Using the Presentation LCD TV with Presentation Computer

1. Turn on the presentation computer on and log in
2. Turn on the TV by pressing the power button on the right edge of the TV
3. Set the TV input to (HDMI 1) by using the input button on the right edge of the TV or the remote control provided
4. The sign located on the computer cart, “Class in session” should be put onto the outside of the door of the classroom.
5. When finished, log out and turn off the TV
6.  Remove the sign from the outside of the classroom door and put it back onto the computer cart.

Using the Presentation LCD TV with Laptop

1.  Connect the VGA cable and the audio cable to the laptop
2.  Turn on the TV by pressing the power button on the right edge of the TV
3.  Set the TV input to (Computer) by using the input button on the right edge of the TV or the remote control provided
4.  The sign located on the computer cart, “Class in session,” should be put onto the outside of the door of the classroom.
5.  When finished, turn off the TV and unplug the VGA and Audio cable and place it on top of the computer cart.
6.  Remove the sign from the outside of the classroom door and put it back onto the computer cart.

Tudy Seistrup maintains a calendar of current reservations for Cordley 3003.  You can view current reservations through the online calendar.   To make a reservation, please e-mail Tudy.  

The computers in Cordley 3003 all have the following software installed:

• 123D Design R2.0

• 7-Zip 16.02

• Adobe Acrobat XI Pro

• ArcGIS 10.3 for Desktop

• AutoCAD 2016

• BioEdit

• Blender

• DIVA-GIS 7.5

• DNA Master

• DnaSP v5

• Epi Info 7

• FileZilla Client 3.21.0

• Foldit

• Gaussian 09W Revision D.01

• GaussView 5.0.9

• Geneious 9.0.5

• Google Chrome

• Google Earth

• GPL Ghostscript

• GSview 5.0

• HyPhy 2.2.4

• IBM SPSS Statistics 23

• ImageMagick 6.7.5-7 Q16

• Inkscape 0.91

• IrfanView

• JMP Pro 11

• Maple 2015

• MATLAB R2014b

• MEGA6 .06

• Microsoft Office Professional Plus 2013

• Microsoft Silverlight

• Mozilla Firefox 45.3.0 ESR

• Mozilla Thunderbird 45.3.0

• Notepad++

• Planform

• PuTTY release 0.67

• PyMOL

• Python 2.7.12

• QuickTime 7

• R for Windows 3.2.0

• RStudio

• SAS 9.4

• Scratch

• SketchUp 2016

• SplitsTree4 4.13.1

• SSH Secure Shell

• STAMP v2.1.3

• Structure

• TIBCO Spotfire S+ 8.2

• TreeView X 0.5.0

• Wing IDE 101 5.1.7-1

• Wolfram Mathematica 9

• XTools Pro 12.0

Before you start: If you are connecting from off campus, you will need to connect through the VPN

Step 1: Open the start menu, scroll down to the bottom and inside (click to open) Windows System choose File Explorer:

Step 2: Select "This PC", then "Computer", then "Map network drive":

Step 3: In the dialog box, select T for the drive letter, paste: "\\cos-dfs.science.oregonstate.edu\dfs-users" as the folder, and check Connect using different credentials (you can tick Reconnect at sign-in if you want) in the folder like so:

Step 4: Click finish.

Step 5: In the dialog box that pops up enter your ONID username (without the greater than or less than signs) and password. You may also check Remember my credentials, especially reccomended if reconnect at sign in is turned on:

Step 6: You are now connected! The folder should pop up like so:

Note: While you may be able to see all of the folders, you will only have access to certain folders.  If you don't have access to a folder that you should, ask your department to submit a ticket to us.

Before you start: If you are connecting from off campus, you will need to connect through the VPN

Step 1: Click finder icon in the dock

Step 2: Click "Connect to server..." from the "Go" menu at the top of the screen

Step 3: Enter "smb://cos-dfs.science.oregonstate.edu/dfs-users" as the Server Address

Step 4: Click Connect

Step 5: In the dialog box that pops up enter your ONID username (without the greater than or less than signs) and password. You may also check Remember this password:

Step 6: Click Connect again.

