content/quickstarts/reusing_ssh_connections_in_linux_or_mac.md

-+++
-title = "Reusing SSH connections in Linux/Mac"
-description = "Reusing connections makes it easier to use multiple terminals"
-weight = "37"
-+++
-
-To make it more convenient for users who use multiple terminal sessions
-simultaneously, SSH can reuse an existing connection if connecting from
-Linux or Mac.  After the initial login, subsequent terminals can use
-that connection, eliminating the need to enter the username and password
-each time for every connection.  To enable this feature, add the
-following lines to your `~/.ssh/config `file:
-
-{{% panel header="`~/.ssh/config`"%}}
-{{< highlight bash >}}
-Host *
-ControlMaster auto
-ControlPath /tmp/%r@%h:%p
-ControlPersist 2h
-{{< /highlight >}}
-{{% /panel %}}
-
-{{% notice info%}}
-You may not have an existing `~/.ssh/config.` If not, simply create the
-file and set the permissions appropriately first:
-`touch ~/.ssh/config && chmod 600 ~/.ssh/config`
-{{% /notice %}}
-
-This will enable connection reuse when connecting to any host via SSH or
-SCP.  

content/quickstarts/submitting_jobs.md

-+++
-title = "Submitting Jobs"
-description =  "How to submit jobs to HCC resources"
-weight = "10"
-+++
-
-Crane and Rhino are managed by
-the [SLURM](https://slurm.schedmd.com) resource manager.  
-In order to run processing on Crane, you
-must create a SLURM script that will run your processing. After
-submitting the job, SLURM will schedule your processing on an available
-worker node.
-
-Before writing a submit file, you may need to
-[compile your application]({{< relref "/guides/running_applications/compiling_source_code" >}}).
-
-- [Ensure proper working directory for job output](#ensure-proper-working-directory-for-job-output)
-- [Creating a SLURM Submit File](#creating-a-slurm-submit-file)
-- [Submitting the job](#submitting-the-job)
-- [Checking Job Status](#checking-job-status)
-  -   [Checking Job Start](#checking-job-start)
-- [Next Steps](#next-steps)
-
-
-### Ensure proper working directory for job output
-
-{{% notice info %}}
-Because the /home directories are not writable from the worker nodes, all SLURM job output should be directed to your /work path.
-{{% /notice %}}
-
-{{% panel theme="info" header="Manual specification of /work path" %}}
-{{< highlight bash >}}
-$ cd /work/[groupname]/[username]
-{{< /highlight >}}
-{{% /panel %}}
-
-The environment variable `$WORK` can also be used.
-{{% panel theme="info" header="Using environment variable for /work path" %}}
-{{< highlight bash >}}
-$ cd $WORK
-$ pwd
-/work/[groupname]/[username]
-{{< /highlight >}}
-{{% /panel %}}
-
-Review how /work differs from /home [here.]({{< relref "/guides/handling_data/_index.md" >}})
-
-### Creating a SLURM Submit File
-
-{{% notice info %}}
-The below example is for a serial job. For submitting MPI jobs, please
-look at the [MPI Submission Guide.]({{< relref "submitting_an_mpi_job" >}})
-{{% /notice %}}
-
-A SLURM submit file is broken into 2 sections, the job description and
-the processing.  SLURM job description are prepended with `#SBATCH` in
-the submit file.
-
-**SLURM Submit File**
-
-{{< highlight batch >}}
-#!/bin/sh
-#SBATCH --time=03:15:00          # Run time in hh:mm:ss
-#SBATCH --mem-per-cpu=1024       # Maximum memory required per CPU (in megabytes)
-#SBATCH --job-name=hello-world
-#SBATCH --error=/work/[groupname]/[username]/job.%J.err
-#SBATCH --output=/work/[groupname]/[username]/job.%J.out
-
-module load example/test
-
-hostname
-sleep 60
-{{< /highlight >}}
-
-- **time**  
-  Maximum walltime the job can run.  After this time has expired, the
-  job will be stopped.
-- **mem-per-cpu**  
-  Memory that is allocated per core for the job.  If you exceed this
-  memory limit, your job will be stopped.
-- **mem**  
-  Specify the real memory required per node in MegaBytes. If you
-  exceed this limit, your job will be stopped. Note that for you
-  should ask for less memory than each node actually has. For Crane, the
-  max is 500GB.
-- **job-name**
-  The name of the job.  Will be reported in the job listing.
-- **partition**  
-  The partition the job should run in.  Partitions determine the job's
