All posts by nicholas

Move git subdirectory into new repo

I had a need to take a folder in one git repository and create a whole new git repository with it, preserving history for all files inside. My desire to keep git history made the process a bit more complicated than simply copying the directory into a new git repository.

First, create a new folder on the git server. I’m all command line, no GUI yet, so I need to make it a bare repository. (Thanks to geeksforgeeks on how to to do this)

#On the main git "server"
mkdir <reponame>.git
cd <reponame>.git
git init --bare

Now, on the desktop (not the git server) clone a copy of the repository with your desired folder into a new directory, remove the git origin server, then strip out everything except that directory (thanks to gbayer.com for the info)

#On the desktop
git clone <initial git repository url> <new_directory_name>
cd <new_directory_name>
git remote rm origin
git filter-branch --subdirectory-filter <directory_to_keep_history_of> -- --all

Lastly, (still on the desktop in the new repository directory) create a new origin with the path of the new repo you created above

#On the desktop, inside new_directory_name
git remote add origin <server>:<path_to_new_repo_folder>
git push --set-upstream origin master

DIY IP KVM

In general I try to buy server-class hardware for my home lab, primarily so that I could have IPMI / Remote access console for remote OS installation & troubleshooting. I recently got a new desktop and found myself with a Threadripper 1950x that would make an excellent addition to my server cluster. The one problem being it’s a desktop-class board, so it does not have any IPMI / remote access device.

I solved my problem with pikvm. It works wonderfully! Pikvm uses a raspberry pi with some additional hardware and software to interface with a system to control power & reset capabilities, as well as KVM functions with the ability to upload OS images and do OS installations remotely. The whole project cost me about $150 since I didn’t have some of the essential items for it. It could definitely be cheaper if I didn’t buy large packs of items or already had some electronics components.

The process was straightforward as outlined on their github page. The only snag I ran into was creating the USB Y (split) cable. It did not work the first time, so I had to tear it all down and start again. One cable I used had more than 4 wires (3 red wires, 1 black, 1 green, 1 white, and 1 yellow.) When I re-assembled to include the yellow wire with the red and black, it all worked.

My custom made Y cable (made from two cables I had lying around)
fully assembled and ready to test
Attached to a test motherboard

I scavenged the metal mounting bracket from some old networking adapter cards. With those I was able to mount the pi and the HDMI-in module to two standard PCI express card slots. I accidentally destroyed one of my SD cards while doing this so be careful if you try it! The PI is mounted at a slight angle so as to not damage the SD card. I had to mount it backwards (ethernet in the back) because I couldn’t get power to it otherwise (power port right up against the motherboard.) My workaround for this was to custom make a short length ethernet cord and use an RJ45 coupler on the outside of the chassis to provide an easy to access network port for the pi.

I wired the power & reset switch, as well as HDD and power LEDs in parallel so they would function with the chassis as well as with the KVM. To do this simply get some male-to-male jumper wires. On one end plug into the chassis wire, and on the other plug into the corresponding positive and negative slots right next to the ones going to the pi.

Cable management nightmare. But it works XD
Finished product

Broadboard pinout: https://github.com/pikvm/pikvm/blob/master/img/v2.png

USB split cable diagram: https://github.com/pikvm/pikvm/blob/master/img/v2_splitter.png

Parts list:

Raspberry Pi 4B 2GB edition: https://www.amazon.com/gp/product/B07TD42S27/ref=ppx_yo_dt_b_asin_title_o04_s00?ie=UTF8&psc=1

Raspberry Pi 4 headsink pack: https://www.amazon.com/gp/product/B07ZLZRDXZ/ref=ppx_yo_dt_b_asin_title_o02_s00?ie=UTF8&psc=1

Raspberry Pi HDMI in Module: https://www.amazon.com/gp/product/B0899L6ZXZ/ref=ppx_yo_dt_b_asin_title_o03_s00?ie=UTF8&psc=1

16GB Micro SD card: https://www.amazon.com/gp/product/B073K14CVB/ref=ppx_yo_dt_b_asin_title_o04_s01?ie=UTF8&psc=1

1 foot HDMI cable: https://www.amazon.com/gp/product/B00DI88XEG/ref=ppx_yo_dt_b_asin_title_o00_s00?ie=UTF8&psc=1

Breadboard 3 pack: https://www.amazon.com/gp/product/B077DN2PS1/ref=ppx_yo_dt_b_asin_title_o04_s01?ie=UTF8&psc=1

Breadboard Jumper Wires: https://www.amazon.com/gp/product/B07GD2BWPY/ref=ppx_yo_dt_b_asin_title_o04_s00?ie=UTF8&psc=1

