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--- cluster_set-up [2016/11/16 14:39] – admin
+++ cluster_set-up [2022/09/21 09:22] (current) – admin
@@ Line 1: / Line 1: @@
 [[sidebar]]
-Listed below are instructions for setting up accounts on deepthought1 (DT1) and deepthought2 (DT2) located at UMD.
+===Instructions depend on the cluster you are using. Click on the link below that is appropriate.===
-Instructions:
+Local Zaratan Cluster: [[ZT1]]
-You will assigned one or both clusters based on your simulation needs by Dr. Klauda. These instructions work for both, so do these on the cluster(s) you are assigned. Dr. Klauda will submit a request to add you as a user to my account on DT1 and/or DT2. Once this is done, you should get a generic email from IT regarding the resource.
+===Details on How to run NAMD on XSEDE with Example Scripts===
-Details of DT1 and DT2 can be found:
+[[Stampede2]]
-http://www.oit.umd.edu/hpcc/
+[[Bridges]]
-Now for the cluster setup:
+[[Comet]]
-If you are not familiar with the use of LINUX, I would first go through some on-line tutorials for commands to use in LINUX and here ([[Linux Guide]]). To login to DT1 (login.deepthought.umd.edu) or DT2 (login.deepthought2.umd.edu) with Windows you will need to have PuTTY ([[Extra Software]]) to connect to deepthought:
+[[Rockfish]]
-http://www.chiark.greenend.org.uk/%7Esgtatham/putty/
+[[Expanse]]
-And the following program will be useful to transfer files between deepthought and your computer
+===Backups of DATA===
-http://winscp.net/eng/index.php
+Data on Zaratan must be backed up.  Click on the link below that describes how to back your data up.
-Built-in commands for MAC users can be used to connect via the command line (scp) and apps for file transfer (eg, cyberduck).
-Then, take a general look at the website of the HPCC OIT to get a general idea on how to login and submit jobs.  Your jobs should not run in your home directory.  They should instead be in the /lustre directory.  You should first make a subdirectory in this with your username (mkdir is the command). Running simulations should be in organized directories.  So think of some naming scheme for simulations. Before starting a simulation, you will need to make a slight change to you .cshrc file in your home directory.  Using the program pico or vm type the following when you are in your home directory:
-<code commend> pico .cshrc.mine </code>
-At the end of the file add the following line:
-<code commend> unset noclobber </code>
-This is needed for the simulations to allow for files to write over existing files.
-One more recent change is that you will need to allow me to look into your /lustre files.  After you've made the directory (described above), you will need to allow access to the files by typing and replacing username with yours:
-<code commend>cd /lustre/username
-chmod a+r .
-chmod -R a+r *
-find . -type d -exec chmod a+x {} \; </code>
+Data Backup: [[Backup]]