-  priority and on what nodes the partition can run on.  See the
-  [Partitions]({{< relref "/guides/submitting_jobs/partitions/_index.md" >}}) page for a list of possible partitions.
-- **error**  
-  Location of the stderr will be written for the job.  `[groupname]`
-  and `[username]` should be replaced your group name and username.
-  Your username can be retrieved with the command `id -un` and your
-  group with `id -ng`.
-- **output**  
-  Location of the stdout will be written for the job.
-
-More advanced submit commands can be found on the [SLURM Docs](https://slurm.schedmd.com/sbatch.html).
-You can also find an example of a MPI submission on [Submitting an MPI Job]({{< relref "submitting_an_mpi_job" >}}).
-
-### Submitting the job
-
-Submitting the SLURM job is done by command `sbatch`.  SLURM will read
-the submit file, and schedule the job according to the description in
-the submit file.
-
-Submitting the job described above is:
-
-{{% panel theme="info" header="SLURM Submission" %}}
-{{< highlight batch >}}
-$ sbatch example.slurm
-Submitted batch job 24603
-{{< /highlight >}}
-{{% /panel %}}
-
-The job was successfully submitted.
-
-### Checking Job Status
-
-Job status is found with the command `squeue`.  It will provide
-information such as:
-
-- The State of the job: 
-    - **R** - Running
-    - **PD** - Pending - Job is awaiting resource allocation.
-    - Additional codes are available
-      on the [squeue](http://slurm.schedmd.com/squeue.html)
-      page.
-- Job Name
-- Run Time
-- Nodes running the job
-
-Checking the status of the job is easiest by filtering by your username,
-using the `-u` option to squeue.
-
-{{< highlight batch >}}
-$ squeue -u <username>
-  JOBID PARTITION     NAME       USER  ST       TIME  NODES NODELIST(REASON)
-  24605     batch hello-wo <username>   R       0:56      1 b01
-{{< /highlight >}}
-
-Additionally, if you want to see the status of a specific partition, for
-example if you are part of a [partition]({{< relref "/guides/submitting_jobs/partitions/_index.md" >}}),
-you can use the `-p` option to `squeue`:
-
-{{< highlight batch >}}
-$ squeue -p esquared
-  JOBID PARTITION     NAME     USER  ST       TIME  NODES NODELIST(REASON)
-  73435  esquared MyRandom tingting   R   10:35:20      1 ri19n10
-  73436  esquared MyRandom tingting   R   10:35:20      1 ri19n12
-  73735  esquared SW2_driv   hroehr   R   10:14:11      1 ri20n07
-  73736  esquared SW2_driv   hroehr   R   10:14:11      1 ri20n07
-{{< /highlight >}}
-
-#### Checking Job Start
-
-You may view the start time of your job with the
-command `squeue --start`.  The output of the command will show the
-expected start time of the jobs.
-
-{{< highlight batch >}}
-$ squeue --start --user lypeng
-  JOBID PARTITION     NAME     USER  ST           START_TIME  NODES NODELIST(REASON)
-   5822     batch  Starace   lypeng  PD  2013-06-08T00:05:09      3 (Priority)
-   5823     batch  Starace   lypeng  PD  2013-06-08T00:07:39      3 (Priority)
-   5824     batch  Starace   lypeng  PD  2013-06-08T00:09:09      3 (Priority)
-   5825     batch  Starace   lypeng  PD  2013-06-08T00:12:09      3 (Priority)
-   5826     batch  Starace   lypeng  PD  2013-06-08T00:12:39      3 (Priority)
-   5827     batch  Starace   lypeng  PD  2013-06-08T00:12:39      3 (Priority)
-   5828     batch  Starace   lypeng  PD  2013-06-08T00:12:39      3 (Priority)
-   5829     batch  Starace   lypeng  PD  2013-06-08T00:13:09      3 (Priority)
-   5830     batch  Starace   lypeng  PD  2013-06-08T00:13:09      3 (Priority)
-   5831     batch  Starace   lypeng  PD  2013-06-08T00:14:09      3 (Priority)
-   5832     batch  Starace   lypeng  PD                  N/A      3 (Priority)
-{{< /highlight >}}
-
-The output shows the expected start time of the jobs, as well as the
-reason that the jobs are currently idle (in this case, low priority of
-the user due to running numerous jobs already).
- 
-#### Removing the Job
-
-Removing the job is done with the `scancel` command.  The only argument
-to the `scancel` command is the job id.  For the job above, the command
-is:
-
-{{< highlight batch >}}
-$ scancel 24605
-{{< /highlight >}}
-
-### Next Steps
-
-{{% children  %}} 

