{"id":214,"date":"2016-10-13T21:45:15","date_gmt":"2016-10-13T21:45:15","guid":{"rendered":"http:\/\/sites.sandiego.edu\/hpc\/?page_id=214"},"modified":"2016-10-13T21:56:17","modified_gmt":"2016-10-13T21:56:17","slug":"214-2","status":"publish","type":"page","link":"https:\/\/sites.sandiego.edu\/hpc\/214-2\/","title":{"rendered":"Schrodinger"},"content":{"rendered":"<h1 id=\"title-heading\" class=\"pagetitle\"><span id=\"title-text\" class=\"page-metadata-modification-info\"> Schrodinger<\/span><\/h1>\n<div id=\"content\" class=\"page view\">\n<div class=\"wiki-content\">\n<div>\n<ul>\n<li>Generate an SSH key<\/li>\n<li>Run Maestro<\/li>\n<li>Schrodinger &#8211; Launching tasks<\/li>\n<li>Schrodinger Glide Batch Submission<\/li>\n<li>Batch Glide Jobs<\/li>\n<li>Batch LigPrep Jobs<\/li>\n<\/ul>\n<\/div>\n<h2><span style=\"color: #000000\"><b>Set up environment<\/b><\/span><\/h2>\n<p>Since Schrodinger working files are large and user home directories are small, we need to set Schrodinger environment variables to change the location of Schrodinger temporary files.<\/p>\n<p>Login to hpcmn submit node<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ ssh -X userid@hpcmn.sandiego.edu\r\n<\/pre>\n<\/div>\n<\/div>\n<p>Set up your .bash_profile. You should add these lines to your .bash_profile to automatically load the what\u2019s in your .bashrc.<\/p>\n<p>Go to your home directory<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ cd\r\n<\/pre>\n<\/div>\n<\/div>\n<p>Show working directory<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ pwd\r\n<\/pre>\n<\/div>\n<\/div>\n<p>Edit your .bash_profile. If you don\u2019t already have one this will create it. nano is a basic editor. Hit Ctrl-o to save from within nano. Hit Ctrl-x to exit the nano editor.<\/p>\n<p>Add the lines to your .bash_profile<\/p>\n<p>$ nano .bash_profile<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\"><span class=\"code-keyword\">if<\/span> [ -e <span class=\"code-quote\">\"${HOME}\/.bashrc\"<\/span> ] ; then\r\n  source <span class=\"code-quote\">\"${HOME}\/.bashrc\"<\/span>\r\nfi\r\n<\/pre>\n<\/div>\n<\/div>\n<p>Set up your .bashrc for Schrodinger.<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ cd\r\n<\/pre>\n<\/div>\n<\/div>\n<p>Add these lines to your .bashrc. Replace USER in lines below with your vega user directory name.<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ nano .bashrc\r\n<\/pre>\n<\/div>\n<\/div>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\"><span class=\"code-keyword\">if<\/span> [ -d <span class=\"code-quote\">\"\/vega\"<\/span> ]; then\r\n    # Yeti\r\n    SCHRODINGER_JOBDB2=\/vega\/stock\/users\/USER\/.jobdb2\r\n    SCHRODINGER_TMPDIR=\/yeti\/tmp\r\nfi\r\nexport SCHRODINGER_JOBDB2\r\nexport SCHRODINGER_TMPDIR\r\n<\/pre>\n<\/div>\n<\/div>\n<h2><a name=\"Yeti-Schrodinger-GenerateanSSHkey\"><\/a>Generate an SSH key<\/h2>\n<p>Creating a passwordless SSH key is necessary and does the following:<\/p>\n<ul>\n<li>Enables you to submit jobs to Saber1 scheduler from within interactive job.<\/li>\n<li>Enables multi-node jobs to communicate across compute nodes<\/li>\n<\/ul>\n<p><b>1.<\/b> Generate a public\/private RSA key pair on a host of your choice, whose home directory is<br \/>\nshared with the remote hosts that you want to run jobs on. Type the following commands while connected to yeti:<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ cd ~\/.ssh\r\n$ ssh-keygen -t rsa\r\n<\/pre>\n<\/div>\n<\/div>\n<p>Note: When asked for a passphrase do not enter one; just press ENTER. If you specify a passphrase it defeats the purpose of configuring passwordless ssh.<\/p>\n<p><b>2.<\/b> Now add your public key to the list of keys allowed to log in to your account:<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ cat id_rsa.pub &gt;&gt; authorized_keys\r\n$ cat id_rsa.pub &gt;&gt; authorized_keys2\r\n<\/pre>\n<\/div>\n<\/div>\n<p><b>3.