute template"
  file:
    encoding: plain
    content: |
      ## template: jinja
      #cloud-config
      merge_how:
      - name: list
        settings: [append]
      - name: dict
        settings: [no_replace, recurse_list]
      users:
        - name: root
          ssh_authorized_keys: {{ ds.meta_data.instance_data.v1.public_keys }}
      write_files:
        - content: ${munge_key}
          path: /etc/munge/munge.key
          permissions: '0400'
          owner: munge:munge
          encoding: base64
      runcmd:
        - systemctl restart munge
        - systemctl restart slurmd
EOF

Once you are done updating cloud-init you can post the file to the cloud-init server.

ochami -k cloud-init group set \
    -f yaml -d @/opt/ohpc/admin/cloud-init/compute.yaml

7.4 Verify Configuration Before Boot

Before booting compute nodes, verify that BSS and cloud-init are configured correctly. These checks catch the most common failures before a wasted boot cycle.

ochami -k bss boot params get \
    | grep -q "ds=nocloud-net" \
    && echo "BSS: OK" \
    || { echo "BSS: FAILED - check boot params"; exit 1; }

Next, confirm that the cloud-init default configuration was uploaded successfully:

ochami -k cloud-init defaults get \
    | grep -q "base-url" \
    && echo "cloud-init defaults: OK" \
    || { echo "cloud-init defaults: FAILED"; exit 1; }

Finally, confirm that the compute group cloud-init configuration is present. This is what delivers the SSH keys and munge key to the node at boot:

ochami -k cloud-init group get raw compute \
    | grep -q "compute" \
    && echo "cloud-init group: OK" \
    || { echo "cloud-init group: FAILED"; exit 1; }

7.5 Node Discovery

OpenCHAMI can do dynamic discovery, but here we will do node discovery by YAML file. The YAML file can be imported by the discover command creating a way for adding nodes that do not have redfish capabilities, or when you just want to provide a list of nodes.

Create the nodes.yaml file the static discovery will use to populate SMD. Also add the compute node names to /etc/hosts for SSH access.

mkdir -p /opt/ohpc/admin/nodes
nf=/opt/ohpc/admin/nodes/nodes.yaml

## Add BMCs
echo "bmcs:" > $nf
for((i=0; i < $num_computes; i++)); do
    nid=$((i+1))
    printf -v mac '%02x:%02x' "$(((nid >> 8) & 0xff))" "$((nid & 0xff))"
    cat >> $nf << EOF
- xname: x1000c0s0b${nid}
  ip: ${c_bmc[$i]}
  mac: 02:00:00:00:${mac}
EOF
done

## Add nodes
echo "nodes:" >> $nf
for((i=0; i < $num_computes; i++)); do
    nid=$((i+1))
    cat >> $nf << EOF
- name: ${c_name[$i]}
  nid: ${nid}
  xname: x1000c0s0b${nid}n0
  bmc: x1000c0s0b${nid}
  groups:
  - compute
  interfaces:
  - mac_addr: ${c_mac[$i]}
    ip_addrs:
    - name: internal
      ip_addr: ${c_ip[$i]}
EOF
done

## Add nodes to /etc/hosts
for((i=0; i < $num_computes; i++)); do
    echo "${c_ip[$i]} ${c_name[$i]}" >> /etc/hosts
done

ochami discover static \
    -f yaml -d @/opt/ohpc/admin/nodes/nodes.yaml

ochami discover static populates SMD components, EthernetInterfaces (under the correct node xname), and group membership from the nodes.yaml file in a single step.

7.6 Boot Compute Nodes

At this point, the head node should be able to boot the newly defined compute nodes. Assuming that the compute node BIOS settings are configured to boot over PXE, all that is required to initiate the provisioning process is to power cycle each of the desired hosts using IPMI access. The following commands use the ipmitool utility to initiate power resets on each of the four compute hosts. Note that the utility requires that the IPMI_PASSWORD environment variable be set with the local BMC password in order to work interactively.

for ((i=0; i<num_computes; i++)) ; do
  ipmitool -E -I lanplus -H "${c_bmc[$i]}" -U "${bmc_username}" \
    -P "${bmc_password}" chassis power reset
done

Once kicked off, the boot process should take less than 5 minutes (depending on BIOS post times) and you can verify that the compute hosts are available via ssh, or via parallel ssh tools to multiple hosts. For example, to run a command on the newly imaged compute hosts using pdsh, execute the following:

pdsh -w ${compute_prefix}[1-${num_computes}] uptime
c1  05:03am  up   0:02,  0 users,  load average: 0.20, 0.13, 0.05
c2  05:03am  up   0:02,  0 users,  load average: 0.20, 0.14, 0.06
c3  05:03am  up   0:02,  0 users,  load average: 0.19, 0.15, 0.06
c4  05:03am  up   0:02,  0 users,  load average: 0.15, 0.12, 0.05

7.7 Wait for Compute Nodes

Wait for all compute nodes to become accessible via SSH. Cloud-init must complete and restart munge and slurmd before the nodes are ready.

until pdsh -w "${compute_prefix}[1-${num_computes}]" true \
    >/dev/null 2>&1; do
    echo "Waiting for compute nodes..."
    sleep 10
done

7.8 Start Slurm

In an earlier section, the Slurm resource manager was installed and configured for use on both the head node and compute node instances. With the cluster nodes up and functional, we can now startup the resource manager services in preparation for running user jobs.

# Start munge and slurm controller on head node
systemctl enable --now munge
systemctl enable --now slurmctld

7.9 Start Slurm on the Compute Nodes

# Start slurm clients on compute hosts
pdsh -w "${compute_prefix}[1-${num_computes}]" systemctl restart munge
pdsh -w "${compute_prefix}[1-${num_computes}]" systemctl restart slurmd

8 Install OpenHPC Development Components

The install procedure outlined in Install OpenHPC Components highlighted the steps necessary to install a head node, assemble and customize a compute image, and provision several compute hosts from bare-metal. With these steps completed, additional OpenHPC-provided packages can now be added to support a flexible HPC development environment including development tools, C/C++/FORTRAN compilers, MPI stacks, and a variety of 3rd party libraries. The following subsections highlight the additional software installation procedures.

