Using OpenMX on Google Compute Engine

Because I have a potato laptop, don't have money to upgrade workspace, want to graduate fast, and understand a little about Compute Engine.

szczynk Created at March 11, 2022 4:42 PM Updated 2 years ago

tech openMX google cloud platform compute engine

Table of Content

Introduction

OpenMX (Open source package for Materials eXplorer) is a software package for nanoscale material simulation based on density function theory (DFT), norm-preserving pseudopotential, and pseudo-atomic localized base functions. OpenMX is the tool I used when I was working on my undergraduate thesis on the electrical and magnetic properties of a monolayer NiBr2 based on density function theory (DFT) but it is very heavy on my Asus K45DR laptop on Ubuntu 20.04 LTS.

The minimum number of cores used by OpenMX is 4 using OpenMPI parallelization to make it faster, even though the minimum specification requirements are met, in fact this is not the case, on my laptop the required SCF calculation is 6 hours to 1 week for 1 configuration file input if it converges. This is very inefficient for the results of the initial research or initial discussion.

Based on my experience of implementing a web server on Google Compute Engine, I ended up using Google Compute Engine as my potato laptop alternative for SCF calculations with OpenMX. Enough with my complaints, let's apply it.

Create a fresh Google Account with Debit or Credit Card

it's a Google service, you must have a Google account, if not, ask Google how to create a Google account.

If you don't have a debit or credit card, you'll need to create one first. In my case, I used the Jenius debit card service. Jenius debit card service registration can be done on your smartphone, online, easy and practical.

Then go to GCP free trial page and fill in what is required.

Create a Ubuntu VM instance

Forgive me, I forgot the first time I logged in Google console, I just followed the popup prompts and suddenly my project name is My First Project. Let's move on.

Let's go to the home page or dashboard or this link
Click the navigation menu button at the very top left
Look for the Compute Engine button and hover over the VM instances button
Click the VM instances button or this link
Click the Create Instance button or this link
Specify Name for your VM, for example openmx
Optional : Change the Zone for this VM. Compute Engine randomizes the list of zones within each region to encourage use across multiple zones. Otherwise, use default value which is us-central1 (Iowa)
Select Configure machine for your VM. For maximum efficiency in SCF calculation :

a. Select Compute-Optimized

b. Select C2 or C2D series

c. Select c2-standard-8 or c2d-standard-8 machine type (8 vCPU equals 4 cores)
Enable display device
In the Boot disk section, click Change, and then do the following :

a. On the Public images tab, choose the following :
- Operating System : Ubuntu
- OS version : Ubuntu 20.04 LTS
- Boot disk type : Balanced Persistent Disk
- Boot disk size : 10 GB
b. To confirm your boot disk options, click Select.
To create and start the VM, click Create.

It takes a few moments to create your instance.

Congratulations you have created and started a VM instance.

Note

the maximum default for all types of Compute Engine vCPUs quotas for each region is 8 vCPUs running at the same time.

You can't request a quota increase. For an overview of Compute Engine quotas, see Resource quotas. You must upgrade your account to perform any of the actions in the preceding list.

The free trial ends when you use all of your credit, or after 3 months, whichever happens first. At that time, the following conditions apply:

You must upgrade to a paid account to continue using Google Cloud. (recommended upgrade before free trial ends)

All resources you created during the trial are stopped.

Any data you stored in Compute Engine is lost.

Your account enters a 30-day grace period, during which you can recover or export manually any resources and data you stored in any Google Cloud services during the trial period.

You might receive a message stating that your account has been canceled, which only indicates that your account has been suspended to prevent charges.

Lots of notes huh? I'm sorry, I'm afraid your calculations and data are lost

Optional : Adding and formating a non-boot disk to your VM

when the boot disk starts to full, you can add a non-boot disk to your VM

Go to the VM instances page.
Check the box and click the name of the instance where you want to add a disk.
On the VM instance details page, click Edit.
Under Additional disks, click Add new disk.
Specify a name for the disk, configure the disk's properties, and select Blank as the Source type.
Click Done to complete the disk's configuration.
Click Save to apply your changes to the instance and add the new disk.
Click the SSH button next to the instance that has the new attached disk. The browser opens a terminal connection to the VM.