<\/b> Remove your known_hosts file:<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ rm known_hosts*\r\n<\/pre>\n<\/div>\n<\/div>\n<p>This is necessary so that the new RSA key-pair mechanism is used for every host. Other-<br \/>\nwise, hosts to which you previously connected using passwords might not use the new<br \/>\nsystem automatically.<\/p>\n<h2><a name=\"Yeti-Schrodinger-RunMaestro\"><\/a>Run Maestro<\/h2>\n<p>Login<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ ssh -X userid@hpcmn.sandiego.edu\r\n<\/pre>\n<\/div>\n<\/div>\n<p>Start an interactive job<br \/>\nNote: for typical use, you can use the default of 1 processor on 1 node. From within this job you can launch completely separate, new jobs to Saber1. You may, if you wish, exit your interactive after submitting tasks to Saber1. To see the results of jobs submitted interactively, just launch another interactive job.<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ qsub -I -W group_list=saber1stock -l walltime=04:00:00,mem=4000mb -X\r\n<\/pre>\n<\/div>\n<\/div>\n<p>Load schrodinger into environment<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ module load schrodinger\r\n<\/pre>\n<\/div>\n<\/div>\n<p>Change to your vega user directory. This will set your default working directory for Schrodinger.<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ cd \/vega\/stock\/users\/USERNAME\r\n<\/pre>\n<\/div>\n<\/div>\n<p>Launch maestro<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ maestro\r\n<\/pre>\n<\/div>\n<\/div>\n<h2><a name=\"Yeti-Schrodinger-SchrodingerLaunchingtasks\"><\/a>Schrodinger &#8211; Launching tasks<\/h2>\n<p>When ready to submit a job from within maestro, for example a Desmond MD job:<\/p>\n<p>Click on the gear icon next to the Run button to select a host entry<\/p>\n<p>If you select a \u201clocal\u201d option, that will run the job with the resources you requested for interactive job with the qsub command. You should only select the local option for shorter tasks that can complete within a few minutes, such as minimization.<\/p>\n<p>For longer tasks that you don\u2019t need to immediately attend to, you should submit a batch job back to Saber1. To do that choose a \u201cSaber1\u201d entry such as:<\/p>\n<ol>\n<li>Select one of the following saber1 entries.<\/li>\n<li>Remember to specify the total # of processors.<\/li>\n<\/ol>\n<ul>\n<li><b>saber1-16<\/b> (16) Total: <b>16<\/b> processors<\/li>\n<li><b>saber2-16<\/b> (32) Total: <b>32<\/b> processors<\/li>\n<li><b>saber4-16<\/b> (64) Total: <b>64<\/b> processors<\/li>\n<li><b>saber1-gpu1<\/b> (1,1) Total: <b>1<\/b> GPU<\/li>\n<\/ul>\n<p>For example, choosing the saber12-16 entry will submit a completely new and unrelated job to the Saber1 scheduler, requesting 2 servers with 16 processors per server, a total of 32 processors.<\/p>\n<p><em>Note: the number of processors you can request may be limited by the number of licenses that are available.<\/em><\/p>\n<p><em>Also note: when requesting more resources, such as 4 nodes, versus 2, your job may have to spend more time waiting in the queue until sufficient resources become available.<\/em><\/p>\n<p>Using a GPU with Desmond can yield a 30 to 80 fold speedup against a single CPU core, so it&#8217;s worth trying it out by selecting: <strong>saber1<\/strong><b>-gpu1<\/b><\/p>\n<p>After you submit the Saber1 job, open up another terminal window and run qstat to search for the new job, replacing userid below with your actual userid.<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ qstat -u USERID<\/pre>\n<\/div>\n<\/div>\n<p>If your job is in the Q state, meaning it\u2019s queued, you can check the status of the job for more information. Replace JOBID below with your actual jobid #.