Resistor Assortment Kit: https://www.amazon.com/gp/product/B0792M83JH/ref=ppx_yo_dt_b_asin_title_o04_s00?ie=UTF8&psc=1

390 OHM resistors: https://www.amazon.com/gp/product/B07QK9NFGT/ref=ppx_yo_dt_b_asin_title_o04_s01?ie=UTF8&psc=1

SSR relays: https://www.digikey.com/product-detail/en/G3VM-61A1/Z2100-ND/673290

windows 10 KERNEL_SECURITY_CHECK_FAILED in qemu vm

I upgraded to a shiny new AMD Ryzen 3rd gen processer (Threadripper 3960x.) After doing so I could not boot up my Windows 10 gaming VM (it uses VFIO / PCI Passthrough for the video card.) The message I kept getting as it tried to boot was:

KERNEL_SECURITY_CHECK_FAILED

After reading this reddit thread and this one It turns out it’s a culmination of a few things:

  • Running Linux kernel greater than 5.4
  • Running QEMU 5
  • Using 3rd gen AMD Ryzen CPU
  • Using host-passthrough CPU mode

The problem comes with a new speculative execution protection hardware feature in the Ryzen Gen 3 chipsets – stibp. Qemu doesn’t know how to handle it properly, thus the bluescreens.

There are two ways to fix it

  • Change host-model from host-passthrough to epyc
  • Add CPU parameters to your Virtual Machine’s XML file instructing it to not use the stibp CPU feature.

Since I have some software that checks CPU model and refuses to work if it’s not in the desktop class (Geforce Experience) I opted for route #2.

First, check the qemu logs to see which CPU parameters your VM was using (pick a time where it worked.) Replace ‘win10’ with the name of your VM.

sudo cat /var/log/libvirt/qemu/win10.log | grep "\-cpu"

in my case, it was -cpu host,migratable=on,topoext=on,kvmclock=on,hv-time,hv-relaxed,hv-vapic,hv-spinlocks=0x1fff,hv-vendor-id=1234567890ab,kvm=off \

Copy everything after -cpu and before the last backslash. Then edit your VM’s XML file (change last argument to the name of your VM)

sudo virsh edit win10

Scroll down to the bottom qemu:commandline section (if it doesn’t exist, create it right above the last line – </domain>. Paste the following information obtained from the above log (ignoring the qemu:commandline lines if they already exist.) In my case it looked like this:

  <qemu:commandline>
    <qemu:arg value='-cpu'/>
    <qemu:arg value='host,topoext=on,kvmclock=on,hv-time,hv-relaxed,hv-vapic,hv-
spinlocks=0x1fff,hv-vendor-id=1234567890ab,kvm=off,-amd-stibp'/>
  </qemu:commandline>

What you’re doing is copying the CPU arguments you found in the log and adding them to the qemu:commandline section, with a twist – adding -amd-stibp which instructs qemu to remove that CPU flag.

This did the trick for me!

KVM with vga passthrough in arch linux

I’ve once again switched from Proxmox to Arch Linux for my desktop machine. Both use KVM so it’s really just a matter of using the different VM manager syntax (virt-manager vs qm.) I used my notes from my previous stint with Arch, my article on GPU Passthrough in Proxmox as well as a thorough reading of the Arch wiki’s PCI Passthrough article.

Enable IOMMU

Configure GRUB to load the necessary iommu modules at boot. Append amd_iommu=on iommu=pt to the end of GRUB_CMDLINE_LINUX_DEFAULT (change accordingly if you have Intel instead of AMD)

sudo vim /etc/default/grub
...
GRUB_CMDLINE_LINUX_DEFAULT="loglevel=3 amd_iommu=on iommu=pt"

Run update-grub

sudo update-grub

Reserve GPU for VFIO

Reserve the GPU you wish to pass through to a VM for use with the vfio kernel driver (so the host OS doesn’t interfere with it)

  1. Determine the PCI address of your GPU
    1. Run lspci -v and look for your card. Mine was 01:00.0 & 01:00.1. You can omit the part after the decimal to include them both in one go – so in that case it would be 01:00
    2. Run lspci -n -s <PCI address from above> to obtain vendor IDs.
      Example :
      lspci -n -s 01:00
      01:00.0 0300: 10de:1b81 (rev a1)
      01:00.1 0403: 10de:10f0 (rev a1)
  2. Assign your GPU to vfio driver using the IDs obtained above.
    Example using above IDs:
    echo "options vfio-pci ids=10de:1b81,10de:10f0" >> /etc/modprobe.d/vfio.conf

Reboot the host to put the kernel / drivers into effect.

