{"id":1987,"date":"2018-09-10T17:57:11","date_gmt":"2018-09-10T08:57:11","guid":{"rendered":"http:\/\/home.hiroshima-u.ac.jp\/~leehs\/?page_id=1987"},"modified":"2023-04-15T10:51:38","modified_gmt":"2023-04-15T01:51:38","slug":"research-tools-%e7%a0%94%e7%a9%b6%e3%83%84%e3%83%bc%e3%83%ab","status":"publish","type":"page","link":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/?page_id=1987","title":{"rendered":"Research Tools"},"content":{"rendered":"\n<h2 class=\"wp-block-heading\">1. Regional Environment Simulator (RES) : Integrated modelling system<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>A meso-scale coupled model system that can be utilized for engineering applications of regional disasters and environmental problems mainly concerning with natural water circulation (developed by Dr. Lee<br>at the Environmental Simulator Project Center, Hiroshima University). RES consists of the following three parts<\/li>\n\n\n\n<li>1) atmosphere-waves-ocean circulation,<\/li>\n\n\n\n<li>2) atmosphere-land surface process-hydrological circulation,<\/li>\n\n\n\n<li>3) coastal and estuarine circulation.<\/li>\n\n\n\n<li>Download: RES manual<\/li>\n<\/ul>\n\n\n\n<h1 class=\"wp-block-heading\">Useful Scientific Software\uff08\u7814\u7a76\u30bd\u30d5\u30c8\uff09<\/h1>\n\n\n\n<p>(used in the CHESS Lab researches)<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">1. Linux Commands and Scripts<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"http:\/\/www.mediacollege.com\/linux\/command\/linux-command.html\" target=\"_blank\" rel=\"noreferrer noopener\">Basic Linux commands<\/a><\/li>\n\n\n\n<li><a href=\"http:\/\/linuxcommand.org\/index.php\" target=\"_blank\" rel=\"noreferrer noopener\">How to write shell scripts<\/a><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">2. Generic Mapping Tool (GMT)<\/h2>\n\n\n\n<p>An open-source collection of ~60 tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing Encapsulated PostScript File (EPS) illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3-D perspective views.<\/p>\n\n\n\n<p>It produces ready-for-publication high-quality postscript images! I use GMT postscript images in almost all of my publications!<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a rel=\"noreferrer noopener\" href=\"http:\/\/www.soest.hawaii.edu\/gmt\/\" target=\"_blank\">Generic Mapping Tool<\/a>&nbsp;(Ver 4.x)<\/li>\n\n\n\n<li><a href=\"https:\/\/www.generic-mapping-tools.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">Generic Mapping Tool<\/a>&nbsp;(Ver 5.x)<\/li>\n\n\n\n<li><a href=\"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/whatisnew.html\">Global Natural Hazards (earthquake, tsunami, and volcanic activities) map&nbsp;<\/a>(produced by Lee with GMT4.3.1)<\/li>\n\n\n\n<li>What we can do with GMT:&nbsp;<a rel=\"noreferrer noopener\" href=\"https:\/\/www.soest.hawaii.edu\/gmt\/gmt\/gmt_examples.html\" target=\"_blank\">more examples<\/a><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">3. GrADS<\/h2>\n\n\n\n<p>An interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data<\/p>\n\n\n\n<p>It deals with meteorological model output: WRF and MM5 output<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"http:\/\/cola.gmu.edu\/grads\/\" target=\"_blank\" rel=\"noreferrer noopener\">The Grid Analysis and Display System<\/a>&nbsp;(GrADS)<\/li>\n\n\n\n<li><a href=\"http:\/\/wind.geophys.tohoku.ac.jp\/index.php?