OpenHPC Install Guide (v2.0)

Authors OpenHPC

Plaintext

OpenHPC (v2.0)
Cluster Building Recipes

OpenSUSE Leap 15.2 Base OS
Warewulf/OpenPBS Edition for Linux* (x86 64)

Document Last Update: 2020-10-06
Document Revision: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Legal Notice

This documentation is licensed under the Creative Commons At-
tribution 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.

2 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Contents
1 Introduction 5
1.1 Target Audience . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.2 Requirements/Assumptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
1.3 Inputs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

2 Install Base Operating System (BOS) 7

3 Install OpenHPC Components 8
3.1 Enable OpenHPC repository for local use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
3.2 Installation template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
3.3 Add provisioning services on master node . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
3.4 Add resource management services on master node . . . . . . . . . . . . . . . . . . . . . . . . 9
3.5 Optionally add InfiniBand support services on master node . . . . . . . . . . . . . . . . . . . 10
3.6 Optionally add Omni-Path support services on master node . . . . . . . . . . . . . . . . . . . 10
3.7 Complete basic Warewulf setup for master node . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.8 Define compute image for provisioning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.8.1 Build initial BOS image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
3.8.2 Add OpenHPC components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
3.8.3 Customize system configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.8.4 Additional Customization (optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.8.4.1 Enable InfiniBand drivers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3.8.4.2 Enable Omni-Path drivers . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.8.4.3 Increase locked memory limits . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.8.4.4 Add BeeGFS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
3.8.4.5 Add Lustre client . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.8.4.6 Enable forwarding of system logs . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.8.4.7 Add Nagios monitoring . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.8.4.8 Add ClusterShell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.8.4.9 Add genders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.8.4.10 Add ConMan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
3.8.4.11 Add NHC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
3.8.5 Import files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
3.9 Finalizing provisioning configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
3.9.1 Assemble bootstrap image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
3.9.2 Assemble Virtual Node File System (VNFS) image . . . . . . . . . . . . . . . . . . . . 20
3.9.3 Register nodes for provisioning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
3.9.4 Optional kernel arguments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
3.9.5 Optionally configure stateful provisioning . . . . . . . . . . . . . . . . . . . . . . . . . 22
3.10 Boot compute nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

4 Install OpenHPC Development Components 23
4.1 Development Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
4.2 Compilers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
4.3 MPI Stacks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
4.4 Performance Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
4.5 Setup default development environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
4.6 3rd Party Libraries and Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
4.7 Optional Development Tool Builds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

3 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

5 Resource Manager Startup 28

6 Run a Test Job 28
6.1 Interactive execution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
6.2 Batch execution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Appendices 32
A Installation Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
B Upgrading OpenHPC Packages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
B.1 New component variants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
C Integration Test Suite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
D Customization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
D.1 Adding local Lmod modules to OpenHPC hierarchy . . . . . . . . . . . . . . . . . . . 37
D.2 Rebuilding Packages from Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
E Package Manifest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
F Package Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

4 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

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, develop-
ment 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 con-
figuration 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:

[sms]# 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:

Tip

Life is a tale told by an idiot, full of sound and fury signifying nothing. –Willy Shakes

1.2 Requirements/Assumptions
This installation recipe assumes the availability of a single head node master, and four compute nodes. The
master node serves as the overall system management server (SMS) and is provisioned with OpenSUSE Leap
15.2 and is subsequently configured to provision the remaining compute nodes with Warewulf in a stateless
configuration. The terms master and SMS are used interchangeably in this guide. For power management,
we assume that the compute node baseboard management controllers (BMCs) are available via IPMI from
the chosen master host. For file systems, we assume that the chosen master server 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 Figure 1 and highlights the high-level
networking configuration. The master host 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

5 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Parallel File System

high speed network

Master compute
(SMS) nodes

Data
Center eth0 eth1 to compute eth interface
Network
to compute BMC interface
tcp networking

Figure 1: Overview of physical cluster architecture.

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.
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 ad-
dresses 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.

6 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

• ${sms name} # Hostname for SMS server
• ${sms ip} # Internal IP address on SMS server
• ${sms eth internal} # Internal Ethernet interface on SMS
• ${eth provision} # Provisioning interface for computes
• ${internal netmask} # Subnet netmask for internal network
• ${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”)
Optional:
• ${sysmgmtd host} # BeeGFS System Management host name
• ${mgs fs name} # Lustre MGS mount name
• ${sms ipoib} # IPoIB address for SMS server
• ${ipoib netmask} # Subnet netmask for internal IPoIB
• ${c ipoib[0]}, ${c ipoib[1]}, ... # IPoIB addresses for computes
• ${kargs} # Kernel boot arguments
• ${nagios web password} # Nagios web access password

2 Install Base Operating System (BOS)
In an external setting, installing the desired BOS on a master SMS host typically involves booting from a
DVD ISO image on a new server. With this approach, insert the OpenSUSE Leap 15.2 DVD, power cycle the
host, and follow the distro provided directions to install the BOS on your chosen master host. Alternatively,
if choosing to use a pre-installed server, please verify that it is provisioned with the required OpenSUSE
Leap 15.2 distribution.

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

[sms]# echo ${sms_ip} ${sms_name} >> /etc/hosts

While it is theoretically possible to enable SELinux on a cluster provisioned with Warewulf, 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 master SMS host. 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.

Finally, provisioning services rely on DHCP, TFTP, and HTTP network protocols. Depending on the
local BOS configuration on the SMS host, default firewall rules may prohibit these services. Consequently,

7 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

this recipe assumes that the local firewall running on the SMS host is disabled. If installed, the default
firewall service can be disabled as follows:

[sms]# systemctl disable SuSEfirewall2
[sms]# systemctl stop SuSEfirewall2

3 Install OpenHPC Components
With the BOS installed and booted, the next step is to add desired OpenHPC packages onto the master
server in order to provide provisioning and resource management services for the rest of the cluster. The
following subsections highlight this process.

3.1 Enable OpenHPC repository for local use
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 master server 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.

[sms]# rpm -ivh http://repos.openhpc.community/OpenHPC/2/Leap_15/x86_64/ohpc-release-2-1.leap15.x86_64.rpm

Tip

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/2.0

In addition to the OpenHPC package repository, the master host also requires access to the standard distro
repositories in order to resolve necessary dependencies.

3.2 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 com-
mands 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 (§ 1.3) and is provided as a convenience
for administrators. For additional information on accessing this script, please see Appendix A.

8 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

3.3 Add provisioning services on master node
With the OpenHPC repository enabled, we can now begin adding desired components onto the master server.
This repository provides a number of aliases that group logical components together in order to help aid
in this process. For reference, a complete list of available group aliases and RPM packages available via
OpenHPC are provided in Appendix E. To add support for provisioning services, the following commands
illustrate addition of a common base package followed by the Warewulf provisioning system.

# Install base meta-packages
[sms]# zypper -n install ohpc-base
[sms]# zypper -n install ohpc-warewulf

Tip

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.

[sms]# ipmitool -E -I lanplus -H ${bmc_ipaddr} -U root chassis bootdev pxe options=persistent

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 SMS host with a specific server ${ntp server},
and allow this server to serve as a local time server for the cluster, issue the following:

[sms]# systemctl enable chronyd.service
[sms]# echo "server ${ntp_server}" >> /etc/chrony.conf
[sms]# echo "allow all" >> /etc/chrony.conf
[sms]# systemctl restart chronyd

Tip

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 SMS host. 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

3.4 Add resource management services on master node
OpenHPC provides multiple options for distributed resource management. The following command adds the
OpenPBS workload manager server components to the chosen master host. Note that client-side components
will be added to the corresponding compute image in a subsequent step.

[sms]# zypper -n install openpbs-server-ohpc

Other versions of this guide are available that describe installation of other resource management systems,
and they can be found in the docs-ohpc package.

9 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

3.5 Optionally add InfiniBand support services on master node
The following command adds OFED and PSM support using base distro-provided drivers to the chosen
master host.

[sms]# zypper -n install libibmad5 librdmacm1 rdma infinipath-psm dapl-devel dapl-utils libibverbs-utils

# Provide udev rules to enable /dev/ipath access for InfiniPath devices
[sms]# cp /opt/ohpc/pub/examples/udev/60-ipath.rules /etc/udev/rules.d/

# Load IB drivers
[sms]# systemctl start rdma

Tip

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 OpenSUSE Leap 15.2 provides the opensm package
should you choose to run it on the master node.

[sms]# cp /opt/ohpc/pub/examples/network/sles/ifcfg-ib0 /etc/sysconfig/network

# Define local IPoIB address and netmask
[sms]# perl -pi -e "s/master_ipoib/${sms_ipoib}/" /etc/sysconfig/network/ifcfg-ib0
[sms]# perl -pi -e "s/ipoib_netmask/${ipoib_netmask}/" /etc/sysconfig/network/ifcfg-ib0

# Initiate ib0
[sms]# ifup ib0

3.6 Optionally add Omni-Path support services on master node
The following command adds Omni-Path support using base distro-provided drivers to the chosen master
host.

[sms]# zypper -n install opa-basic-tools libibmad5

# Load RDMA services
[sms]# systemctl start rdma

Tip

Omni-Path 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 OpenSUSE Leap 15.2 provides the opa-fm package
should you choose to run it on the master node.

10 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

3.7 Complete basic Warewulf setup for master node
At this point, all of the packages necessary to use Warewulf on the master host should be installed. Next,
we need to update several configuration files in order to allow Warewulf to work with OpenSUSE Leap 15.2
and to support local provisioning using a second private interface (refer to Figure 1).

Tip

By default, Warewulf is configured to provision over the eth1 interface and the steps below include updating
this setting to override with a potentially alternatively-named interface specified by ${sms eth internal}.

