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content/events/2017/software_carpentry_workshop_unl_january_5_6_2017.md deleted 100644 → 0
View file @ 2383ec36
+++
title = "SWC Workshop, Jan. 5-6 2017"
description = "SWC Workshop, Jan. 5-6 2017."
+++
**When**: January 5-6, 2017
**Where**: Jackie Gaughan Multicultural Center - room 202 (Ubuntu)
**Quick Link**:
<a href="https://eharstad.github.io/2017-01-05-UNL" class="external-link">https://eharstad.github.io/2017-01-05-UNL</a>
**Materials**
=============
**Introduction:**
**<span
class="confluence-embedded-file-wrapper"><a href="/download/attachments/17041001/SWC-UNL-2017_01_05.pptx?version=1&amp;modificationDate=1483674264000&amp;api=v2" class="confluence-embedded-file"><img src="assets/images/documentConversion/latest/conversion/thumbnail/17041003/1" height="250" /></a></span>**
**<span
class="confluence-embedded-file-wrapper"><a href="/download/attachments/17041001/SWC-UNL-2017_01_05.pdf?version=1&amp;modificationDate=1483674263000&amp;api=v2" class="confluence-embedded-file"><img src="assets/images/documentConversion/latest/conversion/thumbnail/17041002/1" height="250" /></a></span>
**
**Etherpad**:
<a href="https://public.etherpad-mozilla.org/p/2017-01-05-UNL" class="external-link">https://public.etherpad-mozilla.org/p/2017-01-05-UNL</a>
**Shell Lesson**: <span
style="color: rgb(24,54,145);"> </span><a href="https://eharstad.github.io/shell-novice/" class="external-link">https://eharstad.github.io/shell-novice/</a>
**Git Lesson**: <span
style="color: rgb(24,54,145);"> </span><a href="https://eharstad.github.io/git-novice/" class="external-link">https://eharstad.github.io/git-novice/</a>
**R Lesson**:<span
style="color: rgb(24,54,145);"> </span><a href="https://carriebrown.github.io/r-novice-gapminder/" class="external-link">https://carriebrown.github.io/r-novice-gapminder/</a>
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[SWC-UNL-2017\_01\_05.pdf](attachments/17041001/17041002.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[SWC-UNL-2017\_01\_05.pptx](attachments/17041001/17041003.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
content/events/2017/software_carpentry_workshop_unl_march_27_28_2017.md deleted 100644 → 0
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+++
title = "SWC Workshop, March 27-28, 2017"
description = "SWC Workshop, March 27-28, 2017."
+++
**When**: March 27-28, 2017
**Where**: Nebraska Union - Colonial A&B
**Quick Link**:
<a href="https://unlhcc.github.io/2017-03-27-UNL/" class="external-link">https://unlhcc.github.io/2017-03-27-UNL/</a>
**Materials**
=============
**
**
**
**
**
**
**Etherpad**:
<a href="http://pad.software-carpentry.org/2017_03_27_UNL" class="external-link">http://pad.software-carpentry.org/2017_03_27_UNL</a>
**Intro
Slides: [SWC-UNL-20170327.pdf](attachments/17043687/17043692.pdf)**
**Shell Log:**
<a href="http://hcc.unl.edu/swc-history/20170327.html" class="external-link">http://hcc.unl.edu/swc-history/20170327.html</a>
**Shell Lesson**: <span
style="color: rgb(24,54,145);"> </span><a href="https://eharstad.github.io/shell-novice/" class="external-link">https://eharstad.github.io/shell-novice/</a>
**Git Lesson**: <span
style="color: rgb(24,54,145);"> </span><a href="https://eharstad.github.io/git-novice/" class="external-link">https://eharstad.github.io/git-novice/</a>
**Python Lesson**:<span
style="color: rgb(24,54,145);"> </span><a href="https://djw8605.github.io/python-novice-inflammation/" class="external-link">https://djw8605.github.io/python-novice-inflammation/</a>
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[SWC-UNL-2017\_01\_05.pptx](attachments/17043687/17043685.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[SWC-UNL-2017\_01\_05.pdf](attachments/17043687/17043686.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[SWC-UNL-20170327.pdf](attachments/17043687/17043692.pdf)
(application/pdf)
content/events/2017/unk_linear_algebra_feb_28th_2017.md deleted 100644 → 0
View file @ 2383ec36
+++
title = "UNK Linear Algebra, Feb. 28, 2017"
description = "UNK Linear Algebra, Feb. 28, 2017."
+++
**If at any time today you have difficulties or become lost, please
place the <span style="color: rgb(255,0,0);">red</span> sticky note on
top of your monitor and a helper will be around to assist you.**
For these instructions, any commands to be typed into the terminal will be formatted like this.
**What is a cluster:**
----------------------
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042191.png" class="confluence-embedded-image" width="700" height="307" /></span>
(picture courtesy of:
<a href="http://training.h3abionet.org/technical_workshop_2015/?page_id=403" class="external-link">http://training.h3abionet.org/technical_workshop_2015/?page_id=403</a>)
**
**
**To connect to the Crane cluster:**
------------------------------------
- insert the Yubikey into the computer's USB drive. There should be a
small green light in the middle of the Yubikey to indicate it is
inserted correctly.
- Open your preferred web browser and navigate to
<a href="http://go.unl.edu/cranessh" class="external-link">http://go.unl.edu/cranessh</a>
- Click "Start SSH session to crane.unl.edu"
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042178.png" class="confluence-embedded-image" height="400" /></span>
- Click the "Terminal: SSH" icon to begin the SSH session
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042179.png" class="confluence-embedded-image" height="400" /></span>
- Type in the provided Username and Password. Note that the password
will not display on screen, but rest assured that even though
nothing is being output, your password is being entered as you type.
- At the "Passcode:" prompt, press your finger to the gold circle in
the middle of the Yubikey until a string of characters appears on
screen.
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042182.png" class="confluence-embedded-image" height="400" /></span>
- If you logged in successfully, your screen should look similar to
the one belo
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042185/17042183.png" class="confluence-embedded-image" height="400" /></span>
**Linux Commands Reference List:**
----------------------------------
<table>
<colgroup>
<col style="width: 33%" />
<col style="width: 33%" />
<col style="width: 33%" />
</colgroup>
<thead>
<tr class="header">
<th>Command</th>
<th>What it does</th>
<th>Example Uses</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>ls</td>
<td>list: Lists the files and directories located in the current directory</td>
<td><ul>
<li>ls</li>
<li>ls -a
<ul>
<li>shows all the files in the directory, including hidden ones</li>
</ul></li>
<li>ls -l
<ul>
<li>shows contents in a list format including information such as file size, file permissions and date the file was modified</li>
</ul></li>
<li>ls *.txt
<ul>
<li>shows all files in the current directory which end with .txt</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td>cd</td>
<td>change directory: this allows users to in or out of file directories</td>
<td><ul>
<li>cd &lt;folder path&gt;</li>
<li>cd folder_name
<ul>
<li>navigates into directory &quot;folder_name&quot; located in the current directory</li>
</ul></li>
<li>cd ..