8.1 Development Tools

To aid in general development efforts, OpenHPC provides recent versions of the GNU autotools collection, the Valgrind memory debugger, EasyBuild, and Spack. These can be installed as follows:

# Install autotools meta-package
dnf -y install ohpc-autotools
dnf -y install EasyBuild-ohpc
dnf -y install hwloc-ohpc
dnf -y install spack-ohpc
dnf -y install valgrind-ohpc

8.2 Compilers

OpenHPC presently packages the GNU compiler toolchain integrated with the underlying Lmod modules system in a hierarchical fashion. The modules system will conditionally present compiler-dependent software based on the toolchain currently loaded.

dnf -y install gnu15-compilers-ohpc

8.3 MPI Stacks

For MPI development and runtime support, OpenHPC provides pre-packaged builds for a variety of MPI families and transport layers. Currently available options and their applicability to various network transports are summarized in the Available MPI variants table below. The command that follows installs a starting set of MPI families that are compatible with both ethernet and high-speed fabrics.

	Ethernet (TCP)	InfiniBand	Intel Omni-Path
MPICH (ofi)	✓	✓	✓
MPICH (ucx)	✓	✓	✓
MVAPICH2		✓
MVAPICH2 (psm2)			✓
OpenMPI (ofi/ucx)	✓	✓	✓

dnf -y install openmpi5-pmix-gnu15-ohpc mpich-ofi-gnu15-ohpc

Note that OpenHPC 2.x introduces the use of two related transport layers for the MPICH and OpenMPI builds that support a variety of underlying fabrics: UCX (Unified Communication X) and OFI (OpenFabrics interfaces). In the case of OpenMPI, a monolithic build is provided which supports both transports and end-users can customize their runtime preferences with environment variables. For MPICH, two separate builds are provided and the example above highlighted installing the ofi variant. However, the packaging is designed such that both versions can be installed simultaneously and users can switch between the two via normal module command semantics. Alternatively, a site can choose to install the ucx variant instead as a drop-in MPICH replacement:

dnf -y install mpich-ucx-gnu15-ohpc

In the case where both MPICH variants are installed, two modules will be visible in the end-user environment and an example of this configuration is highlighted is below.

module avail mpich

-------------------- /opt/ohpc/pub/moduledeps/gnu15---------------------
   mpich/3.4.3-ofi    mpich/3.4.3-ucx (D)

If your system includes InfiniBand and you enabled underlying support in InfiniBand support and Enable Infiniband Drivers, an additional MVAPICH2 family is available for use:

dnf -y install mvapich2-gnu15-ohpc

Alternatively, if your system includes Intel Omni-Path, use the (psm2) variant of MVAPICH2 instead:

dnf -y install mvapich2-psm2-gnu15-ohpc

8.4 Performance Tools

OpenHPC provides a variety of open-source tools to aid in application performance analysis (refer to Package Manifest for a listing of available packages). This group of tools can be installed as follows:

# Install perf-tools meta-package
dnf -y install ohpc-gnu15-perf-tools

8.5 Setup default development environment

System users often find it convenient to have a default development environment in place so that compilation can be performed directly for parallel programs requiring MPI. This setup can be conveniently enabled via modules and the OpenHPC modules environment is pre-configured to load an ohpc module on login (if present). The following package install provides a default environment that enables autotools, the GNU compiler toolchain, and the OpenMPI stack.

dnf -y install lmod-defaults-gnu15-openmpi5-ohpc

Tip

If you want to change the default environment from the suggestion above, OpenHPC also provides the GNU compiler toolchain with the MPICH and MVAPICH2 stacks:

lmod-defaults-gnu15-mpich-ofi-ohpc
lmod-defaults-gnu15-mpich-ucx-ohpc
lmod-defaults-gnu15-mvapich2-ohpc

8.6 3rd Party Libraries and Tools

OpenHPC provides pre-packaged builds for a number of popular open-source tools and libraries used by HPC applications and developers. For example, OpenHPC provides builds for FFTW and HDF5 (including serial and parallel I/O support), and the GNU Scientific Library (GSL). Again, multiple builds of each package are available in the OpenHPC repository to support multiple compiler and MPI family combinations where appropriate. Note, however, that not all combinatorial permutations may be available for components where there are known license incompatibilities. The general naming convention for builds provided by OpenHPC is to append the compiler and MPI family name that the library was built against directly into the package name. For example, libraries that do not require MPI as part of the build process adopt the following RPM name:

Packages that do require MPI as part of the build expand upon this convention to additionally include the MPI family name as follows:

To illustrate this further, the command below queries the locally configured repositories to identify all of the available PETSc packages that were built with the GNU toolchain. The resulting output that is included shows that pre-built versions are available for each of the supported MPI families presented in MPI Stacks.

dnf search petsc-gnu15 ohpc
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
=========================== N/S matched: petsc-gnu15, ohpc ===========================
petsc-gnu15-impi-ohpc.x86_64 : Portable Extensible Toolkit for Scientific Computation
petsc-gnu15-mpich-ohpc.x86_64 : Portable Extensible Toolkit for Scientific Computation
petsc-gnu15-mvapich2-ohpc.x86_64 : Portable Extensible Toolkit for Scientific Comp...
petsc-gnu15-openmpi5-ohpc.x86_64 : Portable Extensible Toolkit for Scientific Comp...

Tip

OpenHPC-provided 3rd party builds are configured to be installed into a common top-level repository so that they can be easily exported to desired hosts within the cluster. This common top-level path (/opt/ohpc/pub) was previously configured to be mounted on compute nodes in an earlier section, so the packages will be immediately available for use on the cluster after installation on the head node.

For convenience, OpenHPC provides package aliases for these 3rd party libraries and utilities that can be used to install available libraries for use with the GNU compiler family toolchain. For parallel libraries, aliases are grouped by MPI family toolchain so that administrators can choose a subset should they favor a particular MPI stack. Please refer to the Package Manifest appendix for a more detailed listing of all available packages in each of these functional areas. To install all available package offerings within OpenHPC, issue the following:

# Install 3rd party libraries/tools meta-packages built with GNU toolchain
dnf -y install ohpc-gnu15-serial-libs
dnf -y install ohpc-gnu15-io-libs
dnf -y install ohpc-gnu15-python-libs
dnf -y install ohpc-gnu15-runtimes

# Install parallel lib meta-packages for all available MPI toolchains
dnf -y install ohpc-gnu15-mpich-parallel-libs
dnf -y install ohpc-gnu15-openmpi5-parallel-libs

8.7 Optional Development Tool Builds

In addition to the 3rd party development libraries built using the open source toolchains mentioned in an earlier section, OpenHPC also provides optional compatible builds for use with the compilers and MPI stack included in newer versions of the Intel(R) oneAPI HPC Toolkit (using the classic compiler variants). These packages provide a similar hierarchical user environment experience as other compiler and MPI families present in OpenHPC.