# Configure Warewulf provisioning to use desired internal interface
[sms]# perl -pi -e "s/device = eth1/device = ${sms_eth_internal}/" /etc/warewulf/provision.conf

# Configure DHCP server to use desired internal interface
[sms]# perl -pi -e "s/^DHCPD_INTERFACE=\S+/DHCPD_INTERFACE=${sms_eth_internal}/" /etc/sysconfig/dhcpd

# Enable tftp service for compute node image distribution
[sms]# perl -pi -e "s/^\s+disable\s+= yes/ disable = no/" /etc/xinetd.d/tftp

# Configure Warewulf to use the default SLES tftp location
[sms]# perl -pi -e "s#\#tftpdir = /var/lib/#tftpdir = /srv/#" /etc/warewulf/provision.conf

# Update Warewulf http configuration to use the SLES version of Apache modules
[sms]# export MODFILE=/etc/apache2/conf.d/warewulf-httpd.conf
[sms]# perl -pi -e "s#modules/mod_perl.so\$#/usr/lib64/apache2/mod_perl.so#" $MODFILE
[sms]# perl -pi -e "s#modules/mod_version.so\$#/usr/lib64/apache2/mod_version.so#" $MODFILE

# Enable internal interface for provisioning
[sms]# ip link set dev ${sms_eth_internal} up
[sms]# ip address add ${sms_ip}/${internal_netmask} broadcast + dev ${sms_eth_internal}

# Restart/enable relevant services to support provisioning
[sms]# systemctl enable mysql.service
[sms]# systemctl restart mysql
[sms]# systemctl enable apache2.service
[sms]# systemctl restart apache2
[sms]# systemctl enable dhcpd.service
[sms]# systemctl enable tftp.socket
[sms]# systemctl start tftp.socket

3.8 Define compute image for provisioning
With the provisioning services enabled, the next step is to define and customize a system image that can
subsequently be used to provision one or more compute nodes. The following subsections highlight this
process.

3.8.1 Build initial BOS image
The OpenHPC build of Warewulf includes specific enhancements enabling support for OpenSUSE Leap 15.2.
The following steps illustrate the process to build a minimal, default image for use with Warewulf. We begin
by creating a directory structure on the master host that will represent the root filesystem of the compute
node. The default location for this example is in /opt/ohpc/admin/images/leap15.2.

11 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

# Define chroot location
[sms]# export CHROOT=/opt/ohpc/admin/images/leap15.2
# Build initial chroot image
[sms]# mkdir -p -m 755 $CHROOT # create chroot housing dir
[sms]# mkdir -m 755 $CHROOT/dev # create chroot /dev dir
[sms]# mknod -m 666 $CHROOT/dev/zero c 1 5 # create /dev/zero device
[sms]# wwmkchroot -v opensuse-15.2 $CHROOT # create base image
# Enable OpenHPC repo in chroot
[sms]# cp -p /etc/zypp/repos.d/OpenHPC*.repo $CHROOT/etc/zypp/repos.d
# Import GPG keys for chroot repository usage
[sms]# zypper -n --root $CHROOT --no-gpg-checks --gpg-auto-import-keys refresh

3.8.2 Add OpenHPC components
The wwmkchroot process used in the previous step is designed to provide a minimal OpenSUSE Leap 15.2
configuration. Next, we add additional components to include resource management client services, NTP
support, and other additional packages to support the default OpenHPC environment. This process augments
the chroot-based install performed by wwmkchroot to modify the base provisioning image and will access the
BOS and OpenHPC repositories to resolve package install requests. We begin by installing a few common
base packages:

# Install compute node base meta-package
[sms]# zypper -n --root $CHROOT install ohpc-base-compute

To access the remote repositories by hostname (and not IP addresses), the chroot environment needs to
be updated to enable DNS resolution. Assuming that the master host has a working DNS configuration in
place, the chroot environment can be updated with a copy of the configuration as follows:

[sms]# cp -p /etc/resolv.conf $CHROOT/etc/resolv.conf

Now, we can include additional required components to the compute instance including resource manager
client, NTP, and development environment modules support.

# Import GPG keys for chroot repository usage
[sms]# zypper -n --root $CHROOT --no-gpg-checks --gpg-auto-import-keys refresh

# Add OpenPBS client support
[sms]# zypper -n --root $CHROOT install openpbs-execution-ohpc
[sms]# perl -pi -e "s/PBS_SERVER=\S+/PBS_SERVER=${sms_name}/" $CHROOT/etc/pbs.conf
[sms]# echo "PBS_LEAF_NAME=${sms_name}" >> /etc/pbs.conf
[sms]# chroot $CHROOT opt/pbs/libexec/pbs_habitat
[sms]# perl -pi -e "s/\$clienthost \S+/\$clienthost ${sms_name}/" $CHROOT/var/spool/pbs/mom_priv/config
[sms]# echo "\$usecp *:/home /home" >> $CHROOT/var/spool/pbs/mom_priv/config
[sms]# chroot $CHROOT systemctl enable pbs

# Provide udev rules to enable /dev/ipath access for InfiniPath devices
[sms]# cp /opt/ohpc/pub/examples/udev/60-ipath.rules $CHROOT/etc/udev/rules.d/

# Add Network Time Protocol (NTP) support
[sms]# zypper -n --root $CHROOT install chrony
[sms]# chroot $CHROOT systemctl enable chrony
# Identify master host as local NTP server
[sms]# echo "server ${sms_ip}" >> $CHROOT/etc/chrony.conf

# Add kernel drivers
[sms]# zypper -n --root $CHROOT install kernel-default

12 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

# Include modules user environment
[sms]# zypper -n --root $CHROOT install lmod-ohpc

# Enable ssh access
[sms]# chroot $CHROOT systemctl enable sshd.service

# Remove default hostname to allow WW to provision network names
[sms]# mv $CHROOT/etc/hostname $CHROOT/etc/hostname.orig

3.8.3 Customize system configuration
Prior to assembling the image, it is advantageous to perform any additional customization within the chroot
environment created for the desired compute instance. The following steps document the process to add a
local ssh key created by Warewulf to support remote access, identify the resource manager server, configure
NTP for compute resources, and enable NFS mounting of a $HOME file system and the public OpenHPC
install path (/opt/ohpc/pub) that will be hosted by the master host in this example configuration.

# Initialize warewulf database and ssh_keys
[sms]# wwinit database
[sms]# wwinit ssh_keys

# Add NFS client mounts of /home and /opt/ohpc/pub to base image
[sms]# echo "${sms_ip}:/home /home nfs nfsvers=3,nodev,nosuid 0 0" >> $CHROOT/etc/fstab
[sms]# echo "${sms_ip}:/opt/ohpc/pub /opt/ohpc/pub nfs nfsvers=3,nodev 0 0" >> $CHROOT/etc/fstab

# Export /home and OpenHPC public packages from master server
[sms]# echo "/home *(rw,no_subtree_check,fsid=10,no_root_squash)" >> /etc/exports
[sms]# echo "/opt/ohpc/pub *(ro,no_subtree_check,fsid=11)" >> /etc/exports
[sms]# exportfs -a
[sms]# systemctl restart nfs-server
[sms]# systemctl enable nfs-server

3.8.4 Additional Customization (optional)
This section highlights common additional customizations that can optionally be applied to the local cluster
environment. These customizations include:

• Add InfiniBand or Omni-Path drivers • Add Nagios Core monitoring
• Increase memlock limits • Add ClusterShell
• Restrict ssh access to compute resources • Add mrsh
• Add BeeGFS client • Add genders
• Add Lustre client • Add ConMan
• Enable syslog forwarding

Details on the steps required for each of these customizations are discussed further in the following sections.

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

# Add IB support and enable
[sms]# zypper -n --root $CHROOT install rdma-core libibmad5 librdmacm1 dapl-devel dapl-utils libibverbs-utils
[sms]# chroot $CHROOT systemctl enable rdma

13 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

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

# Add OPA support and enable
[sms]# zypper -n --root $CHROOT install opa-basic-tools libibmad5 libibverbs
[sms]# zypper -n --root $CHROOT install libpsm2-2 libpsm2-compat
[sms]# chroot $CHROOT systemctl enable rdma

3.8.4.3 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 updating the /etc/security/limits.conf file and this should be performed
within the compute image and on all job submission hosts. In this recipe, jobs are submitted from the master
host, and the following commands can be used to update the maximum locked memory settings on both the
master host and the compute image:

# Update memlock settings on master
[sms]# perl -pi -e 's/# End of file/\* soft memlock unlimited\n$&/s' /etc/security/limits.conf
[sms]# perl -pi -e 's/# End of file/\* hard memlock unlimited\n$&/s' /etc/security/limits.conf

# Update memlock settings within compute image
[sms]# perl -pi -e 's/# End of file/\* soft memlock unlimited\n$&/s' $CHROOT/etc/security/limits.conf
[sms]# perl -pi -e 's/# End of file/\* hard memlock unlimited\n$&/s' $CHROOT/etc/security/limits.conf

3.8.4.4 Add BeeGFS To add optional support for mounting BeeGFS file systems, an additional ex-
ternal zypper repository provided by the BeeGFS project must be configured. In this recipe, it is assumed
that the file system is hosted by servers that are pre-existing and are not part of the install process. The
${sysmgmtd host} should point the server running the BeeGFS Management Service. Starting the client ser-
vice triggers a build of a kernel module, hence the kernel module development packages must be installed first.
As with Lustre, a default OpenSUSE Leap 15.2 environment may not allow loading of the necessary BeeGFS
kernel modules. Consequently, the example below includes steps which update the /etc/modprobe.d/10-
unsupported-modules.conf file to allow loading of the necessary modules.

# Add BeeGFS client software to master host
[sms]# zypper ar https://www.beegfs.io/release/beegfs 7.2/dists/beegfs-sles15.repo
# install matching kernel-default-devel and beegfs packages
[sms]# version=`rpm -q --qf "%{VERSION}-%{RELEASE}\n" kernel-default`
[sms]# zypper -n install kernel-default-devel-${version}
[sms]# zypper -n install gcc beegfs-client beegfs-helperd beegfs-utils

# Enable OFED support in client
[sms]# perl -pi -e "s/^buildArgs=-j8/buildArgs=-j8 BEEGFS_OPENTK_IBVERBS=1/" \
/etc/beegfs/beegfs-client-autobuild.conf

# Define client's management host
[sms]# /opt/beegfs/sbin/beegfs-setup-client -m ${sysmgmtd_host}

# Update configuration to allow BeeGFS modules to be loaded on master host
[sms]# perl -pi -e "s/^allow_unsupported_modules 0/allow_unsupported_modules 1/" \
/etc/modprobe.d/10-unsupported-modules.conf
[sms]# systemctl start beegfs-helperd
# Build kernel and mount file system
[sms]# systemctl start beegfs-client

14 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

# Add BeeGFS client software to compute node image
[sms]# wget -P $CHROOT/etc/zypp/repos.d https://www.beegfs.io/release/beegfs 7.2/dists/beegfs-sles15.repo
[sms]# zypper -n --root $CHROOT install beegfs-client beegfs-helperd beegfs-utils

# Disable auto-build of kernel module in compute node image
[sms]# perl -pi -e "s/^buildEnabled=true/buildEnabled=false/" $CHROOT/etc/beegfs/beegfs-client-autobuild.conf
[sms]# rm -f $CHROOT/var/lib/beegfs/client/force-auto-build

# Enable client daemons on compute nodes
[sms]# perl -pi -e "s/^allow_unsupported_modules 0/allow_unsupported_modules 1/" \
$CHROOT/etc/modprobe.d/10-unsupported-modules.conf
[sms]# chroot $CHROOT systemctl enable beegfs-helperd beegfs-client

# Copy client config to compute nodes
[sms]# cp /etc/beegfs/beegfs-client.conf $CHROOT/etc/beegfs/beegfs-client.conf

# Include kernel module in warewulf bootstrap
[sms]# echo "drivers += beegfs" >> /etc/warewulf/bootstrap.conf

3.8.4.5 Add Lustre client To add Lustre client support on the cluster, it necessary to install the client
and associated modules on each host needing to access a Lustre file system. In this recipe, it is assumed
that the Lustre file system is hosted by servers that are pre-existing and are not part of the install process.
Outlining the variety of Lustre client mounting options is beyond the scope of this document, but the general
requirement is to add a mount entry for the desired file system that defines the management server (MGS)
and underlying network transport protocol. To add client mounts on both the master server and compute
image, the following commands can be used. Note that the Lustre file system to be mounted is identified
by the ${mgs fs name} variable. In this example, the file system is configured to be mounted locally as
/mnt/lustre. Additionally, note that a default OpenSUSE Leap 15.2 environment may not allow loading
of the necessary Lustre kernel modules. Consequently, the example below includes steps which update the
/etc/modprobe.d/10-unsupported-modules.conf file to allow loading of the necessary modules.