<ul>
<li>navigates out of a directory and into the parent directory</li>
</ul>
cd $HOME (or $WORK)
<ul>
<li>navigates to a user's home (or work) directory</li>
</ul></li>
</ul></td>
</tr>
<tr class="odd">
<td>mv</td>
<td>move: used to move a file or directory to another location</td>
<td><ul>
<li>mv &lt;current file(s)&gt; &lt;target file(s)&gt;</li>
<li>mv * ../
<ul>
<li>moves all files from the current directory into the parent directory</li>
</ul></li>
<li>mv old_filename new_filename
<ul>
<li>renames the file &quot;old_filename&quot; to &quot;new_filename&quot;</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td>man</td>
<td><p>manual: displays documentation for commands</p>
<p><strong>Note:</strong> Use up and down arrows to scroll through the text. To exit the manual display, press 'q'</p></td>
<td><ul>
<li>man &lt;command name&gt;</li>
<li>man ls
<ul>
<li>displays documentation for the ls command</li>
</ul></li>
</ul></td>
</tr>
<tr class="odd">
<td>mkdir</td>
<td>make directory: creates a directory with the specified name</td>
<td><ul>
<li>mkdir &lt;new_folder&gt;
<ul>
<li>creates the directory &quot;new_folder&quot; within the current directory</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td>rmdir</td>
<td><p>remove directory: deletes a directory with the specified name</p>
<p><strong>Note:</strong> rmdir only works on empty directories</p></td>
<td><ul>
<li>rmdir &lt;folder_name&gt;
<ul>
<li>removes the directory &quot;folder_name&quot; if the directory</li>
</ul></li>
<li>rmdir *
<ul>
<li>removes all directories within the current directory</li>
</ul></li>
</ul></td>
</tr>
<tr class="odd">
<td>rm</td>
<td>remove: deletes file or files with the specified name(s)</td>
<td><ul>
<li>rm &lt;file_name&gt;
<ul>
<li>deletes the file &quot;file_name&quot;</li>
</ul></li>
<li>rm *
<ul>
<li>deletes all files in the current directory</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td><p>nano</p></td>
<td><p>nano text editor: opens the nano text editor</p>
<p><strong>Note:</strong> To access the menu options, ^ indicates the control (CTRL) key.</p></td>
<td><ul>
<li>nano
<ul>
<li>opens the text editor in a blank file</li>
</ul></li>
<li>nano &lt;file_name&gt;
<ul>
<li>opens the text editor with &quot;file_name&quot; open. If &quot;file_name&quot; does not exist, it will be created if the file is saved</li>
</ul></li>
</ul></td>
</tr>
<tr class="odd">
<td>clear</td>
<td>clear: clears the screen of all input/output</td>
<td><ul>
<li>clear</li>
</ul></td>
</tr>
<tr class="even">
<td>less</td>
<td><p>less: opens an extended view of a file</p>
<p><strong>Note:</strong> Use up and down arrows to scroll through the text. To exit the extended view, press 'q'</p></td>
<td><ul>
<li>less &lt;file_name&gt;
<ul>
<li>opens an extended view of the file &quot;file_name&quot;</li>
</ul></li>
</ul></td>
</tr>
</tbody>
</table>
**To run MATLAB interactively:**
--------------------------------
- After logging into the cluster, navigate to your $WORK directory:
- cd $WORK
- Request an interactive job:
- srun --reservation=unk --mem=4096 --pty $SHELL
- Load the MATLAB module:
- module load matlab
- Run MATLAB:
- matlab
**To access the MATLAB Tutorial:**
----------------------------------
- Navigate to your $WORK directory:
- cd $WORK
- Clone the github repo containing the tutorial files:
- git clone https://github.com/unlhcc/HCCWorkshops.git
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.10.31 PM.png](attachments/17042185/17042180.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.10.43 PM.png](attachments/17042185/17042181.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.10.31 PM.png](attachments/17042185/17042178.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.10.43 PM.png](attachments/17042185/17042179.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.16.10 PM.png](attachments/17042185/17042182.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.16.37 PM.png](attachments/17042185/17042184.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-02-23 at 5.16.37 PM.png](attachments/17042185/17042183.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2017-2-24 11:14:4.png](attachments/17042185/17042186.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[cluster\_small2.png](attachments/17042185/17042191.png) (image/png)
content/events/2017/unl_r_for_biologists_class_march_8_2017.md deleted 100644 → 0
View file @ 2383ec36
+++
title = "R for Biologists, March 8, 2017"
description = "R for Biologists, March 8, 2017."
+++
**We will be utilizing <span style="color: rgb(255,0,0);">red</span> and
<span style="color: rgb(51,153,102);">green</span> sticky notes today.
If you run into problems or have questions,**
**please place the <span style="color: rgb(255,0,0);">red</span> sticky
note to the back of your computer screen and a helper will assist you.**
If you have not already requested an HCC account under the rcourse998
group, please do so
here: <a href="https://hcc.unl.edu/new-user-request" class="external-link">https://hcc.unl.edu/new-user-request</a>
If you already have an HCC account and need to be added to the
rcourse998 group, please let us know.
If you have not previously set up Duo Authentication, please ask for
assistance.
**Set up Instructions:**
**Windows:**
For Windows will we use two third party
application **PuTTY** and **WinSCP** for demonstration.
PuTTY:
&lt;[putty-0.62-installer.exe](https://hcc-docs.unl.edu/download/attachments/2851288/putty-0.62-installer.exe?version=1&modificationDate=1371067913000&api=v2) or <a href="http://www.putty.org/" class="external-link">http://www.putty.org/</a>&gt;
WinSCP:
&lt;[winscp515setup.exe](https://hcc-docs.unl.edu/download/attachments/2851288/winscp515setup.exe?version=1&modificationDate=1371155133000&api=v2) or <a href="http://winscp.net/eng/download.php" class="external-link">http://winscp.net/eng/download.php</a>&gt;.
**Mac/Linux:**
Mac and Linux users will need to download and install **Cyberduck**.