%B8%F8%B3%AB%BE%F0%CA%F3%2FGrADS%2FGrADS%A4%CETips\" target=\"_blank\" rel=\"noreferrer noopener\">GrADS\u65e5\u672c\u8a9eTips-1<\/a><\/li>\n\n\n\n<li><a href=\"http:\/\/hydro.iis.u-tokyo.ac.jp\/~kei\/?IT%20memo%2FGrADS%20memo\" target=\"_blank\" rel=\"noreferrer noopener\">GrADS\u65e5\u672c\u8a9eTips-2<\/a><\/li>\n\n\n\n<li><a href=\"http:\/\/akyura.sakura.ne.jp\/study\/GrADS\/kouza\/grads.html\" target=\"_blank\" rel=\"noreferrer noopener\">GrADS\u65e5\u672c\u8a9eTips-3<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/atmos.gwnu.ac.kr\/bbs\/board.php?bo_table=j_5_sub1&amp;wr_id=1&amp;sst=wr_hit&amp;sod=asc&amp;sop=and&amp;page=1\" target=\"_blank\" rel=\"noreferrer noopener\">GrADS\ud55c\uad6d\uc5b4Tips<\/a><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">4. Ferret<\/h2>\n\n\n\n<p>An interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets<\/p>\n\n\n\n<p>It open and use a NetCDF format data without any prior treatment: ex. The MITgcm output<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a rel=\"noreferrer noopener\" href=\"https:\/\/ferret.pmel.noaa.gov\/Ferret\/\" target=\"_blank\">Data Visualization and Analysis<\/a><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">5. SciLAB<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"http:\/\/www.scilab.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">The Free Software for Numerical Computation&nbsp;<\/a>: Matlab compatible<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">6. NCO<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"http:\/\/nco.sourceforge.net\/\" target=\"_blank\" rel=\"noreferrer noopener\">The netCDF Operator<\/a>: NCO aids manipulation and analysis of gridded scientific data (e.g., derive new data, average, print, hyperslab, manipulate metadata). The shell-command style of NCO allows users to manipulate and analyze files interactively, or with simple scripts that avoid some overhead (and power) of higher level programming environments.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">7. R and RStudio<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"http:\/\/www.r-project.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">R project<\/a>: a language and environment for statistical computing and graphics<\/li>\n\n\n\n<li><a href=\"https:\/\/www.rstudio.com\/products\/rstudio\/download\/\" target=\"_blank\" rel=\"noreferrer noopener\">R Studio IDE<\/a>: a set of integrated tools designed to help you be more productive with R and Python.<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">8. Hilbert-Huang Transform (HHT)<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"http:\/\/en.wikipedia.org\/wiki\/Hilbert%E2%80%93Huang_transform\" target=\"_blank\" rel=\"noreferrer noopener\">an adaptive time serise analysis method = empirical mode decomposition (EMD) + Hilbert transform<\/a><\/li>\n<\/ul>\n\n\n\n<h1 class=\"wp-block-heading\">High Performance Cluster for GCMs\uff08\u7814\u7a76\u7528\u8a08\u7b97\u6a5f\uff09<\/h1>\n\n\n\n<h2 class=\"wp-block-heading\">1. Simple cluster building starting from one node: ROCKS cluster<\/h2>\n\n\n\n<p>We have two own-build high-performance cluster systems for numerical modelling using the RES. The clusters were built with ROCKS cluster v4.3 and equipped with the software above. Don\u2019t worry!. You can build your own HPC machine as I did from the scratch.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a rel=\"noreferrer noopener\" href=\"http:\/\/www.rocksclusters.org\/\" target=\"_blank\">ROCKS cluster<\/a>&nbsp;: CentOS + Various Rolls<\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">2. Open HPC<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a rel=\"noreferrer noopener\" href=\"https:\/\/openhpc.community\/\" target=\"_blank\">Open-source package for building HPC<\/a>: Community building blocks for<strong>&nbsp;HPC systems<\/strong><\/li>\n<\/ul>\n\n\n\n<h2 class=\"wp-block-heading\">3. High-performance computing platform in the CHESS lab<\/h2>\n\n\n<div class=\"wp-block-image\">\n<figure class=\"alignleft\"><a href=\"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform2.jpg\"><img loading=\"lazy\" decoding=\"async\" width=\"169\" height=\"300\" src=\"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform2-169x300.jpg\" alt=\"\" class=\"wp-image-722\" srcset=\"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform2-169x300.jpg 169w, https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform2-768x1365.jpg 768w, https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform2-576x1024.jpg 