content/redirector.md

----
-title: "Redirector"
----
-
-<script>
-
-// Redirector for hcc-docs links
-// Search for URL parameter 'q' and redirect to top match
-
-var lunrIndex;
-
-function getQueryVariable(variable) {
-    var query = window.location.search.substring(1);
-    var vars = query.split('&');
-
-    for (var i = 0; i < vars.length; i++) {
-        var pair = vars[i].split('=');
-
-        if (pair[0] === variable) {
-            return decodeURIComponent(pair[1].replace(/\+/g, '%20'));
-        }
-    }
-}
-
-// Initialize lunrjs using our generated index file
-function initLunr() {
-    // First retrieve the index file
-    return $.getJSON(baseurl + "/index.json")
-        .done(function(index) {
-            pagesIndex = index;
-            // Set up lunrjs by declaring the fields we use
-            // Also provide their boost level for the ranking
-            lunrIndex = new lunr.Index
-            lunrIndex.ref("uri");
-            lunrIndex.field('title', {
-                boost: 15
-            });
-            lunrIndex.field('tags', {
-                boost: 10
-            });
-            lunrIndex.field("content", {
-                boost: 5
-            });
-
-            // Feed lunr with each file and let lunr actually index them
-            pagesIndex.forEach(function(page) {
-                lunrIndex.add(page);
-            });
-            lunrIndex.pipeline.remove(lunrIndex.stemmer)
-        })
-        .fail(function(jqxhr, textStatus, error) {
-            var err = textStatus + ", " + error;
-            console.error("Error getting Hugo index file:", err);
-        });
-}
-
-function search(query) {
-    // Find the item in our index corresponding to the lunr one to have more info
-    return lunrIndex.search(query).map(function(result) {
-        return pagesIndex.filter(function(page) {
-            return page.uri === result.ref;
-        })[0];
-    });
-}
-
-initLunr().then(function() {
-    var searchTerm = getQueryVariable('q');
-    // Replace non-word chars with space. lunr doesn't like quotes.
-    searchTerm = searchTerm.replace(/[\W_]+/g," ");
-    var results = search(searchTerm);
-
-    if (!results.length) {
-        window.location = baseurl;
-    } else {
-        window.location = results[0].uri;
-    }
-});
-
-</script>

docs/.nav.yml

+ignore: "facilities.md"

docs/Events/.nav.yml

+hide: true

docs/Events/2012/index.md

+---
+title: "2012"
+summary: "Historical listing of various HCC events for the year 2012."
+---
+
+Historical listing of HCC Events
+----------
+
+{{ children('Events/2012') }}

content/events/2012/nebraska_supercomputing_symposium_12.md → docs/Events/2012/nebraska_supercomputing_symposium_12.md

-+++
-title = "Nebraska Supercomputing Symposium '12"
-description = "Nebraska Supercomputing Symposium '12."
-+++
-{{< figure src="/images/2012-11-07.jpg" width="300" class="img-border">}}
-{{< figure src="/images/2012-11-07hdr.jpg" width="300" class="img-border">}}
+---
+title: Nebraska Supercomputing Symposium '12
+summary: "Nebraska Supercomputing Symposium '12."
+---
+<img src="/images/2012-11-07.jpg" width="300" class="img-border">
+<img src="/images/2012-11-07hdr.jpg" width="300" class="img-border">
 