Configure virt-manager

Install virt-manager, dnsmasq & libvirtd:

pacman -Sy libvirtd virt-manager dnsmasq
sudo systemctl enable libvirtd
sudo systemctl start libvirtd

Configure Networking

Assuming you’re using network manager for your connections, create a bridge (thanks to ciberciti.biz & the arch wiki for information on how to do so.) Replace interface names with ones corresponding to your machine:

sudo nmcli connection add type bridge ifname br0 stp no
sudo nmcli connection add type bridge-slave ifname enp4s0 master br0 
sudo nmcli connection show
#Make note of the active connection name
sudo nmcli connection down "Wired connection 2" #from above
sudo nmcli connection up bridge-br0

Create a second bridge bound to lo0 for host-only communication. Change IP as desired:

sudo nmcli connection add type bridge ifname br99 stp no ip4 192.168.2.1/24
sudo nmcli connection add type bridge-slave ifname lo master br99
sudo nmcli connection up bridge-br99

Configure VM

Initial configuration

When creating the passthrough VM, make sure chipset is Q35.

Set the CPU model to host-passthrough (type it in, there is no dropdown for it.)

When adding disks / other devices, set the device model to virtio

Add your GPU by going to Add Hardware and finding it under PCI Host Device.

Windows 10 specific tweaks

If your passthrough VM is going to be windows based, some tweaks are required to get the GPU to work properly within the VM.

Ignore MSRs (blue screen fix)

Later versions of Windows 10 instantly bluescreen with kmode_exception_not_handled unless you pass an option to ignore MSRs. Add the kvm ignore_msrs=1 option in /etc/modprobe.d/kvm.conf to do so. Optionally add the report_ignored_msrs=0 option to squelch massive amounts of kernel messages every time an MSR was ignored.

echo "options kvm ignore_msrs=1" >> /etc/modprobe.d/kvm.conf
#Optional - ignore kernel messages from ignored MSRs
echo "options kvm report_ignored_msrs=0" >> /etc/modprobe.d/kvm.conf

Reboot to make those changes take effect.

NVIDIA Code 43 workaround

Use the virsh edit command to make some tweaks to the VM configuration. We need to hide the fact that this is a VM otherwise the GPU drivers will not load and will throw Error 43. We need to add a vendor_id in the hyperv section, and create a kvm section enabling hidden state, which hides certain CPU flags that the drivers use to detect if they’re in a VM or not.

sudo virsh edit <VM_NAME>

<features>
	<hyperv>
		...
		<vendor_id state='on' value='1234567890ab'/>
		...
	</hyperv>
	...
	<kvm>
	<hidden state='on'/>
	</kvm>
</features>

Optimize CPU

Determine architecture

If you operate on a multi-core system such as my AMD Ryzen Threadripper the you will want to optimize your CPU core configuration in the VM per the CPU Pinning section in the Arch Wiki

Determine your CPU topology by running lscpu -e and lstopo The important things to look for are the CPU number and core number. On my box, it looks like this:

CPU NODE SOCKET CORE L1d:L1i:L2:L3 ONLINE MAXMHZ MINMHZ
0 0 0 0 0:0:0:0 yes 3400.0000 2200.0000
1 0 0 1 1:1:1:0 yes 3400.0000 2200.0000
2 0 0 2 2:2:2:0 yes 3400.0000 2200.0000
3 0 0 3 3:3:3:0 yes 3400.0000 2200.0000
4 0 0 4 4:4:4:1 yes 3400.0000 2200.0000
5 0 0 5 5:5:5:1 yes 3400.0000 2200.0000
6 0 0 6 6:6:6:1 yes 3400.0000 2200.0000
7 0 0 7 7:7:7:1 yes 3400.0000 2200.0000
8 0 0 8 8:8:8:2 yes 3400.0000 2200.0000
9 0 0 9 9:9:9:2 yes 3400.0000 2200.0000
10 0 0 10 10:10:10:2 yes 3400.0000 2200.0000
11 0 0 11 11:11:11:2 yes 3400.0000 2200.0000
12 0 0 12 12:12:12:3 yes 3400.0000 2200.0000
13 0 0 13 13:13:13:3 yes 3400.0000 2200.0000
14 0 0 14 14:14:14:3 yes 3400.0000 2200.0000
15 0 0 15 15:15:15:3 yes 3400.0000 2200.0000
16 0 0 0 0:0:0:0 yes 3400.0000 2200.0000
17 0 0 1 1:1:1:0 yes 3400.0000 2200.0000
18 0 0 2 2:2:2:0 yes 3400.0000 2200.0000
19 0 0 3 3:3:3:0 yes 3400.0000 2200.0000
20 0 0 4 4:4:4:1 yes 3400.0000 2200.0000
21 0 0 5 5:5:5:1 yes 3400.0000 2200.0000
22 0 0 6 6:6:6:1 yes 3400.0000 2200.0000
23 0 0 7 7:7:7:1 yes 3400.0000 2200.0000
24 0 0 8 8:8:8:2 yes 3400.0000 2200.0000
25 0 0 9 9:9:9:2 yes 3400.0000 2200.0000
26 0 0 10 10:10:10:2 yes 3400.0000 2200.0000
27 0 0 11 11:11:11:2 yes 3400.0000 2200.0000
28 0 0 12 12:12:12:3 yes 3400.0000 2200.0000
29 0 0 13 13:13:13:3 yes 3400.0000 2200.0000
30 0 0 14 14:14:14:3 yes 3400.0000 2200.0000
31 0 0 15 15:15:15:3 yes 3400.0000 2200.0000