Step 7: You are now connected! The folder should pop up like this:

 Note: While you may be able to see all of the folders, you will only have access to certain folders.  If you don't have access to a folder that you should, ask your department to submit a ticket to us.

Before you start: If you are connecting from off campus, you will need to connect through the VPN

Step 1: Open the start menu, scroll down to the bottom and inside (click to open) Windows System choose File Explorer:

Step 2: Select "This PC", then "Computer", then "Map network drive":

Step 3: In the dialog box, select Z for the drive letter, paste: "\\pfs.cosine.oregonstate.edu\homes" as the folder, and check Connect using different credentials (you can tick Reconnect at sign-in if you want) in the folder like so

Step 4: Click Finish.

Step 5: In the dialog box that pops up enter your ONID username (without the greater than or less than signs) and password. You may also check Remember my credentials, especially reccomended if reconnect at sign in is turned on:

Step 6: You are now connected! The folder should pop up like so:

Note: These files aren't shared with anyone and you only have 10GB.  If you need more space, let us know.

Before you start: If you are connecting from off campus, you will need to connect through the VPN

Step 1: Click finder icon in the dock

Step 2: Click "Connect to server..." from the "Go" menu at the top of the screen

Step 3: Enter "smb://pfs.cosine.oregonstate.edu/homes" as the Server Address

Step 4: Click connect

Step 5: In the dialog box that pops up enter your ONID username (without the greater than or less than signs) and password. You may also check Remember this password:

Step 7: You are now connected! The folder should pop up like this:

 Note: These files aren't shared with anyone and you only have 10GB.  If you need more space, let us know.

1. From your desktop, navigate through the start menu to open “Secure File Transfer Client”

1.jpg

2. Once the program opens, click on file in the menu bar and then click on “quick connect”.

2.jpg

3. Enter host as shell.cosine.oregonstate.edu along with your username.

3.jpg

4. Click yes to saving the new host key.

4.jpg

5. Enter your password

5.jpg

6. At this point, your files should be shown in the right window. The files on the computer you're currently using are in the left window. Any files you put in your public_html directory will be served to the webserver and be accessible at http://science.oregonstate.edu/~USERNAME/

6.jpg

Please see: https://oregonstate.teamdynamix.com/TDClient/1935/Portal/KB/ArticleDet?ID=101648

1. Open Devices and Printers:
   
2. Find the old printer and right click it, and click remove:
   
3. In the dialog, click yes:
   
4. Contine with the instructions for adding a printer on Windows: Adding a Printer on Windows

There are two ways to add a printer on Windows.  Whenever possible, please add printers using our print server.  If a printer is not on the print server, then add the printer by hostname.  Please do not add printers by IP address as they are subject to change wihtout warning.

1. Press the windows key and search for “Devices and Printers”
   
2. Find the Ricoh Copier in the list of printers and right click it:
   
3. Select the detailed settings tab:
   
4. Click Job Setup:
   
5. Enter your printing code (Same as your copier code) into the user code box:
   
6. Click Ok.  Then send a test print to the printer.  If it doesn’t print then give us a call.

1. Open the settings app, then click "Network & Internet":
   
2. Next open the Wi-Fi Settings:
   
3. Press and hold on OSU_Secure, then tap forget:
   
4. After it forgets the network, reconnect to OSU_Secure:
   
5. Enter the following settings, then click connect:
   EAP Method: PEAP
   Phase 2 authentication: MSCHAPV2
   CA certificate: Use system certificates
   Domain: oregonstate.edu
   Identity: Your ONID Username
   Anoymous Identity: Leave Blank
   Password: Your ONID Password
   

1. Open settings and switch to the WiFi section:
   
2. Select OSU_Secure and forget it.  Click forget at the prompt:
   
   
3. Click OSU_Secure to reconnect to it:
   
4. Enter your new ONID credentials and click join:
   
5. If you're prompted to trust the Oregon State wifi certificate, then click trust:
   

1. Open Network Preferences:
   

1. In the WiFi section, go to Advanced:
   
2. Select OSU_Secure and then hit the minus sign to remove it:
   
   Then click OK to save and close.
3. Back in the WiFi menu, connect to OSU_Secure:
   
