OREGON STATE UNIVERSITY
Open search box
Science accounts provide you with an e-mail account and a Windows Active Directory account. These accounts are for the faculty, staff and graduate students of the College of Science. Guest and undergraduate accounts may be requested, but a sponsor and an expiration date are required.
To request a Science account, fill out the New Accounts form. New accounts are created with your ONID username. If you do not have an ONID username/account, you can request one online here: http://www.onid.orst.edu/docs/gettingstarted/signup.shtml
In general, we create two accounts for each user: an Unix account and a windows domain account. Each type of account can have an email mailbox added. The default is to create a Unix IMAP mailbox unless Exchange is specifically requested.
UNIX Account:
- Personal Home Directory (Z:\ Drive)
- SSH, SFTP Access
- Personal Web Site (must create public_html folder)
- IMAP mailbox
-- Email Address: username@science.oregonstate.edu
-- Email Alias: First.Last@science.oregonstate.edu
Windows Account:
- SCIENCE Domain Login
- Access to Departmental Storage Share (T:\Microbiology)
- Optional Exchange mailbox
-- Email Address: First.Last@oregonstate.edu
* If Exchange email is requested, we typically do not create an IMAP email mailbox. In such
cases, we create a forward for username@science.oregonstate.edu to the Exchange email
address (First.Last@oregonstate.edu).
Global Address List (Outlook Address Book):
- Exchange mailbox users
- Staff
- Faculty
* Exchange users automatically get added to the Global Address List (this can be hidden upon
request). Additionally, for non-Exchange users we publish to the GAL the Unix email address
for staff and faculty. Since mid-2009, the GAL publishing process automatically adds an
email alias First.Last@oregonstate.edu. We can retroactively add an email alias of
First.Last@oregonstate.edu for staff and faculty that do not have one.
Exchange Fees and Quota:
- Standard Mailbox
-- $2/monthly - 1000 MB
-- $2/monthly per each additional 500 MB (allocation increases must be requested)
- Limited Use Mailbox
-- Free - 100 MB
Account Request:
- http://cosine.oregonstate.edu/files/cosine/pdfs/accountrequest.pdf
Password Changes:
- https://secure.science.oregonstate.edu
* The password change tool sets the password on both an user's Unix and windows accounts.
Passwords must have a minimum of 8 characters and must include at least 1 of each of the following:
Password should never include the user or login name (or variation of)
"But I can't remember a non-sense password," you say. Use a song or phrase that you can easily remember, for example "Mary had a little lamb, whose fleece was white as snow". Using the first letter of each word, and selectively replacing some letters with similarly shaped numbers, you could have a secure and memorable password like : Mhall,wfwwa5.
Do not use that example, since it is listed here and publicly available.
If you have forgotten your account password, it must be reset by the Cosine Helpdesk. Due to security/privacy concerns, users must come to the Cosine Helpdesk in person with an official photo ID (e.g. OSU ID card, drivers license, etc.).
Using a web browser that supports secure connections go to: http://secure.science.oregonstate.edu
Log in using your science username and password (you do not need put in science\ before your username)
Click on "Change Password"
Enter in your current password and your new password twice. Click Change Now.
Please read the guidelines for choosing a good password here.
You have changed your Science account password.
When you leave OSU, unless Cosine is notified otherwise by your department, the account you have will remain active for six months. After six months you account and data will be deleted.
Like any shared community resource, the OSU network requires development, enforcement of policy, and standards to assure efficient operation and remediation of issues. Cosine staff use the administrator account to respond to a user's requests, to assure compliance with Network Security Standards, or to investigate and, if appropriate, deal with the anomalous behavior of a machine. Administrator access is not used casually and certainly not for any purpose to invade personal or professional privacy.
If you have questions or concerns regarding this policy, please contact the Cosine Director.
Using the Presentation LCD TV with Presentation Computer
Using the Presentation LCD TV with Laptop
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
The policies that appear on this page are the product of coordinated work by the College of Science Information Network (COSINe) team, the COSINe Advisory Committee for the college, as well as existing University wide computing policies. Computing resources are a critical tool that all of us depend on in the College of Science. Your understanding and cooperation with regard to these policies, as well as your constructive input, is necessary for maintaining efficient and reliable network resources.
Any questions or suggestions you have regarding these policies should be directed to the Director of COSINe or to your department's COSINe Advisory Committee member.
Core Services
Core Services Backup
Online Storage
Standard Backup Schedule
Wired Network Connectivity Standards
Printer Support
Wireless Network Support
PC Hardware Support
Used Equipment Support
Disposal of IT Equipment
IP Address Management
Acceptable Use Policy
Rogue Network Devices
Offsite and Personally Owned PC Support
Departing Employee Procedure
PC Local Administrator Rights
Supported Operating Systems
Application/Software Support
Teaching Lab Support
COSINe Infrastructure Maintenance Schedule
Management of Licensed Software
Guest Accounts
COSINe Advisory Group
Core IT Services are the default services provided by COSINe to faculty, staff and grad students in the College of Science and external customers. Core services include:
Data included in the Standard Backup Schedule include:
All departments fully supported by COSINe are allocated 10 GB of online server storage space per supported user account. The count of the number of user accounts is calculated during the fall term. The server space is backed up according to the standard COSINe backup schedule.