In the terminal, use the lsblk command to list the disks that are attached to your instance and find the disk that you want to format and mount.

sudo lsblk

sda       8:0    0    10G  0 disk
├─sda1    8:1    0   9.9G  0 part /
├─sda14   8:14   0     4M  0 part
└─sda15   8:15   0   106M  0 part /boot/efi
sdb       8:16   0    10G  0 disk

In this example, sdb is the device name for the new blank persistent disk.

Format the disk using the mkfs tool. This command deletes all data from the specified disk, so make sure that you specify the disk device correctly.
```
sudo mkfs.ext4 -m 0 -E lazy_itable_init=0,lazy_journal_init=0,discard /dev/sdb
```
Create a directory that serves as the mount point for the new disk on the VM. You can use any directory. The following example creates a directory under /mnt/disks/.
```
sudo mkdir -p /mnt/disks/openmx
```
Use the mount tool to mount the disk to the instance, and enable the discard option:
```
sudo mount -o discard,defaults /dev/sdb /mnt/disks/openmx
```
Note
You can mount /dev/sdb to any directory you want.
Configure read and write permissions on the disk. For this example, grant write access to the disk for all users.
```
sudo chmod a+w /mnt/disks/openmx
```
Configuring automatic mounting on VM restart by Add the disk to your /etc/fstab file, so that the disk automatically mounts again when the VM restarts. On Linux operating systems, the device name can change with each reboot, but the device UUID always points to the same volume, even when you move disks between systems.

Create a backup of your current /etc/fstab file.
```
sudo cp /etc/fstab /etc/fstab.backup
```

Use the blkid command to list the UUID for the disk.

sudo blkid /dev/sdb

for example output of blkid command

/dev/sdb: UUID="c76cb476-9438-42e4-a31a-2bf428a42043" TYPE="ext4"

Open the /etc/fstab file in a text editor and create an entry that includes the UUID.
```
sudo nano /etc/fstab
```
add this line after last line.
```
UUID=UUID_VALUE /mnt/disks/openmx ext4 discard,defaults,nofail 0 2
```
Replace the following: - UUID_VALUE: the UUID of the disk, listed in the output of the previous step
Use the cat command to verify that your /etc/fstab entries are correct:
```
cat /etc/fstab
```
for example output of cat command
```
LABEL=cloudimg-rootfs /  ext4 defaults 0 1
LABEL=UEFI /boot/efi vfat umask=0077 0 1
UUID="c76cb476-9438-42e4-a31a-2bf428a42043" /mnt/disks/openmx ext4 discard,defaults,nofail 0 2
```
If you detach this disk or create a snapshot from the boot disk for this VM, edit the /etc/fstab file and remove the entry for this disk. Even with MOUNT_OPTION set to nofail or nobootwait, keep the /etc/fstab file in sync with the devices that are attached to your VM and remove these entries before you create your boot disk snapshot or detach the disk.

Setting up desktop environment on Compute Engine

In my humble opinion, life is hard without desktop environment so let's set up Chrome Remote Desktop

Installing Chrome Remote Desktop and Xfce desktop enviroment on the VM instance

For remote connections over slower networks I recommended Xfce because it has minimal graphical elements and few animations.

After the instance has been created, connect to your openmx instance by clicking the SSH button in the instance list :
In the SSH window connected to your VM instance, update the package manager data and install wget :
```
sudo apt update
sudo apt install --assume-yes wget tasksel
```

Download and install the Debian Linux Chrome Remote Desktop installation package :

wget https://dl.google.com/linux/direct/chrome-remote-desktop_current_amd64.deb
sudo apt update
sudo apt-get install --assume-yes ./chrome-remote-desktop_current_amd64.deb

In the SSH window connected to your VM instance, install the Xfce desktop environment and basic desktop components :
```
sudo DEBIAN_FRONTEND=noninteractive \
apt install --assume-yes xfce4 desktop-base dbus-x11 xscreensaver
```

Configure Chrome Remote Desktop to use Xfce by default :

sudo bash -c 'echo "exec /etc/X11/Xsession /usr/bin/xfce4-session" > /etc/chrome-remote-desktop-session'

