UsefulCommands
txt
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School
University of California, Irvine *
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Course
M114L
Subject
Information Systems
Date
Dec 6, 2023
Type
txt
Pages
3
Uploaded by SuperHumanEel3799
<Logging into the server>
1. If you are not on the UCI network, please turn on VPN.
2. Open a terminal window on your laptop, and use the following command to
connect the server with ssh, assuming that your login ID is "team1":
ssh team1@rayl8.bio.uci.edu
Note that the server name is "RAYL8" not "RAY18" in the above command.
<Useful Linux commands on the server>
cd
to change to your home directory
cd .. to change to the parent/upper directory
pwd
to print the current working directory
ls to list all files/directories under the current directory
less
to look at a text file page by page
qsub
to submit a job
qstat
to check the status of your jobs
qdel
to del a job submitted by mistake
Finally you can use up and down arrows to retrieve your previous commands so
you don't have to retype old commands. Another trick is that you can type
"ESC" key twice to auto-complete file/directory names. This also saves you time
when typing.
<Running the test job>
1. Running the job.
cd
to make sure you are in the home directory
cd test
to change to the test directory
qsub subtest
to submit the job script "subtest" to the compute node.
qstat
to check your job
ls
to see whether the output file is written back. You'll see
something like "test.o79821" where the number is the job ID
that is different for each job.
2. Processing the output
When the job is done, i.e. when you see the file "test.o79821", run the
python3 script as follows
python3 extractor.py
Now "ls" again, and you'll see "test.o79821.csv" that is generated by the
script. You can take a look of the file by the following:
less test.o79821.csv
You'll see that Compound with ID "99017" has the most negative score,
"-7.695". This is free energy, so the more negative, the better.
3. Copying files back to your laptop
(a) Do the following in the terminal that is connected to the server by ssh:
cd
to make sure you are in the home directory
cd test
to change to the test directory
pwd
to print out the path to the directory for copy and paste
ls
to list files in the test directory. You'll see file
"1-1653.pdbqt". This is the protein file that need to be
copied back to your laptop.
(b) Open another terminal, but DO NOT ssh to the server. It is best to go to
your Desktop so you can easily find your files. Now do the following, assuming
that your login ID is "team1": scp team1@rayl8.bio.uci.edu:/home/team1/test/1-1653.pdbqt .
Apparently you need to use your own login ID and please copy and paste the path
to the test directory from the server terminal shown above.
Next copy back the docked ligand file, which is under "logs.test" in the
test directory. Suppose you want to copy back compound with ID "99017",
you do the following:
scp team1@rayl8.bio.uci.edu:/home/team1/test/logs.test/99017_out.pdbqt .
On Windows, you'll see these files when using "dir" in this terminal.
On MacOS, you'll see these files when using "ls" in this terminal.
============================================================================
<On Thr, we're going to submit the two production jobs first thing first.>
::::WARNING::::
DO NOT SUBMIT RODUCTION JOBS MORE THAN ONCE.
OTHERWISE THE RESULT FILES MAY BE CORRUPTED.
1. Running the wild type docking job.
cd to make sure you are in the home directory
cd shp2
to change to the shp2 directory
ls
to check what files/directories are there
cd wtshp2
to change to the wild type docking directory
ls
to check what files/directories are there
qsub subwt.team1
to submit the job script "subwt.team1" to the compute node,
assuming the login ID is team1.
qstat to check your job.
If the job is running, we can proceed to submit the mutant docking job.
2. Running the mutant docking job
cd ..
to change to the parent directory shp2
ls
to check what files/directories are there
cd mtshp2
to change to the mutant docking directory
ls
to check what files/directories are there
qsub submt.team1
to submit the job script "submt.team1" to the compute node,
assuming the login ID is team1.
qstat to check your job.
::::WARNING::::
DO NOT SUBMIT RODUCTION JOBS MORE THAN ONCE.
OTHERWISE THE RESULT FILES MAY BE CORRUPTED.
You are supposed to see both of your jobs running. These will take a few
hours. They should be done before Friday and I will collect all data so all
teams can see the docking results from all teams.
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