Running ASReml on Linux

To run ASReml on a Linux system can be very tricky. This software has built its reputation. It then don’t care very much about its custormers. The following valid instructions were after many combination tests. Had you any other alternatives, I would not recommend ASReml, especially on Linux, where most serious computations are carried on nowadays.

The following instructions are to run a cloud instance of AlmaLinux9 one a AlmaLinux 10 system.

AlmaLinux 9 Cloud Image Setup (Alma 10 Host)

Summary of the successful steps to provision an AlmaLinux 9 VM using virt-install and cloud-init.

1. Prerequisites

Ensure virtualization tools are installed and the default network is active:

sudo dnf install -y virt-install libvirt qemu-img libguestfs-tools
sudo systemctl enable --now libvirtd
sudo virsh net-start default

2. Prepare the Image

# Download image
curl -O https://repo.almalinux.org/almalinux/9/cloud/x86_64/images/AlmaLinux-9-GenericCloud-latest.x86_64.qcow2

# Move to storage and resize
sudo mv AlmaLinux-9-GenericCloud-latest.x86_64.qcow2 /var/lib/libvirt/images/almalinux9.qcow2
sudo qemu-img resize /var/lib/libvirt/images/almalinux9.qcow2 20G

3. Create Cloud-Init Configuration

Create a user-data file. Note: Use the correct public key path (e.g., id_ed25519.pub or id_rsa.pub).

#cloud-config
ssh_pwauth: True
users:
  - name: almalinux
    sudo: ALL=(ALL) NOPASSWD:ALL
    lock_passwd: false
    ssh_authorized_keys:
      - ssh-ed25519 AAA... (paste your .pub key here)

4. Provision VM

sudo virt-install 
  --name alma9 
  --memory 12288 
  --vcpus 4 
  --os-variant almalinux9 
  --disk path=/var/lib/libvirt/images/almalinux9.qcow2,format=qcow2 
  --import 
  --network network=default 
  --cloud-init user-data=user-data 
  --graphics none 
  --noautoconsole

5. Accessing the VM

From the Host Machine

Find the IP and SSH in:

sudo virsh net-dhcp-leases default
ssh almalinux@<VM_IP>

From Another Machine (Remote Access)

Since the VM is on a private bridge (192.168.122.x), it is not directly reachable from your local network. Use one of these methods:

Method A: SSH Jump/Proxy (Easiest)

Use the host machine as a gateway. This can also be configured in your .ssh/config:

ssh -J user@host-ip almalinux@<VM_IP>

Install R on the VM

#!/bin/bash

# Install R4.2.3 may cause trouble to install `ASRgenomics` 
# So I removed the R4.2.3 part
# R 4.2.3 Installation Script for AlmaLinux 9
# Based on Posit's pre-compiled binaries

set -e

echo "Enabling EPEL and CRB repositories..."
sudo dnf install -y epel-release
sudo dnf install -y dnf-plugins-core
sudo dnf config-manager --set-enabled crb

#export R_VERSION=4.2.3

#echo "Installing R ${R_VERSION}..."
#sudo dnf install -y https://cdn.posit.co/r/rhel-9/pkgs/R-${R_VERSION}-1-1.x86_64.rpm
echo "Installing R ..."
sudo dnf install R # R 4.5

echo "Verifying installation..."
#/opt/R/${R_VERSION}/bin/R --version

#echo "Creating symbolic links to /usr/local/bin..."
#sudo ln -sf /opt/R/${R_VERSION}/bin/R /usr/local/bin/R
#sudo ln -sf /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript

echo "R installation complete."

Install ASReml-R

Before start R

Start R:

install.packages(c("data.table", "ggplot2", "jsonlite"))
install.packages("path/to/asreml_4.2.0.393_R_x86_64-pc-linux-gnu.tar.gz")

Configure license server route

I had trouble with the license server. ASReml needs to contact the Reprise License Management (RLM) server through port 5053.

sudo ufw status # => inactiave

showing that the port is not blocked by the local computer.

nc -zv ls34.rlmcloud.com 5053 # with wired network
# Ncat: TIMEOUT.
 
nc -zv ls34.rlmcloud.com 5053 # with eduroam
# Ncat: Connected to 54.183.111.138:5053.
# Ncat: 0 bytes sent, 0 bytes received in 0.19 seconds.

confirmed that the port is not open for the wired net at campus level.

Solution

To temporarily force the license request go through eduroam:

sudo ip route add 54.183.111.138 via 10.42.32.1 dev wlo1

To permanently add the route:

nmcli connection show # to find the wifi/eduroam name
sudo nmcli connection modify eduroam +ipv4.routes "54.183.111.138/32 10.42.32.1"
sudo nmcli connection down eduroam && sudo nmcli connection up eduroam

Test ASReml-R

Run the following R script:

# asreml-r basic test script
library(asreml)

# 1. Generate a small simulated dataset
set.seed(42)
n <- 100
data <- data.frame(
  Yield = rnorm(n, mean = 50, sd = 10),
  Variety = factor(sample(paste0("V", 1:5), n, replace = TRUE)),
  Block = factor(sample(paste0("B", 1:4), n, replace = TRUE))
)

# 2. Fit a basic linear mixed model
# Fixed effect: Variety
# Random effect: Block
cat("Fitting model...
")
model <- asreml(
  fixed = Yield ~ Variety,
  random = ~ Block,
  data = data
)

# 3. Print results
cat("
--- Variance Components ---
")
print(summary(model)$varcomp)

cat("
--- Wald Test for Fixed Effects ---
")
print(wald(model))

cat("
ASReml-R test complete.
")