Detailed information for downloading and setting up Cyberduck can be
found here: [For Mac/Linux Users](2851290.html)
**R core and R Studio:**
We will be writing scripts offline in RStudio and then uploading them to
execute them on the cluster. This lesson assumes you have the R core and
RStudio installed. If you do not you can install them here:
R
core: <a href="https://cloud.r-project.org/" class="external-link">https://cloud.r-project.org/</a>
RStudio: <a href="https://www.rstudio.com/products/rstudio/download/" class="external-link">https://www.rstudio.com/products/rstudio/download/</a>
**Required Packages:**
We will also be using the dplyr, ggplot2 and maps package. If you do not
have these installed, please install them now. You can do so using the
following commands inside the RStudio console:
install.packages("dplyr")
install.packages("ggplot2")
install.packages("maps")
**What is a cluster:**
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/17042692/17042703.png" class="confluence-embedded-image" width="700" height="307" /></span></span>
(picture courtesy
of: <a href="http://training.h3abionet.org/technical_workshop_2015/?page_id=403" class="external-link">http://training.h3abionet.org/technical_workshop_2015/?page_id=403</a>)
**Linux Commands Reference List:**
----------------------------------
<table>
<colgroup>
<col style="width: 33%" />
<col style="width: 33%" />
<col style="width: 33%" />
</colgroup>
<thead>
<tr class="header">
<th><div class="tablesorter-header-inner">
Command
</div></th>
<th><div class="tablesorter-header-inner">
What it does
</div></th>
<th><div class="tablesorter-header-inner">
Example Uses
</div></th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>ls</td>
<td>list: Lists the files and directories located in the current directory</td>
<td><ul>
<li>ls</li>
<li>ls -a
<ul>
<li>shows all the files in the directory, including hidden ones</li>
</ul></li>
<li>ls -l
<ul>
<li>shows contents in a list format including information such as file size, file permissions and date the file was modified</li>
</ul></li>
<li>ls *.txt
<ul>
<li>shows all files in the current directory which end with .txt</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td>cd</td>
<td>change directory: this allows users to in or out of file directories</td>
<td><ul>
<li>cd &lt;folder path&gt;</li>
<li>cd folder_name
<ul>
<li>navigates into directory &quot;folder_name&quot; located in the current directory</li>
</ul></li>
<li>cd ..
<ul>
<li>navigates out of a directory and into the parent directory</li>
</ul>
cd $HOME (or $WORK)
<ul>
<li>navigates to a user's home (or work) directory</li>
</ul></li>
</ul></td>
</tr>
<tr class="odd">
<td>mv</td>
<td>move: used to move a file or directory to another location</td>
<td><ul>
<li>mv &lt;current file(s)&gt; &lt;target file(s)&gt;</li>
<li>mv * ../
<ul>
<li>moves all files from the current directory into the parent directory</li>
</ul></li>
<li>mv old_filename new_filename
<ul>
<li>renames the file &quot;old_filename&quot; to &quot;new_filename&quot;</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td>man</td>
<td><p>manual: displays documentation for commands</p>
<p><strong>Note:</strong> Use up and down arrows to scroll through the text. To exit the manual display, press 'q'</p></td>
<td><ul>
<li>man &lt;command name&gt;</li>
<li>man ls
<ul>
<li>displays documentation for the ls command</li>
</ul></li>
</ul></td>
</tr>
<tr class="odd">
<td>mkdir</td>
<td>make directory: creates a directory with the specified name</td>
<td><ul>
<li>mkdir &lt;new_folder&gt;
<ul>
<li>creates the directory &quot;new_folder&quot; within the current directory</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td>rmdir</td>
<td><p>remove directory: deletes a directory with the specified name</p>
<p><strong>Note: </strong>rmdir only works on empty directories</p></td>
<td><ul>
<li>rmdir &lt;folder_name&gt;
<ul>
<li>removes the directory &quot;folder_name&quot; if the directory</li>
</ul></li>
<li>rmdir *
<ul>
<li>removes all directories within the current directory</li>
</ul></li>
</ul></td>
</tr>
<tr class="odd">
<td>rm</td>
<td>remove: deletes file or files with the specified name(s)</td>
<td><ul>
<li>rm &lt;file_name&gt;
<ul>
<li>deletes the file &quot;file_name&quot;</li>
</ul></li>
<li>rm *
<ul>
<li>deletes all files in the current directory</li>
</ul></li>
</ul></td>
</tr>
<tr class="even">
<td><p>nano</p></td>
<td><p>nano text editor: opens the nano text editor</p>
<p><strong>Note: </strong>To access the menu options, ^ indicates the control (CTRL) key.</p></td>
<td><ul>
<li>nano
<ul>
<li>opens the text editor in a blank file</li>
</ul></li>
<li>nano &lt;file_name&gt;
<ul>
<li>opens the text editor with &quot;file_name&quot; open. If &quot;file_name&quot; does not exist, it will be created if the file is saved</li>
</ul></li>
</ul></td>
</tr>
<tr class="odd">
<td>clear</td>
<td>clear: clears the screen of all input/output</td>
<td><ul>
<li>clear</li>
</ul></td>
</tr>
<tr class="even">
<td>less</td>
<td><p>less: opens an extended view of a file</p>
<p><strong>Note: </strong>Use up and down arrows to scroll through the text. To exit the extended view, press 'q'</p></td>
<td><ul>
<li>less &lt;file_name&gt;
<ul>
<li>opens an extended view of the file &quot;file_name&quot;</li>
</ul></li>
</ul></td>
</tr>
</tbody>
</table>
### To download the tutorial files:
- Navigate to your $WORK directory:
- cd $WORK
- Clone the github repo containing the tutorial files:
- git clone https://github.com/unlhcc/HCCWorkshops.git
Take Home Exercise:
[Data Analysis in R](attachments/17042692/17042690.pdf) - Please note
that the on the bottom of page three, there is a missing parenthesis at
the end of the last command.
The final code chunk should read:
# Calculate flight age using birthmonth
age <- data.frame(names(acStart), acStart, stringsAsFactors=FALSE)
colnames(age) <- c("TailNum", "acStart")
flights <- left_join(flights, age, by="TailNum")
flights <- mutate(flights, Age = (flights$Year * 12) + flights$Month - flights$acStart)
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[Big\_Data\_Example.pdf](attachments/17042692/17042690.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-03-08 at 10.19.41 AM.png](attachments/17042692/17042691.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-03-08 at 10.20.51 AM.png](attachments/17042692/17042693.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-03-08 at 10.27.19 AM.png](attachments/17042692/17042695.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-03-08 at 10.28.57 AM.png](attachments/17042692/17042696.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" /> [Screen
Shot 2017-03-08 at 10.30.11 AM.png](attachments/17042692/17042697.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[cluster\_small2.png](attachments/17042692/17042703.png) (image/png)
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+++
title = "UNL STAT802, Jan. 23rd, 2017"
description = "UNL STAT802, Jan. 23rd, 2017."
