OpenHPC (v4.1)

Cluster Building Recipes

AlmaLinux 10 Base OS

Confluent/Slurm Edition for Linux* (x86_64)

Document Last Update: 2026-05-21

Document Revision: e75019d4f697b55036cd8ee416e6793658621ae6

Legal Notice

Copyright © 2016-2026, OpenHPC, a Linux Foundation Collaborative Project. All rights reserved.

This documentation is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0.

Intel, the Intel logo, and other Intel marks are trademarks of Intel Corporation in the U.S. and/or other countries.

*Other names and brands may be claimed as the property of others.

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 confluent 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.

Required variables:

• ${sms_name} - Hostname for head node

• ${sms_ip} - Internal IP address on head node

• ${sms_eth_internal} - Internal Ethernet interface on head node

• ${internal_network} - Subnet network address for internal network

• ${internal_netmask} - Subnet netmask for internal network

• ${internal_prefix_length} - Subnet prefix length for internal network (e.g. 16; must be consistent with ${internal_netmask})

• ${ntp_server} - Local ntp server for time synchronization

• ${bmc_username} - BMC username for use by IPMI

• ${bmc_password} - BMC password for use by IPMI

• ${num_computes} - Total # of desired compute nodes

• ${c_ip[0]}, ${c_ip[1]}, … - Desired compute node addresses

• ${c_bmc[0]}, ${c_bmc[1]}, … - BMC addresses for computes

• ${c_mac[0]}, ${c_mac[1]}, … - MAC addresses for computes

• ${c_name[0]}, ${c_name[1]}, … - Host names for computes

• ${compute_regex} - Regex matching all compute node names (e.g. c*)

• ${compute_prefix} - Prefix for compute node names (e.g. c)

• initialize_options - usklpta

• deployment_protocols - firmware

• ${dns_domain} - DNS domain name for cluster (e.g. local)

• iso_path - location of compute node base os dvd iso (default: AlmaLinux-10.1-x86_64-dvd.iso)

• iso_url - ISO download base URL (optional; overrides default upstream location)

Optional variables:

• ${sysmgmtd_host} - BeeGFS System Management host name
• ${mgs_fs_name} - Lustre MGS mount name
• ${sms_ipoib} - IPoIB address for head node
• ${ipoib_netmask} - Subnet netmask for internal IPoIB
• ${c_ipoib[0]}, ${c_ipoib[1]}, … - IPoIB addresses for computes

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 confluent, 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:

• AlmaLinux-10 (e.g. https://repo.almalinux.org/almalinux/10/)
• EPEL 10 (e.g. http://download.fedoraproject.org/pub/epel/10/)

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

Add the head node name to /etc/hosts so we can make API calls by 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

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.

It is also required by the Confluent provisioner for node deployment.

If an ed25519 key does not already exist, generate one:

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

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

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

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

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.

5 Install Confluent Provisioner

Installation is accomplished in two steps: First, a generic OS image is installed on compute nodes and then, once the nodes are up and running, OpenHPC components are added to both the head node and the nodes at the same time.

5.1 Add provisioning services on head node

To begin, enable use of the public Confluent repository by adding it to the local list of available package repositories. This also requires network access from your head node to the internet, or alternatively, that the repository be mirrored locally. In this case, we use the network.

dnf -y install \
https://hpc.lenovo.com/yum/latest/el10/x86_64/lenovo-hpc-yum-1-1.x86_64.rpm

With the Confluent repository enabled, issue the following to install the provisioning service on the head node:

# Install Confluent and required packages
dnf -y install lenovo-confluent
dnf -y install tftp-server nfs-utils policycoreutils-python-utils yq jq
dnf -y install confluent_ipxe-aarch64 confluent_osdeploy-aarch64

# Enable Confluent and its tools for use in current shell
systemctl enable --now confluent
systemctl enable --now httpd
setsebool -P httpd_can_network_connect on
semanage fcontext -a -t httpd_sys_content_t '/var/lib/confluent(/.*)?'
systemctl enable --now tftp.socket

