Commit d64366a5 authored by Adam Caprez's avatar Adam Caprez
Browse files

Update quickstarts

parent 1f6e2722
+++
title = "HCC Documentation"
description = "HCC Documentation Home"
weight = "1"
+++
HCC Documentation
============================
......@@ -13,7 +19,7 @@ existing resource, acquiring 'priority access'. Finally, several
machines are available via Condor for opportunistic use. This will allow
users almost immediate access, but the job is subject to preemption.
#### <a href="http://hcc.unl.edu/new-user-request" class="external-link">New Users Sign Up</a>
#### [New Users Sign Up](http://hcc.unl.edu/new-user-request)
#### [Quick Start Guides](/quickstarts)
......@@ -31,12 +37,6 @@ campus users. It has 4 CPU/ 64 cores and 256GB RAM per nodes. Two nodes
have 512GB RAM for very large memory jobs. So for jobs requiring more
than 16 cores per node or large memory, Tusker would be a better option.
**Sandhills**: Sandhills is a condominium-style cluster, and the
majority is owned by various research groups on campus. Jobs from
resource owners have first priority in their owned partitions. Users
that do not own resources (Guests) can do opportunistic computation, but
we would recommend using Crane or Tusker.
User Login
----------
......@@ -79,27 +79,19 @@ $ cd $WORK
Resources
---------
- <span style="color: rgb(0,0,0);">Crane</span> - HCC's newest
machine, Crane has 7232 Intel Xeon cores in 452 nodes with 64GB RAM
per node.
- ##### Crane - HCC's newest machine, Crane has 7232 Intel Xeon cores in 452 nodes with 64GB RAM per node.
- Tusker - consists of 106 AMD Interlagos-based nodes (6784 cores)
interconnected with Mellanox QDR Infiniband.
- ##### Tusker - consists of 106 AMD Interlagos-based nodes (6784 cores) interconnected with Mellanox QDR Infiniband.
- Sandhills - has 1440 AMD cores housed in 42 nodes with 128GB per
node and 2 nodes with 256GB per node.
- ##### [Red](http://hcc.unl.edu/red/index.php) - This cluster is the resource for UNL's US CMS Tier-2 site.
- <a href="http://hcc.unl.edu/red/index.php" class="external-link">Red </a>-
This cluster is the resource for UNL's US CMS Tier-2 site.
- [CMS](http://www.uscms.org/)
- [Open Science Grid](http://www.opensciencegrid.org)
- [MyOSG](https://myosg.grid.iu.edu/)
- <a href="http://www.uscms.org/" class="external-link">CMS</a>
- <a href="http://www.opensciencegrid.org/" class="external-link">Open Science Grid</a>
- <a href="https://myosg.grid.iu.edu/" class="external-link">MyOSG</a>
- ##### Anvil - HCC's cloud computing cluster based on Openstack
- [Glidein](The-Open-Science-Grid_11635314.html) - A gateway to
running jobs on the OSG, a collection of computing resources across
the US.
- Anvil - HCC's cloud computing cluster based on Openstack
- ##### [Glidein](The-Open-Science-Grid_11635314.html) - A gateway to running jobs on the OSG, a collection of computing resources across the US.
Resource Capabilities
---------------------
......
1. [HCC-DOCS](index.html)
2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
3. [HCC Documentation](HCC-Documentation_332651.html)
4. [Quick Start Guides](Quick-Start-Guides_1245279.html)
+++
title = "Basic Linux commands"
description = "Simple commands you'll want to know"
weight = "32"
+++
<span id="title-text"> HCC-DOCS : Bash Commands </span>
=======================================================
Basic commands
--------------
Created by <span class="author"> Carrie Brown</span>, last modified on
Oct 26, 2017
[Video Tutorial](#BashCommands-video)
###### [[Jump to the Video Tutorial]](#tutorial-video)
Holland clusters all run on the Linux operating system, similarly to how
your personal computer might run Windows or Mac OS. However, unlike
......@@ -26,12 +24,12 @@ versatility and performance.**
Below, we have compiled a list of common commands and usage examples.