+++
**Lab 1 Time:** 2 - 3:50 PM
**Lab 2 Time:** 4 - 5:50 PM
**Location:** UNL East Campus, Room 49, Hardin Hall
[Slides](attachments/17041326/17041352.pdf)
[Installation Info](attachments/17041326/17041361.pdf)
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat802\_anvil.pptx](attachments/17041326/17041331.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat802\_anvil.pptx](attachments/17041326/17041328.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat802\_anvil.pdf](attachments/17041326/17041352.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat802\_anvil.pptx](attachments/17041326/17041353.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[Installation.pdf](attachments/17041326/17041361.pdf)
(application/pdf)
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+++
title = "UNL STAT802, Fall 2017"
description = "UNL STAT802, Fall 2017."
+++
### Setting Up Anvil Instances for Windows SAS
**Location:** Hardin Hall - Room 49
**Time:** Friday, September 1, 2017 - 10:30 am
[Slides](attachments/21071499/21071500.pdf)
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat802\_anvil.pdf](attachments/21071499/21071603.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat802\_anvil.pptx](attachments/21071499/21071604.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat802\_anvil.pdf](attachments/21071499/21071500.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat802\_anvil.pptx](attachments/21071499/21071501.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[2017-09-06-Anvil.pdf](attachments/21071499/21071618.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[2017-09-06-Anvil.pdf](attachments/21071499/21071629.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[WinSCP-5.11-Setup.exe](attachments/21071499/21071620.exe)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[2017-09-06-Introduction to HCC.pdf](attachments/21071499/21071621.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[KickStartFall17.pdf](attachments/21071499/21071622.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[HCC-Kickstart-Globus-2017095.pdf](attachments/21071499/21071623.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[OSG\_HCCKickstart\_20170906.pdf](attachments/21071499/21071625.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[OSG\_HCCKickstart\_20170906.pdf](attachments/21071499/21071624.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[HCC-Kickstart-Globus-2017095.pdf](attachments/21071499/21071626.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[2017-09-06-Anvil.pdf](attachments/21071499/21071630.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[2017-09-06-Anvil.pdf](attachments/21071499/21071619.pdf)
(application/pdf)
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+++
title = "UNL STAT850, Fall 2017"
description = "UNL STAT850, Fall 2017."
+++
**When: **1:00pm - 1:45pm
**Location:** UNL East Campus, Keim 214
[Slides](attachments/21071482/21071490.pdf)
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat850\_anvil.pdf](attachments/21071482/21071487.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat850\_anvil.pptx](attachments/21071482/21071488.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat850\_anvil.pdf](attachments/21071482/21071490.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat850\_anvil.pptx](attachments/21071482/21071491.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[anyconnect-macosx-4.2.00096-web-deploy-k9.dmg](attachments/21071482/21071492.dmg)
(application/x-diskcopy)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[anyconnect-win-4.2.01022-web-deploy-k9.exe](attachments/21071482/21071493.exe)
(application/octet-stream)
content/events/2017/unl_stat_950_fall_2017.md deleted 100644 → 0
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+++
title = "UNL STAT950, Fall 2017"
description = "UNL STAT950, Fall 2017"
+++
**Date**: 9 am. - 10:15 am 09/19/2017
**Location**: Hardin Hall
**PDF Slides**:
[HCC-Intro](attachments/21072883/21072885.pdf)
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[2017-09-19-STAT950.pdf](attachments/21072883/21072885.pdf)
(application/pdf)
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+++
title = "UNL STAT Alpha Seminar, Fall 2017"
description = "UNL STAT Alpha Seminar, Fall 2017."
+++
**Date**: 11 am. 09/18/2017
**Location**: Keim 264
**PDF Slides**:
[HCC\_Overview](attachments/21072863/21072872.pdf)
[HCC\_Submit\_Jobs](attachments/21072863/21072864.pdf)
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[2017-09-18-Alpha-Seminar.pdf](attachments/21072863/21072870.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[2017-09-18-Alpha-Seminar.pdf](attachments/21072863/21072874.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[Stats2017.pdf](attachments/21072863/21072872.pdf) (application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[2017-09-18-Alpha-Seminar.pdf](attachments/21072863/21072864.pdf)
(application/pdf)
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+++
title = "XSEDE Big Data, Fall 2017"
description = "XSEDE Big Data, Fall 2017."
+++
Morning Session: Recommender with Spark
=======================================
<span
class="confluence-embedded-file-wrapper"><img src="assets/images/18547295/18547296.png" class="confluence-embedded-image" /></span>
Afternoon Session - Deep Learning with TensorFlow
=================================================
<span
class="confluence-embedded-file-wrapper"><img src="assets/images/18547295/18547300.png" class="confluence-embedded-image" /></span>
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2017-5-19\_11-41-42.png](attachments/18547295/18547296.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2017-5-19\_15-42-34.png](attachments/18547295/18547300.png)
(image/png)
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+++
title = "2018"
description = "Listing of various HCC events for the year 2018."
weight = "30"
+++
Historical listing of HCC Events
----------
{{% children %}}
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+++
title = "June Workshop Series 2018"
description = "June Workshop Series 2018."
+++
Introduction to OSG: [Slides(pdf)](attachments/33689824/33689834.pdf)
[Slides(ppt)](attachments/33689824/33689835.pptx)
Introduction to Anvil: [Slides](attachments/33689824/33689825.pdf)
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[Intro\_to\_Anvil.pdf](attachments/33689824/33689825.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[OSG\_HCCWorkshop\_20180626.pdf](attachments/33689824/33689834.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[OSG\_HCCWorkshop\_20180626.pptx](attachments/33689824/33689835.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
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+++
title = "Software Carpentry Workshop Setup"
description = "Software Carpentry Workshop Setup."
+++
For Windows:
============
Bash/Git
--------
1. Download
<a href="https://git-for-windows.github.io/" class="external-link">Git for Windows </a>
2. Run the installer, Click "Yes" if prompted to allow the program to
make changes.
