Cross Linking this website with HTC Condor and OSG

Author: CannonLock

DAGenv.md

@@ -7,11 +7,11 @@ title: Submitting Jobs Using the ChtcRun Package
 To facilitate the submission of large batches of jobs, especially
 batches for Matlab, Python, and R, the CHTC has created the ChtcRun
 package of scripts, files, and directories that will allow you to easily
-construct your own HTCondor workflow (or \"DAG\" batch). By following
+construct your own <a href="http://research.cs.wisc.edu/htcondor/">HTCondor</a> workflow (or \"DAG\" batch). By following
 the ordered set of directions given here, you\'ll be able to easily set
 up and run a set of high-throughput computing jobs on CHTC-available
 resources, including those outside of the CHTC HTCondor Pool in the UW
-Grid and national Open Science Grid.
+Grid and national <a href="http://www.opensciencegrid.org/">Open Science Grid</a>.
 
 1.  From within your home directory on the submit node, in a directory
     of your choice, download the ChtcRun package:

archive_html/DAGenv.shtml

@@ -6,10 +6,11 @@ title: Submitting Jobs Using the ChtcRun Package
 <p>To facilitate the submission of large batches of jobs, especially
  batches for Matlab, Python, and R, the CHTC has created the ChtcRun
  package of scripts, files, and directories that will allow you to easily
- construct your own HTCondor workflow (or "DAG" batch). By following the ordered
+ construct your own <a href="http://research.cs.wisc.edu/htcondor/">HTCondor</a>
+ workflow (or "DAG" batch). By following the ordered
  set of directions given here, you'll be able to easily set up and run
  a set of high-throughput computing jobs on CHTC-available resources,
- including those outside of the CHTC HTCondor Pool in the UW Grid and
+ including those outside of the CHTC <a href="http://research.cs.wisc.edu/htcondor/">HTCondor</a> Pool in the UW Grid and
  national Open Science Grid.
 </p>
 
@@ -163,7 +164,7 @@ the project's job(s),
 as well as control files:
 a DAG input file for describing the DAG 
 (called <code>mydag.dag</code>)
-and an HTCondor job submit description files for each of the node jobs within
+and an <a href="http://research.cs.wisc.edu/htcondor/">HTCondor</a> job submit description files for each of the node jobs within
 the DAG.
 One of the command line arguments to 
 <code>mkdag</code>
@@ -218,7 +219,7 @@ we cannot necessarily trust the return code from MATLAB or R
 to tell us if the job was successful.  
 We determine if a job was successful by checking if at least one 
 file was created that includes the pattern "SubString" in it's 
-filename, for each HTCondor job submitted.
+filename, for each <a href="http://research.cs.wisc.edu/htcondor/">HTCondor</a> job submitted.
 This check is identical to running
 <pre>ls *SubString*
 </pre>
@@ -227,7 +228,7 @@ in a job's output folder after the job completes to see that at least one file i
 
 <li> <code>--parg=ArgumentString</code>
 <br> This optional argument identifies a command line argument that
-is to be passed to each invocation (as an HTCondor job) of the executable.
+is to be passed to each invocation (as an <a href="http://research.cs.wisc.edu/htcondor/">HTCondor</a> job) of the executable.
 This argument will be listed multiple times to define more than one
 command line argument. Optionally, you can use "--parg=<i>unique</i>" to 
 pass the name of the job directory as an argument to your code for each job.

archive_html/chtcjobwrapper.shtml

@@ -6,7 +6,7 @@ title: Submitting Jobs Using chtcjobwrapper
 <p class="underconstruction">This page is under construction</p>
 
 <p>
-Getting your job to run requires submitting an HTCondor job.
+Getting your job to run requires submitting an <a href="http://research.cs.wisc.edu/htcondor/">HTCondor</a> job.
 All HTCondor jobs specify details about the job
 in a file called a submit description file.
 These details include the executable's name, 

archive_html/outside-chtc.shtml

@@ -22,12 +22,13 @@ is space.</p>
 
 <h2>B. The Open Science Grid (OSG)</h2>
 
-<p>The Open Science Grid (OSG) is a group of universities and research labs who have 
+<p>The <a href="http://www.opensciencegrid.org/">Open Science Grid (OSG)</a>
+is a group of universities and research labs who have
 agreed to share their unused computational resources with each other.  If a job is 
 submitted from an OSG submission point, it can run in the OSG pool associated with 
 that submission point.  This OSG pool is the result of going out to other members of 
-the OSG and finding if they have any unused computers that are available to run jobs. 
-These unused computers then form a pool of resources where jobs 
+the OSG and finding if they have any unused computers that are available to run jobs.
+These unused computers then form a pool of resources where jobs
 can go run.</p>
 