From the above output I see my CPU core 0 is shared by CPUs 0 & 16, meaning CPU 0 and CPU 16 (as seen by the Linux kernel) are hyperthreaded to the same physical CPU core.

Especially for gaming, you want to keep all threads on the same CPU cores (for multithreading) and the same CPU die (on my threadripper, CPUs 0-7 reside on one physical die, and CPUs 8-15 reside on the other, within the same socket.)

In my case I want to dedicate one CPU die to my VM with its accompanying hyperthreads (CPUs 0-7 & hyperthreads 16-23) You can accomplish this using the virsh edit command and creating a cputune section (make sure you have a matching vcpu count for the number of cores you’re configuring.) Also edit CPU mode with the proper topology of 1 socket, 1 die, 8 cores with 2 threads. Lastly, configure memory to only be from the proper NUMA node the CPU cores your VM is using (Read here for more info.)

sudo virsh edit <VM_NAME>

<domain type='kvm'>
  ...
  <vcpu placement='static' cpuset='0-7,16-23'>16</vcpu> 
  <cputune>
    <vcpupin vcpu='0' cpuset='0'/>
    <vcpupin vcpu='1' cpuset='16'/>
    <vcpupin vcpu='2' cpuset='1'/>
    <vcpupin vcpu='3' cpuset='17'/>
    <vcpupin vcpu='4' cpuset='2'/>
    <vcpupin vcpu='5' cpuset='18'/>
    <vcpupin vcpu='6' cpuset='3'/>
    <vcpupin vcpu='7' cpuset='19'/>
    <vcpupin vcpu='8' cpuset='4'/>
    <vcpupin vcpu='9' cpuset='20'/>
    <vcpupin vcpu='10' cpuset='5'/>
    <vcpupin vcpu='11' cpuset='21'/>
    <vcpupin vcpu='12' cpuset='6'/>
    <vcpupin vcpu='13' cpuset='22'/>
    <vcpupin vcpu='14' cpuset='7'/>
    <vcpupin vcpu='15' cpuset='23'/>
    <emulatorpin cpuset='0-7','26-23'/>
  </cputune>
  ...
  <cpu mode='host-passthrough' check='none'>
    <topology sockets='1' dies='1' cores='8' threads='2'/>
    <feature policy='require' name='topoext'/>
    <numa>
      <cell id='0' cpus='0-15' memory='16777216' unit='KiB'/>
    </numa>
  </cpu>
  ...
</domain>

Configure NUMA

Non-uniform memory access is essential for 1st and 2nd gen Ryzen chips. It turns out that by default my motherboard hid the real NUMA configuration from the operating system. Remedy this by changing the BIOS setting to set Memory Interleaving = Channel (for my ASRock X399 motherboard it’s in CBS / DF options.) See here: https://www.reddit.com/r/Amd/comments/6vrcq0/psa_threadripper_umanuma_setting_in_bios/

After changing BIOS setting, lstopo now shows proper configuration:

CPU frequency

Change CPU frequency setting to use performance mode:

sudo pacman -S cpupower
sudo cpupower frequency-set -g performance

Enable Hugepages

Append default_hugepagesz=1G hugepagesz=1G hugepages=16 to the kernel line in /etc/default/grub and re-run sudo grub-mkconfig -o /boot/grub/grub.cfg

