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 […]
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 […]
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 […]
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 […]
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 […]
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.
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 […]
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 […]
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, […]
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 […]