Difference between revisions of "Running UCVM on Discovery"

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*[https://carc.usc.edu/user-information/user-guides/high-performance-computing CARC Cluster Documentation]
 
*[https://carc.usc.edu/user-information/user-guides/high-performance-computing CARC Cluster Documentation]
 
*[https://carc.usc.edu/user-information/user-guides/high-performance-computing/running-jobs CARC Running Jobs]
 
*[https://carc.usc.edu/user-information/user-guides/high-performance-computing/running-jobs CARC Running Jobs]
 +
*[https://software-carpentry.org/ Software Carpentry Training Materials]
  
 
== Setting Up UCVM Environment on Discovery ==
 
== Setting Up UCVM Environment on Discovery ==
On discovery, setup your ucvm environment. This is only needed the first time
+
On discovery, setup your ucvm environment. This is only needed the first time. Commands on Linux command line are preceded by %. Don't type the %
  
 
Confirm your test directory exists, if not create it with mkdir command
 
Confirm your test directory exists, if not create it with mkdir command
  
%mkdir /home1/maechlin/test_ucvm
+
%cd /home1/<username>/test_ucvm
 +
 
 +
if not, create a test directory in your account
 +
 
 +
%mkdir /home1/<username/test_ucvm
 +
 
 +
For this training session, copy /home1/maechlin/test_ucvm to your /home1/<username>/test_ucvm
 +
 
 +
%cd /home1/<username>/test_ucvm
 +
 
 +
%cp /home1/maechlin/test_ucvm/* .
 +
 
 +
Confirm the files were copied
 +
 
 +
%ls
 +
 
 +
then return to your login directory
 +
%cd ~
  
 
Then add these aliases into .bashrc file
 
Then add these aliases into .bashrc file
  
*alias 2test="cd /home1/maechlin/test_ucvm"
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*alias 2test="cd /home1/<username>/test_ucvm"
*alias 2project="cd /project/maechlin_162/ucvm/ucvm_bin"
+
*alias 2project="cd /project/scec_608/<username>/ucvm/ucvm_bin"
  
Save the updated .bashrc file
+
Save the updated .bashrc file and run the updated .bashrc file
 
 
then,..
 
  
 
%source ~/.bashrc
 
%source ~/.bashrc
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%ucvm_query -H
 
%ucvm_query -H
 
  
 
This alias should move you to your ucvm installation directory
 
This alias should move you to your ucvm installation directory
  
 
%2project
 
%2project
 +
 +
This alias should move you to your test_ucvm directory
 +
 +
%2test
 +
 +
== Technique to reduce auto logouts ==
 +
$ ssh -o "ServerAliveInterval 60" broadband
  
 
== Running ucvm_query on Discovery ==
 
== Running ucvm_query on Discovery ==
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== Example query format ==
 
== Example query format ==
%ucvm_query -f /project/maechlin_162/ucvm_bin/conf/ucvm.conf -m cvmh < test_pts.in
+
move into your test_ucvm directory where you copied files from /home1/maechlin/test_ucvm
  
== allocation interactive nodes ==
+
You can use alias setup earliers
%salloc --ntasks=1 --time=1:00:00 --account=scec_608
+
%2test
  
== Example profile query ==
+
confirm files referenced are in the current directory
%ucvm_query -f /project/maechlin_162/ucvm_bin/conf/ucvm.conf -m cvmsi < rpv.in > rpv_cvmsi.out
+
%pwd
  
== slurm batch script ==
+
%ucvm_query -f /project/scec_608/<username>/ucvm_bin/conf/ucvm.conf -m cvmh < test_pts.in
%cat ucvm_query.job
 
then..
 
%sbatch ucvm_query.job
 
then ..
 
%squeue -u maechlin
 
then ..
 
%cat rpv_cvmsi.out
 
  
 
== UCVM Basin Query ==
 
== UCVM Basin Query ==
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in a directory on laptop, run this command
 
in a directory on laptop, run this command
 
%scp maechlin@discovery.usc.edu:/home1/maechlin/test_ucvm/*  
 
%scp maechlin@discovery.usc.edu:/home1/maechlin/test_ucvm/*  
</pre>
 
 
== Create Plot using Website - 1D Vertical Profile ==
 
 
Create 1D vertical profile for location in LA Basin (CSU Dominquez Hills):
 
* 33.8628
 
* -118.2525
 
* 0-10k
 
* 100m
 
 
Create Plot using Website:
 
 
* point browser to http://moho.scec.org/UCVM_web/web/viewer.php
 
* select "1D Vertical Profile"
 
* enter 33.8628  for Latitude
 
* enter -118.2525  for Longitude
 
* enter 0  for Z start
 
* enter 10000 for Z ends
 
* enter 100 for Z step
 
 
== Create Plot using Discovery ==
 
Assuiming plotting has been setup for your account, you can Setup the plotting environment,
 
 
%2test
 
 
then..
 