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324402.png" class="confluence-embedded-image" height="250" /></span>
3. Click "Next"
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324403.png" class="confluence-embedded-image" height="400" /></span>
4. Click "Next"
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324405.png" class="confluence-embedded-image" height="400" /></span>
5. Select "Use the Nano editor by default" and click "Next"
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324406.png" class="confluence-embedded-image" height="400" /></span>
6. Ensure "Use Git from the Windows Command Prompt" is selected and
click "Next
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324407.png" class="confluence-embedded-image" height="400" /></span>
7. Click "Next"
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324408.png" class="confluence-embedded-image" height="400" /></span>
8. Ensure "Checkout Windows-style, commit Unix-style line endings" is
selected and click "Next"
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324409.png" class="confluence-embedded-image" height="400" /></span>
9. Click "Next"
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324410.png" class="confluence-embedded-image" height="400" /></span>
10. Click "Install"
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324411.png" class="confluence-embedded-image" height="400" /></span>
11. Click "Finish"
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/35324391/35324412.png" class="confluence-embedded-image" height="400" /></span>
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-8-6\_11-16-17.png](attachments/35324391/35324400.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-8-6\_11-16-41.png](attachments/35324391/35324401.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-8-6\_11-17-16.png](attachments/35324391/35324402.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-8-6\_11-17-41.png](attachments/35324391/35324403.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-8-6\_11-18-8.png](attachments/35324391/35324404.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-8-6\_11-18-14.png](attachments/35324391/35324405.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-8-6\_11-18-55.png](attachments/35324391/35324406.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-8-6\_11-19-47.png](attachments/35324391/35324407.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-8-6\_11-20-40.png](attachments/35324391/35324408.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-8-6\_11-21-8.png](attachments/35324391/35324409.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-8-6\_11-21-25.png](attachments/35324391/35324410.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-8-6\_11-27-58.png](attachments/35324391/35324411.png)
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<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-8-6\_11-29-23.png](attachments/35324391/35324412.png)
(image/png)
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+++
title = "UNL STAT850, Fall 2018"
description = "UNL STAT850, Fall 2018."
+++
**When: **12:30pm - 1:45pm
**Location:** UNL East Campus, Keim 214
[Slides](attachments/35325069/35325093.pdf)
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[anyconnect-win-4.2.01022-web-deploy-k9.exe](attachments/35325069/35325070.exe)
(application/octet-stream)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[anyconnect-macosx-4.2.00096-web-deploy-k9.dmg](attachments/35325069/35325071.dmg)
(application/x-diskcopy)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat850\_anvil.pptx](attachments/35325069/35325072.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat850\_anvil.pdf](attachments/35325069/35325073.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat850\_anvil.pdf](attachments/35325069/35325093.pdf)
(application/pdf)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[stat850\_anvil.pptx](attachments/35325069/35325094.pptx)
(application/vnd.openxmlformats-officedocument.presentationml.presentation)
content/events/_index.md deleted 100644 → 0
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+++
title = "Events"
description = "Historical listing of various HCC events."
weight = "30"
+++
Historical listing of HCC Events
----------
{{% children %}}
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---
title: "Facilities of the Holland Computing Center"
---
This document details the equipment resident in the Holland Computing Center (HCC) as of November 2018.
HCC has two primary locations directly interconnected by a pair of 10 Gbps fiber optic links (20 Gbps total). The 1800 sq. ft. HCC machine room at the Peter Kiewit Institute (PKI) in Omaha can provide up to 500 kVA in UPS and genset protected power, and 160 ton cooling. A 2200 sq. ft. second machine room in the Schorr Center at the University of Nebraska-Lincoln (UNL) can currently provide up to 100 ton cooling with up to 400 kVA of power. One Brocade MLXe router and two Dell Z9264F-ON core switches in each location provide both high WAN bandwidth and Software Defined Networking (SDN) capability. The Schorr machine room connects to campus and Internet2/ESnet at 100 Gbps while the PKI machine room connects at 10 Gbps. HCC uses multiple data transfer nodes as well as a FIONA (flash IO network appliance) to facilitate end-to-end performance for data intensive workflows.
HCC's resources at UNL include two distinct offerings: Sandhills and Red. Sandhills is a linux cluster dedicated to general campus usage with 5,472 compute cores interconnected by low-latency InfiniBand networking. 175 TB of Lustre storage is complemented by 50 TB of NFS storage and 3 TB of local scratch per node.
The largest machine on the Lincoln campus is Red, with 9,536 job slots interconnected by a mixture of 1, 10, and 40 Gbps ethernet. More importantly, Red serves up over 6.6 PB of storage using the Hadoop Distributed File System (HDFS). Red is integrated with the Open Science Grid (OSG), and serves as a major site for storage and analysis in the international high energy physics project known as CMS (Compact Muon Solenoid).
HCC's resources at PKI (Peter Kiewit Institute) in Omaha include Tusker, Crane, Anvil, Attic, and Common storage. Tusker offers 3,712 cores interconnected with Mellanox QDR InfiniBand along with 523TB of Lustre storage. Each compute node is a Dell R815 server with at least 256 GB RAM and 4 Opteron 6272 (2.1 GHz) processors. Tusker and Sandhills are currently being retired and will be moved to the Walter Scott Engineering Center located in Lincoln consolidated into one, new Tusker cluster.
Crane debuted at 474 on the Top500 list with an HPL benchmark or 121.8 TeraFLOPS. Intel Xeon chips (8-core, 2.6 GHz) provide the processing with 4 GB RAM available per core and a total of 12,236 cores. The cluster shares 1.5 PetaBytes of Lustre storage and contains HCC's GPU resources. We have since expanded the existing cluster: 96 nodes with new Intel Xeon E5-2697 v4 chips and 100GB Intel Omni-Path interconnect were added to Crane. Moreover, Crane has 21 GPU nodes with 57 NVIDIA GPUs in total which enables the most state-of-art research, from drug discovery to deep learning.
Anvil is an OpenStack cloud environment consisting of 1,520 cores and 400TB of CEPH storage all connected by 10 Gbps networking. The Anvil cloud exists to address needs of NU researchers that cannot be served by traditional scheduler-based HPC environments such as GUI applications, Windows based software, test environments, and persistent services. In addition, a project to expand Ceph storage by 1.1 PB is in progress.
Attic and Silo form a near line archive with 1.0 PB of usable storage. Attic is located at PKI in Omaha, while Silo acts as an online backup located in Lincoln. Both Attic and Silo are connected with 10 Gbps network connections.
In addition to the cluster specific Lustre storage, a shared common storage space exists between all HCC resources with 1.9PB capacity.
These resources are detailed further below.
