{"id":1347,"date":"2017-11-21T11:08:18","date_gmt":"2017-11-21T11:08:18","guid":{"rendered":"http:\/\/35.198.183.193\/?page_id=1347"},"modified":"2018-04-25T12:40:06","modified_gmt":"2018-04-25T12:40:06","slug":"code-compilation-and-libraries","status":"publish","type":"page","link":"http:\/\/escience.sdu.dk\/index.php\/code-compilation-and-libraries\/","title":{"rendered":"Code compilation &#038; libraries"},"content":{"rendered":"<h4>Compilers<\/h4>\n<ul class=\"nav nav-tabs\">\n<li class=\"active\"><a data-toggle=\"tab\" href=\"#Gcc\">Gcc<\/a><\/li>\n<li><a data-toggle=\"tab\" href=\"#Intel\">Intel<\/a><\/li>\n<\/ul>\n<div class=\"tab-content\">\n<div class=\"tab-pane fade in active\" id=\"Gcc\">The module gcc\/4.8-c7 &#8220;loads&#8221; the default gcc compiler found on our Centos7 system. Other versions of the gcc compiler are also available.To get the currently default version of the gcc module, use<\/p>\n<div class=\"codehilite\">\n<pre><code><span class=\"gp\">testuser@fe1:~$<\/span> module load gcc\/4.8-c7\r\n<\/code><\/pre>\n<\/div>\n<hr>\n<p>Further information:<a href=\"https:\/\/gcc.gnu.org\/\">https:\/\/gcc.gnu.org\/<\/a><br \/>\nVersions available:<\/p>\n<ul>\n<li>gcc\/4.7.4<\/li>\n<li>gcc\/4.8-c7 (default)<\/li>\n<li>gcc\/5.4.0<\/li>\n<li>gcc\/6.2.0<\/li>\n<li>gcc\/6.3.0<\/li>\n<\/ul>\n<\/div>\n<div class=\"tab-pane fade\" id=\"Intel\">This module loads the Intel compiler suite including all packages except for Intel MPI, but including e.g. Intel MKL.Intel MPI may be loaded separately using the module intelmpi.To get the currently default version of the intel module, use<\/p>\n<div class=\"codehilite\">\n<pre><code><span class=\"gp\">testuser@fe1:~$<\/span> module load intel\/2016.05\r\n<\/code><\/pre>\n<\/div>\n<hr>\n<p>Further information:<a href=\"https:\/\/software.intel.com\/en-us\/intel-compilers\">https:\/\/software.intel.com\/en-us\/intel-compilers<\/a><br \/>\nVersions available:<\/p>\n<ul>\n<li>intel\/2015.02<\/li>\n<li>intel\/2015.04<\/li>\n<li>intel\/2016.05 (default)<\/li>\n<li>intel\/2016.11<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<h4>MPI implementations<\/h4>\n<ul class=\"nav nav-tabs\">\n<li class=\"active\"><a data-toggle=\"tab\" href=\"#IntelMPI\">IntelMPI<\/a><\/li>\n<li><a data-toggle=\"tab\" href=\"#MVAPICH2\">MVAPICH2<\/a><\/li>\n<li><a data-toggle=\"tab\" href=\"#OpenMPI\">OpenMPI<\/a><\/li>\n<\/ul>\n<div class=\"tab-content\">\n<div id=\"IntelMPI\" class=\"tab-pane fade in active\">This module loads the Intel MPI compiler path and environment variablesThis module can only be loaded if you first load one of the following modules:<\/p>\n<ul>\n<li>gcc\/4.7.4<\/li>\n<li>gcc\/4.8-c7<\/li>\n<li>gcc\/5.4.0<\/li>\n<li>gcc\/6.2.0<\/li>\n<li>gcc\/6.3.0<\/li>\n<li>intel\/2016.11<\/li>\n<\/ul>\n<p>To get the currently default version of the intelmpi module, use<\/p>\n<div class=\"codehilite\">\n<pre><code><span class=\"gp\">testuser@fe1:~$<\/span> module load intel\/2016.11 intelmpi\/2016.11\r\n<\/code><\/pre>\n<\/div>\n<p>You can replace<span> <\/span><code>intel\/2016.11<\/code><span> <\/span>with other versions of the gcc or intel modules. Note that not all combinations of versions of intelmpi and these modules may be available.