2021-03-24 / Last updated : 2021-03-24 jsasaki 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 […]
2021-03-23 / Last updated : 2021-03-24 jsasaki 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 […]
2021-03-23 / Last updated : 2021-03-24 jsasaki 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 […]
2021-01-23 / Last updated : 2021-01-23 jsasaki Python

Segmentation fault issue when using Miniconda on ITO-A

After installing Miniconda (Anaconda) on the ITO-A supercomputer and creating a virtual environment, a problem of Segmentation fault occurred when running a Python script. A solution to this problem was found and summarized here. How to revolve Segmentation fault issue The problem was probably the conflict with the vendor installed Python. This issue was resolved by appending the following in last part of ~/.bashrc: export PYTHONPATH= The problem was resolved by logging in again and installing Miniconda as usual. The specific method is described here (in Japanese and please translate using an online tool). Occurrence of segmentation fault The environment used to work fine, but when I tried to work […]
2021-01-06 / Last updated : 2021-01-06 jsasaki Research Topics

Knowledge, awareness, and attitudes toward tsunamis: A local survey in the southern coast of Iran

Research Overview The southern coast of Iran (mainly the coastal area facing the Gulf of Oman) is a potential tsunami and storm surge disaster area, but since it is the least developed area in Iran, little work has been done to prevent such disasters. In recent years, the Iranian government has moved to designate this area as a free trade zone, and it is being positioned as an important area. In addition, there are many ethnic minorities living in the area, and religious influences are significant, so it was assumed that ordinary disaster mitigation measures would not work well. In this study, a questionnaire survey, interviews, and focus group discussions […]
2020-12-26 / Last updated : 2020-12-26 jsasaki Research Topics

Assessing the natural recovery of mangroves after human disturbance using neural network classification and Sentinel-2 imagery

Research Overview llegal cultivation of shrimp ponds and rice paddies was carried out in the Wumbaik Reserved Mangrove Forest in Rakhine State, Myanmar; many of them have been abandoned under administrative guidance. Although mangrove reforestation has often been carried out around the world, it is costly and tends to be biased toward specific tree species, resulting in a state that differs from the natural state. This study focuses on how abandoned sites can be regenerated in a natural state without human intervention. AS abandoned areas are generally small in size and low-cost method is required especially in developing countries, we adopted Senitnel-2 imagery, which has relatively high resolution and can […]
2020-09-21 / Last updated : 2020-09-21 jsasaki 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 […]
2020-08-29 / Last updated : 2020-08-29 jsasaki Python

Exporting and rebuilding conda virtual environment

Background After installing Miniconda on a new Windows 10 PC and setting up a virtual environment for running xhycom, xarray.Dataset.hvPlot does not work. There seems to be a problem with the handling of datetime64; pandas get_loc(key) returns a KeyError in datetimes.py. get_loc(key) seems to take an index and there seems to be a confusion between the index and the integer value of datetime64(ns). Since I do not know the solution, I decide to rebuild the virtual environment that is working well. This problem has been discussed in this site. It may be associated with some incompatibility between xarray 0.16 and pandas 1.1 (works with pandas 1.05). Exporting the virtual environment […]
2020-08-21 / Last updated : 2020-08-29 jsasaki Research

HYCOM data download and visualization

The HYCOM database is an oceanic reanalysis dataset often used for open boundary conditions in oceanic circulation models. The Netcdf handling tool of xhycom was developed to facilitate the OPeNDAP download and visualization of Netcdf data using xarray. Data visualization includes creation of still images and time-series movies with matplotlib while interactive visualization with hvPlot. Jupyter Notebook on xhycom may help you to understand how to use it. In terms of visualization, matplotlib is superior in terms of ease of fine tuning and speed, which is better for printed materials. On the other hand, hvPlot is useful for checking values and understanding phenomena interactively; but it is slower.
2020-06-22 / Last updated : 2020-06-22 jsasaki 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 […]