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 […]
Installing NetCDF-Fortran using Intel oneAPI on Ubuntu 22.04 on WSL2
November 5, 2023: Installation environment is updated. Prerequisites It is assumed that Ubuntu 22.04LTS is installed on WSL2 on Windows 11 Pro; Intel oneAPI is installed as well. Referring to this article, libraries other than NetCDF-Fortran are easily installed with apt (compiled with GNU). How to compile NetCDF-C with Intel oneAPI is introduec here in Japanese, but it is time consuming. Install GNU libraries with apt HDF5 (referenced here) and GNU version of NetCDF-C (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 […]
Exporting PowerPoint slide images in high resolution
Saving in PNG is coarse in 96dpi When saving (exporting) images in PNG of PowerPoint slides of Microsoft Office 2016 on Windows 10 Pro, the output is in 96dpi by default; the resolution is too low as a graphic to be inserted into a paper or thesis. A method to increase the resolution was introduced in here. The method is common to any type of images, including PNG and JPEG. Edit Registry Editor Since it operates the registry editor, if you make a mistake, Windows may be damaged at worst. Close all running software and then work carefully. Right-click the "Start button", type regedit in the "Name box" of "Run", […]
Install Intel Parallel Studio XE for Linux 2020
Obtaining the installation package Intel Parallel Studio XE Composer Edition for Fortran and C ++ Linux on Ubuntu 18.04 LTS (WSL1 on Windows 10 Pro 64bit) is being installed. Its version is 2020 Update 1 (Build on March 26, 2020). It is assumed that a tgz file of full package has been downloaded from the license management site and is in an appropriate folder (directory). The default download folder on Windows 10 is C:\Users\username\Downloads (replace username). On Linux, it corresponds to /mnt/c/Users/username/Downloads. The size of this file is 1.7GB. WSL2 has already been released, but I installed it on Ubuntu 18.04 LTS of WSL1. The Intel compiler seems not to […]
Mounting G Suite Google drive on Windows PC
Background FApps has been introduced in the Graduate School of Frontier Sciences, the University of Tokyo. I was considering how to access data on the shared drive (formerly called team drive) of G Suite from a local Python code on Windows 10 Pro using PyDrive. However, it ended in failure. In addition, uninstalling PyDrive installed with conda also failed. Recently, I learned that there is a way to mount Google shared drive locally with Google Drive File Stream as a way to access the data on the shared drive. Google drive file stream Login with your FApps account and open Google Drive. There are My Drive and Shared Drive. Mounting […]
MATLAB on Supercomputer ITO
MATLAB can be used on Supercomputer ITO in GUI (Graphical User Interface) via X-Window or CUI (Command Line Environment). Online manual is here. You cannot install it on your local PC. Loading MATLAB To use MATLAB, your favorite version of MATLAB should be loaded. You can confirm whether it has been loaded using module list command. Available versions are R2019b, R2018a, or R2017a as on April 30, 2020. $ ulimit -v 31457280 $ module load matlab/R2019b $ module list Currently Loaded Modulefiles: 1) intel/2019.4 2) matlab/R2019b MATLAB in CUI CUI is reqcommended considering slow connection in GUI. CUI interactive interface can be invoked by the following: $ matlab -nodisplay It […]
Bar plots on Google Earth Pro
Creating Bar plots kml files for Google Earth Pro using Python googleearthplot referring to this site. Install Suppose pandas is installed. Install simplekml and googleearthplot. pip install simplekml pip install googleearthplot googleearthplot is a Python2 code and some modification is required in Python3 because of an error associated with print statement. First find the location of installed googleearthplot as follows: pip show googleearthplot Edit googleearthplot.py to modify the lines of print statement by converting print **** to print(****) using parentheses. Usage Open a Jupyter Notebook and import packages. Referring to the original site, some examples are shown. Double cricking on created kml file, a plot should be presented on Google […]
Tips for supercomputer ITO-A at Kyushu University
This page is tips for the usage of supercomputer ITO-A at Kyushu University. The service ends in February 2023 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 kbytes(=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 […]
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
Updated on September 23, 2020:There seems a bug in bokeh 2.2.1, in which png files do not contain whole of the graphic area when exporting to png from html. To avoid this error, use bokeh 1.4.0, which can be insalled with conda install -c pyviz bokeh==1.4.0 in a new conda virtual environment 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 […]