Configure FIFO CPU scheduling

The Arch Wiki mentions to run qemu-system-x86_64 with taskset and chrt but doesn’t mention how to do so if you’re using virt-manager. Fortunately this reddit thread outlined how to accomplish it: libvirt hooks. Create the following script and place it in /etc/libvirt/hooks/qemu  , change the VM variable to match the name of your VM, mark that new file as executable (chmod +x /etc/libvirt/hooks/qemu ) and restart libvirtd

#!/bin/bash
#Hook to change VM to FIFO scheduling to decrease latency
#Place this file in /etc/libvirt/hooks/qemu and mark it executable

#Change the VM variable to match the name of your VM
VM="win10"

if [ "$1" == "$VM" ] && [ "$2" == "started" ]; then
  if pid=$(pidof qemu-system-x86_64); then
     chrt -f -p 1 $pid
    echo $(date) changing CPU scheduling to FIFO for VM $1 pid $pid >> /var/log/libvirthook.log
  else
    echo $(date) Unable to acquire PID of $1 >> /var/log/libvirthook.log
  fi
fi
#Additional debug
#echo $(date) libvirt hook arg1=$1 arg2=$2 arg3=$3 arg4=$4 pid=$pid >> /var/log/libvirthook.log 

Isolate CPUs

Update 7/28/20: I no longer do this in favor of the qemu hook script above, which prioritizes to p1 the qemu process for the cores it needs. I’m leaving this section here for historical/additional tweaking purposes.

Update 6/28/20: Additional tuning since I was having some stuttering and framerate issues. Also read here about the emulatorpin option

Dedicate CPUs to the VM (host will not use them) – append isolcups, nohz_full & rcu_nocbs kernel parameters into /etc/default/grub

...
GRUB_CMDLINE_LINUX_DEFAULT=... isolcpus=0-7,16-23 nohz_full=0-7,16-23 rcu_nocbs=0-7,16-23
...

Update grub:

sudo grub-mkconfig -o /boot/grub/grub.cfg

Reboot, then check if it worked:

cat /proc/cmdline
BOOT_IMAGE=/boot/vmlinuz-linux root=/dev/mapper/arch-root rw loglevel=3 amd_iommu=on iommu=pt isolcpus=0-7,16-23 nohz_full=0-7,16-23 rcu_nocbs=0-7,16-23
taskset -cp 1
pid 1's current affinity list: 8-15,24-31

You can still tell programs to use the CPUs the VM has manually with the taskset command:

chrt -r 1 taskset -c <cores to use> <name of program/process>

Low Latency Audio

Upbate 7/8/2020: I found this article and this reddit thread (and this one) on how to use pulseaudio for your guest VM to get low latency guest VM audio piped to the host machine.

Update qemu config

edit /etc/libvirt/qemu.conf: uncomment the line #user = "root" and replace “root” with your username

Update pulseaudio config

Edit /etc/pulse/daemon.conf and uncomment the following lines (remove semicolon)

;default-sample-rate = 44100
;alternate-sample-rate = 48000

Note: Change VM audio settings to match 44100 sample rate

Edit /etc/pulse/default.pa and append auth-anonymous=1 to load-module module-native-protocol-unix

load-module module-native-protocol-unix auth-anonymous=1

The restart pulseaudio:

pulseaudio -k

Update VM XML

remove all audio devices from the virtual hardware details bar (left side in VM info view).

Edit XML via virsh edit <VM_NAME>

Make sure top line reads

<domain type='kvm' xmlns:qemu='http://libvirt.org/schemas/domain/qemu/1.0'>

Add the following after </devices> (bottom of file)

<qemu:commandline>
    <qemu:arg value='-device'/>
    <qemu:arg value='ich9-intel-hda,bus=pcie.0,addr=0x1b'/>
    <qemu:arg value='-device'/>
    <qemu:arg value='hda-micro,audiodev=hda'/>
    <qemu:arg value='-audiodev'/>
    <qemu:arg value='pa,id=hda,server=unix:/run/user/1000/pulse/native'/>
</qemu:commandline>

Replace /user/1000 with the UID of your user (output of id command)