576w, https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform2-1170x2080.jpg 1170w, https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform2.jpg 1575w\" sizes=\"auto, (max-width: 169px) 100vw, 169px\" \/><\/a><figcaption class=\"wp-element-caption\">CHESS lab HPC 1<\/figcaption><\/figure>\n<\/div>\n\n<div class=\"wp-block-image\">\n<figure class=\"alignleft\"><a href=\"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform1.jpg\"><img loading=\"lazy\" decoding=\"async\" width=\"169\" height=\"300\" src=\"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform1-169x300.jpg\" alt=\"\" class=\"wp-image-721\" srcset=\"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform1-169x300.jpg 169w, https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform1-768x1365.jpg 768w, https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform1-576x1024.jpg 576w, https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform1-1170x2079.jpg 1170w, https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2017\/02\/suwave-platform1.jpg 1688w\" sizes=\"auto, (max-width: 169px) 100vw, 169px\" \/><\/a><figcaption class=\"wp-element-caption\">CHESS lab HPC 1<\/figcaption><\/figure>\n<\/div>\n\n<div class=\"wp-block-image\">\n<figure class=\"alignleft size-large\"><a href=\"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2023\/04\/newHPC2-rotated.jpg\"><img loading=\"lazy\" decoding=\"async\" width=\"768\" height=\"1024\" src=\"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2023\/04\/newHPC2-768x1024.jpg\" alt=\"\" class=\"wp-image-5093\" srcset=\"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2023\/04\/newHPC2-768x1024.jpg 768w, https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2023\/04\/newHPC2-225x300.jpg 225w, https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2023\/04\/newHPC2-1152x1536.jpg 1152w, https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2023\/04\/newHPC2-1170x1560.jpg 1170w, https:\/\/home.hiroshima-u.ac.jp\/~leehs\/wp-content\/uploads\/2023\/04\/newHPC2-rotated.jpg 1500w\" sizes=\"auto, (max-width: 768px) 100vw, 768px\" \/><\/a><figcaption class=\"wp-element-caption\">HPC 2<\/figcaption><\/figure>\n<\/div>\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>1. Regional Environment Simulator (RES) : Integrated modelling system Useful Scientific Software\uff08\u7814\u7a76\u30bd\u30d5\u30c8\uff09 (used in the CHESS Lab researches) 1. Linux Commands and Scripts 2. Generic Mapping Tool (GMT) An open-source collection of ~60 tools for manipulating geographic and Cartesian data&#8230;<br \/><a class=\"read-more-button\" href=\"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/?page_id=1987\">Read more<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":20,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-full-width-without-title.php","meta":{"footnotes":""},"class_list":["post-1987","page","type-page","status-publish","hentry"],"rttpg_featured_image_url":null,"rttpg_author":{"display_name":"hslee","author_link":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/?author=1"},"rttpg_comment":0,"rttpg_category":null,"rttpg_excerpt":"1. Regional Environment Simulator (RES) : Integrated modelling system Useful Scientific Software\uff08\u7814\u7a76\u30bd\u30d5\u30c8\uff09 (used in the CHESS Lab researches) 1. Linux Commands and Scripts 2. Generic Mapping Tool (GMT) An open-source collection of ~60 tools for manipulating geographic and Cartesian data...Read more","_links":{"self":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/pages\/1987","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1987"}],"version-history":[{"count":19,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/pages\/1987\/revisions"}],"predecessor-version":[{"id":3814,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/pages\/1987\/revisions\/3814"}],"up":[{"embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/pages\/20"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1987"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}