<\/p>\n<hr>\n<p>Further information:<a href=\"https:\/\/software.intel.com\/en-us\/intel-mpi-library\">https:\/\/software.intel.com\/en-us\/intel-mpi-library<\/a><br \/>\nVersions available:<\/p>\n<ul>\n<li>intelmpi\/2015.02<\/li>\n<li>intelmpi\/2015.04<\/li>\n<li>intelmpi\/2016.05<\/li>\n<li>intelmpi\/2016.11 (default)<\/li>\n<\/ul>\n<\/div>\n<div id=\"MVAPICH2\" class=\"tab-pane fade\">MPI implementation based on MPICH with added Infiniband supportThis module can only be loaded if you first load one of the following modules:<\/p>\n<ul>\n<li>gcc\/4.8-c7<\/li>\n<li>gcc\/5.4.0<\/li>\n<li>gcc\/6.2.0<\/li>\n<li>gcc\/6.3.0<\/li>\n<li>intel\/2016.11<\/li>\n<\/ul>\n<p>To get the currently default version of the mvapich2 module, use<\/p>\n<div class=\"codehilite\">\n<pre><code><span class=\"gp\">testuser@fe1:~$<\/span> module load intel\/2016.11 mvapich2\/2.2\r\n<\/code><\/pre>\n<\/div>\n<p>You can replace<span> <\/span><code>intel\/2016.11<\/code><span> <\/span>with other versions of the gcc or intel modules. Note that not all combinations of versions of mvapich2 and these modules may be available.<\/p>\n<hr>\n<p>Further information:<a href=\"http:\/\/mvapich.cse.ohio-state.edu\/\">http:\/\/mvapich.cse.ohio-state.edu\/<\/a><br \/>\nVersions available:<\/p>\n<ul>\n<li>mvapich2\/2.1<\/li>\n<li>mvapich2\/2.2 (default)<\/li>\n<\/ul>\n<\/div>\n<div id=\"OpenMPI\" class=\"tab-pane fade\">This module loads the OpenMPI compiler path and environment variables. OpenMPI is available in two versions openmpi and openmpi-i8. openmpi-i8 is compiled to use 64-bit integers when using Fortran (the default integer size is 32 bit).You should use the openmpi module unless you are sure that you need the openmpi-i8 version.This module can only be loaded if you first load one of the following modules:<\/p>\n<ul>\n<li>gcc\/4.8-c7<\/li>\n<li>gcc\/5.4.0<\/li>\n<li>gcc\/6.3.0<\/li>\n<li>intel\/2016.11<\/li>\n<\/ul>\n<p>To get the currently default version of the openmpi module, use<\/p>\n<div class=\"codehilite\">\n<pre><code><span class=\"gp\">testuser@fe1:~$<\/span> module load intel\/2016.11 openmpi\/2.0.2\r\n<\/code><\/pre>\n<\/div>\n<p>You can replace<span> <\/span><code>intel\/2016.11<\/code><span> <\/span>with other versions of the gcc or intel modules. Note that not all combinations of versions of openmpi and these modules may be available.<\/p>\n<hr>\n<p>Further information:<a href=\"http:\/\/www.open-mpi.org\/\">http:\/\/www.open-mpi.org\/<\/a><br \/>\nVersions available:<\/p>\n<ul>\n<li>openmpi\/1.8.4<\/li>\n<li>openmpi\/1.8.5<\/li>\n<li>openmpi\/1.8.7<\/li>\n<li>openmpi\/1.8.8<\/li>\n<li>openmpi\/1.10.2<\/li>\n<li>openmpi\/1.10.4<\/li>\n<li>openmpi\/2.0.1<\/li>\n<li>openmpi\/2.0.2 (default)<\/li>\n<li>openmpi-i8\/1.8.5<\/li>\n<li>openmpi-i8\/1.8.7<\/li>\n<li>openmpi-i8\/1.8.8<\/li>\n<li>openmpi-i8\/1.10.2<\/li>\n<li>openmpi-i8\/1.10.4<\/li>\n<li>openmpi-i8\/2.0.1<\/li>\n<li>openmpi-i8\/2.0.2<\/li>\n<\/ul>\n<\/div>\n<\/div>\n<h4>Libraries and Utilities<\/h4>\n<ul class=\"nav nav-tabs\">\n<li class=\"active\"><a data-toggle=\"tab\" href=\"#CUDA\">CUDA<\/a><\/li>\n<li><a data-toggle=\"tab\" href=\"#Cmake\">Cmake<\/a><\/li>\n<li><a data-toggle=\"tab\" href=\"#FFTW\">FFTW<\/a><\/li>\n<li><a data-toggle=\"tab\" href=\"#OpenBabel\">OpenBabel<\/a><\/li>\n<li><a data-toggle=\"tab\" href=\"#Java-Oracle\">Java-Oracle<\/a><\/li>\n<li><a data-toggle=\"tab\" href=\"#TurboVNC\">TurboVNC<\/a><\/li>\n<\/ul>\n<div class=\"tab-content\">\n<div id=\"CUDA\" class=\"tab-pane fade in active\">CUDA is a parallel computing platform and application programming interface (API) model created by NVIDIA. Version 7.5 is installed on all compute nodes. Using this module you can load a specific version of CUDA if necessary. Note that GPU cards are of course only available on the