To take advantage of the available builds, OpenHPC provides a convenience package to enable the oneAPI repository locally along with compatibility packages that integrate oneAPI-generated compiler and MPI modulefiles within the standard OpenHPC user environment. To enable the Intel(R) oneAPI repository and install minimum compiler and MPI requirements for OpenHPC packaging, issue the following:

# Enable Intel oneAPI and install OpenHPC compatibility packages
dnf -y install intel-oneapi-toolkit-release-ohpc
rpm --import \
    https://yum.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
dnf -y install intel-compilers-devel-ohpc
dnf -y install intel-mpi-devel-ohpc

Tip

As noted in an earlier section, the default installation path for OpenHPC (/opt/ohpc/pub) is exported over NFS from the head node to the compute nodes, but the Intel(R) oneAPI HPC Toolkit packages install to a top-level path of /opt/intel. To make the Intel(R) compilers available to the compute nodes one must add an additional NFS export for /opt/intel that is mounted on desired compute nodes.

To enable all 3rd party builds available in OpenHPC that are compatible with the Intel(R) oneAPI classic compiler suite, issue the following:

# Optionally, choose the Omni-Path enabled build for MVAPICH2.
# Otherwise, skip to retain IB variant
dnf -y install mvapich2-psm2-intel-ohpc

# Install 3rd party libraries/tools meta-packages built with Intel toolchain
dnf -y install openmpi5-pmix-intel-ohpc
dnf -y install ohpc-intel-serial-libs
dnf -y install ohpc-intel-geopm
dnf -y install ohpc-intel-io-libs
dnf -y install ohpc-intel-perf-tools
dnf -y install ohpc-intel-python3-libs
dnf -y install ohpc-intel-mpich-parallel-libs
dnf -y install ohpc-intel-mvapich2-parallel-libs
dnf -y install ohpc-intel-openmpi5-parallel-libs
dnf -y install ohpc-intel-impi-parallel-libs

9 Post Provisioning

9.1 Check Cluster Status

After this, check status of the nodes within Slurm by using the sinfo command. All compute nodes should be in an idle state (without asterisk). If the state is reported as unknown, the following might help:

scontrol update partition=normal state=idle

In case of additional Slurm issues, ensure that the configuration file fits your hardware and that it is identical across the nodes. Also, verify that the Slurm user id is the same on the head node and compute nodes. You may also consult Slurm Troubleshooting Guide.

9.2 Add User

We will now add a new user to the cluster. This will be used later to run a test job.

Since OpenCHAMI uses NFS-mounted /home, the new user’s home directory will be immediately available on all compute nodes.

9.3 Update NHC

pdsh -w c1 "/usr/sbin/nhc-genconf -H '*' -c -" | dshbak -c

10 Test Cluster

10.1 Run a Test Job

With the resource manager enabled for production usage, users should now be able to run jobs. To demonstrate this, we will add a “test” user on the head node that can be used to run an example job.

OpenHPC includes a simple “hello-world” MPI application in the /opt/ohpc/pub/examples directory that can be used for this quick compilation and execution. OpenHPC also provides a companion job-launch utility named prun that is installed in concert with the pre-packaged MPI toolchains. This convenience script provides a mechanism to abstract job launch across different resource managers and MPI stacks such that a single launch command can be used for parallel job launch in a variety of OpenHPC environments. It also provides a centralizing mechanism for administrators to customize desired environment settings for their users.

10.2 Interactive Execution

To use the newly created “test” account to compile and execute the application interactively through the resource manager, execute the following (note the use of prun for parallel job launch which summarizes the underlying native job launch mechanism being used):

# Switch to "test" user
su - test

# Compile MPI "hello world" example
[test@sms ~]$ mpicc -O3 /opt/ohpc/pub/examples/mpi/hello.c

# Submit interactive job request and use prun to launch executable
[test@sms ~]$ salloc -n 8 -N 2

[test@c1 ~]$ prun ./a.out

[prun] Master compute host = c1
[prun] Resource manager = slurm
[prun] Launch cmd = mpiexec.hydra -bootstrap slurm ./a.out

 Hello, world (8 procs total)
    --> Process #   0 of   8 is alive. -> c1
    --> Process #   4 of   8 is alive. -> c2
    --> Process #   1 of   8 is alive. -> c1
    --> Process #   5 of   8 is alive. -> c2
    --> Process #   2 of   8 is alive. -> c1
    --> Process #   6 of   8 is alive. -> c2
    --> Process #   3 of   8 is alive. -> c1
    --> Process #   7 of   8 is alive. -> c2

Tip

The following table provides approximate command equivalences between SLURM and OpenPBS:

Command	OpenPBS	SLURM
Submit batch job	qsub [job script]	sbatch [job script]
Request interactive shell	qsub -I /bin/bash	salloc
Delete job	qdel [job id]	scancel [job id]
Queue status	qstat -q	sinfo
Job status	qstat -f [job id]	scontrol show job [job id]
Node status	pbsnodes [node name]	scontrol show node [node id]

10.3 Batch execution

For batch execution, OpenHPC provides a simple job script for reference (also housed in the /opt/ohpc/pub/examples directory. This example script can be used as a starting point for submitting batch jobs to the resource manager and the example below illustrates use of the script to submit a batch job for execution using the same executable referenced in the previous interactive example.

# Copy example job script
[test@sms ~]$ cp /opt/ohpc/pub/examples/slurm/job.mpi .

# Examine contents (and edit to set desired job sizing characteristics)
[test@sms ~]$ cat job.mpi
#!/bin/bash

#SBATCH -J test               # Job name
#SBATCH -o job.%j.out         # Name of stdout output file (%j expands to %jobId)
#SBATCH -N 2                  # Total number of nodes requested
#SBATCH -n 16                 # Total number of mpi tasks #requested
#SBATCH -t 01:30:00           # Run time (hh:mm:ss) - 1.5 hours

# Launch MPI-based executable

prun ./a.out

# Submit job for batch execution
[test@sms ~]$ sbatch job.mpi
Submitted batch job 339

Tip

The use of the %j option in the example batch job script shown is a convenient way to track application output on an individual job basis. The %j token is replaced with the Slurm job allocation number once assigned (job #339 in this example).