# 1. HCC at UNL Resources
## 1.1 Sandhills
* 56 4-socket Opteron 6376 (16-core, 2.3 GHz) with 192 GB RAM
* 42 4-socket Opteron 6128 (8-core, 2.0 GHz) with 128 GB RAM
* 2 4-socket Opteron 6168 (12-core, 1.9 GHz) with 256 GB RAM
* Intel QDR InfiniBand
* 1 and 10 GbE networking
* 5x Dell N3048 switches
* 50 TB shared storage (NFS) -> /home
* 175TB shared scratch storage (Lustre) -> /work
* 3TB local scratch
# 1.2 Red
* USCMS Tier-2 resource, available opportunistically via the Open Science Grid
* 60 2-socket Xeon E5530 (2.4GHz) (16 slots per node)
* 16 2-socket Xeon E5520 (2.27 GHz) (16 slots per node)
* 36 2-socket Xeon X5650 (2.67GHz) (24 slots per node)
* 16 2-socket Xeon E5-2640 v3 (2.6GHz) (32 slots per node)
* 40 2-socket Xeon E5-2650 v3 (2.3GHz) (40 slots per node)
* 24 4-socket Opteron 6272 (2.1 GHz) (64 slots per node)
* 28 2-socket Xeon E5-2650 v2 (2.6GHz) (32 slots per node)
* 48 2-socket Xeon E5-2660 (2.2GHz) (32 slots per node)
* 24 2-socket Xeon E5-2660 v4 (2.0GHz) (56 slots per node)
* 2 2-socket Xeon E5-1660 v3 (3.0GHz) (16 slots per node)
* 6,600 TB HDFS storage (3,300 TB usable)
* Mix of 1, 10, and 40 GbE networking
* 1x Dell S6000-ON switch
* 2x Dell S4048-ON switch
* 5x Dell S3048-ON switches
* 2x Dell S4810 switches
* 2x Dell N3048 switches
# 1.3 Silo (backup mirror for Attic)
* 1 Mercury RM216 2U Rackmount Server 2 Xeon E5-2630 (12-core, 2.6GHz)
* 10 Mercury RM445J 4U Rackmount JBOD with 45x 4TB NL SAS Hard Disks
# 2. HCC at PKI Resources
## 2.1 Tusker
* 58 PowerEdge R815 systems
* 54x with 256 GB RAM, 2x with 512 GB RAM, 2x with 1024 GB RAM
* 4-socket Opteron 6272 Interlagos (64-core, 2.1GHz)
* Mellanox QDR InfiniBand
* 1 GbE networking
* 3x Dell Powerconnect 6248 switches
* 523TB Lustre storage over InfiniBand
# 2.2 Crane
* 452 Relion 2840e systems from Penguin
* 452x with 64 GB RAM
* 2-socket Intel Xeon E5-2670 (8-core, 2.6GHz)
* Intel QDR InfiniBand
* 96 nodes from multiple vendor
* 59x with 256 GB RAM
* 37x with 512 GB RAM
* 2-socket Intel Xeon E5-2697 v4 (18-core, 2.3GHz)
* Intel Omni-Path
* 1 and 10 GbE networking
* 4x 10 GbE switch
* 14x 1 GbE switches
* 1500 TB Lustre storage over InfiniBand
* 3 Supermicro SYS-6016GT systems
* 48 GB RAM
* 2-socket Intel Xeon E5620 (4-core, 2.4GHz)
* 2 Nvidia M2070 GPUs
* 3 Supermicro SYS-1027GR-TSF systems
* 128 GB RAM
* 2-socket Intel Xeon E5-2630 (6-core, 2.3GHz)
* 3 Nvidia K20M GPUs
* 1 Supermicro SYS-5017GR-TF systems
* 32 GB RAM
* 1-socket Intel Xeon E5-2650 v2 (8-core, 2.6GHz)
* 2 Nvidia K40C GPUs
* 5 Supermicro SYS-2027GR-TRF systems
* 64 GB RAM
* 2-socket Intel Xeon E5-2650 v2 (8-core, 2.6GHz)
* 4 Nvidia K40M GPUs
* 2 Supermicro SYS-5018GR-T systems
* 64 GB RAM
* 2-socket Intel Xeon E5-2620 v4 (8-core, 2.1GHz)
* 2 Nvidia P100 GPUs
# 2.3 Attic
* 1 Mercury RM216 2U Rackmount Server 2-socket Xeon E5-2630 (6-core, 2.6GHz)
* 10 Mercury RM445J 4U Rackmount JBOD with 45x 4TB NL SAS Hard Disks
# 2.4 Anvil
* 76 PowerEdge R630 systems
* 76x with 256 GB RAM
* 2-socket Intel Xeon E5-2650 v3 (10-core, 2.3GHz)
* Dual 10Gb Ethernet
* 12 PowerEdge R730xd systems
* 12x with 128 GB RAM
* 2-socket Intel Xeon E5-2630L v3 (8-core, 1.8GHz)
* 12x 4TB NL SAS Hard Disks and 2x200 GB SSD
* Dual 10 Gb Ethernet
* 2 PowerEdge R320 systems
* 2x with 48 GB RAM
* 1-socket Intel E5-2403 v3 (4-core, 1.8GHz)
* Quad 10Gb Ethernet
* 10 GbE networking
* 6x Dell S4048-ON switches
# 2.5 Shared Common Storage
* Storage service providing 1.9PB usable capacity
* 6 SuperMicro 1028U-TNRTP+ systems
* 2-socket Intel Xeon E5-2637 v4 (4-core, 3.5GHz)
* 256 GB RAM
* 120x 4TB SAS Hard Disks
* 2 SuperMicro 1028U-TNRTP+ systems
* 2-socket Intel Xeon E5-2637 v4 (4-core, 3.5GHz)
* 128 GB RAM
* 6x 200 GB SSD
* Intel Omni-Path
* 10 GbE networking
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+++
title = "FAQ"
description = "HCC Frequently Asked Questions"
weight = "20"
+++
- [I have an account, now what?](#i-have-an-account-now-what)
- [How do I change my password?](#how-do-i-change-my-password)
- [I forgot my password, how can I retrieve it?](#i-forgot-my-password-how-can-i-retrieve-it)
- [I just deleted some files and didn't mean to! Can I get them back?](#i-just-deleted-some-files-and-didn-t-mean-to-can-i-get-them-back)
- [How do I (re)activate Duo?](#how-do-i-re-activate-duo)
- [How many nodes/memory/time should I request?](#how-many-nodes-memory-time-should-i-request)
- [I am trying to run a job but nothing happens?](#i-am-trying-to-run-a-job-but-nothing-happens)
- [I keep getting the error "slurmstepd: error: Exceeded step memory limit at some point." What does this mean and how do I fix it?](#i-keep-getting-the-error-slurmstepd-error-exceeded-step-memory-limit-at-some-point-what-does-this-mean-and-how-do-i-fix-it)
- [I want to talk to a human about my problem. Can I do that?](#i-want-to-talk-to-a-human-about-my-problem-can-i-do-that)
---
#### I have an account, now what?
Congrats on getting an HCC account! Now you need to connect to a Holland
cluster. To do this, we use an SSH connection. SSH stands for Secure
Shell, and it allows you to securely connect to a remote computer and
operate it just like you would a personal machine.
