Education
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 […]
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 […]
Time series plotting using hvPlot
hvPlot, a component of PyViz ia a new interactive plotting tool, which is a wrapper of Bokeh. hvPlot is easy to customize plotting options. However, currently there are some drawbacks, such as difficulty in adjusting aspect ratio of graph area, which may be resolved in Bokeh 1.1, slow processing, and cumbersome in exporting high resolution PNG file, comparing to Matplotlib. Default time series plotting Suppose df is a pandas DataFrame having a time series index and columns of 'kion' and 'sped', which are actually a dataset of air temperature and wind speed at Chiba Observatory, Japan, provided by Japan Meteorological Agency. import hvplot.pandas df[['kion','sped']].hvplot() Customized plotting Now one column of […]
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 […]
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 […]
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 the […]
Build FVCOM4.1 (MPI) on ITO Subsystem-A using Intel Compilers
This page is a memorandum of building and executing [cci]FVCOM4.1[/cci] in [cci]MPI[/cci] using Intel compilers on the supercomputer Subsystem-A of ITO at Kyushu University. Those in [cci]Series[/cci] are introduced in this page. The building environment for [cci]Series[/cci] should be prepared. The source files are supposed to exist in [cci]FVCOM4.1/FVCOM_source[/cci] and the test case is [cci]Estuary[/cci] in [cci]FVCOM4.1/Examples/Estuary[/cci]. Preparation for METIS METIS library requires to be installed for building for MPI. First [cci]load[/cci] Intel compilers: [cc] $ module load intel/2018 [/cc] Environmental variables for Intel C compiler should be made as follows: [cc] $ export CC=icc $ export CPP="icc -E" [/cc] Move to the directory of [cci]FVCOM4.1/METIS_source[/cci] where the [cci]METIS[/cci] source […]
Build netcdf-3.6.3-intel on ITO Subsystem-A
This is a memorandum building netcdf-3.6.3 with Intel compilers on Supercomputer ITO Subsystem-A at Kyushu University. The build of netcdf-4.1.2 does not work as found here. Obtaining source of netcdf-3.6.3 Updated on June 13, 2021: The source of netcdf-3.6.3.tar.gz cannot be downloaded now. Suppose you have it. Building netcdf-3.6.3 Create the following bash script of build_netcdf363.sh. #!/bin/bash # build_netcdf363.sh export CC=icc export CXX=icpc export CFLAGS=-O3 export CXXFLAGS=-O3 export F77=ifort export FC=ifort export F90=ifort export FFLAGS=-O3 export CPP='icc -E' export CXXCPP='icpc -E' tar xf netcdf-3.6.3.tar.gz cd netcdf-3.6.3 ./configure --prefix=/home/usr1/account/local/netcdf-3.6.3-intel make make check make install Adding an executable attribute and execute the script. chmod a+x build_netcdf363.sh ./build_netdf363.sh Done! If you use it […]
Build FVCOM4.1 (Series) on ITO Subsystem-A using Intel Compilers
This is a memorandum of how to build and execute FVCOM 4.1 in series (non MPI) using Intel compilers on Supercomputer ITO Subsystem A at Kyushu University. Suppose the source code exists in [cci]FVCOM4.1/FVCOM_source[/cci], and [cci]FVCOM4.1/Examples/Estuary[/cci] is a selected test case. Installing nkf Line feed of some distributed source files is for Windows and need to be fixed using nkf. For installing nkf, download the source of [cci]nkf[/cci] from this site , copy it to [cci] ~/src [/cci], and extract and build it. [cc lang='bash'] $ tar xf nkf-2.1.4.tar.gz $ cd nkf-2.1.4 $ make ### Create ~/local/bin and add its PATH $ cp nkf ~/local/bin/ [/cc] Check line feed of […]