{"id":2730,"date":"2019-11-23T23:44:43","date_gmt":"2019-11-23T14:44:43","guid":{"rendered":"http:\/\/home.hiroshima-u.ac.jp\/~leehs\/?p=2730"},"modified":"2019-11-24T00:18:39","modified_gmt":"2019-11-23T15:18:39","slug":"how-to-setup-a-gerris-server","status":"publish","type":"post","link":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/?p=2730","title":{"rendered":"How to setup a Gerris server"},"content":{"rendered":"\n<p>In this setup example, we used the Ubuntu 18.04 (Bionic Beaver) OS system on a dedicated workstation.<\/p>\n\n\n\n<h4 class=\"wp-block-heading\">Using the pre-built package<\/h4>\n\n\n\n<p> In Ubuntu 18.04 system, type the followings:<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">$ sudo apt install gerris<\/pre>\n\n\n\n<p>But, the pre-built package does not include some of modules such as libmap2D.so, libmap3D.so, libtide2D, and so on.<\/p>\n\n\n\n<p>To have all necessary modules, it has to be compiled from source code (*.tar.gz)<\/p>\n\n\n\n<h4 class=\"wp-block-heading\">Using the source code<\/h4>\n\n\n\n<p>Get the source code at<\/p>\n\n\n\n<figure class=\"wp-block-embed\"><div class=\"wp-block-embed__wrapper\">\nhttp:\/\/gfs.sourceforge.net\/wiki\/index.php\/Installing_from_source\n<\/div><\/figure>\n\n\n\n<p>First, install the Glib development package from repository<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">$ sudo apt-get install libglib2.0-dev <\/pre>\n\n\n\n<p>Then, install dependents packages from Ubuntu repositories.<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">$ sudo apt-get install libglib2.0-dev libnetpbm10-dev m4 libproj-dev \\\nlibgsl0-dev libnetcdf-dev libode-dev libfftw3-dev libhypre-dev libgtkglext1-dev libstartup-notification0-dev ffmpeg<\/pre>\n\n\n\n<pre class=\"wp-block-preformatted\">$ sudo apt-get install libopenmpi-dev<\/pre>\n\n\n\n<p>Next, compiling and installing the GTS<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">$ cd gts\n$ .\/configure (--prefix=... is optional)\n$ make\n$ sudo make install (or just 'make install' if installing locally)<\/pre>\n\n\n\n<p>In order for the system to know that a new dynamic library has been installed, you need to:\n<\/p>\n\n\n\n<ol class=\"wp-block-list\"><li>If installing in <code>\/usr\/local<\/code>:<\/li><li>check that the file <code>\/etc\/ld.so.conf<\/code> exists and contains the line <code>\/usr\/local\/lib<\/code> (if not, add it)<\/li><li>then run\n% sudo \/sbin\/ldconfig\n<\/li><\/ol>\n\n\n\n<p>Finally, compiling and installing the Gerris<\/p>\n\n\n\n<p>Before compiling Gerris you need to decide whether you want to run \nGerris in parallel. The parallel version of Gerris depends on an \nimplementation of the <a href=\"http:\/\/www-unix.mcs.anl.gov\/mpi\/\">MPI<\/a>\n (Message Passing Interface) standard. If you do, you will need to \ninstall the MPI libraries first. On an Ubuntu\/Debian system just do:\n<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">% sudo apt-get install openmpi-bin libopenmpi-dev\n<\/pre>\n\n\n\n<p>Note that the compilation of the parallel version of Gerris requires a working <code>mpicc<\/code> command (i.e. as provided by the <code>openmpi-bin<\/code> package above).\n<\/p>\n\n\n\n<p>Otherwise the process is almost identical to the GTS installation. Again assuming you either downloaded and unpacked a <a href=\"http:\/\/gfs.sourceforge.net\/wiki\/index.php\/Download\">source tarball<\/a> or <a href=\"http:\/\/gfs.sourceforge.net\/wiki\/index.php\/Darcs_installation\">used darcs<\/a> to get a directory called <code>gerris<\/code>, do:\n<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">$ cd gerris\n$ .\/configure\n$ make\n$ sudo make install<\/pre>\n\n\n\n<p>When installing in <code>\/usr\/local<\/code> do not forget to update the dynamic linker database:\n<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">$ sudo \/sbin\/ldconfig<\/pre>\n\n\n\n<p>If everything went well you should be able to run the following (if using a <em>csh<\/em> based shell, remember to <code>rehash<\/code> first):\n<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">$ gerris2D -V<\/pre>\n\n\n\n<h4 class=\"wp-block-heading\">Compiling and installing GfsView <\/h4>\n\n\n\n<p>Install the dependents packages. On an Ubuntu system do: <\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">$ sudo apt-get install libgtk2.0-dev libgtkglext1-dev libstartup-notification0-dev libftgl-dev<\/pre>\n\n\n\n<p>GfsView also provides a non-graphical version (command <code>gfsview-batch<\/code>) which can run without any graphical display. <\/p>\n\n\n\n<p>The batch command is useful for generating on-the-fly animations on systems without a graphical terminal, by using the Gfsview module with GfsOutputView. <\/p>\n\n\n\n<p>To install OSMesa on an Ubuntu system do: <\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">$ sudo apt-get install libosmesa6-dev<\/pre>\n\n\n\n<p>Then as usual do:\n<\/p>\n\n\n\n<pre class=\"wp-block-preformatted\">$ cd gfsview\n$ .\/configure\n$ make\n$ sudo make install<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>In this setup example, we used the Ubuntu 18.04 (Bionic Beaver) OS system on a dedicated workstation. Using the pre-built package In Ubuntu 18.04 system, type the followings: $ sudo apt install gerris But, the pre-built package does not include&#8230;<br \/><a class=\"read-more-button\" href=\"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/?p=2730\">Read more<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[12],"tags":[],"class_list":["post-2730","post","type-post","status-publish","format-standard","hentry","category-tool"],"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":"<a href=\"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/?cat=12\" rel=\"category\">Tool<\/a>","rttpg_excerpt":"In this setup example, we used the Ubuntu 18.04 (Bionic Beaver) OS system on a dedicated workstation. Using the pre-built package In Ubuntu 18.04 system, type the followings: $ sudo apt install gerris But, the pre-built package does not include...Read more","_links":{"self":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/posts\/2730","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/types\/post"}],"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=2730"}],"version-history":[{"count":6,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/posts\/2730\/revisions"}],"predecessor-version":[{"id":2738,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=\/wp\/v2\/posts\/2730\/revisions\/2738"}],"wp:attachment":[{"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2730"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2730"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/home.hiroshima-u.ac.jp\/~leehs\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2730"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}