 
-{{< figure src="/images/PIVOT_Logo.png" width="100" class="img-border">}} Talks
+<img src="/images/PIVOT_Logo.png" width="100" class="img-border>
+
+Talks
 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 
 -   [Intro slides](https://unl.box.com/s/4gctct2jgu2e78y7efld7w39xzbd1j4d)

content/events/2012/supercomputing_mini_workshop_2012.md → docs/Events/2012/supercomputing_mini_workshop_2012.md

-+++
-title = "Supercomputing Mini Workshop 2012"
-description = "Supercomputing Mini Workshop 2012."
-+++
+---
+title: Supercomputing Mini Workshop 2012
+summary: "Supercomputing Mini Workshop 2012."
+---
 
 Presentation
 ============

docs/Events/2013/index.md

+---
+title: "2013"
+summary: "Historical listing of various HCC events for the year 2013."
+---
+
+Historical listing of HCC Events
+----------
+
+{{ children('Events/2013') }}

content/events/2013/june_2013_osg_workshop.md → docs/Events/2013/june_2013_osg_workshop.md

-+++
-title = "HCC OSG Workshop, June 2013"
-description = "HCC OSG Workstop, June 2013."
-+++
+---
+title: HCC OSG Workshop, June 2013
+summary: "HCC OSG Workstop, June 2013."
+---
 
 Location: Unity Room/212 in the Jackie Gaughan Multicultural Center
 

content/events/2013/supercomputing_mini_workshop_february_27_2013.md → docs/Events/2013/supercomputing_mini_workshop_february_27_2013.md

-+++
-title = "Supercomputing Mini Workshop 2013"
-description = "Supercomputing Mini Workshop 2013."
-+++
+---
+title: Supercomputing Mini Workshop 2013
+summary: "Supercomputing Mini Workshop 2013."
+---
 
 Supercomputing Mini Workshop - February 27, 2013
 ================================================
 
-{{% notice info %}}The materials found on this page were applicable at the time of the event. When referencing these, 
+!!! noteThe materials found on this page were applicable at the time of the event. When referencing these, 
 please check current documentation to ensure the resources are still available.A list of currently available resources can be found on the
- [Submitting Jobs page](https://hcc.unl.edu/docs/#resource-capabilities){{% /notice %}}
+ [Submitting Jobs page](https://hcc.unl.edu/docs/#resource-capabilities)
 
 In this hour-long mini workshop, you will obtain hands-on experience
 performing a simple calculation (summing from 1 to 16) with a
@@ -22,7 +22,7 @@ state-of-the-art supercomputing resources.
 **Logging In**
 
 ``` syntaxhighlighter-pre
-ssh tusker.unl.edu -l demoXXXX
+ssh crane.unl.edu -l demoXXXX
 ```
 
 **[Cypwin Link](http://cygwin.com/install.html)**
@@ -49,7 +49,7 @@ two folders, `serial\_f90` and `parallel\_f90`, in this folder
 
 ``` syntaxhighlighter-pre
 $ ls
-$ scp -r ./demo_code <username>@tusker.unl.edu:/work/demo/<username>
+$ scp -r ./demo_code <username>@crane.unl.edu:/work/demo/<username>
 <enter password>
 ```
 
@@ -59,7 +59,7 @@ Serial Job
 First, you need to login to the cluster
 
 ``` syntaxhighlighter-pre
-$ ssh <username>@tusker.unl.edu
+$ ssh <username>@crane.unl.edu
 <enter password>
 ```
 
@@ -133,14 +133,14 @@ code.  It uses MPI for communication between the parallel processes.
 $ mpif90 fortran_mpi.f90 -o fortran_mpi.x
 ```
 
-Next, we will submit the MPI application to the Tusker cluster scheduler
+Next, we will submit the MPI application to the cluster scheduler
 using the file `submit_tusker.mpi`.
 