# Add Lustre client software to master host
[sms]# zypper -n install lustre-client-ohpc

# Update configuration to allow Lustre modules to be loaded on master host
[sms]# perl -pi -e "s/^allow_unsupported_modules 0/allow_unsupported_modules 1/" \
/etc/modprobe.d/10-unsupported-modules.conf

# Include Lustre client software in compute image
[sms]# zypper -n --root $CHROOT install lustre-client-ohpc

# Update configuration to allow Lustre modules to be loaded on compute hosts
[sms]# perl -pi -e "s/^allow_unsupported_modules 0/allow_unsupported_modules 1/" \
$CHROOT/etc/modprobe.d/10-unsupported-modules.conf

# Include mount point and file system mount in compute image
[sms]# mkdir $CHROOT/mnt/lustre
[sms]# echo "${mgs_fs_name} /mnt/lustre lustre defaults,_netdev,localflock 0 0" >> $CHROOT/etc/fstab

15 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Tip

The suggested mount options shown for Lustre leverage the localflock option. This is a Lustre-specific
setting that enables client-local flock support. It is much faster than cluster-wide flock, but if you have an
application requiring cluster-wide, coherent file locks, use the standard flock attribute instead.

The default underlying network type used by Lustre is tcp. If your external Lustre file system is to be
mounted using a network type other than tcp, additional configuration files are necessary to identify the de-
sired network type. The example below illustrates creation of modprobe configuration files instructing Lustre
to use an InfiniBand network with the o2ib LNET driver attached to ib0. Note that these modifications
are made to both the master host and compute image.

[sms]# echo "options lnet networks=o2ib(ib0)" >> /etc/modprobe.d/lustre.conf
[sms]# echo "options lnet networks=o2ib(ib0)" >> $CHROOT/etc/modprobe.d/lustre.conf

With the Lustre configuration complete, the client can be mounted on the master host as follows:

[sms]# mkdir /mnt/lustre
[sms]# mount -t lustre -o localflock ${mgs_fs_name} /mnt/lustre

16 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

3.8.4.6 Enable forwarding of system logs It is often desirable to consolidate system logging infor-
mation 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 stateless compute node’s memory footprint. The following commands highlight
the steps necessary to configure compute nodes to forward their logs to the SMS, and to allow the SMS to
accept these log requests.

# Configure SMS to receive messages and reload rsyslog configuration
[sms]# echo ’module(load="imudp")’ >> /etc/rsyslog.d/ohpc.conf
[sms]# echo ’input(type="imudp" port="514")’ >> /etc/rsyslog.d/ohpc.conf
[sms]# systemctl restart rsyslog

# Define compute node forwarding destination
[sms]# echo "*.* @${sms_ip}:514" >> $CHROOT/etc/rsyslog.conf
[sms]# echo "Target=\"${sms_ip}\" Protocol=\"udp\"" >> $CHROOT/etc/rsyslog.conf

# Disable most local logging on computes. Emergency and boot logs will remain on the compute nodes
[sms]# perl -pi -e "s/^\*\.info/\\#\*\.info/" $CHROOT/etc/rsyslog.conf
[sms]# perl -pi -e "s/^authpriv/\\#authpriv/" $CHROOT/etc/rsyslog.conf
[sms]# perl -pi -e "s/^mail/\\#mail/" $CHROOT/etc/rsyslog.conf
[sms]# perl -pi -e "s/^cron/\\#cron/" $CHROOT/etc/rsyslog.conf
[sms]# perl -pi -e "s/^uucp/\\#uucp/" $CHROOT/etc/rsyslog.conf

3.8.4.7 Add Nagios monitoring Nagios is an open source infrastructure network monitoring package
designed to watch servers, switches, and various services and offers user-defined alerting facilities for mon-
itoring various aspects of an HPC cluster. The core Nagios daemon and a variety of monitoring plugins
are provided by the underlying OS distro and the following commands can be used to install and configure
a Nagios server on the master node, and add the facility to run tests and gather metrics from provisioned
compute nodes. This simple configuration example is intended to be illustrative to walk through defining a
compute host group and enabling an ssh check for the computes. Users are encouraged to consult Nagios
documentation for more information and can install additional plugins as desired on login nodes, service
nodes, or compute hosts.

# Install nagios, nrep, and all available plugins on master host
[sms]# zypper -n install nagios nrpe monitoring-plugins-*

# Install nrpe and an example plugin into compute node image
[sms]# zypper -n --root $CHROOT install nrpe monitoring-plugins-ssh

# Enable and configure Nagios NRPE daemon in compute image
[sms]# chroot $CHROOT systemctl enable nrpe
[sms]# perl -pi -e "s/^allowed_hosts=/# allowed_hosts=/" $CHROOT/etc/nagios/nrpe.cfg
[sms]# echo "nrpe : ${sms_ip} : ALLOW" >> $CHROOT/etc/hosts.allow
[sms]# echo "nrpe : ALL : DENY" >> $CHROOT/etc/hosts.allow

# Copy example Nagios config file to define a compute group and ssh check
# (note: edit as desired to add all desired compute hosts)
[sms]# cp /opt/ohpc/pub/examples/nagios/compute.cfg /etc/nagios/objects
# Register the config file with nagios
[sms]# echo "cfg_file=/etc/nagios/objects/compute.cfg" >> /etc/nagios/nagios.cfg

# Update location of mail binary for alert commands
[sms]# perl -pi -e "s/ \/bin\/mail/ \/usr\/bin\/mailx/g" /etc/nagios/objects/commands.cfg

# Update email address of contact for alerts
[sms]# perl -pi -e "s/nagios\@localhost/root\@${sms_name}/" /etc/nagios/objects/contacts.cfg

# Add check_ssh command for remote hosts

17 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

[sms]# echo command[check_ssh]=/usr/lib64/nagios/plugins/check_ssh localhost $CHROOT/etc/nagios/nrpe.cfg

# define password for nagiosadmin to be able to connect to web interface
[sms]# htpasswd -bc /etc/nagios/passwd nagiosadmin ${nagios_web_password}

# Enable Nagios on master, and configure
[sms]# systemctl enable nagios
[sms]# systemctl start nagios
# Update permissions on ping command to allow nagios user to execute
[sms]# chmod u+s `which ping`

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

# Install ClusterShell
[sms]# zypper -n install clustershell

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

3.8.4.9 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
[sms]# zypper -n install genders-ohpc

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

3.8.4.10 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
[sms]# zypper -n install conman-ohpc

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

18 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

# Enable and start conman
[sms]# systemctl enable conman
[sms]# systemctl start conman

Note that an additional kernel boot option is typically necessary to enable serial console output. This option
is highlighted in §3.9.4 after compute nodes have been registered with the provisioning system.

3.8.4.11 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 master and compute nodes
[sms]# zypper -n install nhc-ohpc
[sms]# zypper -n --root $CHROOT install nhc-ohpc

3.8.5 Import files
The Warewulf system includes functionality to import arbitrary files from the provisioning server for distri-
bution to managed hosts. This is one way to distribute user credentials to compute nodes. To import local
file-based credentials, issue the following:

[sms]# wwsh file import /etc/passwd
[sms]# wwsh file import /etc/group
[sms]# wwsh file import /etc/shadow

Finally, to add optional support for controlling IPoIB interfaces (see §3.5), OpenHPC includes a template
file for Warewulf that can optionally be imported and used later to provision ib0 network settings.

[sms]# wwsh file import /opt/ohpc/pub/examples/network/sles/ifcfg-ib0.ww
[sms]# wwsh -y file set ifcfg-ib0.ww --path=/etc/sysconfig/network/ifcfg-ib0

3.9 Finalizing provisioning configuration
Warewulf employs a two-stage boot process for provisioning nodes via creation of a bootstrap image that
is used to initialize the process, and a virtual node file system capsule containing the full system image.
This section highlights creation of the necessary provisioning images, followed by the registration of desired
compute nodes.

3.9.1 Assemble bootstrap image
The bootstrap image includes the runtime kernel and associated modules, as well as some simple scripts to
complete the provisioning process. The following commands highlight the inclusion of additional drivers and
creation of the bootstrap image based on the running kernel.

19 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

# (Optional) Include drivers from kernel updates; needed if enabling additional kernel modules on computes
[sms]# export WW_CONF=/etc/warewulf/bootstrap.conf
[sms]# echo "drivers += updates/kernel/" >> $WW_CONF

# Build bootstrap image
[sms]# wwbootstrap `uname -r`

3.9.2 Assemble Virtual Node File System (VNFS) image
With the local site customizations in place, the following step uses the wwvnfs command to assemble a VNFS
capsule from the chroot environment defined for the compute instance.