For a more information, check out one of these references:
- <a href="https://eharstad.github.io/shell-novice/" class="external-link">Software Carpentry's &quot;Introduction to the Bash Shell&quot; Lesson</a> -
- [Software Carpentrys "Introduction to the Bash Shell" Lesson](https://eharstad.github.io/shell-novice) -
a great walkthrough of the basics of Bash designed for novice users
- <a href="http://www.comptechdoc.org/os/linux/usersguide/" class="external-link">Linux Users Guide</a> -
- [Linux Users Guide](http://www.comptechdoc.org/os/linux/usersguide) -
detailed information about the Linux command line and how to utilize
it
- <a href="https://www.cheatography.com/davechild/cheat-sheets/linux-command-line/" class="external-link">Linux Command Line Cheat Sheet</a> -
- [Linux Command Line Cheat Sheet](https://www.cheatography.com/davechild/cheat-sheets/linux-command-line) -
a quick reference for Linux commands. Offers a PDF version that you
can print out.
......@@ -210,8 +208,7 @@ cd $HOME (or $WORK)
</tbody>
</table>
<span id="BashCommands-video" class="confluence-anchor-link"></span>
Document generated by Confluence on Oct 24, 2018 14:47
Tutorial Video
--------------
[Atlassian](http://www.atlassian.com/)
{{< youtube B0VdKiHNjU4 >}}
+++
title = "For Mac/Linux Users"
description = "Quickstart Guide for Mac/Linux Users"
weight = "30"
weight = "22"
+++
##### Use of Duo two-factor authentication is **required** to access HCC resources.
......@@ -16,7 +16,7 @@ with the HCC supercomputers.
If you are running Windows, please use the quickstart [For Windows
Users]({{< relref "for_windows_users" >}}).
Accessing to HCC Supercomputers
Access to HCC Supercomputers
-------------------------------
For Mac/Linux users, use the system program Terminal to assess to the
......
+++
title = "Fortran/C on HCC"
description = "How to compile and run Fortran/C program on HCC machines"
weight = "50"
+++
This quick start demonstrates how to implement a Fortran/C program on
HCC supercomputers. The sample codes and submit scripts can be
downloaded from [serial_dir.zip](/attachments/serial_dir.zip).
#### Login to a HCC Cluster (Tusker or Crane) 
Log in to a HCC cluster through PuTTY ([For Windows Users]({{< relref "/quickstarts/for_windows_users">}})) or Terminal ([For Mac/Linux
Users]({{< relref "/quickstarts/for_maclinux_users">}})) and make a subdirectory called `serial_dir` under the `$WORK` directory. 
{{< highlight bash >}}
$ cd $WORK
$ mkdir serial_dir
{{< /highlight >}}
In the subdirectory `serial_dir`, save all the relevant Fortran/C codes. Here we include two demo
programs, `demo_f_serial.f90` and `demo_c_serial.c`, that compute the sum from 1 to 20. 