GPU nodes.To get the currently default version of the cuda module, use<\/p>\n<div class=\"codehilite\">\n<pre><code><span class=\"gp\">testuser@fe1:~$<\/span> module load cuda\/7.5\r\n<\/code><\/pre>\n<\/div>\n<hr>\n<p>Further information:<a href=\"http:\/\/www.nvidia.com\/object\/cuda_home_new.html\">http:\/\/www.nvidia.com\/object\/cuda<em>home<\/em>new.html<\/a><br \/>\nVersions available:<\/p>\n<ul>\n<li>cuda\/7.0<\/li>\n<li>cuda\/7.5 (default)<\/li>\n<li>cuda\/8.0.44<\/li>\n<\/ul>\n<\/div>\n<div id=\"Cmake\" class=\"tab-pane fade\">CMake is a cross-platform, open-source build systemTo get the currently default version of the cmake module, use<\/p>\n<div class=\"codehilite\">\n<pre><code><span class=\"gp\">testuser@fe1:~$<\/span> module load cmake\/3.5.2\r\n<\/code><\/pre>\n<\/div>\n<hr>\n<p>Further information:<a href=\"http:\/\/www.cmake.org\/\">http:\/\/www.cmake.org\/<\/a><br \/>\nVersions available:<\/p>\n<ul>\n<li>cmake\/3.2.2<\/li>\n<li>cmake\/3.5.2 (default)<\/li>\n<li>cmake\/3.7.0<\/li>\n<li>cmake\/3.7.2<\/li>\n<\/ul>\n<\/div>\n<div id=\"FFTW\" class=\"tab-pane fade\">FFTW &#8211; Fastest Fourier Transform in the WestThis module can only be loaded if you first load one of the following modules:<\/p>\n<ul>\n<li>gcc\/4.8-c7 intelmpi\/2016.11<\/li>\n<li>gcc\/4.8-c7 mvapich2\/2.2<\/li>\n<li>gcc\/4.8-c7 openmpi-i8\/1.10.4<\/li>\n<li>gcc\/4.8-c7 openmpi-i8\/2.0.2<\/li>\n<li>gcc\/4.8-c7 openmpi\/1.10.4<\/li>\n<li>gcc\/4.8-c7 openmpi\/2.0.2<\/li>\n<li>gcc\/5.4.0 intelmpi\/2016.11<\/li>\n<li>gcc\/5.4.0 mvapich2\/2.2<\/li>\n<li>gcc\/5.4.0 openmpi-i8\/1.10.4<\/li>\n<li>gcc\/5.4.0 openmpi-i8\/2.0.2<\/li>\n<li>gcc\/5.4.0 openmpi\/1.10.4<\/li>\n<li>gcc\/5.4.0 openmpi\/2.0.2<\/li>\n<li>gcc\/6.3.0 intelmpi\/2016.11<\/li>\n<li>gcc\/6.3.0 mvapich2\/2.2<\/li>\n<li>gcc\/6.3.0 openmpi-i8\/1.10.4<\/li>\n<li>gcc\/6.3.0 openmpi-i8\/2.0.2<\/li>\n<li>gcc\/6.3.0 openmpi\/1.10.4<\/li>\n<li>gcc\/6.3.0 openmpi\/2.0.2<\/li>\n<li>intel\/2016.11 intelmpi\/2016.11<\/li>\n<li>intel\/2016.11 mvapich2\/2.2<\/li>\n<li>intel\/2016.11 openmpi-i8\/1.10.4<\/li>\n<li>intel\/2016.11 openmpi-i8\/2.0.2<\/li>\n<li>intel\/2016.11 openmpi\/1.10.4<\/li>\n<li>intel\/2016.11 openmpi\/2.0.2<\/li>\n<\/ul>\n<p>To get the currently default version of the fftw module, use<\/p>\n<div class=\"codehilite\">\n<pre><code><span class=\"gp\">testuser@fe1:~$<\/span> module load intel\/2016.11 openmpi\/2.0.2 fftw\/3.3.6\r\n<\/code><\/pre>\n<\/div>\n<p>You can replace<span> <\/span><code>intel\/2016.11 openmpi\/2.0.2<\/code><span> <\/span>with other versions of the , gcc, intel, intelmpi, mvapich2, openmpi or openmpi-i8 modules. Note that not all combinations of versions of fftw and these modules may be available.<\/p>\n<hr>\n<p>Further information:<a href=\"http:\/\/www.fftw.org\/\">http:\/\/www.fftw.org\/<\/a><br \/>\nVersions available:<\/p>\n<ul>\n<li>fftw\/3.3.4<\/li>\n<li>fftw\/3.3.5<\/li>\n<li>fftw\/3.3.6 (default)<\/li>\n<\/ul>\n<\/div>\n<div id=\"OpenBabel\" class=\"tab-pane fade\">Open Babel: The Open Source Chemistry ToolboxTo get the currently default version of the openbabel module, use<\/p>\n<div class=\"codehilite\">\n<pre><code><span class=\"gp\">testuser@fe1:~$<\/span> module load openbabel\/2.3.2\r\n<\/code><\/pre>\n<\/div>\n<hr>\n<p>Further information:<a href=\"http:\/\/openbabel.org\/\">http:\/\/openbabel.org\/<\/a><br \/>\nVersions available:<\/p>\n<ul>\n<li>openbabel\/2.3.2 (default)<\/li>\n<li>openbabel\/2.4.1<\/li>\n<\/ul>\n<\/div>\n<div id=\"Java-Oracle\" class=\"tab-pane fade\">Java SE Development KitJava Platform, Standard Edition or Java SE is a widely used platform for development and deployment of portable applications for desktop and server environments. Java SE uses the object-oriented Java programming language.This module contains the Java SE development kit from Oracle.