[sms]# wwvnfs --chroot $CHROOT

3.9.3 Register nodes for provisioning
In preparation for provisioning, we can now define the desired network settings for four example compute
nodes with the underlying provisioning system and restart the dhcp service. Note the use of variable names
for the desired compute hostnames, node IPs, and MAC addresses which should be modified to accommodate
local settings and hardware. By default, Warewulf uses network interface names of the eth# variety and adds
kernel boot arguments to maintain this scheme on newer kernels. Consequently, when specifying the desired
provisioning interface via the $eth provision variable, it should follow this convention. Alternatively, if
you prefer to use the predictable network interface naming scheme (e.g. names like en4s0f0), additional
steps are included to alter the default kernel boot arguments and take the eth# named interface down after
bootstrapping so the normal init process can bring it up again using the desired name.
Also included in these steps are commands to enable Warewulf to manage IPoIB settings and correspond-
ing definitions of IPoIB addresses for the compute nodes. This is typically optional unless you are planning
to include a Lustre client mount over InfiniBand. The final step in this process associates the VNFS image
assembled in previous steps with the newly defined compute nodes, utilizing the user credential files and
munge key that were imported in §3.8.5.

# Set provisioning interface as the default networking device
[sms]# echo "GATEWAYDEV=${eth_provision}" > /tmp/network.$$
[sms]# wwsh -y file import /tmp/network.$$ --name network
[sms]# wwsh -y file set network --path /etc/sysconfig/network --mode=0644 --uid=0

# Add nodes to Warewulf data store
[sms]# for ((i=0; i<$num_computes; i++)) ; do
wwsh -y node new ${c_name[i]} --ipaddr=${c_ip[i]} --hwaddr=${c_mac[i]} -D ${eth_provision}
done

# Additional step required if desiring to use predictable network interface
# naming schemes (e.g. en4s0f0). Skip if using eth# style names.
[sms]# export kargs="${kargs} net.ifnames=1,biosdevname=1"
[sms]# wwsh provision set --postnetdown=1 "${compute_regex}"

# Define provisioning image for hosts
[sms]# wwsh -y provision set "${compute_regex}" --vnfs=leap15.2 --bootstrap=`uname -r` \
--files=dynamic_hosts,passwd,group,shadow,network

20 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

# Optionally define IPoIB network settings (required if planning to mount Lustre/BeeGFS over IB)
[sms]# for ((i=0; i<$num_computes; i++)) ; do
wwsh -y node set ${c_name[$i]} -D ib0 --ipaddr=${c_ipoib[$i]} --netmask=${ipoib_netmask}
done
[sms]# wwsh -y provision set "${compute_regex}" --fileadd=ifcfg-ib0.ww

Tip

Warewulf includes a utility named wwnodescan to automatically register new compute nodes versus the
outlined node-addition approach which requires hardware MAC addresses to be gathered in advance. With
wwnodescan, nodes will be added to the Warewulf database in the order in which their DHCP requests are
received by the master, so care must be taken to boot nodes in the order one wishes to see preserved in the
Warewulf database. The IP address provided will be incremented after each node is found, and the utility
will exit after all specified nodes have been found. Example usage is highlighted below:

[sms]# wwnodescan --netdev=${eth_provision} --ipaddr=${c_ip[0]} --netmask=${internal_netmask} \
--vnfs=leap15.2 --bootstrap=`uname -r` --listen=${sms_eth_internal} ${c_name[0]}-${c_name[3]}

# Restart dhcp / update PXE
[sms]# systemctl restart dhcpd
[sms]# wwsh pxe update

21 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

3.9.4 Optional kernel arguments
If you chose to enable ConMan in §3.8.4.10, additional warewulf configuration is needed as follows:

# Define node kernel arguments to support SOL console
[sms]# wwsh -y provision set "${compute_regex}" --console=ttyS1,115200

If any components have added to the boot time kernel command line arguments for the compute nodes, the
following command is required to store the configuration in Warewulf:

# Set optional compute node kernel command line arguments.
[sms]# wwsh -y provision set "${compute_regex}" --kargs="${kargs}"

3.9.5 Optionally configure stateful provisioning
Warewulf normally defaults to running the assembled VNFS image out of system memory in a stateless
configuration. Alternatively, Warewulf can also be used to partition and format persistent storage such that
the VNFS image can be installed locally to disk in a stateful manner. This does, however, require that a
boot loader (GRUB) be added to the image as follows:

# Add GRUB2 bootloader and re-assemble VNFS image
[sms]# zypper -n --root $CHROOT install grub2
[sms]# wwvnfs --chroot $CHROOT

Enabling stateful nodes also requires additional site-specific, disk-related parameters in the Warewulf con-
figuration, and several example partitioning scripts are provided in the distribution.

# Select (and customize) appropriate parted layout example
[sms]# cp /etc/warewulf/filesystem/examples/gpt_example.cmds /etc/warewulf/filesystem/gpt.cmds
[sms]# wwsh provision set --filesystem=gpt "${compute_regex}"
[sms]# wwsh provision set --bootloader=sda "${compute_regex}"

Tip

Those provisioning compute nodes in UEFI mode will install a slightly different set of packages in to the
VNFS. Warewulf also provides an example EFI filesystem layout.

# Add GRUB2 bootloader and re-assemble VNFS image
[sms]# zypper -n --root $CHROOT install grub2-efi grub2-efi-modules
[sms]# wwvnfs --chroot $CHROOT
[sms]# cp /etc/warewulf/filesystem/examples/efi_example.cmds /etc/warewulf/filesystem/efi.cmds
[sms]# wwsh provision set --filesystem=efi "${compute_regex}"
[sms]# wwsh provision set --bootloader=sda "${compute_regex}"

Upon subsequent reboot of the modified nodes, Warewulf will partition and format the disk to host the
desired VNFS image. Once the image is installed to disk, warewulf can be configured to use the nodes’ local
storage as the boot device.

# Configure local boot (after successful provisioning)
[sms]# wwsh provision set --bootlocal=normal "${compute_regex}"

22 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

3.10 Boot compute nodes
At this point, the master server 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.

[sms]# 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:

[sms]# pdsh -w c[1-4] 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

Tip

While the pxelinux.0 and lpxelinux.0 files that ship with Warewulf to enable network boot support a wide
range of hardware, some hosts may boot more reliably or faster using the BOS versions provided via the
syslinux package. If you encounter PXE issues, consider replacing the pxelinux.0 and lpxelinux.0 files
supplied with warewulf-provision-ohpc with versions from syslinux.

4 Install OpenHPC Development Components
The install procedure outlined in §3 highlighted the steps necessary to install a master host, 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.

4.1 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
[sms]# zypper -n install ohpc-autotools

[sms]# zypper -n install EasyBuild-ohpc
[sms]# zypper -n install hwloc-ohpc
[sms]# zypper -n install spack-ohpc
[sms]# zypper -n install valgrind-ohpc

23 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

4.2 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.

[sms]# zypper -n install gnu9-compilers-ohpc

4.3 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 trans-
ports are summarized in Table 1. The command that follows installs a starting set of MPI families that are
compatible with both ethernet and high-speed fabrics.

Table 1: Available MPI variants

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

[sms]# zypper -n install openmpi4-gnu9-ohpc mpich-ofi-gnu9-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:

[sms]# zypper -n install mpich-ucx-gnu9-ohpc

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

[sms]# module avail mpich

-------------------- /opt/ohpc/pub/moduledeps/gnu9 ---------------------
mpich/3.3.2-ofi mpich/3.3.2-ucx (D)

If your system includes InfiniBand and you enabled underlying support in §3.5 and §3.8.4, an additional
MVAPICH2 family is available for use:

[sms]# zypper -n install mvapich2-gnu9-ohpc

24 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

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

[sms]# zypper -n install mvapich2-psm2-gnu9-ohpc

An additional OpenMPI build variant is listed in Table 1 which enables PMIx job launch support for use
with Slurm. This optional variant is available as openmpi4-pmix-slurm-gnu9-ohpc.

4.4 Performance Tools
OpenHPC provides a variety of open-source tools to aid in application performance analysis (refer to Ap-
pendix E for a listing of available packages). This group of tools can be installed as follows:

# Install perf-tools meta-package
[sms]# zypper -n install ohpc-gnu9-perf-tools

Tip

OpenHPC includes the Likwid performance analysis toolkit in the perf-tools meta-package. This package
requires the MSR kernel driver, which is not enabled by default on SUSE distributions. To enable:

# Load MSR driver
[sms]# modprobe msr

4.5 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.

[sms]# zypper -n install lmod-defaults-gnu9-openmpi4-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-gnu9-mpich-ofi-ohpc
• lmod-defaults-gnu9-mpich-ucx-ohpc
• lmod-defaults-gnu9-mvapich2-ohpc

4.6 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

25 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

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 §4.3.

[sms]# zypper search -t package petsc-gnu7-*-ohpc
Loading repository data...
Reading installed packages...

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 §3.8.3, so the packages will be immediately
available for use on the cluster after installation on the master host.

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 Appendix E 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
[sms]# zypper -n install ohpc-gnu9-serial-libs
[sms]# zypper -n install ohpc-gnu9-io-libs
[sms]# zypper -n install ohpc-gnu9-python-libs
[sms]# zypper -n install ohpc-gnu9-runtimes

# Install parallel lib meta-packages for all available MPI toolchains
[sms]# zypper -n install ohpc-gnu9-mpich-parallel-libs
[sms]# zypper -n install ohpc-gnu9-openmpi4-parallel-libs

26 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

4.7 Optional Development Tool Builds
In addition to the 3rd party development libraries built using the open source toolchains mentioned in §4.6,
OpenHPC also provides optional compatible builds for use with the compilers and MPI stack included in
newer versions of the Intel® Parallel Studio XE software suite. 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, the Parallel Studio software suite must be obtained and installed
separately. Once installed locally, the OpenHPC compatible packages can be installed using standard package
manager semantics. Note that licenses are provided free of charge for many categories of use. In particular,
licenses for compilers and developments tools are provided at no cost to academic researchers or developers
contributing to open-source software projects. More information on this program can be found at:

https://software.intel.com/en-us/qualify-for-free-software

Tip

As noted in §3.8.3, the default installation path for OpenHPC (/opt/ohpc/pub) is exported over
NFS from the master to the compute nodes, but the Parallel Studio installer defaults to a path of
/opt/intel. To make the Intel® compilers available to the compute nodes one must either customize
the Parallel Studio installation path to be within /opt/ohpc/pub, or alternatively, 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 Intel® Parallel Studio, issue
the following:

# Install OpenHPC compatibility packages (requires prior installation of Parallel Studio)
[sms]# zypper -n install intel-compilers-devel-ohpc
[sms]# zypper -n install intel-mpi-devel-ohpc

# Optionally, choose the Omni-Path enabled build for MVAPICH2. Otherwise, skip to retain IB variant
[sms]# zypper -n install mvapich2-psm2-intel-ohpc

# Install 3rd party libraries/tools meta-packages built with Intel toolchain
[sms]# zypper -n install ohpc-intel-serial-libs
[sms]# zypper -n install ohpc-intel-geopm
[sms]# zypper -n install ohpc-intel-io-libs
[sms]# zypper -n install ohpc-intel-perf-tools
[sms]# zypper -n install ohpc-intel-python3-libs
[sms]# zypper -n install ohpc-intel-runtimes
[sms]# zypper -n install ohpc-intel-mpich-parallel-libs
[sms]# zypper -n install ohpc-intel-mvapich2-parallel-libs
[sms]# zypper -n install ohpc-intel-openmpi4-parallel-libs
[sms]# zypper -n install ohpc-intel-impi-parallel-libs

27 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

5 Resource Manager Startup
In section §3, the OpenPBS workload manager was installed and configured for use on both the master host
and compute node instances. With the cluster nodes up and functional, we can now startup the resource
manager services on the master host in preparation for running user jobs.
The following command can be used to startup the necessary services to support resource management
under OpenPBS.

