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Tips for supercomputer ITO-A at Kyushu University

This page is tips for usage of supercomputer ITO-A at Kyushu University. About disk quota Check status of disk usage You may encounter an error message like disk quota exceeded when the disk used exceeds its quota. You can check the disk status: lfs quota -g group_name /home Displayed something like as follows: Disk quotas for group ******* (gid *****): Filesystem kbytes quota limit grace files quota limit grace /home 10738166000* 10737418240 10737418240 – 2307227 8000000 10000000 – Where kbyte(=10738166000*): used (kbytes), quota(=10737418240): disk quota (software limit), limit (=10737418240): disk quota (hardware limit),grace (-): Approved duration with exceeded disk quota status,files (=2307227): the number of files used. In this example, …

Build Delft3D on Ubuntu 16.04 of WSL using GNU compiler

This post is a memorandum on building Delft3D on Ubuntu 16.04 of WSL on Windows 10 Pro. I tried to build Delft3D on Ubuntu 18.04 with Intel compiler, but it did not work, and thus following the information here, I built Delft3D on Ubuntu 16.04 with the GNU compiler. (Posted on June 12, 2019) Preparation First, set the Windows shared folder. Add the following to the end of ~/.bashrc so that you can access the Windows C drive as ~/winc. if [ -d winc ]; then   echo “Windows shared folders ready” else   ln -s /mnt/c winc fi In order to reflect the changed .bashrc , execute the following in your …

File output in Bokeh

This article is targeted for Windows 10. Although Matplotlib is a conventional plotting tool in Python, Bokeh is a relatively new package that makes it easy to create interactive plots. Unfortunately, the image output for pasting into PowerPoint or Word is low resolution by default, and it is necessary to enhance the resolution by setting the value of vertical and horizontal pixels to be large at the stage of creating graph. However, since the size of the character does not change in this way, it is very troublesome to set the size of the character each time the pixel values are changed. I found an easy solution for this issue …

Setup GitLab using Git for Windows

Register GitLab Firstly, register GitLab and create a project. No contents are required at this moment as this project will be cloned to Windows directory. Install Git for Windows Download Git for Windows from this site and install it. Default settings are recommended except Adjusting your PATH environment where Use Git from Git Bash only is recommended to choose for safety. Initial setting for Git Open Git Bash and set as follows. Here, Hidemaru Editor is chosen. user.name and user.email should be those registered in GitLab. Quotation marks are also required. git config –global core.editor "’/C/Program Files (x86)/Hidemaru/Hidemaru.exe’ //fu8" git config –global user.name "Your Name" git config –global user.email "your@email.com" …

APNG Animation using APNG Assembler (CUI)

GIF animation has been popular since long ago, but in recent years APNG animation (Animation consisting of a time series of PNG files) seems to be becoming popular and supported by the latest major browsers, including Google Chrome. As software to create APNG, APNG Assembler (apngasm) is a standard. Although there is a GUI version on Windows, from the consistency with the Linux environment, I will summarize the creation method using the CUI version. Install APNG Assembler APNG Assembler web site. Download an appropriate file from List of files. For example, Windows 64 bit CUI binary is apngasm-2.91-bin-win64.zip and Linux CUI binary is apngasm-2.91-bin-linux.zip. Although you may install it on …

Set up ITO-A@kyushu-u supercomputer

This is a memorandum report for seting up an environment on ITO-A at Kyushu University Supercomputer Center. How to login On Windows, you need a terminal emulator to login and MobaXterm is recommended to use, which also has a function of X11 forwarding for displaying X Window screen. Its installation method is introduced in this site (in Japanese). Change file access permission You may change the permission of your directories and files as follows so that group members can read and execute files and help you: $ chmod -R 750 /home/usr_num/account where the first, second, and third digits are types of permissions for user, group, and all the others, and …

Setup Ubuntu 18.04 on WSL on Windows 10 Pro

Install Ubuntu 18.04 Install Ubuntu 18.04 through Microsoft Store on Windows Subsystem for Linux (WSL) on Windows 10 Pro (ver. 1803). It is very simple. Update and upgrade Ubuntu 18.04 Update and upgrade Ubuntu 18.04 as follows. It will take a long time. username@HOSTNAME:~$ sudo apt update && sudo apt upgrade -y [sudo] password for username: Get:1 http://security.ubuntu.com/ubuntu bionic-security InRelease [83.2 kB] Get:2 http://archive.ubuntu.com/ubuntu bionic InRelease [242 kB] … (Long lines continued) You can check the version. username@HOSTNAME:~$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description:    Ubuntu 18.04 LTS Release:        18.04 Codename:       bionic Sharing Windows’ folders To make it easy …

Install Intel Parallel Studio XE 2018 Composer on WSL Ubuntu on Windows10

I installed Inte Parallel Studio XE 2018 Composer on WSL Ubuntu on Windows 10. In November, 2017, I tried to install it as posted here (in Japanese), it was not successful. This time I successfully installed it on Windows 10 ver. 1803 issued in April, 2018. Installation Download Version 2018 (Update 2) March 21, 2018 from the license administration server in here and save it in an appropriate directory and extract it. Move to the extracted directory and invoke install_sh. $ tar xf parallel_studio_xe_2018_update2_composer_edition_online.tgz $ cd parallel_studio_xe_2018_update2_composer_edition_online $ sudo ./install.sh Just follow the instruction. Basically the default values are fine. After completing the installation, invoke a tool as follows to …

Upgrade Ubuntu on WSL on Windows10

Windows10 was upgraded to 1803 at the end of April 2018. It seems that Windows Sybsystem for Linux (WSL) has been enhanced, and we will also upgrade WSL’s Unbutu to the latest version. Confirm version Start up Ubuntu terminal and check the version. $ uname -a Linux T470-S 4.4.0-17134-Microsoft #1-Microsoft Tue Apr 10 18:04:00 PST 2018 x86_64 x86_64 x86_64 GNU/Linux $ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 16.04.3 LTS Release: 16.04 Codename: xenial Local cache update Update the local cache of the installed packages. In my environment, this setting prompted me to enter root’s password. $ sudo apt update Update to latest version Update …

DEM and Coastline data

DEM Digital Elevation Model ASTER GDEM 30 m DEM SRTM at CGIAR-CSI 90 m DEM and re-sampled 250 m, 500 m, and 1km DEM Coastline Data NOAA GEODASS NOAA’s online coastline extractor is no longer recommended to use. Instead, download GSHHG in binary file and manipulate it on a software geodas-ng. Also GEODASS coastlines may be downloaded and processed using geodas-ng. geodas-ng can draw a map of specified lon & lat ranges and then export it in a various file format, including GMT text format and ESRI shape file format.

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