Computing

Computing
Install Intel oneAPI on Ubuntu 20.04 LTS

In order to use Intel C compiler and Intel Fortran compiler for numerical computation, Intel oneAPI Base Toolkit and HPC Toolkit (Intel Fortran) on Ubuntu 20.04 LTS of WSL2 of Windows 10 Pro were installed. This site (in Japanese) was referred. The Intel compilers are now available free of charge, and can be installed using apt, which is very convenient. Install the required drivers Install the required drivers by referring to here. # Add package repository sudo apt-get install -y gpg-agent wget wget -qO - https://repositories.intel.com/graphics/intel-graphics.key | sudo apt-key add - sudo apt-add-repository 'deb [arch=amd64] https://repositories.intel.com/graphics/ubuntu focal main' # Install run-time packages sudo apt-get update sudo apt-get install intel-opencl-icd intel-level-zero-gpu […]

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Computing
Installing GMT 6 on Ubuntu 20.04 LTS

GMT 6 is a popular plotting tool in regional and earth sciences, and it is a great software to draw the most beautiful figures with print quality. This is a memorandum of the build and installation on Ubuntu 20.04 LTS on WLS2 of Windows 10 Pro. I referred to this site (in Japanese). You may be able to install it with apt, but it is easy to build and recommended in the official site. Install dependent packages The first step is to install dependent packages. If some package is already installed, it will be skipped. sudo apt update sudo apt upgrade -y sudo apt install -y build-essential cmake libcurl4-gnutls-dev libnetcdf-dev […]

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Computing
Install Ubuntu 20.04 LTS on WSL2 of Windows 10

This is a memorandum of the installation of Ubuntu 20.04 LTS on WSL2 of Windows 10 Pro. It is assumed that WSL2 can be used. Get Ubuntu 20.04 LTS from Microsoft Store Go to the Microsoft Store, search for Linux, and find Ubuntu 20.04 LTS. There should be no confusion in the installation. When you register your user name, you will be asked to set a password, which you will enter when you run as root using sudo. It is convenient to pin it to the taskbar. Install packages Launch the Ubuntu 20.04 LTS terminal. After updating to the latest version, install the necessary packages. sudo apt update sudo apt […]

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Computing
Change font color settings in Ubuntu terminal on WSL

I found it difficult to see some of the colors of the terminals on WSL2 Ubuntu 18.04LTS on Windows 10 Pro. So you can customize the text color. Install Windows Terminal Install from Microsoft Store. Register in the start menu. Start Windows Terminal Start Windows Terminal from the Start menu, then Windows PowerShell terminal will be launched. Click on the downward-facing symbol to the right of the "+" on the right of the tab to open the menu. Click on Settings in the menu, edit it (Append "colorScheme": "One Half Dark",) as follows: { "guid": "{c6eaf9f4-32a7-5fdc-b5cf-066e8a4b1e40}", "hidden": false, "name": "Ubuntu-18.04", "colorScheme": "One Half Dark", "source": "Windows.Terminal.Wsl" }, Color setting using […]

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Computing
Making vim (vi) text color easier to see on WSL-Ubuntu

Comments in .bashrc hard to see I'm using WSL-Ubuntu session of MobaXterm on Ubuntu 18.04LTS on WSL, but when I open .bashrc with vi (vim), comments are hard to see. So make the text color easier to see. Referring to this site (in Japanese), let's introduce a color scheme of molokai to make it easier to see. Installing molokai Start a terminal, create vim's personal setting directory .vim in the home directory, install molokai, and open .vimrc using vi. $ mkdir .vim $ cd .vim $ mkdir colors $ git clone https://github.com/tomasr/molokai Cloning into'molokai'... remote: Enumerating objects: 148, done. remote: Total 148 (delta 0), reused 0 (delta 0), pack-reused 148 […]

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Computing
Working on GitLab by mirroring open source model

Clone open source model to GitLab Taking an ocean model ROMS as an example, let's consider the best practice of operating the ROMS repositories by cloning (not forking) the original ROMS repository to GitLab, where the mirroring is set to automatically import the update of the original repository. Please refer to this article for the settings up to this point. I will create and operate my own devel branch to avoid changing the repository cloned from the original repository on GitLab. Now the remote repository is GitLab cloning (mirroring) the original ROMS repository; local repository is operated using GitBash on Windows 10 Pro and Git on Supercomputer ITO. Final workflow […]

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Computing
Git for Windows

Install Install Git for Windows on Windows 10 Pro and manage version control with Git Bash. It is assumed that the compilation and execution will be done on Ubuntu 18.04 LTS on WSL on Windows 10 Pro. Therefore, the linefeed code should always be in Linux format. This linefeed code stuff is a trap for beginners, so be careful. Download Git for Windows from here and start installation by double-clicking. Basically, the default is OK, but in the question about line endings appearing nearly at the end (Configuring line ending conversions), click the third option below. This allows you to work while always maintaining the Linux linefeed code. Checkout as-is, […]

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Computing
Using Markdown editor StackEdit on GSuite

StackEdit initial settings Our lab members use GSuite; it is convenient if README.MD is prepared in Markdown in a shared folder and can be viewed. This can be realized by StackEdit. Here and here (both in Japanese) are helpful. StackEdit is a browser-based (confirmed using Chrome) Markdown editor and can be used standalone. You do not need to register; access here, read the explanation, and start writing with START WRITING at the top. At first, the following Welcome to StackEdit document appears, the left is the manuscript in Markdown notation while the right is its display. There are Toggle explorer buttons in the upper left and upper right. As shown […]

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Computing
HYCOM dataset usage

HYCOM Datasets In HYCOM Data Server, the results of HYCOM's global ocean flow field reproduction prediction results are available as a dataset. The two main ones are: They are Analysis and Reanalysis. The difference in contents is written in here. The items are the same for both, SSH (sea surface height), zonal velocity (east-west velocity), meridional velocity (north-north velocity), temperature (in-situ water temperature), and salinity. GOFS 3.1: 41-layer HYCOM + NCODA Global 1/12 ° Analysis Archive from July 2014 to the present. Details are here. Be careful that there are Missing days. GOFS 3.1: 41-layer HYCOM + NCODA Global 1/12 ° Reanalysis This is an archive every 3 hours from […]

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Computing
Building NetCDF-Fortran using Intel compiler on Ubuntu 18.04 on WSL

Prerequisites It is assumed that Ubuntu 18.04LTS is installed on WSL on Windows 10 Pro; Intel Parallel Studio XE 2020 Composer Edition is installed. Referring to this article, libraries other than NetCDF-Fortran are easily installed with apt (compiled with GNU). Install GNU libraries with apt HDF5 (referenced here) and GNU version of NetCDF-4 (libnetcdf-dev) and NetCDF-Fortran (libnetcdff-dev, refer to here) are installed as follows. libnetcdff-dev should not be installed as building Intel version failed. $ sudo apt update $ sudo apt install hdf5-tools hdf5-helpers libhdf5-dev libhdf5-doc libhdf5-serial-dev $ sudo apt install libnetcdf-dev Check whether the installation was successful. $ nc-config --all This netCDF 4.6.0 has been built with the following […]

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