# start PBS daemons on master host
[sms]# systemctl enable pbs
[sms]# systemctl start pbs

In the default configuration, the compute hosts have not been added to the OpenPBS resource man-
ager. To add the compute hosts, execute the following to register each host and apply several key global
configuration options.

# initialize PBS path
[sms]# . /etc/profile.d/pbs.sh
# enable user environment propagation (needed for modules support)
[sms]# qmgr -c "set server default_qsub_arguments= -V"
# enable uniform multi-node MPI task distribution
[sms]# qmgr -c "set server resources_default.place=scatter"
# enable support for job accounting
[sms]# qmgr -c "set server job_history_enable=True"
# register compute hosts with PBS
[sms]# for host in "${c_name[@]}"; do
qmgr -c "create node $host"
done

6 Run a Test Job
With the resource manager enabled for production usage, users should now be able to run jobs. To demon-
strate this, we will add a “test” user on the master host that can be used to run an example job.

[sms]# useradd -m test

Warewulf installs a utility on the compute nodes to automatically synchronize known files from the
provisioning server at five minute intervals. In this recipe, recall that we previously registered credential files
with Warewulf (e.g. passwd, group, and shadow) so that these files would be propagated during compute
node imaging. However, with the addition of a new “test” user above, the files have been outdated and we
need to update the Warewulf database to incorporate the additions. This re-sync process can be accomplished
as follows:

[sms]# wwsh file resync passwd shadow group

28 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Tip

After re-syncing to notify Warewulf of file modifications made on the master host, it should take approximately
5 minutes for the changes to propagate. However, you can also manually pull the changes from compute nodes
via the following:

[sms]# pdsh -w $compute_prefix[1-4] /warewulf/bin/wwgetfiles

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.

6.1 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 mpiexec for parallel job launch which summarizes
the underlying native job launch mechanism being used):

# Switch to "test" user
[sms]# 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 ~]$ qsub -I -l select=2:mpiprocs=4

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

[prun] Master compute host = c1
[prun] Resource manager = openpbs
[prun] Launch cmd = mpiexec.hydra -rmk pbs ./a.out

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

29 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Tip

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

Command OpenPBS SLURM

Submit batch job qsub [job script] sbatch [job script]
Request interactive shell qsub -I /bin/bash srun –pty /bin/bash
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]

30 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

6.2 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/openpbs/job.mpi .

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

# Name of stdout output file
#PBS -o job.out

# Total number of nodes and MPI tasks/node requested
#PBS -l select=2:mpiprocs=4

# Run time (hh:mm:ss) - 1.5 hours
#PBS -l walltime=01:30:00
#----------------------------------------------------------

# Change to submission directory
cd $PBS_O_WORKDIR

# Launch MPI-based executable
prun ./a.out

# Submit job for batch execution
[test@sms ~]$ qsub job.mpi
5.master

31 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Appendices
A 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 §1.3. 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 SMS master host 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

[sms]# zypper -n install docs-ohpc

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

[sms]# cp /opt/ohpc/pub/doc/recipes/leap15/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.

[sms]# cp -p /opt/ohpc/pub/doc/recipes/leap15/x86_64/warewulf/OpenPBS/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.

[sms]# export OHPC_INPUT_LOCAL=./input.local
[sms]# ./recipe.sh

32 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

B 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 v2, you will first need to update your local OpenHPC repository configuration to point against
the v2 release (or update your locally hosted mirror). Refer to §3.1 for more details on enabling the latest
repository. In contrast, when upgrading between micro releases on the same branch (e.g. from v2 to 2.2),
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 in chroot location(s)). Package man-
agers 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.

[sms]# zypper clean -a
[sms]# zypper --root $CHROOT clean

2. Upgrade master (SMS) node

[sms]# zypper -n up "*-ohpc"

# Any new Base OS provided dependencies can be installed by
# updating the ohpc-base metapackage
[sms]# zypper -n up "ohpc-base"

Tip

The version of Warewulf included in OpenHPC v1.3.6 added a new architecture-specific package con-
taining iPXE files. Upgraders will need to install this package on the SMS node.

[sms]# zypper -n install warewulf-provision-server-ipxe-x86 64-ohpc

3. Upgrade packages in compute image

[sms]# zypper -n --root $CHROOT up "*-ohpc"

# Any new compute-node Base OS provided dependencies can be installed by
# updating the ohpc-base-compute metapackage
[sms]# zypper -n --root $CHROOT up "ohpc-base-compute"

4. Rebuild image(s)

[sms]# wwvnfs --chroot $CHROOT

In the case where packages were upgraded within the chroot compute image, you will need to reboot the
compute nodes when convenient to enable the changes.

33 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

B.1 New component variants
As newer variants of key compiler/MPI stacks are released, OpenHPC will periodically add toolchains
enabling the latest variant. To stay consistent throughout the build hierarchy, minimize recompilation
requirements for existing binaries, and allow for multiple variants to coexist, unique delimiters are used to
distinguish RPM package names and module hierarchy.
In the case of a fresh install, OpenHPC recipes default to installation of the latest toolchains available
in a given release branch. However, if upgrading a previously installed system, administrators can opt-in
to enable new variants as they become available. To illustrate this point, consider the previous OpenHPC
1.3.5 release as an example which contained GCC 7.3.0 along with runtimes and libraries compiled with
this toolchain. In the case where an admin would like to enable the newer “gnu8” toolchain, installation of
these additions is simplified with the use of OpenHPC’s meta-packages (see Table 2 in Appendix E). The
following example illustrates adding the complete “gnu8” toolchain. Note that we leverage the convenience
meta-packages containing MPI-dependent builds, and we also update the modules environment to make it
the default.

# Install GCC 8.x-compiled meta-packages with dependencies
[sms]# zypper -n install ohpc-gnu8-perf-tools \
ohpc-gnu8-io-libs \
ohpc-gnu8-python-libs \
ohpc-gnu8-runtimes \
ohpc-gnu8-serial \
ohpc-gnu8-parallel-libs

# Update default environment
[sms]# zypper -n remove lmod-defaults-gnu7-openmpi3-ohpc
[sms]# zypper -n install lmod-defaults-gnu8-openmpi3-ohpc

34 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

C 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.

[sms]# zypper -n 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 OpenPBS 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. Example output is
shown below (some output is omitted for the sake of brevity).

[sms]# 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 ............. : OpenPBS
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.

35 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

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 (OpenPBS/gnu9/mpich)
ok 2 [libs/FFTW] MPI C binary runs under resource manager (OpenPBS/gnu9/mpich)
ok 3 [libs/FFTW] Serial Fortran binary runs under resource manager (OpenPBS/gnu9/mpich)
PASS rm_execution (exit status: 0)
1..3
ok 1 [libs/FFTW] Serial C binary runs under resource manager (OpenPBS/gnu9/mvapich2)
ok 2 [libs/FFTW] MPI C binary runs under resource manager (OpenPBS/gnu9/mvapich2)
ok 3 [libs/FFTW] Serial Fortran binary runs under resource manager (OpenPBS/gnu9/mvapich2)
PASS rm_execution (exit status: 0)
1..3
ok 1 [libs/FFTW] Serial C binary runs under resource manager (OpenPBS/gnu9/openmpi4)
ok 2 [libs/FFTW] MPI C binary runs under resource manager (OpenPBS/gnu9/openmpi4)
ok 3 [libs/FFTW] Serial Fortran binary runs under resource manager (OpenPBS/gnu9/openmpi4)
PASS rm_execution (exit status: 0)

36 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

D Customization
D.1 Adding local Lmod modules to OpenHPC hierarchy
Locally installed applications can easily be integrated in to OpenHPC systems by following the Lmod con-
vention laid out by the provided packages. Two sample module files are included in the examples-ohpc
package—one representing an application with no compiler or MPI runtime dependencies, and one depen-
dent on OpenMPI and the GNU toolchain. Simply copy these files to the prescribed locations, and the lmod
application should pick them up automatically.

[sms]# mkdir /opt/ohpc/pub/modulefiles/example1
[sms]# cp /opt/ohpc/pub/examples/example.modulefile \
/opt/ohpc/pub/modulefiles/example1/1.0
[sms]# mkdir /opt/ohpc/pub/moduledeps/gnu7-openmpi3/example2
[sms]# cp /opt/ohpc/pub/examples/example-mpi-dependent.modulefile \
/opt/ohpc/pub/moduledeps/gnu7-openmpi3/example2/1.0
[sms]# module avail

----------------------------------- /opt/ohpc/pub/moduledeps/gnu7-openmpi3 -----------------------------------
adios/1.12.0 imb/2018.0 netcdf-fortran/4.4.4 ptscotch/6.0.4 sionlib/1.7.1
boost/1.65.1 mpi4py/2.0.0 netcdf/4.4.1.1 scalapack/2.0.2 slepc/3.7.4
example2/1.0 mpiP/3.4.1 petsc/3.7.6 scalasca/2.3.1 superlu_dist/4.2
fftw/3.3.6 mumps/5.1.1 phdf5/1.10.1 scipy/0.19.1 tau/2.26.1
hypre/2.11.2 netcdf-cxx/4.3.0 pnetcdf/1.8.1 scorep/3.1 trilinos/12.10.1

--------------------------------------- /opt/ohpc/pub/moduledeps/gnu7 ----------------------------------------
R/3.4.2 metis/5.1.0 ocr/1.0.1 pdtoolkit/3.24 superlu/5.2.1
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 valgrind/3.13.0
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".

37 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

D.2 Rebuilding Packages from Source
Users of OpenHPC may find it desirable to rebuild one of the supplied packages to apply build customizations
or satisfy local requirements. 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 zypper 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.

