Differences

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--- zt1 [2022/09/21 09:21] – created admin
+++ zt1 [2023/10/03 14:42] (current) – admin
@@ Line 23: / Line 23: @@
 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 nano or vim type the following when you are in your home directory:
+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 /scratch directory.  A subdirectory is already made for you on scratch (/scratch/zt1/project/energybio/user). 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 nano or vim type the following when you are in your home directory:
 <code commend> nano .cshrc.mine </code>
@@ Line 33: / Line 33: @@
 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 /scratch 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 below. Please copy and paste these commands after the first, as if you omit a '.' this will now work properly.
+One more recent change is that you will need to allow users to look into your /scratch and /shell files.  You will need to allow access to the files by typing and replacing username with yours below. Please copy and paste these commands after the first, as if you omit a '.' this will now work properly.
 <code commend>cd /scratch/zt1/project/energybio/user/username
 chmod a+r .
 chmod -R a+r *
-find . -type d -exec chmod a+x {} \; </code>
+find . -type d -exec chmod a+x {} \;
+mkdir /afs/shell.umd.edu/project/energybio/shared/username
+cd /afs/shell.umd.edu/project/energybio/user/username
+chmod a+r .
+chmod -R a+r *
+find . -type d -exec chmod a+x {} \;
+</code>
+The scratch filesystem is **ONLY** for current jobs running and analysis. We have a smaller quota on this resource which you can see how much with the command scratch_quota. Most data that is for a current project but not yet published should be placed in the SHELL shared directory. You will need to make your own directory in /afs/shell.umd.edu/project/energybio/shared with your username (this is the last line in the code above).