Estuarine and Coastal Environment, Coastal Engineering and Management, Sustainability Science

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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.

Build FVCOM4.1 (MPI) on ITO Subsystem-A using Intel Compilers

This page is a memorandum of building and executing FVCOM4.1 in MPI using Intel compilers on the supercomputer Subsystem-A of ITO at Kyushu University. Those in Series are introduced in this page. The building environment for Series should be prepared. The source files are supposed to exist in FVCOM4.1/FVCOM_source and the test case is Estuary in FVCOM4.1/Examples/Estuary. Preparation for METIS METIS library requires to be installed for building for MPI. First load Intel compilers: $ module load intel/2018 Environmental variables for Intel C compiler should be made as follows: $ export CC=icc $ export CPP="icc -E" Move to the directory of FVCOM4.1/METIS_source where the METIS source code exists and extract …

Build makedepf90 on ITO Subsystem-A

This page is a memorandum for building makedepf90 with Intel compiler on Subsystem-A of Supercomputer ITO at Kyushu University, which is used in building FVCOM. Obtaining source code Source code can be downloaded from Github by clicking the green button of Clone or download at the right-hand side. Copy it in a directory, e.g., ~/src/ . Then set environmental variables for Intel compilers as introduced in this page. Extract the source code, build it and copy the created executable file of makedepf90 to, e.g., ~/local/bin that is added to PATH. $ unzip makedepf90.zip $ cd makedepf90-master $ make $ cp makedepf90 ~/local/bin Usage When makedepends for FVCOM needs to be …

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 The source of netcdf-3.6.3 can be downloaded from this site. Extract it in a directory: tar xf netcdf-3.6.3.tar.gz Set environmental variables Environmental variables requires to be set for using Intel compilers. You may temporarily set them in .bashrc and invoke $ . .bashrc. $ 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’ Building netcdf-3.6.3 Now you can …

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 FVCOM4.1/FVCOM_source, and FVCOM4.1/Examples/Estuary 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 nkf from this site , copy it to  ~/src, and extract and build it. $ 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/ Check line feed of source …

Setup environment on ITO at Kyushu University Supercomputer

The following is a memo of initial setup for subsystem A on ITO at Kyushu University. Login environment If you are using in Japanese, in .bashrc, the following setting should be implemented to avoid garbled characters in the terminal. export LANG=en_US.UTF-8 Install Anaconda To avoid conflict with the pre-installed Python system, pyenv is installed and used to create a virtual environment. Install pyenv Pyenv can be easily installed as follows: $ cd ~ $ git clone git://github.com/yyuu/pyenv.git .pyenv Edit ~/.bashrc Add the following in .bashrc: export PYENV_ROOT="${HOME}/.pyenv" if [ -d "${PYENV_ROOT}" ]; then     export PATH=${PYENV_ROOT}/bin:$PATH     eval "$(pyenv init -)" fi You can take a look at …

Handling SQLite database using Python

Suppose that the file name of SQLite’s database is mpos_S.sqlite, its table (like a sheet of Excel) name is mpos_S, and mpos_S contains column data. If the column name of water temperature data is tp, this column tp contains water temperature data. In order to handle it from Python, you need to import sqlite3. First connect to the database and get the cursor cur. >>> import sqlite3 >>> conn = sqlite3.connect(‘mpos_S.sqlite’) >>> cur = conn.cursor() Check information of columns. >>> cur.execute("PRAGMA TABLE_INFO(mpos_S)")  ### Gets information about columns of table mpos_S >>> cols = cur.fetchall()  ### Information of a column is a tuple containing 6 elements. >>> print(cols) To get only …

Install PyMC3 on Windows 10 (Anaconda)

I tried installing PyMC on Windows 10 to learn materials in the book of “Bayesian Methods for Hackers”, but I encountered problems, which seems owing to suspension of maintenance. I first created a virtual environment of pymc3 and then installed necessary packages using conda: > conda create -n pymc3 python=3.6 > activate pymc3 > conda install matplotlib > conda install pymc3 However, import pymc3 lead to ModuleNotFoundError. So did import pymc(installing pymc2). Fortunately I found a solution from this article (in Japanese) and summarized how I accommodated below. First I recreated a virtual environment for pymc3 and then started installing Python3.5 instead of Python 3.6. > deactivate > conda remove …

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