Appendices

11 Installation Template

This appendix highlights the availability of a companion installation script that is included with OpenHPC documentation. This script, when combined with local site inputs, can be used to implement a starting recipe for bare-metal system installation and configuration. This template script is used during validation efforts to test cluster installations and is provided as a convenience for administrators as a starting point for potential site customization.

Tip

Note that the template script provided is intended for use during initial installation and is not designed for repeated execution. If modifications are required after using the script initially, we recommend running the relevant subset of commands interactively.

The template script relies on the use of a simple text file to define local site variables that were outlined in the Inputs section. By default, the template installation script attempts to use local variable settings sourced from the /opt/ohpc/pub/doc/recipes/vanilla/input.local file, however, this choice can be overridden by the use of the ${OHPC_INPUT_LOCAL} environment variable. The template install script is intended for execution on the head node and is installed as part of the docs-ohpc package into /opt/ohpc/pub/doc/recipes/vanilla/recipe.sh. After enabling the OpenHPC repository and reviewing the guide for additional information on the intent of the commands, the general starting approach for using this template is as follows:

dnf -y install docs-ohpc

cp /opt/ohpc/pub/doc/recipes/almalinux10/input.local input.local

cp -p /opt/ohpc/pub/doc/recipes/almalinux10/x86_64/openchami/slurm/recipe.sh .

export OHPC_INPUT_LOCAL=./input.local
./recipe.sh

12 Upgrading OpenHPC Packages

As newer OpenHPC releases are made available, users are encouraged to upgrade their locally installed packages against the latest repository versions to obtain access to bug fixes and newer component versions. This can be accomplished with the underlying package manager as OpenHPC packaging maintains versioning state across releases. Also, package builds available from the OpenHPC repositories have “-ohpc” appended to their names so that wild cards can be used as a simple way to obtain updates. The following general procedure highlights a method for upgrading existing installations. When upgrading from a minor release older than v4, you will first need to update your local OpenHPC repository configuration to point against the v4 release (or update your locally hosted mirror). Refer to an earlier section for more details on enabling the latest repository. In contrast, when upgrading between micro releases on the same branch (e.g. from v4 to 4.2), there is no need to adjust local package manager configurations when using the public repository as rolling updates are pre-configured.

dnf clean expire-cache

dnf -y upgrade "*-ohpc"

# Any new Base OS provided dependencies can be installed by
# updating the ohpc-base metapackage
dnf -y upgrade "ohpc-base"

Update the image layer YAML configurations as needed, then rebuild the production compute image and reboot compute nodes to apply the changes.

podman run \
    --rm \
    --device /dev/fuse \
    --network host \
    -e S3_ACCESS=admin \
    -e S3_SECRET=password1234 \
    -v /opt/ohpc/admin/images/data:/data \
    -v /opt/ohpc/admin/images/compute-prod.yaml:/home/builder/config.yaml \
    ghcr.io/openchami/image-build:latest \
        image-build \
        --config config.yaml

After the image is rebuilt and published to S3, reboot the compute nodes to apply the changes.

13 Integration Test Suite

This appendix details the installation and basic use of the integration test suite used to support OpenHPC releases. This suite is not intended to replace the validation performed by component development teams, but is instead, devised to confirm component builds are functional and interoperable within the modular OpenHPC environment. The test suite is generally organized by components and the OpenHPC CI workflow relies on running the full suite using Jenkins to test multiple OS configurations and installation recipes. To facilitate customization and running of the test suite locally, we provide these tests in a standalone RPM.

dnf -y install test-suite-ohpc

The RPM installation creates a user named ohpc-test to house the test suite and provide an isolated environment for execution. Configuration of the test suite is done using standard GNU autotools semantics and the BATS shell-testing framework is used to execute and log a number of individual unit tests. Some tests require privileged execution, so a different combination of tests will be enabled depending on which user executes the top-level configure script. Non-privileged tests requiring execution on one or more compute nodes are submitted as jobs through the SLURM resource manager. The tests are further divided into “short” and “long” run categories. The short run configuration is a subset of approximately 180 tests to demonstrate basic functionality of key components (e.g. MPI stacks) and should complete in 10-20 minutes. The long run (around 1000 tests) is comprehensive and can take an hour or more to complete.

Most components can be tested individually, but a default configuration is setup to enable collective testing. To test an isolated component, use the configure option to disable all tests, then re-enable the desired test to run. The --help option to configure will display all possible tests. By default, the test suite will endeavor to run tests for multiple MPI stacks where applicable. To restrict tests to only a subset of MPI families, use the --with-mpi-families option (e.g. --with-mpi-families="openmpi4"). Example output is shown below (some output is omitted for the sake of brevity).

su - ohpc-test
[test@sms ~]$ cd tests
[test@sms ~]$ ./configure --disable-all --enable-fftw
checking for a BSD-compatible install... /bin/install -c
checking whether build environment is sane... yes

------------------------------------ SUMMARY -----------------------------------

Package version............... : test-suite-2.0.0

Build user.................... : ohpc-test
Build host.................... : sms001
Configure date................ : 2020-10-05 08:22
Build architecture............ : x86_64
Compiler Families............. : gnu9
MPI Families.................. : mpich mvapich2 openmpi4
Python Families............... : python3
Resource manager ............. : SLURM
Test suite configuration...... : short

Libraries:
    Adios .................... : disabled
    Boost .................... : disabled
    Boost MPI................. : disabled
    FFTW...................... : enabled
    GSL....................... : disabled
    HDF5...................... : disabled
    HYPRE..................... : disabled

Many OpenHPC components exist in multiple flavors to support multiple compiler and MPI runtime permutations, and the test suite takes this in to account by iterating through these combinations by default. If make check is executed from the top-level test directory, all configured compiler and MPI permutations of a library will be exercised. The following highlights the execution of the FFTW related tests that were enabled in the previous step.