# Source the confluent profile to setup env
source /etc/profile.d/confluent_env.sh

5.2 Complete Basic Confluent Setup for the Head Node

At this point, all of the packages necessary to use Confluent on the head node should be installed. Confluent requires a network domain name specification for system-wide name resolution. This value can be set to match your local DNS schema or given a unique identifier such as local. A default group called everything is automatically added to every node. It provides a method to indicate global settings. Attributes may all be specified on the command line, and an example set could be:

nodegroupattrib everything \
    deployment.useinsecureprotocols=${deployment_protocols:-firmware} \
    dns.domain=${dns_domain:-local}
nodegroupattrib everything \
    dns.servers=${dns_servers} net.ipv4_gateway=${ipv4_gateway}

5.3 Download ISO Image for Compute Node Deployment

The osdeploy import command (below) requires a local copy of the AlmaLinux 10 ISO image (AlmaLinux-10.1-x86_64-dvd.iso), available from the AlmaLinux 10 download page. If the ISO is not already present locally, download it:

iso_file="AlmaLinux-10.1-x86_64-dvd.iso"
iso_url="${iso_url:=https://repo.almalinux.org/almalinux/10/isos/x86_64}"
[[ -f "${iso_file}" ]] || curl -fO "${iso_url}/${iso_file}"

5.4 Build Initial Compute Base OS image

With the provisioning services enabled, the next step is to define a system image that can subsequently be used to provision one or more compute nodes. To begin, you will first need to have a local copy of the ISO image available for the underlying OS. In this recipe, the relevant ISO image is AlmaLinux-10.1-x86_64-dvd.iso (available from the AlmaLinux 10 download page). We initialize the image creation process using the osdeploy command assuming that the necessary ISO image is available locally in ${iso_path} as follows:

The osdeploy initialize command is used to prepare a Confluent server to deploy operating systems. For first time setup, run osdeploy initialize interactively to be walked through the various options using: osdeploy initialize -i

osdeploy initialize -${initialize_options:-usklpta}
osdeploy import ${iso_path:-AlmaLinux-10.1-x86_64-dvd.iso}
restorecon -Rv /var/lib/confluent/

Once completed, the OS image should be available for use within Confluent. These can be queried via:

# Query available images
osdeploy list

We now update the kernel arguments to remove the quiet option and add serial console. You could also add debug here as well to increase debug messages.

# Update kernel arguments
yq -i '.kernelargs = "console=ttyS0,115200 console=tty0 rd.shell"' \
  /var/lib/confluent/public/os/alma-10.1-x86_64-default/profile.yaml
osdeploy updateboot alma-10.1-x86_64-default

If needing to copy files from the head node to the compute nodes during deployment, this can be done by modifying the syncfiles file that is created when osdeploy import command is run. For an environment that has no DNS server and needs to have /etc/hosts file synced amongst all the nodes, the following command should be run.

echo "/etc/hosts -> /etc/hosts" >> \
    /var/lib/confluent/public/os/alma-10.1-x86_64-default/syncfiles

5.5 Add Compute Nodes

Next, we add compute nodes to the and define their properties as attributes in the Confluent database. These hosts are grouped logically into a group named compute to facilitate group-level commands used later in the recipe. The compute group has to be defined first before we can add any nodes to the group using the nodegroup define command. Note the use of variable names for the desired compute hostnames, node IPs, MAC addresses, and BMC login credentials, which should be modified to accommodate local settings and hardware. To enable serial console access via Confluent, console.method property is also defined.

# Define the compute group
nodegroupdefine compute

# Define nodes as objects in Confluent database
for ((i=0; i<$num_computes; i++)) ; do
    nodedefine ${c_name[$i]} groups=everything,compute \
    hardwaremanagement.manager=${c_bmc[$i]} \
    secret.hardwaremanagementuser=${bmc_username} \
    secret.hardwaremanagementpassword=${bmc_password} \
    net.hwaddr=${c_mac[$i]} net.bootable=true net.ipv4_method=static \
    net.ipv4_address=${c_ip[$i]}/${internal_prefix_length}
done

If enabling optional IPoIB functionality (e.g. to support Lustre over InfiniBand), additional settings are required to define the IPoIB network with Confluent and specify desired IP settings for each compute. This can be accomplished as follows for the ib0 interface:

# Register desired IPoIB IPs per compute
for ((i=0; i<$num_computes; i++)) ; do
    nodeattrib ${c_name[i]} net.ib0.ipv4_address=${c_ipoib[i]}/${ipoib_netmask}
done

confluent2hosts can be used to help generate /etc/hosts entries for a noderange. It can read from the Confluent database, using -a. In this mode, each net.value.attribute group is pulled together into hosts lines. ipv4 and ipv6 address fields are associated with the corresponding hostname attributes.