<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ checkjob -v JOBID\r\n<\/pre>\n<\/div>\n<\/div>\n<h2><a name=\"Yeti-Schrodinger-SchrodingerGlideBatchSubmission\"><\/a>Schrodinger Glide Batch Submission<\/h2>\n<p>Note: text after $ denotes what is typed into the terminal command line<\/p>\n<h2><a name=\"Yeti-Schrodinger-BatchGlideJobs\"><\/a>Batch Glide Jobs<\/h2>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ ssh -X \u2018your userid\u2019@hpcmn.sandiego.edu\r\n$ cd \/vega\/stock\/users\/\u2019you\u2019\r\n$ qsub -q interactive -I -W group_list=saber1stock -l walltime=04:00:00,mem=4000mb -X\r\n$ module load schrodinger\/2015-3\r\n$ maestro -SGL\r\n<\/pre>\n<\/div>\n<\/div>\n<ul>\n<li>Set up glide docking job (chose grid, ligands, force field, etc.)<\/li>\n<li>Click on cog to change job name and chose number of subjobs, click OK (not run)<\/li>\n<li>Click on arrow next to cog and click WRITE<\/li>\n<li>In Fetch, make sure a folder with the name of your job has written and contains \u2018job name\u2019.in and \u2018job name\u2019.sh<\/li>\n<li>Launch another terminal window and ssh into Saber1<\/li>\n<li>cd into job directory (eg. $ cd \/vega\/stock\/users\/\u2019you\u2019\/\u2019job name\u2019)<\/li>\n<\/ul>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ nano \u2018job name\u2019.sh\r\n<\/pre>\n<\/div>\n<\/div>\n<ul>\n<li>In this window, delete the line of script paste in the following, modified to your job:<\/li>\n<li>modify amount of walltime and\/or memory (max amount shown below)<\/li>\n<li>change input file to your directory<\/li>\n<\/ul>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">#!\/bin\/sh\r\n#Torque directives\r\n#PBS -W group_list=saber1stock\r\n#PBS -l nodes=1:ppn=16,walltime=48:00:00,mem=60gb\r\n#PBS -M \u2018your userid\u2019@hpcmn.sandiego.edu\r\n#PBS -m abe\r\n#PBS -V\r\n# Set output and error directories\r\n#PBS -o localhost:$PBS_O_WORKDIR\/\r\n#PBS -e localhost:$PBS_O_WORKDIR\/\r\nmodule load schrodinger\/2015-3\r\nexport SCHRODINGER_TMPDIR=\/hpcmn\/tmp\r\nINPUT=\/vega\/stock\/users\/\u2019you\u2019\/\u2019job name\u2019\/\u2019job name\u2019.in\r\n<span class=\"code-quote\">\"${SCHRODINGER}\/glide\"<\/span> -WAIT -OVERWRITE -HOST <span class=\"code-quote\">\"localhost:16\"<\/span> -NJOBS 16 <span class=\"code-quote\">\"${INPUT}\"<\/span>\r\n<\/pre>\n<\/div>\n<\/div>\n<ul>\n<li>hit CONTROL+X to exit window<\/li>\n<li>hit Y to save changes, hit ENTER to write file<\/li>\n<\/ul>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">$ qsub \u2018job name\u2019.sh\r\n<\/pre>\n<\/div>\n<\/div>\n<ul>\n<li>a job number should be generated<\/li>\n<li>to monitor job, use $ qstat &#8211;u \u2018your uni\u2019 to monitor job<\/li>\n<li>if you need to delete this job, use $ qdel \u2018job number\u2019<\/li>\n<li>to make sure shell script has modified correctly, use $ cat \u2018job name\u2019.sh<\/li>\n<li>to make sure input file has correct information, use $ cat \u2018job name\u2019.in<\/li>\n<\/ul>\n<h2><a name=\"Yeti-Schrodinger-BatchLigPrepJobs\"><\/a>Batch LigPrep Jobs<\/h2>\n<p>Same as Glide jobs, write the input and shell script files modify shell script as below:<\/p>\n<div class=\"code panel\">\n<div class=\"codeContent panelContent\">\n<pre class=\"code-java\">#!\/bin\/sh\r\n#Torque directives\r\n#PBS -W group_list=saber1stock\r\n#PBS -l nodes=1:ppn=16,walltime=48:00:00,mem=60gb\r\n#PBS -M \u2018your userid\u2019@hpcmn.sandiego.edu\r\n#PBS -m abe\r\n#PBS -V\r\n# Set output and error directories\r\n#PBS -o localhost:$PBS_O_WORKDIR\/\r\n#PBS -e localhost:$PBS_O_WORKDIR\/\r\nmodule load schrodinger\/2015-3\r\nexport SCHRODINGER_TMPDIR=\/hpcmn\/tmp\r\nINPUT=\/vega\/stock\/users\/\u2019you\u2019\/\u2019job name\u2019\/\u2019job name\u2019.in\r\n<span class=\"code-quote\">\"${SCHRODINGER}\/ligprep\"<\/span> -WAIT -OVERWRITE -HOST <span class=\"code-quote\">\"localhost:16\"<\/span> -NJOBS 16 <span class=\"code-quote\">\"${INPUT}\"<\/span>\r\n<\/pre>\n<p>&nbsp;<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Schrodinger Generate an SSH key Run Maestro Schrodinger &#8211; 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