[test@sms ~]$ make check
make --no-print-directory check-TESTS
PASS: libs/fftw/ohpc-tests/test_mpi_families
============================================================================
Testsuite summary for test-suite 2.0.0
============================================================================
# TOTAL: 1
# PASS:  1
# SKIP:  0
# XFAIL: 0
# FAIL:  0
# XPASS: 0
# ERROR: 0
============================================================================
[test@sms ~]$ cat libs/fftw/tests/family-gnu*/rm_execution.log
1..3
ok 1 [libs/FFTW] Serial C binary runs under resource manager (SLURM/gnu9/mpich)
ok 2 [libs/FFTW] MPI C binary runs under resource manager (SLURM/gnu9/mpich)
ok 3 [libs/FFTW] Serial Fortran binary runs under resource manager (SLURM/gnu9/mpich)
PASS rm_execution (exit status: 0)
1..3
ok 1 [libs/FFTW] Serial C binary runs under resource manager (SLURM/gnu9/mvapich2)
ok 2 [libs/FFTW] MPI C binary runs under resource manager (SLURM/gnu9/mvapich2)
ok 3 [libs/FFTW] Serial Fortran binary runs under resource manager (SLURM/gnu9/...
PASS rm_execution (exit status: 0)
1..3
ok 1 [libs/FFTW] Serial C binary runs under resource manager (SLURM/gnu9/openmpi4)
ok 2 [libs/FFTW] MPI C binary runs under resource manager (SLURM/gnu9/openmpi4)
ok 3 [libs/FFTW] Serial Fortran binary runs under resource manager (SLURM/gnu9/...
PASS rm_execution (exit status: 0)

14 Customization

14.1 Adding local Lmod modules to OpenHPC hierarchy

Administrators may wish to add locally built software packages to the OpenHPC module hierarchy. This can be accomplished by creating module files in the appropriate locations under /opt/ohpc/pub/moduledeps or /opt/ohpc/pub/modulefiles. Two sample module files are included in the examples-ohpc package—one representing an application with no compiler or MPI runtime dependencies, and one dependent on OpenMPI and the GNU toolchain. Simply copy these files to the prescribed locations, and the lmod application should pick them up automatically.

# Create a simple example module
mkdir /opt/ohpc/pub/modulefiles/example1
cp /opt/ohpc/pub/examples/example.modulefile \
    /opt/ohpc/pub/modulefiles/example1/1.0

# Create an example module with a dependency
mkdir /opt/ohpc/pub/moduledeps/gnu7-openmpi3/example2
cp /opt/ohpc/pub/examples/example-mpi-dependent.modulefile \
    /opt/ohpc/pub/moduledeps/gnu7-openmpi3/example2/1.0

# Show modules
module avail

14.2 Rebuilding Packages from Source

OpenHPC packages can be rebuilt from source using the source RPMs available from the OpenHPC repository. This allows administrators to customize package builds for their specific needs. One way to accomplish this is to install the appropriate source RPM, modify the spec file as needed, and rebuild to obtain an updated binary RPM. OpenHPC spec files contain macros to facilitate local customizations of compiler, compilation flags and MPI family. A brief example using the FFTW library is highlighted below. Note that the source RPMs can be downloaded from the community repository server at http://repos.openhpc.community via a web browser or directly via dnf as highlighted below. In this example we make an explicit change to FFTW’s configuration, as well as modifying the CFLAGS environment variable. The package is also tagged with an additional delimiter to allow easy co-installation and use.

# Install rpm-build package and dnf tools from base OS distro
sudo dnf -y install rpm-build dnf-plugins-core

# Install FFTW's build dependencies
sudo dnf builddep fftw-gnu15-openmpi5-ohpc

# Download SRPM from OpenHPC repository and install locally
dnf download --source fftw-gnu15-openmpi5-ohpc
rpm -i ./fftw-gnu15-openmpi5-ohpc-*.rpm

# Modify spec file as desired
cd ~/rpmbuild/SPECS
sed -i "s/enable-static=no/enable-static=yes/" fftw.spec

# Increment RPM release so the package manager will see an update
sed -i "s/Release:   400.ohpc.3.1/Release:   400.ohpc.3.2/" fftw.spec

# Rebuild binary RPM. Note that additional directives can be specified to modify build
rpmbuild -bb --define "OHPC_CFLAGS '-O3 -mtune=native'" \
        --define "OHPC_CUSTOM_DELIM static" fftw.spec

# Install the new package
sudo dnf -y install \
        ../RPMS/$(uname -m)/fftw-gnu15-openmpi5-static-ohpc-*.$(uname -m).rpm

15 Package Manifest

This appendix provides a summary of available meta-package groupings and all of the individual RPM packages that are available as part of this OpenHPC release. The meta-packages provide a mechanism to group related collections of RPMs by functionality and provide a convenience mechanism for installation. A list of the available meta-packages and a brief description is presented in the table below.