Depending on your operating system, you may need to install software to
make this connection. Check out on Quick Start Guides for information on
how to install the necessary software for your operating system
- [For Mac/Linux Users]({{< relref "for_maclinux_users" >}})
- [For Windows Users]({{< relref "for_windows_users" >}})
#### How do I change my password?
#### I forgot my password, how can I retrieve it?
Information on how to change or retrieve your password can be found on
the documentation page: [How to change your
password]({{< relref "how_to_change_your_password" >}})
All passwords must be at least 8 characters in length and must contain
at least one capital letter and one numeric digit. Passwords also cannot
contain any dictionary words. If you need help picking a good password,
consider using a (secure!) password generator such as
[this one provided by Random.org](https://www.random.org/passwords)
To preserve the security of your account, we recommend changing the
default password you were given as soon as possible.
#### I just deleted some files and didn't mean to! Can I get them back?
That depends. Where were the files you deleted?
**If the files were in your $HOME directory (/home/group/user/):** It's
possible.
$HOME directories are backed up daily and we can restore your files as
they were at the time of our last backup. Please note that any changes
made to the files between when the backup was made and when you deleted
them will not be preserved. To have these files restored, please contact
HCC Support at
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
as soon as possible.
**If the files were in your $WORK directory (/work/group/user/):** No.
Unfortunately, the $WORK directories are created as a short term place
to hold job files. This storage was designed to be quickly and easily
accessed by our worker nodes and as such is not conducive to backups.
Any irreplaceable files should be backed up in a secondary location,
such as Attic, the cloud, or on your personal machine. For more
information on how to prevent file loss, check out [Preventing File
Loss]({{< relref "preventing_file_loss" >}}).
#### How do I (re)activate Duo?
**If you have not activated Duo before:**
Please stop by
[our offices](http://hcc.unl.edu/location)
along with a photo ID and we will be happy to activate it for you. If
you are not local to Omaha or Lincoln, contact us at
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
and we will help you activate Duo remotely.
**If you have activated Duo previously but now have a different phone
number:**
Stop by our offices along with a photo ID and we can help you reactivate
Duo and update your account with your new phone number.
**If you have activated Duo previously and have the same phone number:**
Email us at
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
from the email address your account is registered under and we will send
you a new link that you can use to activate Duo.
#### How many nodes/memory/time should I request?
**Short answer:** We don’t know.
**Long answer:** The amount of resources required is highly dependent on
the application you are using, the input file sizes and the parameters
you select. Sometimes it can help to speak with someone else who has
used the software before to see if they can give you an idea of what has
worked for them.
But ultimately, it comes down to trial and error; try different
combinations and see what works and what doesn’t. Good practice is to
check the output and utilization of each job you run. This will help you
determine what parameters you will need in the future.
For more information on how to determine how many resources a completed
job used, check out the documentation on [Monitoring Jobs]({{< relref "monitoring_jobs" >}}).
#### I am trying to run a job but nothing happens?
Where are you trying to run the job from? You can check this by typing
the command \`pwd\` into the terminal.
**If you are running from inside your $HOME directory
(/home/group/user/)**:
Move your files to your $WORK directory (/work/group/user) and resubmit
your job.
The worker nodes on our clusters have read-only access to the files in
$HOME directories. This means that when a job is submitted from $HOME,
the scheduler cannot write the output and error files in the directory
and the job is killed. It appears the job does nothing because no output
is produced.
**If you are running from inside your $WORK directory:**
Contact us at
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
with your login, the name of the cluster you are running on, and the
full path to your submit script and we will be happy to help solve the
issue.
##### I keep getting the error "slurmstepd: error: Exceeded step memory limit at some point." What does this mean and how do I fix it?
This error occurs when the job you are running uses more memory than was
requested in your submit script.
If you specified `--mem` or `--mem-per-cpu` in your submit script, try
increasing this value and resubmitting your job.
If you did not specify `--mem` or `--mem-per-cpu` in your submit script,
chances are the default amount allotted is not sufficient. Add the line
{{< highlight batch >}}
#SBATCH --mem=<memory_amount>
{{< /highlight >}}
to your script with a reasonable amount of memory and try running it again. If you keep
getting this error, continue to increase the requested memory amount and
resubmit the job until it finishes successfully.
For additional details on how to monitor usage on jobs, check out the
documentation on [Monitoring Jobs]({{< relref "monitoring_jobs" >}}).
If you continue to run into issues, please contact us at
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)
for additional assistance.
#### I want to talk to a human about my problem. Can I do that?
Of course! We have an open door policy and invite you to stop by
[either of our offices](http://hcc.unl.edu/location)
anytime Monday through Friday between 9 am and 5 pm. One of the HCC
staff would be happy to help you with whatever problem or question you
have. Alternatively, you can drop one of us a line and we'll arrange a
time to meet: [Contact Us](https://hcc.unl.edu/contact-us).
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title = "Guides"
weight = "20"
+++
In-depth guides to using HCC resources
--------------------------------------
{{% children description="true" %}}
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+++
title = "Available images"
description = "HCC-provided images for Anvil"
+++
HCC provides pre-configured images available to researchers. Below is a
list of available images.