The intended use of this server space is as a repository for user data files, not as space to save full desktop/notebook backups, or large quantities of research data.
Storage capacity beyond the 3 GB per user limit is described here: Expanded Online Storage
Users are also given personal storage space in their home directory.
* Users also have access to 1TB of temporary storage on T:\Scratch (also accessible via /mnt/scratch on the linux command line). This space will be monitored and anything older than 30 days will be removed.
Core IT services data, managed servers and other managed network hosts (see Network Host Backup below) are backed up according to the following schedule on a monthly cycle:
| Monthly | Full | All user files are backed up |
| Weekly | Differential | All user files changed since the last full backup are saved |
| Daily | Incremental | All user files changed since the last backup are saved |
Effectively, this means that user data can be restored to the state it was in at the end-of-day, for any of the previous 30 days.
Computers connected to the wired network must meet the following minimum standards:
*Exceptions may be granted only by the COSINe Director in instances where there are sound technical reasons that justify a static system; e.g. instrumentation software requirements preclude operating system updates
The preferred method of wireless access is through the OSU_Secure wireless network, which is delivered by OSU-IS to many areas on campus. There are situations or conditions in which OSU_Secure is not suitable. In such cases, COSINe will install and manage wireless routers providing the following are met:
Because of the diverse array of printer hardware and associated repair skills, COSINe provides only limited support for printers. Printer services are limited to:
Diagnosis of problems and recommending actions that might resolve hardware issues can be provided at users' request. But requesting service--either from the Campus repair service, or from the printer hardware vendor--is the responsibility of the department to which the printer belongs
Modern PCs, even those from established manufacturers, are typically a hodgepodge of parts from various sources. Not surprisingly, there are occasions when the quality assurance processes of major vendors fail to find an incompatibility or outright failure prior to shipping. In these cases, where a user has purchased a machine or upgrade from a recommended vendor, COSINe will work to resolve hardware issue(s) that arise through direct troubleshooting, or by working with the vendor.
More challenging are the cases where a PC has been specified and ordered piecemeal by a user in an effort to either save money or to obtain some unique set of features. While COSINe is happy to order the parts and provide up to 3 hours troubleshooting hardware issues for such machines, beyond that time limit users must provide an index against which time can be billed at the current technical services rate. Users are responsible for assembly and configuration of a piecemeal machine, and are ultimately responsible for resolution of hardware issues.
Users should be aware that in today's market, with the exception of high-end or uniquely specialized PCs, little can be gained by building a machine from "scratch." In fact, when hardware specification, assembly and configuration are factored in, the cost of a piecemeal machine will far exceed a preassembled machine from a major vendor. Piecemeal machines also come with no warranty for the assembled unit.
All used equipment must be evaluated and approved by COSINe staff as to suitability for its intended use prior to installation. Such equipment must comply with the Network Connectivity Standards.
The COSINe Helpdesk is happy to facilitate the disposal of IT equipment to OSU surplus, providing:
To avoid the disposal fee for CRT monitors (currently $8 ea) users may take the monitors to the recycling center on Walnut Blvd. There is a bin clearly marked for IT equipment where monitors, and other such equipment, may be deposited at no charge.
College of Science IP address space is managed by COSINe in cooperation with OSU Network Engineering. OSU has strict policies and procedures regarding assignment of IP addresses. Users may not independently assign OSU IP addresses. Violators of this policy will have their network port and account permanently disabled.
COSINe follows the OSU Network Engineering Acceptable Use Policy. Please consult this link if you have questions.
http://fa.oregonstate.edu/gen-manual
Rogue devices will be denied access to the network as they are discovered. A Rogue network device is defined as a device on the Campus network which meets either of the following criteria:
Note: mitigation of rogue network devices will be pursued at the finest level of granularity possible. There are cases where multiple machines may be denied network access so that a single device can be taken offline; e.g. a user-installed router masking multiple machines may be taken offline if one of the machines it masks has been compromised or is generating anomalous traffic. This will result in all machines behind the device being denied network access until the problem can be addressed.
Users who purposely implement rogue devices will have their user accounts and network access revoked.
COSINe must be notified of a users impending departure by the respective department(s) prior to the departure date.
In the event the departing employee's personal computer is configured as part of the science domain, it is critical--and the employee's responsibility--to bring the machine to the COSINe Helpdesk so that it can be removed from the domain prior to departure.
Unless notified to the contrary by the respective department, accounts of users leaving the College of Science will be held open for a period of 6 months following the user's official departure date. This provides departed users with access to their Email account--or to forward Email delivered to their science account--and access to files stored on the COS file server. Beyond this period, unless special arrangements have been made with approval from the department chair to hold the account open for a period of up to a year, the science.oregonstate.edu account will be closed and all Email and stored files purged.