 <p>CHTC is a member of the Open Science Grid, so our submit servers, besides sending 

archive_html/scaling-htc.shtml

@@ -41,7 +41,8 @@ is space.</p>
 <a name="osg"></a>
 <h2>B. The Open Science Grid (OSG)</h2>
 
-<p>The Open Science Grid (OSG) is a group of universities and research labs who have 
+<p>The <a href="http://www.opensciencegrid.org/">Open Science Grid (OSG)</a> is a
+group of universities and research labs who have
 agreed to share their unused computational resources with each other.  If a job is 
 submitted from an OSG submission point, it can run in the OSG pool associated with 
 that submission point.  This OSG pool is the result of going out to other members of 

archive_html/tensorflow-singularity-wait.shtml

@@ -5,7 +5,7 @@ title: Running Tensorflow Jobs
 
 <p>This guide describes how to use a pre-built Tensorflow environment 
 (implemented as a <a href="http://singularity.lbl.gov/">Singularity container</a>)
-to run Tensorflow jobs in CHTC and on the Open Science Grid (OSG).</p>
+to run Tensorflow jobs in CHTC and on the <a href="http://www.opensciencegrid.org/">Open Science Grid (OSG)</a>.</p>
 
 <h2>Overview</h2>
 

dev_website/troubleshooting.shtml

@@ -111,7 +111,7 @@ output = <i>outfile.out</i>
 error = <i>errfile.err</i>
 </pre>
 
-<p>HTCondor will produce these files and they can be used for troubleshooting.  
+<p><a href="http://research.cs.wisc.edu/htcondor/">HTCondor</a> will produce these files and they can be used for troubleshooting.
 Here is the kind of information you can find in each file. </p>
 
 <b>Output</b>
@@ -143,7 +143,7 @@ your code triggered an error. </p>
 
 <b>Log</b>
 
-<p>The log file contains information that HTCondor tracks for each job, including 
+<p>The log file contains information that <a href="http://research.cs.wisc.edu/htcondor/">HTCondor</a> tracks for each job, including
 when it was submitted, started, and stopped.  It also describes resource use, 
 and where the job ran. </p>
 

file-availability.md

@@ -56,7 +56,7 @@ portion of the data. By default, the submit file `executable`,
 * Advantages:  
 HTCondor file transfer is robust and is available on ANY of CHTC\'s
 accessible HTC resources including the UW Grid of campus pools, and the
-Open Science Grid.
+<a href="http://www.opensciencegrid.org/">Open Science Grid</a>.
 
 * Data Security:  
 Files transferred with HTCondor transfer are owned by the job and

gpu-jobs.md

@@ -359,7 +359,7 @@ for running GPU jobs:
 
 ## 3. Using GPUs on the Open Science Grid
 
-CHTC, as a member of the Open Science Grid (OSG) can access GPUs that
+CHTC, as a member of the <a href="http://www.opensciencegrid.org/">Open Science Grid (OSG)</a> can access GPUs that
 are available on the OSG. See [this guide](/scaling-htc.shtml) to know
 whether your jobs are good candidates for the OSG and then get in touch
 with CHTC's Research Computing Facilitators to discuss details. 

julia-jobs.md

@@ -22,7 +22,7 @@ You will need the 64-bit, tarball compiled for general use on a Linux x86 system
 file name will resemble something like `julia-#.#.#-linux-x86_64.tar.gz`.
 
     * Tip: use `wget` to download directly to your `/home` directory on the 
-submit server, **OR** use `transfer_input_files = url` in your HTCondor submit files.
+submit server, **OR** use `transfer_input_files = url` in your <a href="http://research.cs.wisc.edu/htcondor/">HTCondor</a> submit files.
 