{{%expand "demo_f_serial.f90" %}}
{{< highlight bash >}}
Program demo_f_serial
implicit none
integer, parameter :: N = 20
real*8 w
integer i
common/sol/ x
real*8 x
real*8, dimension(N) :: y
do i = 1,N
w = i*1d0
call proc(w)
y(i) = x
write(6,*) 'i,x = ', i, y(i)
enddo
write(6,*) 'sum(y) =',sum(y)
Stop
End Program
Subroutine proc(w)
real*8, intent(in) :: w
common/sol/ x
real*8 x
x = w
Return
End Subroutine
{{< /highlight >}}
{{% /expand %}}
{{%expand "demo_c_serial.c" %}}
{{< highlight c >}}
//demo_c_serial
#include <stdio.h>
double proc(double w){
double x;
x = w;
return x;
}
int main(int argc, char* argv[]){
int N=20;
double w;
int i;
double x;
double y[N];
double sum;
for (i = 1; i <= N; i++){
w = i*1e0;
x = proc(w);
y[i-1] = x;
printf("i,x= %d %lf\n", i, y[i-1]) ;
}
sum = 0e0;
for (i = 1; i<= N; i++){
sum = sum + y[i-1];
}
printf("sum(y)= %lf\n", sum);  
 
return 0;
}
{{< /highlight >}}
{{% /expand %}}
---
#### Compiling the Code
The compiling of a Fortran/C++ code to executable is usually done behind
the scene in a Graphical User Interface (GUI) environment, such as
Microsoft Visual Studio. In a HCC cluster, the compiling is done
explicitly by first loading a choice compiler and then executing the
corresponding compiling command. Here we will use the GNU Complier
Collection, `gcc`, for demonstration. Other available compilers such as
`intel` or `pgi` can be looked up using the command
line `module avail`. Before compiling the code, make sure there is no
dependency on any numerical library in the code. If invoking a numerical
library is necessary, contact a HCC specialist
({{< icon name="envelope" >}}[hcc-support@unl.edu] (mailto:hcc-support@unl.edu)) to
discuss implementation options.
{{< highlight bash >}}
$ module load compiler/gcc/8.2
$ gfortran demo_f_serial.f90 -o demo_f_serial.x
$ gcc demo_c_serial.c -o demo_c_serial.x
{{< /highlight >}}
The above commends load the `gcc` complier and use the compiling
commands `gfortran` or `gcc` to compile the codes to`.x` files
(executables). 
#### Creating a Submit Script
Create a submit script to request one core (default) and 1-min run time
on the supercomputer. The name of the main program enters at the last
line.
{{% panel header="`submit_f.serial`"%}}
{{< highlight bash >}}
#!/bin/sh
#SBATCH --mem-per-cpu=1024
#SBATCH --time=00:01:00
#SBATCH --job-name=Fortran
#SBATCH --error=Fortran.%J.err
#SBATCH --output=Fortran.%J.out
module load compiler/gcc/4.9
./demo_f_serial.x
{{< /highlight >}}
{{% /panel %}}
{{% panel header="`submit_c.serial`"%}}
{{< highlight bash >}}
#!/bin/sh
#SBATCH --mem-per-cpu=1024
#SBATCH --time=00:01:00
#SBATCH --job-name=C
#SBATCH --error=C.%J.err
#SBATCH --output=C.%J.out
module load compiler/gcc/4.9
./demo_c_serial.x
{{< /highlight >}}
{{% /panel %}}
#### Submit the Job
The job can be submitted through the command `sbatch`. The job status
can be monitored by entering `squeue` with the `-u` option.
{{< highlight bash >}}
$ sbatch submit_f.serial
$ sbatch submit_c.serial
$ squeue -u <username>
{{< /highlight >}}
Replace `<username>` with your HCC username.
#### Sample Output
The sum from 1 to 20 is computed and printed to the `.out` file (see
below). 