 
%plot_depth_profile.py -s 33.8628,-118.2525 -b 0 -e 10000 -d vs,vp,density -v 100 -c cvmh -o depth.png
 
 
Then, you can view the plots with
 
 
%view_png.py -f depth.png
 
 
== Setting up Plotting Environment for the first time ==
 
<pre>
 
if you see ucvmPlotting,
 
do this,
 
  %conda activate ucvmPlotting
 
  skip to  NEXT
 
else,
 
  %conda env create -f ucvmPlotting.yml
 
  this will take a while..
 
 
  %conda env list
 
 
  should see ucvmPlotting as one of the environment
 
 
  %conda activate ucvmPlotting
 
 
  %2project
 
  %git clone https://github.com/SCECcode/ucvm_plotting.git
 
  %cd ucvm_plotting
 
  %./unpack-dist
 
 
NEXT:
 
check if ucvm_plotting is there,
 
 
%2project
 
%cd ucvm_plotting/ucvm_plotting
 
%./run_depth.sh
 
 
to run manually,
 
%plot_horizontal_slice.py -b 33.35,-118 -u 34.35,-117 -e 1000 -d vs -c cvmh -a s -s 0.01 -o horizontal.png
 
%view_png.py -f horizontal.png
 
 
 
</pre>
 
</pre>
  

Latest revision as of 02:53, 22 April 2021

CARC Getting Started Documentation

Setting Up UCVM Environment on Discovery

On discovery, setup your ucvm environment. This is only needed the first time. Commands on Linux command line are preceded by %. Don't type the %

Confirm your test directory exists, if not create it with mkdir command

%cd /home1/<username>/test_ucvm

if not, create a test directory in your account

%mkdir /home1/<username/test_ucvm

For this training session, copy /home1/maechlin/test_ucvm to your /home1/<username>/test_ucvm

%cd /home1/<username>/test_ucvm

%cp /home1/maechlin/test_ucvm/* .

Confirm the files were copied

%ls

then return to your login directory %cd ~

Then add these aliases into .bashrc file

  • alias 2test="cd /home1/<username>/test_ucvm"
  • alias 2project="cd /project/scec_608/<username>/ucvm/ucvm_bin"

Save the updated .bashrc file and run the updated .bashrc file

%source ~/.bashrc

then,..

%env |grep UCVM

should see setting of UCVM related environment variable like these..

UCVM_SRC_PATH=...

UCVM_INSTALL_PATH=...

then, these command should return useful information..

%which ucvm_query

%ucvm_query -H

This alias should move you to your ucvm installation directory

%2project

This alias should move you to your test_ucvm directory

%2test

Technique to reduce auto logouts

$ ssh -o "ServerAliveInterval 60" broadband

Running ucvm_query on Discovery

This is the contents of the README.md on discovery

(base) [maechlin@discovery1 test_ucvm]$ cat README.md
== Linux Command Syntax ==
Example commands on Linux system. Don't type the % sign
%ls
%pwd

== ucvm query Input format ==
lon, lat, depth
-118.0, 34.0 0.0

== Example query format ==
move into your test_ucvm directory where you copied files from /home1/maechlin/test_ucvm

You can use alias setup earliers
%2test

confirm files referenced are in the current directory
%pwd

%ucvm_query -f /project/scec_608/<username>/ucvm_bin/conf/ucvm.conf -m cvmh < test_pts.in

== UCVM Basin Query ==
*[https://github.com/SCECcode/UCVMC/wiki/Test-Cases-Basin-Query Basin Query Examples]

== Example basin_query Command on Discovery ==
%basin_query -f /project/maechlin_162/ucvm_bin/conf/ucvm.conf -m cvmh -v 2500 < basin_pts.in > basin_pts_cvmh.out
then..
%cat basin_pts_cvmh.out 
which shows returns 3 depth values tuple that is, first-crossing, second crossing and the last crossing with the threshold.

== Transfer files between Discovery and laptop ==
Assume file on laptop, copy it to directory on discovery
Issue this command from directory on laptop that contains the file ucvmPlotting.yml that you want to copy
%scp ucvmPlotting.yml maechlin@discovery.usc.edu:/home1/maechlin/test_ucvm/.

or, copy files from directory on discovery.usc.edu to laptop
in a directory on laptop, run this command
%scp maechlin@discovery.usc.edu:/home1/maechlin/test_ucvm/* 

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