Final Win10 XML tweaks for 1950x threadripper

<domain type='kvm' id='1' xmlns:qemu='http://libvirt.org/schemas/domain/qemu/1.0'>
 ...
  <memory unit='KiB'>16777216</memory>
  <currentMemory unit='KiB'>16777216</currentMemory>
  <memoryBacking>
    <hugepages/>
  </memoryBacking>
  <vcpu placement='static'>16</vcpu>
  <cputune>
    <vcpupin vcpu='0' cpuset='0'/>
    <vcpupin vcpu='1' cpuset='16'/>
    <vcpupin vcpu='2' cpuset='1'/>
    <vcpupin vcpu='3' cpuset='17'/>
    <vcpupin vcpu='4' cpuset='2'/>
    <vcpupin vcpu='5' cpuset='18'/>
    <vcpupin vcpu='6' cpuset='3'/>
    <vcpupin vcpu='7' cpuset='19'/>
    <vcpupin vcpu='8' cpuset='4'/>
    <vcpupin vcpu='9' cpuset='20'/>
    <vcpupin vcpu='10' cpuset='5'/>
    <vcpupin vcpu='11' cpuset='21'/>
    <vcpupin vcpu='12' cpuset='6'/>
    <vcpupin vcpu='13' cpuset='22'/>
    <vcpupin vcpu='14' cpuset='7'/>
    <vcpupin vcpu='15' cpuset='23'/>
    <emulatorpin cpuset='8-15,24-31'/>
  </cputune>
  <numatune>
    <memory mode='strict' nodeset='0'/>
  </numatune>
  ...
  <features>
     ...
    <hyperv>
     ...
      <vendor_id state='on' value='1234567890ab'/>
    </hyperv>
    <kvm>
      <hidden state='on'/>
    </kvm>
    ...
  </features>
  <cpu mode='host-passthrough' check='none'>
    <topology sockets='1' dies='1' cores='8' threads='2'/>
    <feature policy='require' name='topoext'/>
    <numa>
      <cell id='0' cpus='0-15' memory='16777216' unit='KiB'/>
    </numa>
  </cpu>
   ...
  <qemu:commandline>
    <qemu:arg value='-device'/>
    <qemu:arg value='ich9-intel-hda,bus=pcie.0,addr=0x1b'/>
    <qemu:arg value='-device'/>
    <qemu:arg value='hda-micro,audiodev=hda'/>
    <qemu:arg value='-audiodev'/>
    <qemu:arg value='pa,id=hda,server=unix:/run/user/1000/pulse/native'/>
  </qemu:commandline>
</domain>

Profit

I’m very pleased with my current setup. It works well!

arch install notes 2020-06

My install notes to get Arch Linux set up just the way I like it, June 2020 edition. Reference: https://wiki.archlinux.org/index.php/Installation_guide

Change to dvorak layout:
loadkeys dvorak

Sync NTP time:
timedatectl set-ntp true

Configure disk:
fdisk
#create separate efi partition, LVM root & swap
pvcreate <dev>
vgcreate arch <dev>
lvcreate -L+2G arch -n swap
lvcreate -l100%FREE -n root arch

Initialize swap:
mkswap /dev/arch/swap
swapon /dev/arch/swap

Format & Mount root:
mkfs.ext4 /dev/arch/root
mount /dev/arch/root /mnt

Create EFI partition
mkdosfs -F32 <partition 1>
mkdir /mnt/efi
mount <partition 1> /mnt/efi

Make mirrorlist use only xmission
sed -i 's/^Server/#Server/g;s/#Server\(.*xmission.*\)/Server\1/g' /etc/pacman.d/mirrorlist

Install base system plus extra packages:
pacstrap /mnt base linux linux-firmware lvm2 efibootmgr samba vim htop networkmanager inetutils man-db man-pages texinfo openssh grub

Generate fstab
genfstab -U /mnt >> /mnt/etc/fstab

Enter new environment chroot
arch-chroot /mnt

Set timezone
ln -sf /usr/share/zoneinfo/America/Boise /etc/localtime

Configure en_US locales
sed -i 's/^#en_US\(.*\)/en_US\1/g' /etc/locale.gen
locale-gen

Make dvorak layout permanent
echo "KEYMAP=dvorak" > /etc/vconsole.conf

Set hostname
echo "_HOSTNAME_" > /etc/hostname
echo "127.0.1.1 _HOSTNAME_._DOMAIN_ _HOSTNAME_" >> /etc/hosts

Enable lvm2 hook for initial ramdisk (boot)
sed -i 's/HOOKS=(.*\<block\>/& lvm2/' /etc/mkinitcpio.conf

Generate initial ramdisk
mkinitcpio -P

Set password for root user:
passwd

Install Grub (EFI)
grub-install --target=x86_64-efi --efi-directory=/efi --bootloader-id=GRUB
grub-mkconfig -o /boot/grub/grub.cfg

Enable networking & SSH on bootup:
systemctl enable NetworkManager sshd

Configure NTP
yum -y install ntp
#modify /etc/ntp.conf for timeservers as desired
systemctl enable ntpd

Exit chroot & reboot
exit
reboot

Zimbra expired ldap certificate fix

I started getting SSL errors with my Zimbra mail server despite having a valid SSL certificate everywhere I knew where to check. When I tried to use zmcontrol status I got this error:

Unable to start TLS: SSL connect attempt failed error:14090086:SSL routines:ssl3_get_server_certificate:certificate verify failed when connecting to ldap master.