<\/p>\n<p>To get the currently default version of the java-oracle module, use<\/p>\n<div class=\"codehilite\">\n<pre><code><span class=\"gp\">testuser@fe1:~$<\/span> module load java-oracle\/1.8.0-91\r\n<\/code><\/pre>\n<\/div>\n<hr>\n<p>Further information:<a href=\"http:\/\/www.oracle.com\/technetwork\/java\/javase\/overview\/\">http:\/\/www.oracle.com\/technetwork\/java\/javase\/overview\/<\/a><br \/>\nVersions available:<\/p>\n<ul>\n<li>java-oracle\/1.7.0-45<\/li>\n<li>java-oracle\/1.8.0-51<\/li>\n<li>java-oracle\/1.8.0-66<\/li>\n<li>java-oracle\/1.8.0-91 (default)<\/li>\n<li>java-oracle\/1.8.0-112<\/li>\n<li>java-oracle\/1.8.0-121<\/li>\n<li>java-oracle\/1.8.0-144<\/li>\n<\/ul>\n<\/div>\n<div id=\"TurboVNC\" class=\"tab-pane fade\">TurboVNC can be used to speed up X\/GUI connections running over ssh making GUI programs running on our compute nodes actually usable. This is particularly useful for e.g. Matlab which is otherwise too slow to be used using the GUI.For this to work, you must install a corresponding VNC client running on your own computer, e.g.,<span> <\/span><a href=\"http:\/\/www.turbovnc.org\/\">TurboVNC<\/a>.The TurboVNC package also include MESA libraries (software 3D) which in some cases are required to make this run smoothly.<\/p>\n<p>Note that you are only allowed to start a VNC server on the compute nodes.<\/p>\n<p>To start a VNC job run the command<span> <\/span><code>sinteractive-vnc<\/code>, e.g.,<span> <\/span><code>sinteractive-vnc --time 0-4 --account sdutest_slim<\/code><\/p>\n<p>To get the currently default version of the turbovnc module, use<\/p>\n<div class=\"codehilite\">\n<pre><code><span class=\"gp\">testuser@fe1:~$<\/span> module load turbovnc\/2.0\r\n<\/code><\/pre>\n<\/div>\n<hr>\n<p>Further information:<a href=\"http:\/\/www.turbovnc.org\/\">http:\/\/www.turbovnc.org\/<\/a><br \/>\nVersions available:<\/p>\n<ul>\n<li>turbovnc\/2.0 (default)<\/li>\n<\/ul>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Compilers Gcc Intel The module gcc\/4.8-c7 &#8220;loads&#8221; the default gcc compiler found on our Centos7 system. Other versions of the gcc compiler are also available.To get the currently default version of the gcc module, use<a class=\"moretag\" href=\"http:\/\/escience.sdu.dk\/index.php\/code-compilation-and-libraries\/\"> Read more&hellip;<\/a><\/p>\n","protected":false},"author":1,"featured_media":3986,"parent":0,"menu_order":30,"comment_status":"closed","ping_status":"closed","template":"page-templates\/template-fullwidth.php","meta":[],"_links":{"self":[{"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/pages\/1347"}],"collection":[{"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/comments?post=1347"}],"version-history":[{"count":7,"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/pages\/1347\/revisions"}],"predecessor-version":[{"id":3990,"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/pages\/1347\/revisions\/3990"}],"wp:featuredmedia":[{"embeddable":true,"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/media\/3986"}],"wp:attachment":[{"href":"http:\/\/escience.sdu.dk\/index.php\/wp-json\/wp\/v2\/media?parent=1347"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}