| Image Name | Username to Connect | Access instructions | Description |
| ------------------------ | -------------------- | ------------------------------------ | --------------------------------------------------------------------------------- |
| Cloudera 5.12 GNOME | `cloudera` | [X2Go instructions]({{< relref "connecting_to_linux_instances_using_x2go" >}}) | Cloudera 5.12 QuickStart VM. *Note*: Follow the X2Go instructions, but choose GNOME for the Session type instead of Xfce.|
| CentOS 7.4 | `centos` | `ssh -l centos@<ip address>` | The CentOS Linux distribution is a stable, predictable, manageable and reproducible platform derived from the sources of Red Hat Enterprise Linux (RHEL).|
| CentOS 6.9 | `centos` | `ssh -l centos@<ip address>` | **HCC Standard OS**. The CentOS Linux distribution is a stable, predictable, manageable and reproducible platform derived from the sources of Red Hat Enterprise Linux (RHEL).|
| Fedora 26 Cloud | `fedora` | `ssh -l fedora <ipaddress>` | Fedora is a Linux distribution developed by the community-supported Fedora Project and sponsored by the Red Hat company.|
| Fedora 26 RStudio (Xfce) | `fedora` |[X2Go instructions]({{< relref "connecting_to_linux_instances_using_x2go" >}}) | Fedora 26 with the Xfce Desktop Environment pre-installed.|
| CentOS 7.4 Xfce | `centos` |[X2Go instructions]({{< relref "connecting_to_linux_instances_using_x2go" >}}) | CentOS 7.4 with the Xfce Desktop Environment pre-installed.|
| CentOS 6.9 Xfce | `centos` |[X2Go instructions]({{< relref "connecting_to_linux_instances_using_x2go" >}}) | CentOS 6.9 with the Xfce Desktop Environment pre-installed.|
| Ubuntu 14.04 Xfce | `ubuntu` |[X2Go instructions]({{< relref "connecting_to_linux_instances_using_x2go" >}}) | Ubuntu 14.04 with the Xfce Desktop Environment pre-installed.|
| Ubuntu 16.04 Xfce | `ubuntu` |[X2Go instructions]({{< relref "connecting_to_linux_instances_using_x2go" >}}) | Ubuntu 16.04 with the Xfce Desktop Environment pre-installed.|
| Ubuntu 17.04 Xfce | `ubuntu` |[X2Go instructions]({{< relref "connecting_to_linux_instances_using_x2go" >}}) | Ubuntu 17.04 with the Xfce Desktop Environment pre-installed.|
| Windows 7 | `cloud-user` |[Windows instructions]({{< relref "connecting_to_windows_instances" >}}) | Windows 7 Enterprise edition with remote desktop access.|
| Windows 10 | `cloud-user` |[Windows instructions]({{< relref "connecting_to_windows_instances" >}}) | Windows 10 LTSB edition with remote desktop access.|
| Windows 7 Matlab | `cloud-user` |[Windows instructions]({{< relref "connecting_to_windows_instances" >}}) | Windows 7 Enterprise with Matlab r2013b, r2014b, r2015b, r2016b, r2017a pre-installed.|
| Windows 10 Matlab | `cloud-user` |[Windows instructions]({{< relref "connecting_to_windows_instances" >}}) | Windows 10 LTSB with Matlab r2013b, r2014b, r2015b, r2016b, r2017a pre-installed.|
| Windows 7 SAS | `cloud-user` |[Windows instructions]({{< relref "connecting_to_windows_instances" >}}) | Windows 7 Enterprise with SAS 9.3, 9.4 pre-installed.|
| Windows 10 SAS | `cloud-user` |[Windows instructions]({{< relref "connecting_to_windows_instances" >}}) | Windows 10 LTSB with Matlab r2013b, r2014b, r2015b, r2016b, r2017a pre-installed.|
| Windows 7 Mathematica | `cloud-user` |[Windows instructions]({{< relref "connecting_to_windows_instances" >}}) | Windows 7 Enterprise with Mathematica 10.4 and 11.0 pre-installed.|
| Windows 10 Mathematica | `cloud-user` |[Windows instructions]({{< relref "connecting_to_windows_instances" >}}) | Windows 10 LTSB with Mathematica 10.4 and 11.0 pre-installed.|
| Ubuntu Cloud 14.04 LTS | `ubuntu` | `ssh -l ubuntu <ipaddress>` | Ubuntu Cloud Image from the 14.04 Long Term Support release.|
| Ubuntu Cloud 16.04 LTS | `ubuntu` | `ssh -l ubuntu <ipaddress>` | Ubuntu Cloud Image from the 16.04 Long Term Support release.|
| Ubuntu Cloud 17.04 LTS | `ubuntu` | `ssh -l ubuntu <ipaddress>` | Ubuntu Cloud Image from the 17.04 Long Term Support release.|
Additional images can be produced by HCC staff by request at
{{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu).
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title = "Formatting and mounting a volume in Linux"
description = "How to format and mount volume as a hard drive in Linux."
+++
{{% notice info %}}
This guide assumes you associated your SSH Key Pair with the instance
when it was created, and that you are connected to the [Anvil VPN]({{< relref "connecting_to_the_anvil_vpn" >}}).
{{% /notice %}}
Once you have [created and attached]({{< relref "creating_and_attaching_a_volume" >}})
your volume, it must be formatted and mounted in your Linux instance to be usable. This
procedure is identical to what would be done when attaching a second
hard drive to a physical machine. In this example, a 10GB volume was
created and attached to the instance. Note that the majority of this
guide is for a newly created volume.
{{% notice note %}}
**If you are attaching an existing volume with data already on it,
skip to [creating a directory and mounting the volume](#mounting-the-volume).**
{{% /notice %}}
#### Formatting the volume
Follow the relevant guide
([Windows]({{< relref "connecting_to_linux_instances_from_windows">}})
| [Mac]({{< relref "connecting_to_linux_instances_from_mac" >}})) for your
operating system to connect to your instance. Formatting and mounting
the volume requires root privileges, so first run the
command `sudo su -` to get a root shell.
{{% panel theme="danger" header="**Running commands as root**" %}}**Extreme care should be taken when running commands as `root.`** It is very easy to permanently delete data or cause irreparable damage to your instance.{{% /panel %}}
{{< figure src="/images/13599376.png" width="700" >}}
Next, you will need to determine what device the volume is presented as
within Linux. Typically this will be `/dev/vdb`, but it is necessary to
verify this to avoid mistakes, especially if you have more than one
volume attached to an instance. The command `fdisk -l` will list the
hard drive devices.
{{< figure src="/images/13599470.png" width="700" >}}
Here there is a completely empty (no partitions) disk device matching
the 10GB size of the volume, so `/dev/vdb` is the correct device.
The `fdisk` utility will first be used to create a single partition.
Run the command `fdisk /dev/vdb` to start the program using the volume
disk device.
{{< figure src="/images/13599477.png" width="700" >}}
Press `n` for new partition and hit enter.
{{< figure src="/images/13599479.png" width="700" >}}
Press `p` for primary partition and hit enter.
{{< figure src="/images/13599482.png" width="700" >}}
Enter `1` for the partition number.
{{< figure src="/images/13599528.png" width="700" >}}
At the next two prompts hit enter to accept the defaults and return to
the main command prompt.
{{< figure src="/images/13599530.png" width="700" >}}
Finally, press `w` followed by return to save the changes and
exit `fdisk`.
{{< figure src="/images/13599533.png" width="700" >}}
Now that a partition has been created, it can be formatted. Here, the
EXT4 filesystem will be used. This is the default filesystem used by
many Linux distributions including CentOS and Ubuntu, and is a good
general choice. An alternate filesystem may be used by running a
different format command. To format the partition using EXT4, run the
command `mkfs.ext4 /dev/vdb1`. You will see a progress message and then
be returned to the shell prompt.
{{< figure src="/images/13599540.png" width="700" >}}
#### Mounting the volume
{{% notice note %}}
If you are attaching a pre-existing volume, start here.
{{% /notice %}}
Finally, the formatted partition must be mounted as a directory to be
used. By convention this is done under `/mnt`, but you may choose to
mount it elsewhere depending on the usage. Here, a directory
called `myvolume` will be created and the volume mounted there. Run the
following commands to make the directory and mount the volume:
{{< highlight bash >}}
mkdir /mnt/myvolume
mnt /dev/vdb1 /mnt/myvolume
{{< /highlight >}}
{{< figure src="/images/13599546.png" width="700" >}}
Running the command `df -h` should then show the new mounted empty
volume.
{{< figure src="/images/13599549.png" width="700" >}}
The volume can now be used.