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Data Exercise 2.1: Using a Web Proxy for Large Shared Input

Continuing the series of exercises blasting mouse genetic sequences, the objective of this exercise is to use a web proxy to stage the large database, which will be downloaded into each of many jobs that use the split input files from the last exercise (Exercise 1.3).

Setup

  • Make sure you are logged into login04.osgconnect.net
  • Make sure you are in the same directory as the previous exercise, Exercise 1.3 directory named blast-split.

Place the Large File on the Proxy

First, you'll need to put the pdbaa_files.tar.gz file onto the Stash web directory. Use the following command:

[email protected] $ cp pdbaa_files.tar.gz /public/<USERNAME>

Replacing <USERNAME> with your username

Test a download of the file

Once the file is placed in your /public directory, it can be downloaded from a corresponding URL such as http://stash.osgconnect.net/public/<USERNAME>/pdbaa_files.tar.gz, where <USERNAME> is your username on login04.osgconnect.net.

Using the above convention (and from a different directory on login04.osgconnect.net, any directory), you can test the download of your pdbaa_files.tar.gz file with a command like the following:

[email protected] $ wget http://stash.osgconnect.net/public/<USERNAME>/pdbaa_files.tar.gz

Again, replacing <USERNAME> with your own username. You may realize that you've been using wget to download files from a web proxy for many of the previous exercises at the school!

Run a New Test Job

Now, you'll repeat the last exercise (with a single input query file) but have HTCondor download the pdbaa_files.tar.gz file from the web proxy, instead of having the file transferred from the submit server.

Modify the submit file and wrapper script

In the wrapper script, we have to add some special lines so that we can pull from the HTTP proxy and see where they are coming from. Normally, we would let HTCondor do the HTTP transfer, but we want to see the download and to see where it came from. In blast_wrapper.sh, we will have to add commands to pull the data file:

#!/bin/bash

# Set the http_proxy environment which wget uses
export http_proxy=$OSG_SQUID_LOCATION

# Copy the pdbaa_files.tar.gz to the worker node
# Add the -S argument, so we can see if it was a cache HIT or MISS
wget -S http://stash.osgconnect.net/public/<USERNAME>/pdbaa_files.tar.gz

tar xvzf pdbaa_files.tar.gz

./blastx -db pdbaa -query $1 -out $1.result

rm pdbaa*

Be sure to replace <USERNAME> with your own username.

The new line will download the pdbaa_files.tar.gz from the HTTP proxy, using the closest cache (because wget will look at the environment variable http_proxy for the newest cache).

Also notice the final line of the wrapper script has been modified to delete the pdbaa data files as well as the pdbaa_files.tar.gz file so that it will not be transferred back to the submit server when the job finishes.

In your submit file, you will need to remove the pdbaa_files.tar.gz file from the transfer_input_files, because we are now transferring the tarball via the wget command in our wrapper script.

Submit the test job

You may wish to first remove the log, result, output, and error files from the previous tests, which will be overwritten when the new test job completes.

[email protected] $ rm *.error *.out *.result *.log

Submit a single test job! (If your submit file uses a queue .. matching statement, a simple way to submit a single job is to temporarily change it to queue inputfile matching mouse_rna.fa.1.

When the job starts, the wrapper will download the pdbaa_files.tar.gz file from the web proxy. If the jobs takes longer than two minutes, you can assume that it will complete successfully, and then continue with the rest of the exercise.

After the job completes examine the error file generated by the submission. At the top of the file, you will find something like:

--2021-07-23 10:35:51--  http://stash.osgconnect.net/public/dweitzel/pdbaa_files.tar.gz
Resolving iitgrid.iit.edu (iitgrid.iit.edu)... 216.47.155.220
Connecting to iitgrid.iit.edu (iitgrid.iit.edu)|216.47.155.220|:3128... connected.
Proxy request sent, awaiting response... 
  HTTP/1.1 200 OK
  Server: nginx/1.16.1
  Content-Type: application/octet-stream
  Content-Length: 22105180
  Last-Modified: Fri, 23 Jul 2021 14:27:49 GMT
  ETag: "60fad1e5-1514c5c"
  Accept-Ranges: bytes
  Age: 0
  Date: Fri, 23 Jul 2021 15:35:51 GMT
  X-Cache: HIT from iitgrid.iit.edu
  Via: 1.1 iitgrid.iit.edu (squid/frontier-squid-4.10-2.1)
  Connection: close
Length: 22105180 (21M) [application/octet-stream]
Saving to: 'pdbaa_files.tar.gz.1'
...

Notice the X-Cache line. It says it was a cache HIT from the proxy iitgrid.iit.edu. Yay! You successfully used a proxy to cache data near your worker node! Notice, the name of the cache may be different, and it may be a MISS the first time you request the data from the cache.

Get HTCondor to do the wget for you!

The transfer_input_files command in the submit file can also be an HTTP address. Instead of using wget in your blast_wrapper.sh file, remove it and add the HTTP address to the transfer_input_files line in your blast_split.sub

executable = blast_wrapper.sh
transfer_input_files = blastx, $(inputfile), http://stash.osgconnect.net/public/<USERNAME>/pdbaa_files.tar.gz
output = $(inputfile).out
...

Run all 100 Jobs!

If all of the previous tests have gone okay, you can prepare to run all 100 jobs that will use the split input files. To make sure you're not going to generate too much data, use the size of files from the previous test to calculate how much total data you're going to add to the blast-split directory for 100 jobs.

Make sure you remove pdbaa_files.tar.gz from the transfer_input_files in the split submit file.

Submit all 100 jobs! They may take a while to all complete, but it will still be faster than the many hours it would have taken to blast the single, large mouse_rna.fa file without splitting it up. In the meantime, as long as the first several jobs are running for longer than two minutes, you can move on to the next exercise