4. Enter your ONID Username and Password when you're prompted:
   
5. Click Join.  If you are still unable to connect to the wireless then give us a call or stop by our office.

Most of the time, Windows will smoothly prompt you for your new credentials when you attempt to connect to OSU_Secure from on campus. If for some reason this doesn't happen, then there's a few steps to force Windows to perform a fresh connection:

1. First, Open the networking menu by clicking the wifi icon in the lower right hand corner:
   
2. Open Network Settings:
   
3. Select "Manage Wi-fi Settings":
   
4. Select OSU Secure and click forget:
   
   
5. Reopen the wifi menu:
   
   Select OSU_Secure:
   
   Then click connect:
   
6. You will most likely get a warning asking if you expect to find OSU_Secure in your area.  If you're on campus, then click connect:
   
7. Then enter your ONID credentials and click ok:
   

If all goes well, on Ubuntu you should simply be prompted for your new password with a dialog like this:

If you don't get one of those or you need to start connecting from scratch do this:

1. Open the wifi settings and click the gear icon next to "eduroam":
   
2. Click forget network:
   
3. Click on the eduroam SSID to open the connection dialog:
   
4. Enter the following connection information:
   Wi-Fi Security: Leave as "WPA & WPA2 Enterprise"
   Authentication: Change to "Protected EAP (PEAP)"
   Anonymous identity: Leave this field blank
   Domain: Enter "oregonstate.edu"
   CA certificate: Leave as "(None)"
   CA certificate password: Leave this field blank
   No CA certificate is required: Check this checkbox
   PEAP version: Leave as "Automatic"
   Inner authentication: Leave as "MSCHAPv2"
   Username: Enter your ONID username followed by "@oregonstate.edu" here
   Password: Enter your ONID password here
   
5. Lastly, click connect.  If you are unable to connect then please give us a call or stop by our helpdesk.  If the password or username is incorrect then you should see the username and password dialog from the first screenshot.

If you are currently a Cosine customer you already have access to our cluster. To access the server, SSH into submit.hpc.cosine.oregonstate.edu using your cosine/science username and password.

 If connecting from Off campus, please refer to I can't connect to the cluster from off campus.

Join the Cosine HPC mailing list for notifications about software updates and maintenance. Visit http://lists.science.oregonstate.edu/mailman/listinfo/cosine-hpc

User home directories on the cluster are provided by a dedicated server with 26TB of disk space. For performance reasons, this space is not backed up.

1. Create a directory in your home for the z drive mount point
2. sshfs shell.cosine.oregonstate.edu: <your mount point>
3. Please copy files from zdrive to cluster home before execution

Example

mkdir ~/zdrive

sshfs shell.cosine.oregonstate.edu: ~/zdrive

The cluster uses the environments module to provide an easy way to switch between software revisions. These modules configure environmental variables such as PATH for each piece of software. 

To get a list of available modules to load, execute:

module avail

To get a list of what modules are currently loaded, execute:

module list 

To load the Matlab 2014b module, execute

module load matlab/R2014b 

To display modules set to load during login:

module initlist

To set a module to automatically load during login:

module initadd matlab/R2014b

To remove a module from loading during login:

module initrm matlab/R2014b

Jobs should be submitted using a special sh script which tells the scheduler how to handle the job.