15.1 Available OpenHPC Meta-packages

Group Name	Description
ohpc-autotools	Collection of GNU autotools packages.
ohpc-base	Collection of base packages.
ohpc-base-compute	Collection of compute node base packages.
ohpc-gnu15-io-libs	Collection of IO library builds for use with GNU compiler toolchain.
ohpc-gnu15-mpich-io-libs	Collection of IO library builds for use with GNU compiler toolchain and the MPICH runtime.
ohpc-gnu15-mpich-parallel-libs	Collection of parallel library builds for use with GNU compiler toolchain and the MPICH runtime.
ohpc-gnu15-mpich-perf-tools	Collection of performance tool builds for use with GNU compiler toolchain and the MPICH runtime.
ohpc-gnu15-mvapich2-io-libs	Collection of IO library builds for use with GNU compiler toolchain and the MVAPICH2 runtime.
ohpc-gnu15-mvapich2-parallel-libs	Collection of parallel library builds for use with GNU compiler toolchain and the MVAPICH2 runtime.
ohpc-gnu15-mvapich2-perf-tools	Collection of performance tool builds for use with GNU compiler toolchain and the MVAPICH2 runtime.
ohpc-gnu15-openmpi5-io-libs	Collection of IO library builds for use with GNU compiler toolchain and the OpenMPI runtime.
ohpc-gnu15-openmpi5-parallel-libs	Collection of parallel library builds for use with GNU compiler toolchain and the OpenMPI runtime.
ohpc-gnu15-openmpi5-perf-tools	Collection of performance tool builds for use with GNU compiler toolchain and the OpenMPI runtime.
ohpc-gnu15-parallel-libs	Collection of parallel library builds for use with GNU compiler toolchain.
ohpc-gnu15-perf-tools	Collection of performance tool builds for use with GNU compiler toolchain.
ohpc-gnu15-python-libs	Collection of python related library builds for use with GNU compiler toolchain.
ohpc-gnu15-python3-libs	Collection of python3 related library builds for use with GNU compiler toolchain.
ohpc-gnu15-runtimes	Collection of runtimes for use with GNU compiler toolchain.
ohpc-gnu15-serial-libs	Collection of serial library builds for use with GNU compiler toolchain.
ohpc-intel-impi-io-libs	Collection of IO library builds for use with Intel(R) oneAPI Toolkit and Intel(R) MPI runtime.
ohpc-intel-impi-parallel-libs	Collection of parallel library builds for use with Intel(R) oneAPI Toolkit and the Intel(R) MPI Library.
ohpc-intel-impi-perf-tools	Collection of performance tool builds for use with Intel(R) oneAPI Toolkit compiler toolchain and the Intel(R) MPI runtime.
ohpc-intel-io-libs	Collection of IO library builds for use with Intel(R) oneAPI Toolkit.
ohpc-intel-mpich-io-libs	Collection of IO library builds for use with Intel(R) oneAPI Toolkit and MPICH runtime.
ohpc-intel-mpich-parallel-libs	Collection of parallel library builds for use with Intel(R) oneAPI Toolkit and the MPICH runtime.
ohpc-intel-mpich-perf-tools	Collection of performance tool builds for use with Intel(R) oneAPI Toolkit compiler toolchain and the MPICH runtime.
ohpc-intel-mvapich2-io-libs	Collection of IO library builds for use with Intel(R) oneAPI Toolkit and MVAPICH2 runtime.
ohpc-intel-mvapich2-parallel-libs	Collection of parallel library builds for use with Intel(R) oneAPI Toolkit and the MVAPICH2 runtime.
ohpc-intel-mvapich2-perf-tools	Collection of performance tool builds for use with Intel(R) oneAPI Toolkit compiler toolchain and the MVAPICH2 runtime.
ohpc-intel-openmpi5-io-libs	Collection of IO library builds for use with Intel(R) oneAPI Toolkit and OpenMPI runtime.
ohpc-intel-openmpi5-parallel-libs	Collection of parallel library builds for use with Intel(R) oneAPI Toolkit and the OpenMPI runtime.
ohpc-intel-openmpi5-perf-tools	Collection of performance tool builds for use with Intel(R) oneAPI Toolkit compiler toolchain and the OpenMPI runtime.
ohpc-intel-perf-tools	Collection of performance tool builds for use with Intel(R) oneAPI Toolkit.
ohpc-intel-python3-libs	Collection of python3 related library builds for use with Intel(R) oneAPI Toolkit.
ohpc-intel-serial-libs	Collection of serial library builds for use with Intel(R) oneAPI Toolkit.
ohpc-slurm-client	Collection of client packages for SLURM.
ohpc-slurm-server	Collection of server packages for SLURM.
ohpc-warewulf	Collection of base packages for Warewulf provisioning.

15.2 RPM Packages

What follows next in this Appendix is a series of tables that summarize the underlying RPM packages available in this OpenHPC release. These packages are organized by groupings based on their general functionality and each table provides information for the specific RPM name, version, brief summary, and the web URL where additional information can be obtained for the component. Note that many of the 3rd party community libraries that are pre-packaged with OpenHPC are built using multiple compiler and MPI families. In these cases, the RPM package name includes delimiters identifying the development environment for which each package build is targeted. Additional information on the OpenHPC package naming scheme is presented in Section 3rd Party Packages. The relevant package groupings and associated references are as follows:

15.2.1 Administrative Tools

RPM Package Name	Version	Info/URL
conman	0.3.1	ConMan: The Console Manager. http://dun.github.io/conman
docs	4.0.0	OpenHPC documentation. https://github.com/openhpc/ohpc
docs	4.1.0	OpenHPC documentation. https://github.com/openhpc/ohpc
examples	2.0	Example source code and templates for use within OpenHPC environment. https://github.com/openhpc/ohpc
genders	1.32	Static cluster configuration database. https://github.com/chaos/genders
hpc-workspace	1.5.0	Temporary workspace management. https://github.com/holgerBerger/hpc-workspace
lmod-defaults	2.0	OpenHPC default login environments. https://github.com/openhpc/ohpc
lmod	9.2	Lua based Modules (lmod). https://github.com/TACC/Lmod
losf	0.56.0	A Linux operating system framework for managing HPC clusters. https://github.com/hpcsi/losf
nhc	1.4.3	LBNL Node Health Check. https://github.com/mej/nhc
ohpc-release	4	OpenHPC release files. https://github.com/openhpc/ohpc
pdsh	2.36	Parallel remote shell program. https://github.com/chaos/pdsh
prun	2.2	Convenience utility for parallel job launch. https://github.com/openhpc/ohpc
test-suite	4.1.0	Integration test suite for OpenHPC. https://github.com/openhpc/ohpc

15.2.2 Resource Management

RPM Package Name	Version	Info/URL
magpie	3.2	Scripts for running Big Data software in HPC environments. https://github.com/LLNL/magpie
openpbs-client	23.06.06	OpenPBS for a client host. http://www.openpbs.org
openpbs-execution	23.06.06	OpenPBS for an execution host. http://www.openpbs.org
openpbs-server	23.06.06	OpenPBS for a server host. http://www.openpbs.org
pmix	4.2.9	An extended/exascale implementation of PMI. https://pmix.org
slurm-contribs	25.05.7	Perl tool to print Slurm job state information. https://slurm.schedmd.com
slurm-devel	25.05.7	Development package for Slurm. https://slurm.schedmd.com
slurm-example-configs	25.05.7	Example config files for Slurm. https://slurm.schedmd.com
slurm-libpmi	25.05.7	Slurm's implementation of the pmi libraries. https://slurm.schedmd.com
slurm	25.05.7	Slurm Workload Manager. https://slurm.schedmd.com
slurm-openlava	25.05.7	openlava/LSF wrappers for transition from OpenLava/LSF to Slurm. https://slurm.schedmd.com
slurm-pam_slurm	25.05.7	PAM module for restricting access to compute nodes via Slurm. https://slurm.schedmd.com
slurm-perlapi	25.05.7	Perl API to Slurm. https://slurm.schedmd.com
slurm-sackd	25.05.7	Slurm authentication daemon. https://slurm.schedmd.com
slurm-slurmctld	25.05.7	Slurm controller daemon. https://slurm.schedmd.com
slurm-slurmd	25.05.7	Slurm compute node daemon. https://slurm.schedmd.com
slurm-slurmdbd	25.05.7	Slurm database daemon. https://slurm.schedmd.com
slurm-sview	25.05.7	Graphical user interface to view and modify Slurm state. https://slurm.schedmd.com
slurm-torque	25.05.7	Torque/PBS wrappers for transition from Torque/PBS to Slurm. https://slurm.schedmd.com