Tip

Packages modified locally will not be cryptographically signed like the packages in the OpenHPC repository.
Zypper requires and additional flag (--no-gpg-checks) to install unsigned packages.

# Install rpm-build package from base OS distro
sms:~ # zypper -n install rpm-build

# Download SRPM from OpenHPC repository and install locally
sms001:~ # zypper source-install fftw-gnu9-openmpi4-ohpc

# Modify spec file as desired
sms001:~ # cd ~/rpmbuild/SPECS
sms:~rpmbuild/SPECS # perl -pi -e "s/enable-static=no/enable-static=yes/" fftw.spec

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

# Install the new package
sms ~rpmbuild/SPECS # zypper --no-gpg-checks in \
../RPMS/x86_64/fftw-gnu9-openmpi4-static-ohpc.2.0-3.3.8-6.1.x86_64.rpm

# The new module file appears along side the default
sms ~ # module avail fftw

--------------------------/opt/ohpc/pub/moduledeps/gnu9-openmpi4 ---------------------------
fftw/3.3.8-static fftw/3.3.8 (D)

38 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

E 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 Table 2.

39 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 2: 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-gnu9-geopm Global Extensible Open Power Manager for use with GNU compiler toolchain.
ohpc-gnu9-io-libs Collection of IO library builds for use with GNU compiler toolchain.
ohpc-gnu9-mpich-io-libs Collection of IO library builds for use with GNU compiler toolchain and the
MPICH runtime.
ohpc-gnu9-mpich-parallel-libs Collection of parallel library builds for use with GNU compiler toolchain and
the MPICH runtime.
ohpc-gnu9-mpich-perf-tools Collection of performance tool builds for use with GNU compiler toolchain
and the MPICH runtime.
ohpc-gnu9-mvapich2-io-libs Collection of IO library builds for use with GNU compiler toolchain and the
MVAPICH2 runtime.
ohpc-gnu9-mvapich2-parallel-libs Collection of parallel library builds for use with GNU compiler toolchain and
the MVAPICH2 runtime.
ohpc-gnu9-mvapich2-perf-tools Collection of performance tool builds for use with GNU compiler toolchain
and the MVAPICH2 runtime.
ohpc-gnu9-openmpi4-io-libs Collection of IO library builds for use with GNU compiler toolchain and the
OpenMPI runtime.
ohpc-gnu9-openmpi4-parallel-libs Collection of parallel library builds for use with GNU compiler toolchain and
the OpenMPI runtime.
ohpc-gnu9-openmpi4-perf-tools Collection of performance tool builds for use with GNU compiler toolchain
and the OpenMPI runtime.
ohpc-gnu9-parallel-libs Collection of parallel library builds for use with GNU compiler toolchain.
ohpc-gnu9-perf-tools Collection of performance tool builds for use with GNU compiler toolchain.
ohpc-gnu9-python-libs Collection of python related library builds for use with GNU compiler
toolchain.
ohpc-gnu9-python3-libs Collection of python3 related library builds for use with GNU compiler
toolchain.
ohpc-gnu9-runtimes Collection of runtimes for use with GNU compiler toolchain.
ohpc-gnu9-serial-libs Collection of serial library builds for use with GNU compiler toolchain.
ohpc-intel-geopm Global Extensible Open Power Manager for use with Intel(R) Parallel Studio
XE software suite.
ohpc-intel-impi-io-libs Collection of IO library builds for use with Intel(R) Parallel Studio XE soft-
ware suite and Intel(R) MPI runtime.
ohpc-intel-impi-parallel-libs Collection of parallel library builds for use with Intel(R) Parallel Studio XE
toolchain and the Intel(R) MPI Library.
ohpc-intel-impi-perf-tools Collection of performance tool builds for use with Intel(R) Parallel Studio XE
compiler toolchain and the Intel(R) MPI runtime.
ohpc-intel-io-libs Collection of IO library builds for use with Intel(R) Parallel Studio XE soft-
ware suite.
ohpc-intel-mpich-io-libs Collection of IO library builds for use with Intel(R) Parallel Studio XE soft-
ware suite and MPICH runtime.
ohpc-intel-mpich-parallel-libs Collection of parallel library builds for use with Intel(R) Parallel Studio XE
toolchain and the MPICH runtime.
ohpc-intel-mpich-perf-tools Collection of performance tool builds for use with Intel(R) Parallel Studio XE
compiler toolchain and the MPICH runtime.

40 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 2 (cont): Available OpenHPC Meta-packages

Group Name Description
ohpc-intel-mvapich2-io-libs Collection of IO library builds for use with Intel(R) Parallel Studio XE software
suite and MVAPICH2 runtime.
ohpc-intel-mvapich2-parallel-libs Collection of parallel library builds for use with Intel(R) Parallel Studio XE
toolchain and the MVAPICH2 runtime.
ohpc-intel-mvapich2-perf-tools Collection of performance tool builds for use with Intel(R) Parallel Studio XE
compiler toolchain and the MVAPICH2 runtime.
ohpc-intel-openmpi4-io-libs Collection of IO library builds for use with Intel(R) Parallel Studio XE software
suite and OpenMPI runtime.
ohpc-intel-openmpi4-parallel-libs Collection of parallel library builds for use with Intel(R) Parallel Studio XE
toolchain and the OpenMPI runtime.
ohpc-intel-openmpi4-perf-tools Collection of performance tool builds for use with Intel(R) Parallel Studio XE
compiler toolchain and the OpenMPI runtime.
ohpc-intel-perf-tools Collection of performance tool builds for use with Intel(R) Parallel Studio XE
toolchain.
ohpc-intel-python3-libs Collection of python3 related library builds for use with Intel(R) Parallel Stu-
dio XE toolchain.
ohpc-intel-runtimes Collection of runtimes for use with Intel(R) Parallel Studio XE toolchain.
ohpc-intel-serial-libs Collection of serial library builds for use with Intel(R) Parallel Studio XE
toolchain.
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.

41 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

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 §4.6. The relevant package groupings and associated Table references are as follows:

• Administrative tools (Table 3)
• Provisioning (Table 4)
• Resource management (Table 5)
• Compiler families (Table 6)
• MPI families (Table 7)
• Development tools (Table 8)
• Performance analysis tools (Table 9)
• IO Libraries (Table 10)
• Runtimes (Table 11)
• Serial/Threaded Libraries (Table 12)
• Parallel Libraries (Table 13)

42 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 3: Administrative Tools

RPM Package Name Version Info/URL
ConMan: The Console Manager.
conman-ohpc 0.3.0
http://dun.github.io/conman
OpenHPC documentation.
docs-ohpc 2.0.0
https://github.com/openhpc/ohpc
Example source code and templates for use within OpenHPC
examples-ohpc 2.0
environment. https://github.com/openhpc/ohpc
Static cluster configuration database.
genders-ohpc 1.27
https://github.com/chaos/genders
lmod-defaults-gnu9-impi-ohpc
lmod-defaults-gnu9-mpich-ofi-ohpc
lmod-defaults-gnu9-mpich-ucx-ohpc
lmod-defaults-gnu9-mvapich2-ohpc
OpenHPC default login environments.
lmod-defaults-gnu9-openmpi4-ohpc 2.0
https://github.com/openhpc/ohpc
lmod-defaults-intel-impi-ohpc
lmod-defaults-intel-mpich-ohpc
lmod-defaults-intel-mvapich2-ohpc
lmod-defaults-intel-openmpi4-ohpc
Lua based Modules (lmod).
lmod-ohpc 8.2.10
https://github.com/TACC/Lmod
A Linux operating system framework for managing HPC clus-
losf-ohpc 0.56.0
ters. https://github.com/hpcsi/losf
Remote shell program that uses munge authentication.
mrsh-ohpc 2.12
https://github.com/chaos/mrsh
LBNL Node Health Check.
nhc-ohpc 1.4.2
https://github.com/mej/nhc
OpenHPC release files.
ohpc-release 2
https://github.com/openhpc/ohpc
Parallel remote shell program.
pdsh-ohpc 2.34
https://github.com/chaos/pdsh
Convenience utility for parallel job launch.
prun-ohpc 2.0
https://github.com/openhpc/ohpc
Integration test suite for OpenHPC.
test-suite-ohpc 2.0.0
https://github.com/openhpc/ohpc/tests

43 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 4: Provisioning

RPM Package Name Version Info/URL
Scalable systems management suite for high performance
warewulf-common-ohpc 3.9.0
clusters. http://warewulf.lbl.gov
Warewulf - Add IPMI to aarch64 initramfs.
warewulf-ipmi-ohpc-initramfs-aarch64 3.9.0
http://warewulf.lbl.gov
Warewulf - Add IPMI to x86 64 initramfs.
warewulf-ipmi-ohpc-initramfs-x86 64 3.9.0
http://warewulf.lbl.gov
Warewulf - GPL sources used in Warewulf provisioning.
warewulf-provision-ohpc-gpl sources 3.9.0
http://warewulf.lbl.gov
Warewulf - HPC cluster configuration.
warewulf-cluster-ohpc 3.9.0
http://warewulf.lbl.gov
Warewulf - IPMI support.
warewulf-ipmi-ohpc 3.9.0
http://warewulf.lbl.gov
Warewulf - Install local database server.
warewulf-common-ohpc-localdb 3.9.0
http://warewulf.lbl.gov
Warewulf - System provisioning core.
warewulf-provision-ohpc 3.9.0
http://warewulf.lbl.gov
Warewulf - System provisioning server.
warewulf-provision-ohpc-server 3.9.0
http://warewulf.lbl.gov
Warewulf - Virtual Node File System support.
warewulf-vnfs-ohpc 3.9.0
http://warewulf.lbl.gov
Warewulf - iPXE Bootloader for aarch64.
warewulf-provision-ohpc-server-ipxe-aarch64 3.9.0
http://warewulf.lbl.gov
Warewulf - iPXE Bootloader for x86 64.
warewulf-provision-ohpc-server-ipxe-x86 64 3.9.0
http://warewulf.lbl.gov
Warewulf - initramfs base for aarch64.
warewulf-provision-ohpc-initramfs-aarch64 3.9.0
http://warewulf.lbl.gov
Warewulf - initramfs base for x86 64.
warewulf-provision-ohpc-initramfs-x86 64 3.9.0
http://warewulf.lbl.gov