An example with common options can be seen below: 

 submit.sh

#!/bin/sh

# Give the job a name
#$ -N example_job

# set the shell
#$ -S /bin/sh

# set working directory on all host to
# directory where the job was started
#$ -cwd

# send all process STDOUT (fd 2) to this file
#$ -o job_output.txt

# send all process STDERR (fd 3) to this file
#$ -e job_output.err

# email information
#$ -m e
 
# Just change the email address. You will be emailed when the job has finished.
#$ -M myusername@science.oregonstate.edu

# generic parallel environment with 2 cores requested
#$ -pe orte 2

# Load a module, if needed
module load sprng/5

# Commands
./my_program

If necessary, make my_program executable

chmod +x my_program

Submit the job

qsub submit.sh

qstat is used to check the status of jobs on the cluster. By itself it will show a brief overview

qstat

To show the status of all nodes and queued processes, execute

qstat -u '*'

The state codes that dare displayed in the last column of qstat are as follows:

If a job is currently running:

qstat -j <jobId>

After a job has been executed:

qacct -j <jobId>

The command:

qdel <job id of process>

Is used to remove a job from the queue. If the job is in a dr state the -f flag must be used to force the job to stop. The job ID is supplied as an argument to qdel.

Nodes in the all.q have mixed memory sizes. To ensure that a job lands on a node with enough memory, the mem_free resource can be used.

For example. to execute on nodes with at least 60GB of RAM available:

qsub -l mem_free=60G submit.sh

Create a Submission File

Place the following code into a .sh file (i.e. submit.sh):

#!/bin/sh
# Give the job a name
$ -N JOB_NAME
# set the shell
$ -S /bin/sh
# set working directory on all host to directory where the job was started
$ -cwd
# send all ERROR messages to this file
$ -e errors.txt
# Change the email address to YOUR email, and you will be emailed when the job has finished.
$ -m e
$ -M email_address@oregonstate.edu
# Ask for 1 core, as R can only use 1 core for processing
$ -pe orte 1
# Load the R Module
module load R
# Commands to run job
R inputFile.r > outputFile.out

Submit the Job to the Cluster

Type the following commands, replacing "submit.sh" with the name of your .sh file:

qsub submit.sh

R Examples

can be found on the cluster inside the /cm/shared/examples/R folder

You can download and install any R Libraries which you might need to run on the cluster into your home directory and simply use them from there. These instructions give you the steps to accomplish this.

 ssh to the cluster

1.  Load R module
   

   module load R

2. Launch R
   

   R
   

3. Type the command to install the desired package
   

   install.packages("package_name") 

If this is the first time you have run the install.packages() command, you will be asked if you want to create a personal library.  Answer 'y'.

 Follow the prompts to pick a mirror, etc.

R will download and install the library into the newly created personal library (in your home directory).

To use this library, use the library command (like any other installed library):

library(library_name)

Create a Submission File

Place the following code into a .sh file (i.e. submit.sh):

#!/bin/sh
# Give the job a name
$ -N JOB_NAME
# set the shell
$ -S /bin/sh
# set working directory on all host to directory where the job was started
$ -cwd
# send all ERROR messages to this file
$ -e errors.txt
# Change the email address to YOUR email, and you will be emailed when the job has finished.
$ -m e
$ -M email_address@oregonstate.edu
# Use 4 cores for processing
$ -pe orte 4
# Load the Gaussian Module
module load gaussian/g16
# Commands to run job
g16 < inputFile.com > outputFile.out

Submit the Job to the Cluster

Type the following commands, replacing "submit.sh" with the name of your .sh file:

qsub submit.sh

Gaussian Examples

Examples for Gaussian can be found on the cluster inside the /cm/shared/examples/g09 folder

The node cosine004 has two NVIDIA Tesla K40m GPU Computing Accelerators. Each card provides 2880 cores and 12GB of RAM. Each card has been set to exclusive mode, meaning only one process can access the gpu at a time.

The device names of these cards are /dev/nvidia0 and /dev/nvidia1. 

A dedicated queue, gpu.q has been created for these resources. 

For interactive use, use qlogin and specify the queue:

 qlogin -q gpu.q

For batch use, use qsub in the standard fashion, but specify the queue:

 qsub -q gpu.q submit.sh

CUDA 7.5 tools are installed, but must be loaded with the modules system, typically you will include the toolkit and the gdk

module load cuda75/toolkit/7.5.18
module load cuda75/gdk/352.79

NOTE: when comping software with nvcc, there is a module conflict with gcc/5.1.0, remove this module to use the system gcc 4.8.5 

module unload gcc/5.1.0

CUDA Example

A simple CUDA example can be found in the directory: /cm/shared/examples/cuda

The Cosine cluster is protected by a firewall which blocks access from off campus. Users need to establish a VPN connection or first ssh into a campus server before connecting to the submit node.