15.2.3 Compiler Families

RPM Package Name	Version	Info/URL
gnu15-compilers	15.2.0	The GNU C Compiler and Support Files. http://gcc.gnu.org
intel-compilers-devel	2025.0	OpenHPC compatibility package for Intel(R) oneAPI HPC Toolkit. https://github.com/openhpc/ohpc
intel-oneapi-toolkit-release	2025.0	Intel(R) oneAPI HPC Toolkit Repository Setup. https://github.com/openhpc/ohpc

15.2.4 MPI Families / Communication Libraries

RPM Package Name	Version	Info/URL
intel-mpi-devel	2025.0	OpenHPC compatibility package for Intel(R) oneAPI MPI Library. https://github.com/openhpc/ohpc
mpich	5.0.1	MPICH MPI implementation. http://www.mpich.org
mvapich2	4.1	OSU MVAPICH2 MPI implementation. http://mvapich.cse.ohio-state.edu
openmpi5	5.0.10	A powerful implementation of MPI/SHMEM. http://www.open-mpi.org
ucx	1.20.0	UCX is a communication library implementing high-performance messaging. http://www.openucx.org

15.2.5 Development Tools

RPM Package Name	Version	Info/URL
EasyBuild	5.3.0	Software build and installation framework. https://easybuilders.github.io/easybuild
autoconf	2.71	A GNU tool for automatically configuring source code. http://www.gnu.org/software/autoconf
automake	1.16.5	A GNU tool for automatically creating Makefiles. http://www.gnu.org/software/automake
cmake	4.3.1	CMake is an open-source, cross-platform family of tools designed to build, test and package software. https://cmake.org
cuda-devel	25.9	OpenHPC compatibility package for cuda. https://github.com/openhpc/ohpc
cuda-repo	25.9	Cuda toolkit online repository. https://github.com/openhpc/ohpc
hwloc	2.13.0	Portable Hardware Locality. http://www.open-mpi.org/projects/hwloc
libtool	2.4.6	The GNU Portable Library Tool. http://www.gnu.org/software/libtool
python3-mpi4py	4.1.1	Python bindings for the Message Passing Interface (MPI) standard. https://github.com/mpi4py/mpi4py
python3-numpy	2.4.4	NumPy array processing for numbers, strings, records and objects. https://github.com/numpy/numpy
spack	1.1.1	HPC software package management. https://github.com/spack/spack
valgrind	3.26.0	Valgrind Memory Debugger. http://www.valgrind.org

15.2.6 Performance Analysis Tools

RPM Package Name	Version	Info/URL
dimemas	5.5.0	Dimemas tool. https://tools.bsc.es
extrae	5.0.4	Extrae tool. https://tools.bsc.es
imb	2021.11	Intel MPI Benchmarks (IMB). https://software.intel.com/en-us/articles/intel-mpi-benchmarks
likwid	5.5.1	Performance tools for the Linux console. https://github.com/RRZE-HPC/likwid
omb	7.5.2	OSU Micro-benchmarks. https://mvapich.cse.ohio-state.edu/benchmarks
papi	7.2.0	Performance Application Programming Interface. http://icl.cs.utk.edu/papi
paraver	4.12.0	Paraver. https://tools.bsc.es
pdtoolkit	3.25.1	PDT is a framework for analyzing source code. http://www.cs.uoregon.edu/Research/pdt
scalasca	2.6.2	Toolset for performance analysis of large-scale parallel applications. http://www.scalasca.org
scorep	9.4	Scalable Performance Measurement Infrastructure for Parallel Codes. http://www.vi-hps.org/projects/score-p
tau	2.35.1	Tuning and Analysis Utilities Profiling Package. http://www.cs.uoregon.edu/research/tau/home.php

15.2.7 IO Libraries

RPM Package Name	Version	Info/URL
adios2	2.12.0	The Adaptable IO System v2 (ADIOS2). https://adios2.readthedocs.io/en/latest/index.html
cubew	4.9.1	CUBE Uniform Behavioral Encoding generic presentation writer component. http://www.scalasca.org/software/cube-4.x/download.html
hdf5	2.1.1	A general purpose library and file format for storing scientific data. http://www.hdfgroup.org/HDF5
netcdf-cxx	4.3.1	C++ Libraries for the Unidata network Common Data Form. http://www.unidata.ucar.edu/software/netcdf
netcdf-fortran	4.6.2	Fortran Libraries for the Unidata network Common Data Form. http://www.unidata.ucar.edu/software/netcdf
netcdf	4.10.0	C Libraries for the Unidata network Common Data Form. http://www.unidata.ucar.edu/software/netcdf
otf2	3.1.1	Open Trace Format 2 library. http://score-p.org
phdf5	2.1.1	A general purpose library and file format for storing scientific data (parallel version). http://www.hdfgroup.org/HDF5
pnetcdf	1.14.1	A Parallel NetCDF library (PnetCDF). http://cucis.ece.northwestern.edu/projects/PnetCDF
sionlib	1.7.7	Scalable I/O Library for Parallel Access to Task-Local Files. https://apps.fz-juelich.de/jsc/sionlib/docu/index.html

15.2.8 Distro Packages

RPM Package Name	Version	Info/URL
python3-Cython	3.2.4	The Cython compiler for writing C extensions for the Python language. http://www.cython.org

