{"id":965,"date":"2012-05-15T15:02:00","date_gmt":"2012-05-15T13:02:00","guid":{"rendered":"http:\/\/oldblogs.uct.ac.za\/blog\/big-bytes\/2012\/05\/15\/hyphy-in-hi-fidelity"},"modified":"2022-09-26T20:15:43","modified_gmt":"2022-09-26T18:15:43","slug":"hyphy-in-hi-fidelity","status":"publish","type":"post","link":"https:\/\/ucthpc.uct.ac.za\/index.php\/2012\/05\/15\/hyphy-in-hi-fidelity\/","title":{"rendered":"HyPhy in hi-fidelity"},"content":{"rendered":"HyPhy<\/a>\u00a0is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. \u00a0We installed HiPhy a while back but could not get it to run correctly in MPI mode. \u00a0It took a while to puzzle out all the problems, turned out we needed to recompile from scratch, but as the source relied on cmake this required us to remove our old version and upgrade to cmake 2.8. \u00a0In addition the source required GLIBCXX_3.4.15 which required gcc4.6 to be referenced. \u00a0Once that was done the compile was simple:\r\n\r\ncmake -DINSTALL_PREFIX=\/opt\/exp_soft\/<dest> .<\/span>\r\n\r\nmake MPI \u00a0(or MP2)<\/span>\r\n\r\nmake install<\/span>\r\n\r\nDon't leave off the final '.' in the cmake command above!\r\n\r\nTo run this as MPI requires the use of the mpirun facility:\r\n\r\nmpirun -machinefile ${PBS_NODEFILE} HYPHYMPI data.bf<\/span>\r\n\r\nAnd depending on the directives the appropriate resources are assigned:\r\n\r\n\"HyPhy\"\r\n\r\n ","protected":false},"excerpt":{"rendered":"

HyPhy<\/a> is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.  We installed HiPhy a while back but could not get it to run correctly in MPI mode.  It took a while to puzzle out all the problems, turned out we needed to recompile from scratch, but as the source relied on cmake this required us to remove our old version and upgrade to cmake 2.8.  In addition the source required GLIBCXX_3.4.15 which required gcc4.6 to be referenced.  Once that was done the compile was simple:<\/p>\n

cmake -DINSTALL_PREFIX=\/opt\/exp_soft\/<dest> .<\/span><\/p>\n

make MPI  (or MP2)<\/span><\/p>\n

make install<\/span><\/p>\n

Don’t leave off the final ‘.’ in the cmake command above!<\/p>\n

To run this as MPI requires the use of the mpirun facility:<\/p>\n

mpirun -machinefile ${PBS_NODEFILE} HYPHYMPI data.bf<\/span><\/p>\n

And depending on the directives the appropriate resources are assigned:<\/p>\n

\"HyPhy\"<\/p>\n

 <\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[4],"tags":[],"yoast_head":"\nHyPhy in hi-fidelity - UCT HPC<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2012\/05\/15\/hyphy-in-hi-fidelity\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"HyPhy in hi-fidelity - UCT HPC\" \/>\n<meta property=\"og:description\" content=\"HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning.  We installed HiPhy a while back but could not get it to run correctly in MPI mode.  It took a while to puzzle out all the problems, turned out we needed to recompile from scratch, but as the source relied on cmake this required us to remove our old version and upgrade to cmake 2.8.  In addition the source required GLIBCXX_3.4.15 which required gcc4.6 to be referenced.  Once that was done the compile was simple:cmake -DINSTALL_PREFIX=\/opt\/exp_soft\/<dest> .make MPI  (or MP2)make installDon't leave off the final '.' in the cmake command above!To run this as MPI requires the use of the mpirun facility:mpirun -machinefile ${PBS_NODEFILE} HYPHYMPI data.bfAnd depending on the directives the appropriate resources are assigned: \" \/>\n<meta property=\"og:url\" content=\"https:\/\/ucthpc.uct.ac.za\/index.php\/2012\/05\/15\/hyphy-in-hi-fidelity\/\" \/>\n<meta property=\"og:site_name\" content=\"UCT HPC\" \/>\n<meta property=\"article:published_time\" content=\"2012-05-15T13:02:00+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2022-09-26T18:15:43+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/ucthpc.uct.ac.za\/wp-content\/uploads\/2015\/07\/hyphy.png\" \/>\n<meta name=\"author\" content=\"Andrew Lewis\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Andrew Lewis\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2012\/05\/15\/hyphy-in-hi-fidelity\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2012\/05\/15\/hyphy-in-hi-fidelity\/\"},\"author\":{\"name\":\"Andrew Lewis\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#\/schema\/person\/c183ad1c0a1063124a72d63963ae9c7e\"},\"headline\":\"HyPhy in hi-fidelity\",\"datePublished\":\"2012-05-15T13:02:00+00:00\",\"dateModified\":\"2022-09-26T18:15:43+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2012\/05\/15\/hyphy-in-hi-fidelity\/\"},\"wordCount\":155,\"publisher\":{\"@id\":\"https:\/\/ucthpc.uct.ac.za\/#organization\"},\"articleSection\":[\"hpc\"],\"inLanguage\":\"en-ZA\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2012\/05\/15\/hyphy-in-hi-fidelity\/\",\"url\":\"https:\/\/ucthpc.uct.ac.za\/index.php\/2012\/05\/15\/hyphy-in-hi-fidelity\/\",\"name\":\"HyPhy in hi-fidelity - 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