{{%expand "Fortran.out" %}}
{{< highlight batchfile>}}
i,x = 1 1.0000000000000000
i,x = 2 2.0000000000000000
i,x = 3 3.0000000000000000
i,x = 4 4.0000000000000000
i,x = 5 5.0000000000000000
i,x = 6 6.0000000000000000
i,x = 7 7.0000000000000000
i,x = 8 8.0000000000000000
i,x = 9 9.0000000000000000
i,x = 10 10.000000000000000
i,x = 11 11.000000000000000
i,x = 12 12.000000000000000
i,x = 13 13.000000000000000
i,x = 14 14.000000000000000
i,x = 15 15.000000000000000
i,x = 16 16.000000000000000
i,x = 17 17.000000000000000
i,x = 18 18.000000000000000
i,x = 19 19.000000000000000
i,x = 20 20.000000000000000
sum(y) = 210.00000000000000
{{< /highlight >}}
{{% /expand %}}
{{%expand "C.out" %}}
{{< highlight batchfile>}}
i,x= 1 1.000000
i,x= 2 2.000000
i,x= 3 3.000000
i,x= 4 4.000000
i,x= 5 5.000000
i,x= 6 6.000000
i,x= 7 7.000000
i,x= 8 8.000000
i,x= 9 9.000000
i,x= 10 10.000000
i,x= 11 11.000000
i,x= 12 12.000000
i,x= 13 13.000000
i,x= 14 14.000000
i,x= 15 15.000000
i,x= 16 16.000000
i,x= 17 17.000000
i,x= 18 18.000000
i,x= 19 19.000000
i,x= 20 20.000000
sum(y)= 210.000000
{{< /highlight >}}
{{% /expand %}}
This diff is collapsed.
1. [HCC-DOCS](index.html)
2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
3. [HCC Documentation](HCC-Documentation_332651.html)
4. [Quick Start Guides](Quick-Start-Guides_1245279.html)
<span id="title-text"> HCC-DOCS : How to change your password </span>
=====================================================================
Created by <span class="author"> Adam Caprez</span>, last modified by
<span class="editor"> Carrie Brown</span> on Oct 24, 2018
<span
class="aui-icon aui-icon-small aui-iconfont-info confluence-information-macro-icon"></span>
Your account must be active with Duo authentication setup in order for
the following instructions to work.
- [HCC password
requirements](#Howtochangeyourpassword-HCCpasswordrequirements)
- [Changing a known HCC
password](#Howtochangeyourpassword-ChangingaknownHCCpassword)
- [Change your password via the command
line](#Howtochangeyourpassword-Changeyourpasswordviathecommandline)
- [Change your password using the myHCC User
Portal](#Howtochangeyourpassword-ChangeyourpasswordusingthemyHCCUserPortal)
- [Resetting a forgotten HCC
password](#Howtochangeyourpassword-ResettingaforgottenHCCpassword)
- [Tutorial Video](#Howtochangeyourpassword-TutorialVideo)
+++
title = "Changing Your Password"
description = "How to change your HCC password"
weight = "30"
+++
How to change your password
---------------------------
{{% notice info%}}
**Your account must be active with Duo authentication setup in order for
the following instructions to work.**
{{% /notice %}}
- [HCC password requirements](#hcc-password-requirements)
- [Changing a known HCC password](#changing-a-known-hcc-password)
- [Change your password via the command line](#change-your-password-via-the-command-line)
- [Change your password using the myHCC User Portal](#change-your-password-using-the-myhcc-user-portal)
- [Resetting a forgotten HCC password](#resetting-a-forgotten-hcc-password)
- [Tutorial Video](#tutorial-video)
Every HCC user has a password that is same on all HCC machines
(Sandhills, Tusker, Crane). This password needs to satisfy the HCC
password requirements.<span style="line-height: 1.42857;"> </span>
(Tusker, Crane, Anvil). This password needs to satisfy the HCC
password requirements.
### **HCC password requirements**
### HCC password requirements
All HCC passwords must meet the following requirements when they are
created or changed:
......@@ -39,36 +31,33 @@ created or changed:
- at least 8 characters long
- at least 1 capital letter
- at least 1 number
- **can not**<span style="line-height: 1.42857;"> contain an existing
dictionary word</span>
- **can not**<span style="line-height: 1.42857;"> contain information
from user's account details (</span>*username*<span
style="line-height: 1.42857;">, </span>*email*<span
style="line-height: 1.42857;">)</span>
- **can not** contain an existing dictionary word
- **can not** contain information from user's account details (*username*,
*email*)
Using special characters in the password is not required, but it is
allowed. Also, the system keeps a history of the user's previous two
passwords, and their reuse is not allowed.
