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Purpose

A proof-of-concept high-performance server for primary and secondary NGS analyses with reasonable TAT and a USD $3000 budget.

Hardware and OS

Acquired a Dell XPS 8950 tower desktop in mid 2022 with the following specs. To support ECC memory, we could have gotten a Dell Precision 3660, but that goes over budget.

  • Intel Core i9-12900K (best single-thread performance; added liquid cooling option)
  • 64GB DDR5-4400 Memory (sufficient for most NGS algorithms, except maybe de novo assembly)
  • 1x 960GB Intel Optane 905P PCIe NVMe SSD (nvme2n1) (overkill for a boot disk; regular SSD is fine)
  • 2x 2TB Samsung 980 Pro PCIe NVMe SSD (nvme0n1, nvme1n1)

We'll choose to install Clear Linux for the latest kernel optimized for performance on Intel CPUs.

  1. On a Windows PC, download the Clear Linux Desktop ISO image.
  2. Boot into BIOS on the server (press F2 during Dell logo), and ensure that:
    • SATA Operation is set to AHCI (disables hardware RAID)
    • Secure Boot is disabled (does not work with Clear Linux)
    • AC Recovery is set to Last Power State
    • POST Behaviour is set to Continue on Warnings and Keyboard Error Detection is disabled
    • Virtualization, VT for Direct I/O, and Trusted Execution are enabled
  3. Follow these instructions to create a bootable USB stick.
  4. Plug in the USB stick and boot into it (press F12 during Dell logo).
  5. After the live desktop image boots, click "Clear Linux OS installer" on the dock and follow instructions.
  6. Use the smaller SSD (nvme2n1) as the installation media and add yourself as a sudo user.
  7. Click "Advanced Options" to set the hostname, make sure other options are set to your preference, and click "Install".
  8. After booting into the installed OS, start Terminal and install the following: 
    sudo swupd update
sudo swupd bundle-add -y openssh-server storage-utils clr-network-troubleshooter
sudo systemctl enable --now sshd.socket
  9. Create a unix group for your team (E.g. dx below) and make it your primary group: 
    sudo groupadd dx
sudo usermod -g dx $USER
sudo groupdel $USER
  10. Create a level 0 RAID using the two larger SSDs and make it writable for your team: 
    sudo mdadm --create --verbose --level=0 --raid-devices=2 /dev/md0 /dev/nvme0n1 /dev/nvme1n1
sudo mkfs.ext4 -F /dev/md0
sudo blkid -o value /dev/md0 | head -n1 | xargs -I{} echo "UUID={} /hot ext4 defaults,noatime 0 2" | sudo tee -a /etc/fstab
sudo mount /hot
sudo chown $USER:dx /hot
sudo chmod 775 /hot
  11. Use Samba and NetBIOS to share the folder /hot over the network: 
    sudo mkdir -p /etc/samba
echo -e "[hot]\n  path=/hot\n  writeable=yes" | sudo tee -a /etc/samba/smb.conf
sudo systemctl enable --now smb
sudo systemctl enable --now nmb
  12. Set a samba password for your username using sudo smbpasswd -a $USER