 1. Submit an "interactive build" job to create a Julia project and 
 install packages, else skip to the next step.
@@ -166,7 +166,7 @@ julia> exit()
 ## Save Installed Packages For Later Jobs
 
 To use this project, and the associated installed packages, in 
-subsequent jobs, we need to have HTCondor return some files to 
+subsequent jobs, we need to have <a href="http://research.cs.wisc.edu/htcondor/">HTCondor</a> return some files to 
 the submit server by converting the `my-project/` directory
 to a tarball, before exiting the interactive job session:
 
@@ -195,11 +195,11 @@ my-project.tar.gz
 # Submit Julia Jobs
 
 To submit a job that runs a Julia script, create a bash 
-script and HTCondor submit file following the examples in this section.
+script and <a href="http://research.cs.wisc.edu/htcondor/">HTCondor</a> submit file following the examples in this section.
 
 ## Create Executable Bash Script
 
-Your job will use a bash script as the HTCondor `executable`. This script 
+Your job will use a bash script as the <a href="http://research.cs.wisc.edu/htcondor/">HTCondor</a> `executable`. This script 
 will contain all the steps needed to unpack the Julia binaries and 
 execute your Julia script (`script.jl`). Below are two example bash script, 
 one which can be used to execute a script with base Julia, and one that 

outside-chtc.md

@@ -27,7 +27,7 @@ We call sending jobs to other pools on campus *flocking*.
 B. The Open Science Grid (OSG)
 ------------------------------
 
-The Open Science Grid (OSG) is a group of universities and research labs
+The <a href="http://www.opensciencegrid.org/">Open Science Grid (OSG)</a> is a group of universities and research labs
 who have agreed to share their unused computational resources with each
 other. If a job is submitted from an OSG submission point, it can run in
 the OSG pool associated with that submission point. This OSG pool is the

scaling-htc.md

@@ -51,7 +51,7 @@ We call sending jobs to other pools on campus *flocking*.
 B. The Open Science Grid (OSG)
 ------------------------------
 
-The Open Science Grid (OSG) is a group of universities and research labs
+The <a href="http://www.opensciencegrid.org/">Open Science Grid (OSG)</a> is a group of universities and research labs
 who have agreed to share their unused computational resources with each
 other. If a job is submitted from an OSG submission point, it can run in
 the OSG pool associated with that submission point. This OSG pool is the

tensorflow-singularity-wait.md

@@ -6,7 +6,7 @@ title: Running Tensorflow Jobs
 
 This guide describes how to use a pre-built Tensorflow environment
 (implemented as a [Singularity container](http://singularity.lbl.gov/))
-to run Tensorflow jobs in CHTC and on the Open Science Grid (OSG).
+to run Tensorflow jobs in CHTC and on the <a href="http://www.opensciencegrid.org/">Open Science Grid</a>.
 
 Overview
 --------

testing-jobs.md

@@ -33,7 +33,7 @@ effective high-throughput computing in the following ways:
 -   **Making good choices:** knowing how big and how long your jobs are,
     and the size of input/output files will show you how to most
     effectively use CHTC resources. Jobs under 2 hrs or so? Allow your
-    jobs to flock and glide to the UW Grid and Open Science Grid. Input
+    jobs to flock and glide to the UW Grid and <a href="http://www.opensciencegrid.org/">Open Science Grid</a>. Input
     files of more than 5 GB? You should probably be using the CHTC large
     file staging area. Longer jobs? Include a line in your submit file
     restricting your jobs to the CHTC servers that guarantee 72 hours.
@@ -75,7 +75,7 @@ of CHTC servers, jobs are guaranteed to run for 72 hours. Jobs that run
 for longer than 72 hours will fail, unless they have implemented a
 self-checkpointing method that allows them to resume after being
 evicted. Jobs that are shorter, around 2-4 hours, are good candidates to
-run on the UW Grid and/or Open Science Grid.
+run on the UW Grid and/or <a href="http://www.opensciencegrid.org/">Open Science Grid</a>.
 
 Input and output file size will impact how your files will be
 transferred to and from the execute nodes. Large input files will need