44 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 5: Resource Management

RPM Package Name Version Info/URL
OpenPBS for an execution host.
openpbs-execution-ohpc 20.0.0
http://www.openpbs.org
OpenPBS for a client host.
openpbs-client-ohpc 20.0.0
http://www.openpbs.org
OpenPBS for a server host.
openpbs-server-ohpc 20.0.0
http://www.openpbs.org
An extended/exascale implementation of PMI.
pmix-ohpc 3.1.4
https://pmix.github.io/pmix
Development package for Slurm.
slurm-devel-ohpc 20.02.5
https://slurm.schedmd.com
Example config files for Slurm.
slurm-example-configs-ohpc 20.02.5
https://slurm.schedmd.com
PAM module for restricting access to compute nodes via Slurm.
slurm-pam slurm-ohpc 20.02.5
https://slurm.schedmd.com
Perl API to Slurm.
slurm-perlapi-ohpc 20.02.5
https://slurm.schedmd.com
Perl tool to print Slurm job state information.
slurm-contribs-ohpc 20.02.5
https://slurm.schedmd.com
Slurm Workload Manager.
slurm-ohpc 20.02.5
https://slurm.schedmd.com
Slurm compute node daemon.
slurm-slurmd-ohpc 20.02.5
https://slurm.schedmd.com
Slurm controller daemon.
slurm-slurmctld-ohpc 20.02.5
https://slurm.schedmd.com
Slurm database daemon.
slurm-slurmdbd-ohpc 20.02.5
https://slurm.schedmd.com
Slurmś implementation of the pmi libraries.
slurm-libpmi-ohpc 20.02.5
https://slurm.schedmd.com
Torque/PBS wrappers for transition from Torque/PBS to Slurm.
slurm-torque-ohpc 20.02.5
https://slurm.schedmd.com
openlava/LSF wrappers for transition from OpenLava/LSF to
slurm-openlava-ohpc 20.02.5
Slurm. https://slurm.schedmd.com

Table 6: Compiler Families

RPM Package Name Version Info/URL
The GNU C Compiler and Support Files.
gnu9-compilers-ohpc 9.3.0
http://gcc.gnu.org
OpenHPC compatibility package for Intel(R) Parallel Studio
intel-compilers-devel-ohpc 2020
XE. https://github.com/openhpc/ohpc

45 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 7: MPI Families / Communication Libraries

RPM Package Name Version Info/URL
OpenHPC compatibility package for Intel(R) MPI Library.
intel-mpi-devel-ohpc 2020
https://github.com/openhpc/ohpc
User-space RDMA Fabric Interfaces.
libfabric-ohpc 1.10.1
http://www.github.com/ofiwg/libfabric
mpich-ofi-gnu9-ohpc MPICH MPI implementation.
3.3.2
mpich-ofi-intel-ohpc http://www.mpich.org
mpich-ucx-gnu9-ohpc MPICH MPI implementation.
3.3.2
mpich-ucx-intel-ohpc http://www.mpich.org
mvapich2-gnu9-ohpc
mvapich2-intel-ohpc OSU MVAPICH2 MPI implementation.
2.3.2
mvapich2-psm2-gnu9-ohpc http://mvapich.cse.ohio-state.edu
mvapich2-psm2-intel-ohpc
openmpi4-gnu9-ohpc A powerful implementation of MPI/SHMEM.
4.0.4
openmpi4-intel-ohpc http://www.open-mpi.org
UCX is a communication library implementing high-
ucx-ohpc 1.8.0
performance messaging. http://www.openucx.org

46 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 8: Development Tools

RPM Package Name Version Info/URL
Software build and installation framework.
EasyBuild-ohpc 4.3.0
https://easybuilders.github.io/easybuild
A GNU tool for automatically creating Makefiles.
automake-ohpc 1.16.1
http://www.gnu.org/software/automake
A GNU tool for automatically configuring source code.
autoconf-ohpc 2.69
http://www.gnu.org/software/autoconf
CMake is an open-source, cross-platform family of tools
cmake-ohpc 3.16.2
designed to build, test and package software. https:
//cmake.org
Portable Hardware Locality.
hwloc-ohpc 2.1.0
http://www.open-mpi.org/projects/hwloc
The GNU Portable Library Tool.
libtool-ohpc 2.4.6
http://www.gnu.org/software/libtool
python3-scipy-gnu9-mpich-ohpc
Scientific Tools for Python.
python3-scipy-gnu9-mvapich2-ohpc 1.5.1
http://www.scipy.org
python3-scipy-gnu9-openmpi4-ohpc
python3-numpy-gnu9-ohpc NumPy array processing for numbers, strings, records
1.19.0
python3-numpy-intel-ohpc and objects. https://github.com/numpy/numpy
python3-mpi4py-gnu9-impi-ohpc
python3-mpi4py-gnu9-mpich-ohpc
python3-mpi4py-gnu9-mvapich2-ohpc
Python bindings for the Message Passing Interface
python3-mpi4py-gnu9-openmpi4-ohpc
3.0.3 (MPI) standard.
python3-mpi4py-intel-impi-ohpc
https://bitbucket.org/mpi4py/mpi4py
python3-mpi4py-intel-mpich-ohpc
python3-mpi4py-intel-mvapich2-ohpc
python3-mpi4py-intel-openmpi4-ohpc
HPC software package management.
spack-ohpc 0.15.0
https://github.com/LLNL/spack
Valgrind Memory Debugger.
valgrind-ohpc 3.15.0
http://www.valgrind.org

47 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 9: Performance Analysis Tools

RPM Package Name Version Info/URL
dimemas-gnu9-impi-ohpc
dimemas-gnu9-mpich-ohpc
dimemas-gnu9-mvapich2-ohpc
dimemas-gnu9-openmpi4- Dimemas tool.
5.4.2
ohpc https://tools.bsc.es
dimemas-intel-impi-ohpc
dimemas-intel-mpich-ohpc
dimemas-intel-mvapich2-ohpc
dimemas-intel-openmpi4-ohpc
extrae-gnu9-impi-ohpc
extrae-gnu9-mpich-ohpc
extrae-gnu9-mvapich2-ohpc
extrae-gnu9-openmpi4-ohpc Extrae tool.
3.7.0
extrae-intel-impi-ohpc https://tools.bsc.es
extrae-intel-mpich-ohpc
extrae-intel-mvapich2-ohpc
extrae-intel-openmpi4-ohpc
geopm-gnu9-impi-ohpc
geopm-gnu9-mpich-ohpc
geopm-gnu9-mvapich2-ohpc
geopm-gnu9-openmpi4-ohpc Global Extensible Open Power Manager.
1.1.0
geopm-intel-impi-ohpc https://geopm.github.io
geopm-intel-mpich-ohpc
geopm-intel-mvapich2-ohpc
geopm-intel-openmpi4-ohpc
imb-gnu9-impi-ohpc
imb-gnu9-mpich-ohpc
imb-gnu9-mvapich2-ohpc
Intel MPI Benchmarks (IMB).
imb-gnu9-openmpi4-ohpc
2019.6 https://software.intel.com/en-us/articles/
imb-intel-impi-ohpc
intel-mpi-benchmarks
imb-intel-mpich-ohpc
imb-intel-mvapich2-ohpc
imb-intel-openmpi4-ohpc
likwid-gnu9-ohpc Performance tools for the Linux console.
5.0.1
likwid-intel-ohpc https://github.com/RRZE-HPC/likwid
Allows safer access to model specific registers (MSRs).
msr-safe-ohpc 1.4.0
https://github.com/LLNL/msr-safe
Allows safer access to model specific registers (MSRs).
msr-safe-ohpc-kmp-default 1.4.0 k5.3.18 lp152.19
https://github.com/LLNL/msr-safe
omb-gnu9-impi-ohpc
omb-gnu9-mpich-ohpc
omb-gnu9-mvapich2-ohpc
omb-gnu9-openmpi4-ohpc OSU Micro-benchmarks.
5.6.2
omb-intel-impi-ohpc http://mvapich.cse.ohio-state.edu/benchmarks
omb-intel-mpich-ohpc
omb-intel-mvapich2-ohpc
omb-intel-openmpi4-ohpc
Paraver.
paraver-ohpc 4.8.2
https://tools.bsc.es
Performance Application Programming Interface.
papi-ohpc 5.7.0
http://icl.cs.utk.edu/papi

48 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 9 (cont): Performance Analysis Tools

RPM Package Name Version Info/URL
pdtoolkit-gnu9-ohpc PDT is a framework for analyzing source code.
3.25.1
pdtoolkit-intel-ohpc http://www.cs.uoregon.edu/Research/pdt
scalasca-gnu9-impi-ohpc
scalasca-gnu9-mpich-ohpc
scalasca-gnu9-mvapich2-ohpc
Toolset for performance analysis of large-scale parallel
scalasca-gnu9-openmpi4-ohpc
2.5 applications.
scalasca-intel-impi-ohpc
http://www.scalasca.org
scalasca-intel-mpich-ohpc
scalasca-intel-mvapich2-ohpc
scalasca-intel-openmpi4-ohpc
scorep-gnu9-impi-ohpc
scorep-gnu9-mpich-ohpc
scorep-gnu9-mvapich2-ohpc
Scalable Performance Measurement Infrastructure for
scorep-gnu9-openmpi4-ohpc
6.0 Parallel Codes.
scorep-intel-impi-ohpc
http://www.vi-hps.org/projects/score-p
scorep-intel-mpich-ohpc
scorep-intel-mvapich2-ohpc
scorep-intel-openmpi4-ohpc
tau-gnu9-impi-ohpc
tau-gnu9-mpich-ohpc
tau-gnu9-mvapich2-ohpc
tau-gnu9-openmpi4-ohpc Tuning and Analysis Utilities Profiling Package.
2.29
tau-intel-impi-ohpc http://www.cs.uoregon.edu/research/tau/home.php
tau-intel-mpich-ohpc
tau-intel-mvapich2-ohpc
tau-intel-openmpi4-ohpc