Eventually I found this blog post explaining the problem – it’s with the LDAP component in Zimbra. You have to switch it from ldap to ldaps. Why did this change? I do not know.

ZIMBRA_HOSTNAME=_your_mail_server_dns_hostname_

sudo -u zimbra bash
zmlocalconfig -e ldap_master_url=ldaps://$ZIMBRA_HOSTNAME:636
zmlocalconfig -e ldap_url=ldaps://$ZIMBRA_HOSTNAME:636
zmlocalconfig -e ldap_starttls_supported=0
zmlocalconfig -e ldap_port=636
zmcontrol stop
zmcontrol start

This did the trick. The errors went away.

Threadripper / Epyc processor core optimization

I had a pet project (folding@home) where I wanted to maximize computing power. I became frustrated with default CPU scheduling of my folding@home threads. Ideal performance would keep similar threads on the same CPU, but the threads were jumping all over the place, which was impacting performance.

Step one was to figure out which threads belonged to which physical cores. I found on this site that you can use cat to find out what your “sibling threads” are:

cat /sys/devices/system/cpu/cpu{0..15}/topology/thread_siblings_list

The above command is for my Threadripper & Epyc systems, which each have 16 cores hyperthreaded to 32 cores. Adjust the {0..15} number to match your number of cores (core 0 being the fist core.) This was my output:

cat /sys/devices/system/cpu/cpu{0..15}/topology/thread_siblings_list

0,16
1,17
2,18
3,19
4,20
5,21
6,22
7,23
8,24
9,25
10,26
11,27
12,28
13,29
14,30
15,31

Now that I know the sibling threads are offset by 16, I can use this information to optimize my folding@home VMs. I modified my CPU pinning script to take this into consideration. The script ensures that each VM is pinned to only use sibling threads (ensuring they all stay on the same physical CPU.)

This script should be used with caution. It pins processes to specific CPUs, which limits the kernel scheduler’s ability to move things around if needed. If configured badly this can cause the machine to lock up or VMs to be terminated.

I saw some impressive results spinning up four separate 8 core VMs and pinning them to sibling cores using this script. It almost doubled the rate at which I completed folding@home work units.

And now, the script:

#!/bin/bash
#Properly assign CPU cores to their respective die for EPYC/Threadripper systems
#Based on how hyperthreads are done in these systems
#cat /sys/devices/system/cpu/cpu{0..15}/topology/thread_siblings_list

#The script takes two arguments - the ID of the Proxmox VM to modify, and the core to begin the VM on
#If running this against multiple VMs, make sure to increment this second number by half of the cores of the previous VM
#For example, if I have one 8 core VM and I run this script specifying 0 for the offset, if I spin up a second VM, the second argument would be 4
#this would ensure the second VM starts on core 4 (the 5th core) and assigns sibling cores to match

set -eo pipefail

#take First argument as which VMID to pin CPU cores to, the second argument is which core to start pinning to
VMID=$1
OFFSET=$2

#Determine offset for sibling threads
SIBLING_THREAD_OFFSET=$(cat /sys/devices/system/cpu/cpu0/topology/thread_siblings_list| sed 's/,/ /g' | awk '{print $2}')

#Function to determine number of CPU cores a VM has
cpu_tasks() {
	expect <<EOF | sed -n 's/^.* CPU .*thread_id=\(.*\)$/\1/p' | tr -d '\r' || true
spawn qm monitor $VMID
expect ">"
send "info cpus\r"
expect ">"
EOF
}

#Only act if VMID & OFFSET are set
if [[ -z $VMID  || -z $OFFSET ]]
then
	echo "Usage: cpupin.sh <VMID> <OFFSET>"
	exit 1
else
	#Get PIDs of each CPU core for VM, count number of VM cores, and get even/odd PIDs for assignment
	VCPUS=($(cpu_tasks))
	VCPU_COUNT="${#VCPUS[@]}"
	VCPU_EVEN_THREADS=($(for EVEN_THREAD in "${VCPUS[@]}"; do echo $EVEN_THREAD; done | awk '!(NR%2)'))
	VCPU_ODD_THREADS=($(for ODD_THREAD in "${VCPUS[@]}"; do echo $ODD_THREAD; done | awk '(NR%2)'))

	if [[ $VCPU_COUNT -eq 0 ]]; then
		echo "* No VCPUS for VM$VMID"
		exit 1
	fi

	echo "* Detected ${#VCPUS[@]} assigned to VM$VMID..."
	echo "* Resetting cpu shield..."