We recommend connecting using the VPN. However, if you cannot use the OSU VPN but are able to remote into a campus PC, you can SSH from the campus PC to access the cluster.
If you prefer to work locally when submitting jobs and accessing the cluster, you can also set up SSH multi-hopping.

If you run into an issue where:

[root@cluster-submit ~]# qmon
Warning: Cannot convert string "-adobe-helvetica-medium-r-*--14-*-*-*-p-*-*-*" to type FontStruct
Warning: Cannot convert string "-adobe-helvetica-bold-r-*--14-*-*-*-p-*-*-*" to type FontStruct
Warning: Cannot convert string "-adobe-helvetica-medium-r-*--20-*-*-*-p-*-*-*" to type FontStruct
Warning: Cannot convert string "-adobe-helvetica-medium-r-*--12-*-*-*-p-*-*-*" to type FontStruct
Warning: Cannot convert string "-adobe-helvetica-medium-r-*--24-*-*-*-p-*-*-*" to type FontStruct
Warning: Cannot convert string "-adobe-courier-medium-r-*--14-*-*-*-m-*-*-*" to type FontStruct
Warning: Cannot convert string "-adobe-courier-bold-r-*--14-*-*-*-m-*-*-*" to type FontStruct
Warning: Cannot convert string "-adobe-courier-medium-r-*--12-*-*-*-m-*-*-*" to type FontStruct
Warning: Cannot convert string "-adobe-helvetica-medium-r-*--10-*-*-*-p-*-*-*" to type FontStruct
X Error of failed request: BadName (named color or font does not exist)
Major opcode of failed request: 45 (X_OpenFont)
Serial number of failed request: 525
Current serial number in output stream: 536

Appears when attempting to run qmon, then you will need to install a package on your machine.

For machines running Ubuntu:

apt-get install xfstt
service xfstt start
apt-get install xfonts-75dpi
xset +fp /usr/share/fonts/X11/75dpi
xset fp rehash

- Where cores are allocated to more than one queue the investor queues take precedence during scheduling.

GPU Resources

cosine004: gpu.q 2 NVIDIA Tesla K40m GPUs 2880 cores and 12GB of RAM.

cosine004: hendrix-gpu.q 2 NVIDIA Tesla K40c GPUs 2880 cores and 12GB of RAM.

cosine001: sun-gpu.q 1 NVIDIA Tesla K40m GPUs 2880 cores and 12GB of RAM.

If this error occurs, you need to load an a newer version of gcc that has an updated libstdc++so.6 library. In your submit script, add the following lines to switch from gcc 5.1.0 to 9.2.0

module unload gcc/5.1.0
module load gcc/9.2.0

We have moved our web structure to a more robust environment. In doing so all authenticated users on Drupal will be on the Secure port which requires a Certificate for each site. If the site is of the form oregonstate.edu we can get a Cert for free and you will not get a warning.

If it is not of that form there are two options, first is we create one but this will give the warning. Secondly is to purchase one for that site name.

With the new system we cache web pages, this way the site is more responsive.  The downside is some times the cache doesn't know that the pages changed and it will still send out the old page.  To request the new page hold down the Shift key and click refresh (pres F5 on the keboard) and this will get the most up-to-date page.

Clear Internet Cache

In Google Chrome + New Edge:

Step 1: While in Chrome or the new Edge, press Ctrl + Shift + Del, this should bring up the 'Clear browsing data' prompt.

Step 2: Select the time range for which you'd like to delete data for (1), and then select 'Clear data / Clear now' (2):

In Firefox:

Step 1: While in Firefox, open the hamburger menu on the top right and select 'options':

Step 2: Select 'Privacy & Security':

Step 3: Scroll down until you find the 'History' section. Select "Clear History...':

 Step 4: Select the time range for which you'd like to delete data for (1), and then select 'OK' (2):