### **Changing a known HCC password**
### Changing a known HCC password
If you know your current HCC password, you can use one of two approaches
to change it:
#### **Change your password via the command line **
#### Change your password via the command line
To change a current or temporary password, the user needs to login to
any HCC cluster (Crane or Tusker) and use the ***passwd*** command: 
**Change HCC password**
``` syntaxhighlighter-pre
{{< highlight bash >}}
$ passwd
Changing password for user <username>.
Current Password:
New password:
New password:
```
{{< /highlight >}}
With this command, the user is first prompted for his/her old password.
If the "*Current Password*" is correct, then the user is asked twice for
......@@ -77,30 +66,24 @@ needs to fulfill the HCC password requirements.
#### Change your password using the myHCC User Portal
1. Login to the
<a href="https://hcc.unl.edu/myhcc/" class="external-link">myHCC User Portal</a>
1. Login to the [myHCC User Portal](https://hcc.unl.edu/myhcc)
with your HCC credentials.
2. Click **Update Account** in the top menu
<span
class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/13041705/35326617.png" class="confluence-embedded-image image-center" height="150" /></span>
{{< figure src="/images/35326617.png" height="150" >}}
3. Enter your new password in the **Password** and **Retype Password**
boxes and click **Modify** to save
<span
class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/13041705/35326618.png" class="confluence-embedded-image image-center" height="150" /></span>
{{< figure src="/images/35326618.png" height="150" >}}
### **Resetting a forgotten HCC password**
### Resetting a forgotten HCC password
To reset your password, navigate to the
<a href="https://hcc.unl.edu/myhcc/" class="external-link">myHCC User Portal</a>
in your browser
To reset your password, navigate to the [myHCC User Portal](https://hcc.unl.edu/myhcc/) in your browser
Click the link to reset your forgotten password
<span
class="confluence-embedded-file-wrapper image-center-wrapper confluence-embedded-manual-size"><img src="assets/images/13041705/35326619.png" class="confluence-embedded-image image-center" height="400" /></span>
{{< figure src="/images/35326619.png" height="400" >}}
Fill in the requested information (your HCC user name and email
associated with your account) and click **Reset Password**. A reset link
......@@ -109,24 +92,4 @@ onscreen prompts to set a new password.
### Tutorial Video
<span id="Howtochangeyourpassword-Video"
class="confluence-anchor-link"></span>
Attachments:
------------
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-10-18\_13-25-46.png](attachments/13041705/35326617.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-10-18\_13-27-34.png](attachments/13041705/35326618.png)
(image/png)
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[image2018-10-18\_13-31-22.png](attachments/13041705/35326619.png)
(image/png)
Document generated by Confluence on Oct 24, 2018 14:47
[Atlassian](http://www.atlassian.com/)
{{< youtube eaTW6FDhpsM >}}
1. [HCC-DOCS](index.html)
2. [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
3. [HCC Documentation](HCC-Documentation_332651.html)
4. [Quick Start Guides](Quick-Start-Guides_1245279.html)
+++
title = "How to setup X11 forwarding"
description = "Use X11 forwarding to view GUI programs remotely"
weight = "35"
+++
<span id="title-text"> HCC-DOCS : How to setup X11 forwarding </span>
=====================================================================
Created by <span class="author"> Jingchao Zhang</span>, last modified by
<span class="editor"> Adam Caprez</span> on Jun 20, 2018
If you are connecting to HCC clusters via a PC running Windows, please take the following steps to setup X11 forwarding.
------------------------------------------------------------------------------------------------------------------------
##### If you are connecting to HCC clusters via a PC running Windows, please take the following steps to setup X11 forwarding.