	#Start at offset CPU number, assign odd numbered PIDs to their own CPU thread, then increment CPU core number
	#0-3 if offset is 0, 4-7 if offset is 4, etc
	ODD_CPU_INDEX=$OFFSET
	for PID in "${VCPU_ODD_THREADS[@]}"
	do
		echo "* Assigning ODD thread $ODD_CPU_INDEX to $PID..."
		taskset -pc "$ODD_CPU_INDEX" "$PID"
		((ODD_CPU_INDEX+=1))
	done

	#Start at offset + CPU count, assign even number PIDs to their own CPU thread, then increment CPU core number
	#16-19 if offset is 0,	20-23 if offset is 4, etc
	EVEN_CPU_INDEX=$(($OFFSET + $SIBLING_THREAD_OFFSET))
	for PID in "${VCPU_EVEN_THREADS[@]}"
	do
		echo "* Assigning EVEN thread $EVEN_CPU_INDEX to $PID..."
		taskset -pc "$EVEN_CPU_INDEX" "$PID"
		((EVEN_CPU_INDEX+=1))
	done
fi

UBUNTU 20.04 cloned VM same DHCP IP fix

I cloned an Ubuntu 20.04 VM and was frustrated to see both boxes kept getting the same DHCP IP address despite having different network MAC addresses. I finally found on this helpful post which states Ubuntu 20.04 uses systemd-networkd for DHCP leases which behaves differently than dhclient. As wickedchicken states,

systemd-networkd uses a different method to generate the DUID than dhclientdhclient by default uses the link-layer address while systemd-networkd uses the contents of /etc/machine-id. Since the VMs were cloned, they have the same machine-id and the DHCP server returns the same IP for both.

To fix, replace the contents of one or both of /etc/machine-id. This can be anything, but deleting the file and running systemd-machine-id-setup will create a random machine-id in the same way done on machine setup.

So my fix was to run the following on the cloned machine:

sudo rm /etc/machine-id
sudo systemd-machine-id-setup
sudo reboot

That did the trick!


For the systems that registered their hostnames under the wrong IPs, I had to take the following action for my Ubuntu 20.04 desktop as well as my Ubiquiti USG-Pro 4

Ubiquiti: Clear DHCP lease

clear dhcp lease ip <ip_address>

Ubuntu desktop: Flush DNS

sudo systemd-resolve --flush-caches

Folding@home opencl error fix

I decided to contribute my GPU on my Ubuntu-based system to the Folding@Home effort for COVID-19. I kept getting this error message for my NVIDIA GeForce GTX 1050 TI when I tried:

ERROR:WU00:FS00:Failed to start core: OpenCL device matching slot 0 not found, make sure the OpenCL driver is installed or try setting 'opencl-index' manually

I had the nvidia opencl packages installed but apparently missed something. I finally found on the folding at home forum what I was missing – ocl-icd-opencl-dev

sudo apt install ocl-icd-opencl-dev

After running the above command and restarting the FAHClient service, the GPU started folding. For science!


EDIT 5/6/2020: After a re-install I had the issue where the GPU wouldn’t show up at all. It addition to ocl-icd-opencl-dev, it looks like you also need nvidia-cuda-dev.

sudo apt install ocl-icd-opencl-dev nvidia-cuda-dev

Sort by middle of a string

I had a list of items I wanted to sort in a non-standard way:

app-function1.site1.jeppson.org
app-function2.site3.jeppson.org
app-function3.site4.jeppson.org
app-function4.site2.jeppson.org
app-function1.site6.jeppson.org
app-function3.site9.jeppson.org
app-function4.site7.jeppson.org

It’s a generalized list for publication but you get the idea. I wanted to sort by site name. Thanks to this post I found it’s relatively easy. You can tell the sort command to use a character as a tab delimiter (-t) and then specify which key “column” to sort by (-k)

In my case I sorted by site by specifying the dot character '.' as the delimiter, and the second “column” as the key '-k2'

The end result was this:

cat apps-by-site-unsorted.txt | sort -t. -k2
app-function1.site1.jeppson.org
app-function4.site2.jeppson.org
app-function2.site3.jeppson.org
app-function3.site4.jeppson.org
app-function1.site6.jeppson.org
app-function4.site7.jeppson.org
app-function3.site9.jeppson.org

Success