# Add nodes to /etc/hosts
confluent2hosts -a compute

With the desired compute nodes and domain identified, the remaining steps in the provisioning configuration process are to define the provisioning mode and image for the compute group and use Confluent commands to complete configuration for network services like DNS and DHCP. These tasks are accomplished as follows:

# Associate desired provisioning image for computes
nodedeploy -n compute -p alma-10.1-x86_64-default

5.6 Boot Compute Nodes

Prior to booting the compute hosts, we configure them to use PXE as their next boot mode. After the initial PXE, ensuing boots will return to using the default boot device specified in the BIOS.

nodesetboot compute network

At this point, the head node should be able to boot the newly defined compute nodes. This is done by using the nodepower Confluent command leveraging IPMI protocol set up during the compute node definition in the previous section. The following power cycles each of the desired hosts.

nodepower compute boot

Once kicked off, the boot process should take about 5-10 minutes (depending on BIOS post times). You can monitor the provisioning by using the nodeconsole command, which displays serial console for a selected node. Note that the escape sequence is CTRL-e c . typed sequentially.

Successful provisioning can be verified by a parallel command on the compute nodes. The Confluent-provided nodeshell command uses Confluent node names and groups. For example, to run a command on the newly imaged compute hosts using nodeshell, execute the following:

nodeshell compute uptime
c1:  12:56:50 up 14 min,  0 users,  load average: 0.00, 0.01, 0.04
c2:  12:56:50 up 13 min,  0 users,  load average: 0.00, 0.02, 0.05
c3:  12:56:50 up 14 min,  0 users,  load average: 0.00, 0.02, 0.05
c4:  12:56:50 up 14 min,  0 users,  load average: 0.00, 0.01, 0.04

5.7 Setup Compute Nodes

We now need to configure the compute nodes. We leverage the Confluent-provided nodeshell command that runs the command on the compute nodes.

We first disable the firewall on the compute nodes.

# Disable firewall for computes
nodeshell compute systemctl disable --now firewalld

We next add the kernel drivers.

# Add kernel drivers
nodeshell compute dnf -y install kernel

The compute nodes need access to the EPEL repository, a required dependency for OpenHPC packages.

# Add EPEL repo
nodeshell compute dnf -y install epel-release
# Enable CRB
nodeshell compute "/usr/bin/crb enable"

And add additional packages.

# Add Network Time Protocol (NTP) support
nodeshell compute dnf -y install chrony

# Include nfs-utils
nodeshell compute dnf -y install nfs-utils

5.7.1 InfiniBand Support (Optional)

Optionally add the InfiniBand support.

# Optionally add IB support and enable
nodeshell compute dnf -y groupinstall "InfiniBand Support"

5.8 Deploy OpenHPC Components on Compute Notes

The next step is adding OpenHPC components to the compute nodes that at this point are running basic OSes. This process will leverage two Confluent-provided commands: nodeshell to run the package installer on all the nodes in parallel and nodersync to distribute configuration files from the head node to the compute nodes.

We first add the OpenHPC repository to the compute nodes:

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

Additionally, a workaround is needed for OpenHPC documentation files, which are installed into a read-only NFS share /opt/ohpc/pub. Any package attempting to write to that directory will fail to install. The following prevents that by directing rpm not to install documentation files on the compute nodes:

nodeshell compute 'echo "%_excludedocs 1" >> \
  "$HOME/.rpmmacros"'

Now OpenHPC and other cluster-related software components can be installed on the nodes. The first step is to install a base compute package on the compute nodes:

# Install compute node base meta-package
nodeshell compute dnf -y install ohpc-base-compute

Next, we can include additional components:

# Include modules user environment
nodeshell compute dnf -y install lmod-ohpc

5.9 Install Slurm

In the previous section, the Slurm resource manager was installed and configured on the head node.