Disable the display manager service on your instance. There is no display connected to your instance, so the display manager service won't start.
```
sudo systemctl disable lightdm.service
```

Optional: install the Chrome browser on your instance :

wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
sudo apt install --assume-yes ./google-chrome-stable_current_amd64.deb

Finish with GUI for File Compression and Mousepad text editor

sudo apt update
sudo apt install --assume-yes thunar-archive-plugin mousepad

Configuring and starting the Chrome Remote Desktop service

To start the remote desktop server, you need to have an authorization key for the Google account that you want to use to connect to it :

On your local computer, using the Chrome browser, go to the Chrome Remote Desktop command line setup page :
```
https://remotedesktop.google.com/headless
```
If you're not already signed in, sign in with a Google Account. This is the account that will be used for authorizing remote access.
On the Set up another computer page, click Begin.
On the Download and install Chrome Remote Desktop page, click Next. Do not download and click Windows and Debian Linux link
Click Authorize.

You need to allow Chrome Remote Desktop to access your account. If you approve, the page displays a command line for Debian Linux that looks like the following :
```
DISPLAY= /opt/google/chrome-remote-desktop/start-host \
--code="4/xxxxxxxxxxxxxxxxxxxxxxxx" \
--redirect-url="https://remotedesktop.google.com/_/oauthredirect" \
--name=$(hostname)
```
You use this command to set up and start the Chrome Remote Desktop service on your VM instance, linking it with your Google Account using the authorization code.

Note
The authorization code in the command line is valid for only a few minutes, and you can use it only once. Otherwise restart this step again.
You can know your hostname by looking at your SSH like this username@hostname , if you name your VM instance openmx your hostname is openmx
Copy the command to the SSH window that's connected to your instance, and then run the command.
When you're prompted, enter a 6-digit PIN. This number will be used for additional authorization when you connect later. You might see errors like No net_fetcher or Failed to read. You can ignore these errors.

Verify that the service is running using the following command.

sudo systemctl status chrome-remote-desktop@$USER

If the service is running, you see output that includes the state active :

chrome-remote-desktop.service - LSB: Chrome Remote Desktop service
Loaded: loaded (/lib/systemd/system/chrome-remote-desktop@USER.service; enabled; vendor preset: enabled)
Active: active (running) since DATE_TIME; ELAPSED_TIME

To restart the service, use the following command in the SSH window :

sudo systemctl restart chrome-remote-desktop@$USER

You can exit SSH window at this point by type exit or click the x button.

Connecting to the VM instance

You can connect to the VM instance using the Chrome Remote Desktop web application.

On your local computer, go to the Chrome Remote Desktop web site.
Click Access my computer.
If you're not already signed in to Google, sign in with the same Google Account that you used to set up the Chrome Remote Desktop service. You see your VM instance openmx in the Remote Devices list.
Click the name of the remote desktop instance. if you name your VM instance openmx, click openmx
When you're prompted, enter the PIN that you created earlier, and then click the arrow button to connect. You are now connected to the desktop environment on your remote Compute Engine instance.
The first time you connect, you are prompted to set up the desktop panels. Click Use Default Config to get the standard taskbar at the top and the quick launch panel at the bottom.

Optional : Improving the remote desktop experience

Install the Remote Desktop Chrome app

The Remote Desktop Chrome app gives a separate windowed experience and allows keyboard shortcuts that would normally be intercepted by Chrome to be used on the remote system.

If this app is not installed, do the following :

Open the Session Options panel using the button chevron_left that appears when you move the mouse to the side of the window.
In the Install App section, click Begin.
Click Install. The remote desktop session reopens in its own application window.

Disable screensavers and lock screens

Because you're accessing your desktop from a remote computer, it's normally not necessary to use a screensaver or screen locker, so you can disable these. If this screensaver is not fisabled, it will take some cpu resources

In the Applications menu, select Settings then select Screensaver.
Set Mode to Disable Screen Saver.