49 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 10: IO Libraries

RPM Package Name Version Info/URL
adios-gnu9-impi-ohpc
adios-gnu9-mpich-ohpc
adios-gnu9-mvapich2-ohpc
adios-gnu9-openmpi4-ohpc The Adaptable IO System (ADIOS).
1.13.1
adios-intel-impi-ohpc http://www.olcf.ornl.gov/center-projects/adios
adios-intel-mpich-ohpc
adios-intel-mvapich2-ohpc
adios-intel-openmpi4-ohpc
hdf5-gnu9-ohpc A general purpose library and file format for storing scientific
1.10.6
hdf5-intel-ohpc data. http://www.hdfgroup.org/HDF5
netcdf-cxx-gnu9-impi-ohpc
netcdf-cxx-gnu9-mpich-ohpc
netcdf-cxx-gnu9-mvapich2-ohpc
netcdf-cxx-gnu9-openmpi4-ohpc C++ Libraries for the Unidata network Common Data Form.
4.3.1
netcdf-cxx-intel-impi-ohpc http://www.unidata.ucar.edu/software/netcdf
netcdf-cxx-intel-mpich-ohpc
netcdf-cxx-intel-mvapich2-ohpc
netcdf-cxx-intel-openmpi4-ohpc
netcdf-fortran-gnu9-impi-ohpc
netcdf-fortran-gnu9-mpich-ohpc
netcdf-fortran-gnu9-mvapich2-ohpc
Fortran Libraries for the Unidata network Common Data
netcdf-fortran-gnu9-openmpi4-ohpc
4.5.2 Form.
netcdf-fortran-intel-impi-ohpc
http://www.unidata.ucar.edu/software/netcdf
netcdf-fortran-intel-mpich-ohpc
netcdf-fortran-intel-mvapich2-ohpc
netcdf-fortran-intel-openmpi4-ohpc
netcdf-gnu9-impi-ohpc
netcdf-gnu9-mpich-ohpc
netcdf-gnu9-mvapich2-ohpc
netcdf-gnu9-openmpi4-ohpc C Libraries for the Unidata network Common Data Form.
4.7.3
netcdf-intel-impi-ohpc http://www.unidata.ucar.edu/software/netcdf
netcdf-intel-mpich-ohpc
netcdf-intel-mvapich2-ohpc
netcdf-intel-openmpi4-ohpc
phdf5-gnu9-impi-ohpc
phdf5-gnu9-mpich-ohpc
phdf5-gnu9-mvapich2-ohpc
A general purpose library and file format for storing scientific
phdf5-gnu9-openmpi4-ohpc
1.10.6 data.
phdf5-intel-impi-ohpc
http://www.hdfgroup.org/HDF5
phdf5-intel-mpich-ohpc
phdf5-intel-mvapich2-ohpc
phdf5-intel-openmpi4-ohpc

50 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 10 (cont): IO Libraries

RPM Package Name Version Info/URL
pnetcdf-gnu9-impi-ohpc
pnetcdf-gnu9-mpich-ohpc
pnetcdf-gnu9-mvapich2-ohpc
pnetcdf-gnu9-openmpi4-ohpc A Parallel NetCDF library (PnetCDF).
1.12.1
pnetcdf-intel-impi-ohpc http://cucis.ece.northwestern.edu/projects/PnetCDF
pnetcdf-intel-mpich-ohpc
pnetcdf-intel-mvapich2-ohpc
pnetcdf-intel-openmpi4-ohpc
sionlib-gnu9-impi-ohpc
sionlib-gnu9-mpich-ohpc
sionlib-gnu9-mvapich2-ohpc
Scalable I/O Library for Parallel Access to Task-Local Files.
sionlib-gnu9-openmpi4-ohpc
1.7.4 http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/
sionlib-intel-impi-ohpc
Software/SIONlib/ node.html
sionlib-intel-mpich-ohpc
sionlib-intel-mvapich2-ohpc
sionlib-intel-openmpi4-ohpc

51 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 11: Runtimes

RPM Package Name Version Info/URL
Lightweight user-defined software stacks for high-performance
charliecloud-ohpc 0.15
computing. https://hpc.github.io/charliecloud
Application and environment virtualization.
singularity-ohpc 3.4.2
https://www.sylabs.io/singularity

Table 12: Serial/Threaded Libraries

RPM Package Name Version Info/URL
R is a language and environment for statistical computing and
R-gnu9-ohpc 3.6.3
graphics (S-Plus like). http://www.r-project.org
gsl-gnu9-ohpc GNU Scientific Library (GSL).
2.6
gsl-intel-ohpc http://www.gnu.org/software/gsl
metis-gnu9-ohpc Serial Graph Partitioning and Fill-reducing Matrix Ordering.
5.1.0
metis-intel-ohpc http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
An optimized BLAS library based on GotoBLAS2.
openblas-gnu9-ohpc 0.3.7
http://www.openblas.net
plasma-gnu9-ohpc Parallel Linear Algebra Software for Multicore Architectures.
2.8.0
plasma-intel-ohpc https://bitbucket.org/icl/plasma
scotch-gnu9-ohpc Graph, mesh and hypergraph partitioning library.
6.0.6
scotch-intel-ohpc http://www.labri.fr/perso/pelegrin/scotch
superlu-gnu9-ohpc A general purpose library for the direct solution of linear
5.2.1
superlu-intel-ohpc equations. http://crd.lbl.gov/∼xiaoye/SuperLU

52 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 13: Parallel Libraries

RPM Package Name Version Info/URL
boost-gnu9-impi-ohpc
boost-gnu9-mpich-ohpc
boost-gnu9-mvapich2-ohpc
boost-gnu9-openmpi4-ohpc Boost free peer-reviewed portable C++ source libraries.
1.73.0
boost-intel-impi-ohpc http://www.boost.org
boost-intel-mpich-ohpc
boost-intel-mvapich2-ohpc
boost-intel-openmpi4-ohpc
fftw-gnu9-impi-ohpc
fftw-gnu9-mpich-ohpc A Fast Fourier Transform library.
3.3.8
fftw-gnu9-mvapich2-ohpc http://www.fftw.org
fftw-gnu9-openmpi4-ohpc
hypre-gnu9-impi-ohpc
hypre-gnu9-mpich-ohpc
hypre-gnu9-mvapich2-ohpc
hypre-gnu9-openmpi4-ohpc Scalable algorithms for solving linear systems of equations.
2.18.1
hypre-intel-impi-ohpc http://www.llnl.gov/casc/hypre
hypre-intel-mpich-ohpc
hypre-intel-mvapich2-ohpc
hypre-intel-openmpi4-ohpc
mfem-gnu9-impi-ohpc
mfem-gnu9-mpich-ohpc
mfem-gnu9-mvapich2-ohpc
Lightweight, general, scalable C++ library for finite element
mfem-gnu9-openmpi4-ohpc
4.1 methods.
mfem-intel-impi-ohpc
http://mfem.org
mfem-intel-mpich-ohpc
mfem-intel-mvapich2-ohpc
mfem-intel-openmpi4-ohpc
mumps-gnu9-impi-ohpc
mumps-gnu9-mpich-ohpc
mumps-gnu9-mvapich2-ohpc
mumps-gnu9-openmpi4-ohpc A MUltifrontal Massively Parallel Sparse direct Solver.
5.2.1
mumps-intel-impi-ohpc http://mumps.enseeiht.fr
mumps-intel-mpich-ohpc
mumps-intel-mvapich2-ohpc
mumps-intel-openmpi4-ohpc
opencoarrays-gnu9-impi-ohpc
ABI to leverage the parallel programming features of the
opencoarrays-gnu9-mpich-ohpc
2.8.0 Fortran 2018 DIS.
opencoarrays-gnu9-mvapich2-ohpc
http://www.opencoarrays.org
opencoarrays-gnu9-openmpi4-ohpc
petsc-gnu9-impi-ohpc
petsc-gnu9-mpich-ohpc
petsc-gnu9-mvapich2-ohpc
petsc-gnu9-openmpi4-ohpc Portable Extensible Toolkit for Scientific Computation.
3.13.1
petsc-intel-impi-ohpc http://www.mcs.anl.gov/petsc
petsc-intel-mpich-ohpc
petsc-intel-mvapich2-ohpc
petsc-intel-openmpi4-ohpc

53 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

Table 13 (cont): Parallel Libraries

RPM Package Name Version Info/URL
ptscotch-gnu9-impi-ohpc
ptscotch-gnu9-mpich-ohpc
ptscotch-gnu9-mvapich2-ohpc
ptscotch-gnu9-openmpi4-ohpc Graph, mesh and hypergraph partitioning library using MPI.
6.0.6
ptscotch-intel-impi-ohpc http://www.labri.fr/perso/pelegrin/scotch
ptscotch-intel-mpich-ohpc
ptscotch-intel-mvapich2-ohpc
ptscotch-intel-openmpi4-ohpc
scalapack-gnu9-impi-ohpc
scalapack-gnu9-mpich-ohpc
scalapack-gnu9-mvapich2-ohpc
A subset of LAPACK routines redesigned for heterogenous
scalapack-gnu9-openmpi4-ohpc
2.1.0 computing.
scalapack-intel-impi-ohpc
http://www.netlib.org/lapack-dev
scalapack-intel-mpich-ohpc
scalapack-intel-mvapich2-ohpc
scalapack-intel-openmpi4-ohpc
slepc-gnu9-impi-ohpc
slepc-gnu9-mpich-ohpc
slepc-gnu9-mvapich2-ohpc
slepc-gnu9-openmpi4-ohpc A library for solving large scale sparse eigenvalue problems.
3.13.2
slepc-intel-impi-ohpc http://slepc.upv.es
slepc-intel-mpich-ohpc
slepc-intel-mvapich2-ohpc
slepc-intel-openmpi4-ohpc
superlu dist-gnu9-impi-ohpc
superlu dist-gnu9-mpich-ohpc
superlu dist-gnu9-mvapich2-ohpc
A general purpose library for the direct solution of linear
superlu dist-gnu9-openmpi4-ohpc
6.1.1 equations.
superlu dist-intel-impi-ohpc
http://crd-legacy.lbl.gov/∼xiaoye/SuperLU
superlu dist-intel-mpich-ohpc
superlu dist-intel-mvapich2-ohpc
superlu dist-intel-openmpi4-ohpc
trilinos-gnu9-impi-ohpc
trilinos-gnu9-mpich-ohpc
trilinos-gnu9-mvapich2-ohpc
trilinos-gnu9-openmpi4-ohpc A collection of libraries of numerical algorithms.
13.0.0
trilinos-intel-impi-ohpc https://trilinos.org
trilinos-intel-mpich-ohpc
trilinos-intel-mvapich2-ohpc
trilinos-intel-openmpi4-ohpc

54 Rev: 1e970dd16
Install Guide (v2.0): OpenSUSE Leap 15.2/x86 64 + Warewulf + OpenPBS

F 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: 5392 744D 3C54 3ED5 7847 65E6 8A30 6019 DA565C6C

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.

[sms]# rpm --checksig -v docs-ohpc-*.rpm
docs-ohpc-2.0.0-72.1.ohpc.2.0.x86_64.rpm:
Header V3 RSA/SHA1 Signature, key ID da565c6c: OK
Header SHA256 digest: OK
Header SHA1 digest: OK
Payload SHA256 digest: OK
V3 RSA/SHA1 Signature, key ID da565c6c: OK
MD5 digest: OK

55 Rev: 1e970dd16