ITO
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 […]
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 […]
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 […]
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 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 […]