We now install the Slurm clients and configure them. The Slurm and munge configuration files need to be copied to the nodes. This can be accomplished as follows:

# Add Slurm client support meta-package
nodeshell compute dnf -y install ohpc-slurm-client

Copy the slurm.conf and munge keys to the compute nodes.

nodersync /etc/slurm/slurm.conf compute:/etc/slurm/slurm.conf
nodersync /etc/munge/munge.key compute:/etc/munge/munge.key

5.10 Configure NFS Mounts on Compute Nodes

Configure NFS mounts to access the head node’s shared filesystems on compute nodes.

# Add NFS mounts for /home and /opt/ohpc/pub
MOUNT_OPTIONS="nfsvers=3,nodev,nosuid 0 0"
NFS_PUB="${sms_ip}:/opt/ohpc/pub /opt/ohpc/pub nfs ${MOUNT_OPTIONS}"
nodeshell compute "echo ${sms_ip}:/home /home nfs ${MOUNT_OPTIONS} >> /etc/fstab"
nodeshell compute "echo ${NFS_PUB} >> /etc/fstab"
# Create mount point and mount filesystems
nodeshell compute "mkdir -p /opt/ohpc/pub"
nodeshell compute "mount -a"

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
nodeshell compute dnf -y 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
nodeshell compute dnf -y install opa-basic-tools
nodeshell compute dnf -y 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
nodeshell compute 'echo "* soft memlock unlimited" >> \
  "/etc/security/limits.d/40-ohpc-limits.conf"'
nodeshell compute 'echo "* hard memlock unlimited" >> \
  "/etc/security/limits.d/40-ohpc-limits.conf"'

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:

nodeshell compute 'echo "account    required     pam_slurm.so" >> \
  "/etc/pam.d/sshd"'

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
nodeshell compute dnf -y install cuda-repo-ohpc

# Install the GPU driver on the compute nodes
nodeshell compute dnf -y install nvidia-driver:latest-dkms

# Enable DKMS service to automatically rebuild driver
nodeshell compute "systemctl enable dkms"

# Install the toolkit on the head node
nodeshell compute dnf -y install cuda-devel-ohpc nvidia-driver-cuda

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
nodeshell compute "echo '*.* @${sms_ip}:514' > /etc/rsyslog.d/ohpc-forward.conf"

# Disable most local logging on computes.
# Emergency and boot logs will remain on the compute nodes
nodeshell compute sed -i 's/^\*\.info/#\*\.info/' \
  "/etc/rsyslog.conf"
nodeshell compute sed -i 's/^authpriv/#authpriv/' \
  "/etc/rsyslog.conf"
nodeshell compute sed -i 's/^mail/#mail/' \
  "/etc/rsyslog.conf"
nodeshell compute sed -i 's/^cron/#cron/' \
  "/etc/rsyslog.conf"
nodeshell compute sed -i 's/^uucp/#uucp/' \
  "/etc/rsyslog.conf"

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
nodeshell compute 'echo "${sms_ip}:/opt/intel /opt/intel nfs nfsvers=4,nodev 0 0" >> \
  "/etc/fstab"'

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
nodeshell compute dnf -y install nhc-ohpc

# 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

7.1 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

Running systems may need to restart slurmctld to pickup any changes.

7.2 Start Slurm on Compute Nodes

With Slurm configured, we can now startup the resource manager services in preparation for running user jobs. Generally, this is a two-step process that requires starting up the controller daemons on the head node and the client daemons on each of the compute nodes. 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.

We now start the Slurm daemon on the compute nodes.

# Start munge and slurm controller on head node
nodeshell compute "systemctl enable --now munge"
nodeshell compute "systemctl enable --now slurmd"

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 Slurm user id is the same on the head node and compute nodes. You may also consult Slurm Troubleshooting Guide.

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.

Table: Available MPI variants

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

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:

package-<compiler_family>-ohpc-<package_version>-<release>.rpm

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

package-<compiler_family>-<mpi_family>-ohpc-<package_version>-<release>.rpm

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...