1. Download Xming to your local PC and install. Download
link: <a href="http://sourceforge.net/project/downloading.php?group_id=156984&amp;filename=Xming-6-9-0-31-setup.exe" class="external-link">http://sourceforge.net/project/downloading.php?group_id=156984&amp;filename=Xming-6-9-0-31-setup.exe</a>
2. Download PuTTY to your local PC and install.  Download
link: <a href="http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe" class="external-link">http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe</a>
link: https://downloads.sourceforge.net/project/xming/Xming/6.9.0.31/Xming-6-9-0-31-setup.exe
2. Download PuTTY to your local PC and install.  Download link: http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe
3. Open Xming and keep it running in the background.
4. Configure PuTTY as below:
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/11637375/11637370.png" class="confluence-embedded-image" height="400" /></span><span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/11637375/11637371.jpg" class="confluence-embedded-image" height="400" /></span>
5. To test your X11 setup, after login, type command "xeyes" and press
{{< figure src="/images/11637370.png" height="400" >}}
{{< figure src="/images/11637371.jpg" height="400" >}}
5. To test your X11 setup, after login, type command `xeyes` and press
enter.
<span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/11637375/11637372.png" class="confluence-embedded-image" height="400" /></span>
{{< figure src="/images/11637372.png" height="400" >}}
6. Close the xeyes application by "Ctrl + c" from the terminal or click
the close button on the up-right corner of the graphical window.
 
If you are connecting to HCC clusters via a Macintosh, please take the following steps to setup X11 forwarding.
---------------------------------------------------------------------------------------------------------------
##### If you are connecting to HCC clusters via a Macintosh, please take the following steps to setup X11 forwarding.
- <span style="color: rgb(51,51,51);font-size: 14.0px;line-height: 1.42857;">Check the OS version on your Mac, if it's below 10.8., you can simply type "ssh -Y username@hostname" in your terminal to login.</span>
------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
<span
style="color: rgb(51,51,51);font-size: 14.0px;line-height: 1.42857;">
</span>
- Check the OS version on your Mac, if it's below 10.8., you can simply type `ssh -Y username@hostname` in your terminal to login.
- If your OS version is newer than 10.8, please do the following:
1. Download and install XQuartz.
Download link: <a href="http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.7.dmg" class="external-link">http://xquartz.macosforge.org/downloads/SL/XQuartz-2.7.7.dmg</a>
2. Type "ssh -Y username@hostname" in your terminal to login.
3. To test your X11 setup, after login, type command "xeyes" and press
1. Download and install XQuartz.
Download link: https://dl.bintray.com/xquartz/downloads/XQuartz-2.7.11.dmg
2. Type `ssh -Y username@hostname` in your terminal to login.
3. To test your X11 setup, after login, type command "xeyes" and press
enter.
 <span
class="confluence-embedded-file-wrapper confluence-embedded-manual-size"><img src="assets/images/11637375/11637374.png" class="confluence-embedded-image" height="400" /></span>
4. Close the xeyes application by "control + c" from the terminal or
{{< figure src="/images/11637374.png" height="400" >}}
4. Close the xeyes application by "Control + c" from the terminal or
click the close button on the up-left corner of the graphical
window.
If you are connecting to HCC clusters via a Linux laptop, please take the following steps to setup X11 forwarding.
------------------------------------------------------------------------------------------------------------------
##### If you are connecting to HCC clusters via a Linux laptop, please take the following steps to setup X11 forwarding.
1. Open the remote client terminal.
2. Type "ssh -Y username@hostname" in your terminal to login.
2. Type `ssh -Y username@hostname`" in your terminal to login.
3. To test your X11 setup, after login, type command "xeyes" and press
enter.
4. Close the xeyes application by "Ctrl + c" from the terminal or click
......@@ -66,37 +50,10 @@ If you are connecting to HCC clusters via a Linux laptop, please take the follo
 
Related articles
----------------
<a href="http://www.straightrunning.com/XmingNotes/" class="external-link">X11 on Windows</a>
<a href="https://en.wikipedia.org/wiki/XQuartz" class="external-link">X11 on Mac</a>