Congrats, you have Compute Engine with Xfce desktop Environment

Installing OpenMX on Google Compute Engine

Installing OpenMX from Github Release

Connect to your openmx instance by clicking the SSH button in the instance list
In the SSH window connected to your VM instance or your terminal, update the package manager data
```
sudo apt update
```
Note
You need SSH window to get sudo command

Do not close your SSH window yet

Download OpenMX version 3.9 with patch version 3.9.9 from github release

wget https://github.com/Ncmexp2717/OpenMX-deb/releases/download/v3.9.9-2/openmx_3.9.9-2_amd64.deb

Install them with apt or dpkg

sudo apt install ./openmx_3.9.9-2_amd64.deb

Connect your VM instance using the Chrome Remote Desktop web application by clicking the name of the remote desktop instance for example openmx.
OpenMX has been installed and you can use it on desktop terminal.

Note

The default value for a input keyword of DATA.PATH is changed to /usr/share/openmx/DFT_DATA19.

The 2019 database of fully relativistic pseudopotentials (VPS) and pseudo-atomic orbitals (PAO), which could be an input data of openmx. It is installed on /usr/share/openmx/DFT_DATA19.

Examples of inputs and computational results are also contained. They are installed on /usr/share/openmx/work.

Installing OpenMX from source

Connect to your openmx instance by clicking the SSH button in the instance list
In the SSH window connected to your VM instance or your terminal, update the package manager data and install build-essential and library package that openmx need to build
```
sudo apt update
sudo apt install --assume-yes build-essential gcc-7 gfortran-7 libfftw3-dev libopenmpi-dev liblapack-dev libblas-dev libscalapack-mpi-dev
```
Do not close your SSH window yet

Download OpenMX version 3.9 with patch version 3.9.9

wget http://t-ozaki.issp.u-tokyo.ac.jp/openmx3.9.tar.gz

wget http://www.openmx-square.org/bugfixed/21Oct17/patch3.9.9.tar.gz

now you close your SSH window

Note
You need SSH window to get sudo command

Connect your VM instance using the Chrome Remote Desktop web application by clicking the name of the remote desktop instance for example openmx.
Click the File Manager :
Right click and then click Extract Here on openmx3.9.tar.gz
Right click and then click Cut on patch3.9.9.tar.gz
Navigate to openmx3.9 / source folder and paste patch3.9.9.tar.gz
Right click and then click Extract Here on patch3.9.9.tar.gz
Click Yes or Replace to patch the source code
Find kpoint.in file and move to openmx3.9 / work folder
Go back to openmx3.9 / source folder and find makefile file

Edit makefile file by Right click, then click Open With "Mousepad" and Change line 8 to line 14 with this config

makefile

# MKLROOT = /opt/intel/mkl
# CC = mpicc -O3 -xHOST -ip -no-prec-div -qopenmp -I/opt/intel/mkl/include/fftw
CC = mpicc -O3 -fopenmp
# FC = mpif90 -O3 -xHOST -ip -no-prec-div -qopenmp
FC = mpif90 -O3 -fopenmp
# LIB= -L${MKLROOT}/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_openmpi_lp64 -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -liomp5 -lpthread -lm -ldl
LIB= -L/usr/lib -L/usr/lib/x86_64-linux-gnu -llapack -lblas -lfftw3 -lmpi -lmpi_mpifh -lgfortran -lscalapack-openmpi

Open Terminal at blank space inside file manager by Right click and then click Open Terminal Here
Build openmx using the following command.
```
make clean
make all
make install
```
It takes a few moments to build openmx. You might see some errors. You can ignore these errors.
Finally grant executable permission on openmx :
```
chmod +x openmx
```
OpenMX has been installed and you can use it on desktop terminal.

Optional : Building other supportive program on OpenMX source

Navigate to openmx3.9 / source folder
Open Terminal at blank space inside file manager by Right click and then click Open Terminal Here
Build other supportive program on OpenMX source

Band Dispersion
```
gcc bandgnu13.c -lm -o bandgnu13
```
Density of States
```
make DosMain
```
Analysis of Spin Texture
```
make kSpin
```

Tips

Read through the OpenMX manual for various details.

OpenMX viewer can help you choose certain parameters for the input file e.g., basis configuration. You may also consult this reference table.

SeeK-path tool can help you build the k-path.

VESTA and xcrysden tool can be used for the visualization.

The work directory under OpenMX installation contains lots of example files for your reference.

Introduction Collecting Watches As a Hobby