15.2.9 Runtimes

RPM Package Name	Version	Info/URL
charliecloud	0.44	Lightweight user-defined software stacks for high-performance computing. https://charliecloud.io

15.2.10 Serial/Threaded Libraries

RPM Package Name	Version	Info/URL
R	4.5.3	R is a language and environment for statistical computing and graphics (S-Plus like). http://www.r-project.org
cubelib	4.9.1	CUBE Uniform Behavioral Encoding generic presentation library component. http://www.scalasca.org/software/cube-4.x/download.html
gotcha	1.0.8	A library for wrapping function calls to shared libraries. https://github.com/llnl/gotcha
gsl	2.8	GNU Scientific Library (GSL). http://www.gnu.org/software/gsl
metis	5.1.0	Serial Graph Partitioning and Fill-reducing Matrix Ordering. http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
opari2	2.0.9	An OpenMP runtime performance measurement instrumenter. https://www.vi-hps.org/projects/score-p
openblas	0.3.32	An optimized BLAS library based on GotoBLAS2. http://www.openblas.net
plasma	25.5.27	Parallel Linear Algebra Software for Multicore Architectures. https://github.com/icl-utk-edu/plasma
scotch	7.0.11	Graph, mesh and hypergraph partitioning library. https://gitlab.inria.fr/scotch/scotch
superlu	7.0.1	A general purpose library for the direct solution of linear equations. http://crd.lbl.gov/~xiaoye/SuperLU

15.2.11 Parallel Libraries

RPM Package Name	Version	Info/URL
boost	1.90.0	Free peer-reviewed portable C++ source libraries. http://www.boost.org
fftw	3.3.10	A Fast Fourier Transform library. http://www.fftw.org
hypre	3.1.0	Scalable algorithms for solving linear systems of equations. http://www.llnl.gov/casc/hypre
mfem	4.9	Lightweight, general, scalable C++ library for finite element methods. http://mfem.org
mumps	5.8.2	A MUltifrontal Massively Parallel Sparse direct Solver. https://mumps-solver.org
petsc	3.25.0	Portable Extensible Toolkit for Scientific Computation. http://www.mcs.anl.gov/petsc
ptscotch	7.0.11	Graph, mesh and hypergraph partitioning library using MPI. https://gitlab.inria.fr/scotch/scotch
scalapack	2.2.3	A subset of LAPACK routines redesigned for heterogeneous computing. https://netlib.org/scalapack
slepc	3.25.0	A library for solving large scale sparse eigenvalue problems. http://slepc.upv.es
superlu_dist	9.2.1	A general purpose library for the direct solution of linear equations. https://portal.nersc.gov/project/sparse/superlu
trilinos	17.0.0	A collection of libraries of numerical algorithms. https://trilinos.org

16 Package Signatures

All of the RPMs provided via the OpenHPC repository are signed with a GPG signature. By default, the underlying package managers will verify these signatures during installation to ensure that packages have not been altered. The RPMs can also be manually verified and the public signing key fingerprint for the latest repository is shown below:

The following command can be used to verify an RPM once it has been downloaded locally by confirming if the package is signed, and if so, indicating which key was used to sign it. The example below highlights usage for a local copy of the docs-ohpc package and illustrates how the key ID matches the fingerprint shown above.

rpm --checksig -v ohpc-release-4-1.el10.x86_64.rpm
ohpc-release-4-1.el10.x86_64.rpm:
    Header V3 RSA/SHA256 Signature, key ID d722a692: OK
    Header SHA256 digest: OK
    Header SHA1 digest: OK
    Payload SHA256 digest: OK
    V3 RSA/SHA256 Signature, key ID d722a692: OK
    MD5 digest: OK

Legal Notice

1 Introduction

1.1 Target Audience

1.2 Requirements/Assumptions

1.3 Inputs

1.4 Installation Template

2 Install Base Operating System

2.1 Install OS

2.2 Configure HTTPS Proxy (Optional)

2.3 Enable EL Package Repositories

2.4 Configure Firewall

2.5 Add Hostname

2.6 Configure NTP

2.7 Generate SSH Key Pair

2.8 Setup NFS Server

2.9 Optionally add InfiniBand support services on head node

2.10 Optionally add Omni-Path support services on head node

3 Install OpenHPC Components

3.1 Enable OpenHPC Repository

3.2 Install OpenHPC Base Packages

4 Install Slurm

4.1 Add Slurm on Head Node

5 Install OpenCHAMI Provisioner

5.1 Install OpenCHAMI

5.2 Certificate Creation

5.3 Setting no proxy

5.4 Setup DHCP

5.5 Complete basic OpenCHAMI setup for head node

5.6 s3cmd Setup

5.7 OpenCHAMI Client Install

5.8 Starting OpenCHAMI

5.9 Compute Image Configuration

5.10 Configure Slurm Client

5.11 Building the Base OS Image

6 Additional Customization

6.1 Enable InfiniBand drivers

6.2 Enable Omni-Path drivers

6.3 Increase locked memory limits

6.4 Enable ssh control via resource manager

6.5 GPU Drivers

6.6 Enable System Log Forwarding

6.7 Intel oneAPI Compiler Runtime

6.8 Cluster Admin Tools

6.8.1 Add ClusterShell

6.8.2 Add genders

6.8.3 Add ConMan

6.8.4 Add NHC

6.9 Add Magpie

6.10 Charliecloud

7 Deploy Cluster

7.1 Rebuild Image

7.2 Setting Boot Parameters

7.3 Building cloud-init Image

7.3.1 Create Default Configuration

7.3.2 Configure Munge

7.4 Verify Configuration Before Boot

7.5 Node Discovery

7.6 Boot Compute Nodes

7.7 Wait for Compute Nodes

7.8 Start Slurm

7.9 Start Slurm on the Compute Nodes

8 Install OpenHPC Development Components

8.1 Development Tools

8.2 Compilers

8.3 MPI Stacks

8.4 Performance Tools

8.5 Setup default development environment

8.6 3rd Party Libraries and Tools

8.7 Optional Development Tool Builds

9 Post Provisioning

9.1 Check Cluster Status

9.2 Add User

9.3 Update NHC

10 Test Cluster

10.1 Run a Test Job

10.2 Interactive Execution

10.3 Batch execution

Appendices

11 Installation Template

12 Upgrading OpenHPC Packages