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

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.

useradd -m test

Next, the user’s credentials need to be distributed across the cluster. Confluent’s nodeapply has a merge functionality that adds new entries into credential files on compute nodes:

# Create a sync file for pushing user credentials to the nodes
echo "/etc/passwd -> /etc/passwd" >> \
    /var/lib/confluent/public/os/alma-10.1-x86_64-default/syncfiles
echo "/etc/group -> /etc/group" >> \
    /var/lib/confluent/public/os/alma-10.1-x86_64-default/syncfiles

# Use Confluent to distribute credentials to nodes
nodeapply -F compute

9.3 Update NHC

Generate NHC configuration file based on compute node environment

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

10 Test Cluster

We now run some simple tests on the cluster to ensure it is operational.

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

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

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.

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:

1. Install the docs-ohpc package

dnf -y install docs-ohpc

2. Copy the provided template input file to use as a starting point to define local site settings:

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

3. Update input.local with desired settings

4. Copy the template installation script which contains command-line instructions culled from this guide.

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

5. Review and edit recipe.sh to suite.

6. Use environment variable to define local input file and execute recipe.sh to perform a local installation.

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.

1. (Optional) Ensure repo metadata is current (on head node and compute nodes). Package managers will naturally do this on their own over time, but if you are wanting to access updates immediately after a new release, the following can be used to sync to the latest.

dnf clean expire-cache
nodeshell compute dnf clean expire-cache

2. Upgrade head node

dnf -y upgrade "*-ohpc"

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

3. Upgrade packages on compute nodes

nodeshell compute dnf -y upgrade "*-ohpc"

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

Note that to update running services such as a resource manager, a service restart is required on the compute nodes.

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

Example Output

----------------------- /opt/ohpc/pub/moduledeps/gnu7-openmpi3 ------------------------
   adios/1.12.0    imb/2018.0          netcdf-fortran/4.4.4    ptscotch/6.0.4
   boost/1.65.1    mpi4py/2.0.0        netcdf/4.4.1.1          scalapack/2.0.2
   example2/1.0    mpiP/3.4.1          petsc/3.7.6             scalasca/2.3.1
   fftw/3.3.6      mumps/5.1.1         phdf5/1.10.1            scipy/0.19.1
   hypre/2.11.2    netcdf-cxx/4.3.0    pnetcdf/1.8.1           scorep/3.1

--------------------------- /opt/ohpc/pub/moduledeps/gnu7 -----------------------------
   R/3.4.2        metis/5.1.0     ocr/1.0.1              pdtoolkit/3.24
   gsl/2.4        mpich/3.2       openblas/0.2.20        plasma/2.8.0
   hdf5/1.10.1    numpy/1.13.1    openmpi3/3.0.0  (L)    scotch/6.0.4

---------------------------- /opt/ohpc/admin/modulefiles ------------------------------
   spack/0.10.0

----------------------------- /opt/ohpc/pub/modulefiles -------------------------------
   EasyBuild/3.4.1         cmake/3.9.2         hwloc/1.11.8        pmix/1.2.3
   autotools        (L)    example1/1.0 (L)    llvm5/5.0.0         prun/1.2        (L)
   clustershell/1.8        gnu7/7.2.0   (L)    ohpc         (L)    singularity/2.4

  Where:
   L:  Module is loaded

Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of
the "keys".

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

The new module file now appears along side the default.

$ module -t spider fftw
fftw/3.3.10-static
fftw/3.3.10

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

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:

• Administrative Tools

• Resource Management

• Compiler Families

• MPI Families / Communication Libraries

• Development Tools

• Performance Analysis Tools

• IO Libraries

• Distro Packages

• Runtimes

• Serial/Threaded Libraries

• Parallel Libraries

15.2.1 Administrative Tools

15.2.2 Resource Management

15.2.3 Compiler Families

15.2.4 MPI Families / Communication Libraries

15.2.5 Development Tools

15.2.6 Performance Analysis Tools

15.2.7 IO Libraries

15.2.8 Distro Packages

15.2.9 Runtimes

15.2.10 Serial/Threaded Libraries

15.2.11 Parallel Libraries

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:

Fingerprint: 5E33 3CA3 A1BD BBC9 DF14 9D74 09AD FAE4 **D722A692**

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