 ``` syntaxhighlighter-pre
 $ qsub submit_tusker.mpi
 ```
 
-The Tusker cluster scheduler will pick machines (possibly several,
+The cluster scheduler will pick machines (possibly several,
 depending on availability) to run the parallel MPI application.  You can
 check the status of the job the same way you did with the Serial job:
 

content/events/2014/august_2014_uno_hcc_workshop.md → docs/Events/2014/august_2014_uno_hcc_workshop.md

-+++
-title = "August 2014 UNO Workshop"
-description = "August 2014 UNO Workshop."
-+++
+---
+title: August 2014 UNO Workshop
+summary: "August 2014 UNO Workshop."
+---
 
 When: August 29, 2014
 

docs/Events/2014/index.md

+---
+title: "2014"
+summary: "Historical listing of various HCC events for the year 2014."
+---
+
+Historical listing of HCC Events
+----------
+
+{{ children('Events/2014') }}

content/events/2014/july_2014_bioinformatics_workshop.md → docs/Events/2014/july_2014_bioinformatics_workshop.md

-+++
-title = "July 2014 Bioinformatics Workshop"
-description = "July 2014 Bioinformatics Workshop"
-+++
+---
+title: July 2014 Bioinformatics Workshop
+summary: "July 2014 Bioinformatics Workshop"
+---
 
 
 Monday - Wednesday, July 28 -30 (lunch will be provided)

content/events/2014/june_2014_bioinformatics_workshop.md → docs/Events/2014/june_2014_bioinformatics_workshop.md

-+++
-title = "HCC Bioinformatics Workshop, June 2013"
-description = "HCC Bioinformatics Workshop, June 2013."
-+++
+---
+title: HCC Bioinformatics Workshop, June 2013
+summary: "HCC Bioinformatics Workshop, June 2013."
+---
 
 Thursday, June 26 \| 10am-4pm (lunch will be provided)
 
@@ -23,16 +23,16 @@ Filley Hall, Room 302
  
 
 [Click to download ppt of
-presentation.](https://unl.box.com/s/3raqcvv00x0m4qbn7ubukitu8b7q9e5r)
+presentation.](https://uofnelincoln.sharepoint.com/:p:/s/UNL-HollandComputingCenter/EQ8ETtcUhFtAsyk9XT40QQ0BAWTj1m-WAnN2F4r9H_bzRQ?e=8wyeDr)
 
 
 [Click to download PDF of
-presentation.](https://unl.box.com/s/bkozojpnt8hcwnnsc6eww1muy4fv9wb3)
+presentation.](https://uofnelincoln.sharepoint.com/:b:/s/UNL-HollandComputingCenter/EfMi5y35e7tDtRiWMM_vQWABRyoub4njO7AnE0qupD8k6Q?e=fNu2Gs)
  
 
-[Click to download BLAST presentation](https://unl.box.com/s/e8juelxpeomhehhm2zg57102s9aeqhuy)
+[Click to download BLAST presentation](https://uofnelincoln.sharepoint.com/:b:/s/UNL-HollandComputingCenter/EYV5vp-DdLtKjLMqjTpwjxIBtfRe2QAvpiJU-LzPhnriLw?e=LPzhST)
  
 
 [Click to download example query
-file](https://unl.box.com/s/nk0bybekzqon368pxbfd77xykbuk1ywb)
+file](https://uofnelincoln.sharepoint.com/:u:/s/UNL-HollandComputingCenter/EeazfOASF8VFsmjappZeqv8BBpxP0GuSdCVB51jBEbkZrw?e=4C8aL5)
 

content/events/2014/october_2014_hcc_workshop_college_of_engineering.md → docs/Events/2014/october_2014_hcc_workshop_college_of_engineering.md

-+++
-title = "October 2014 HCC Workshop - CoE"
-description = "October 2014 HCC Workshop - CoE."
-+++
+---
+title: October 2014 HCC Workshop - CoE
+summary: "October 2014 HCC Workshop - CoE."
+---
 
 When:    October 10th, 2014    3:00 - 5:00