Emeritus faculty who are no longer actively participating in research or teaching activities, may, with departmental approval, retain their email address, but only as a forwarding address to another, external email account for as long as they wish. This will allow them to continue to receive email sent to their science address.
Users are provided local administrator rights to their COSINe supported PC. This allows users to install software and generally manage their own machine.
Operating systems supported by COSINe include those supported by Microsoft, Apple, Redhat (CentOS) or Ubuntu with regularly released security patches and updates.
Users are responsible for learning and understanding the operation and features of the applications they use. COSINe does not provide support for applications (e.g. MS Word or other MS Office products, Photoshop, web applications, etc.) beyond installation for any software other than Operating System Support as outlined above.
Installation and configuration of software on teaching lab PCs is performed between August 1 and September 15 of each year.
COSINe Helpdesk will email a request for specifications to Lab Managers in early summer, and are encouraged to submit their final specification early as scheduling of lab PC builds is on a first come, first served basis.
Maintenance on COSINe managed infrastructure is scheduled for Friday evenings between 7 PM and 12 AM. Notification of a scheduled maintenance period will be Emailed to the affected population no less than 24 hours in advance, and will be announced on the COSINe general announcement page.
COSINe strictly follows software license agreements. License agreements typically restrict on which machines respective software can be installed, and how copies of the software are managed. Because of software license restrictions, note that:
Note: OSUWare, a collection of free and site licensed software for use by OSU employees and students, is described here: http://oregonstate.edu/helpdocs/software/recommended-software/osuware
To accommodate the basic connectivity needs of visitors to COS a generic departmental "guest" account can be setup which can be used to log on to a PC. Following are the attributes of these accounts:
The mission of the COSINe Advisory Group is to act as the interface between COSINe supported units and COSINe management to assure ongoing, 2-way communication regarding IT directions and strategies.
Oregonstate provides users with unlimited storage on Box, but it isn't suitable for research documents. Box is also a good way of transfering files between colleagues who are off campus as long as the data isn't confidential. For how to setup box and what it's best uses are, check this: box.oregonstate.edu
Step 0: If you are connecting from off campus, you will need to connect through the VPN
Step 1: Open the start menu. Then right click on Computer and select map network drive.
Step 2: In the dialog box, select T for the drive letter, tick Connect using different credentials (you can tick Reconnect at logon if you want) and paste: "\\cos-dfs.science.oregonstate.edu\dfs-users" in the folder like so:
Step 2.5: Click finish.
Step 3: In the dialog box that pops up enter your ONID username and password (leave out the angle brackets):
Step 3.75: It should open up the folder 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.
Step 0: If you are connecting from off campus, you will need to connect through the VPN
Step 1: Click finder icon in the dock
Step 1.5: Click "Connect to server..." from the "Go" menu at the top of the screen
Step 2: Enter "smb://cos-dfs.science.oregonstate.edu/dfs-users" as the Server Address
Step 2.95: Click connect
Step 3: Enter your ONID credentials
Step 3.5: Click connect again.
Step 4: It should look something 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.
Step 0: If you are connecting from off campus, you will need to connect through the VPN
Step 1: Open the start menu. Then right click on Computer and select map network drive.
Step 2: In the dialog box, select Z for the drive letter, tick Connect using different credentials (you can tick Reconnect at logon if you want) and paste: "\\pfs.cosine.oregonstate.edu\homes" in the folder like so:
Step 2.5: Click finish.
Step 3: In the dialog box that pops up enter your ONID username and password:
Step 3.75: It should open up the folder like this:
Note: These files aren't shared with anyone and you only have 10GB. If you need more space, let us know.
Step 0: If you are connecting from off campus, you will need to connect through the VPN
Step 1: Click finder icon in the dock
Step 1.5: Click "Connect to server..." from the "Go" menu at the top of the screen
Step 2: Enter "smb://pfs.cosine.oregonstate.edu/homes" as the Server Address
Step 2.95: Click connect
Step 3: Enter your ONID credentials
Step 4: It should look 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”
2. Once the program opens, click on file in the menu bar and then click on “quick connect”.
3. Enter host as shell.cosine.oregonstate.edu along with your username.
4. Click yes to saving the new host key.
5. Enter your password
6. At this point your files should be shown in the right window. The files in your public_html directory will be related to the files served be the webserver at http://science.oregonstate.edu/~USERNAME/
The science mail servers can be connected to using the following settings:
Follow directions below to set up your exchange account on your iPhone, iPad, or iPod.
NOTE: If you do not know the pertinent information above, please contact your Department Computer Administrator (DCA)
To search for people, click on the Addresses button at the top of your Outlook Express window. *Make sure you have the proper address book selected when searching for contacts. The default address book can be changed, while inside the address book window, by navigating to Tools menu and selecting Options... and changing the dropdown menu beneath "Show this address list first".
To search for people, click on the Addresses Book button at the top-right area of your Outlook Express window. *Make sure you have the proper address book selected when searching for contacts. The default address book can be changed, while inside the address book window, by navigating to the Tools menu and selecting Options... Next, select the Custom radio button and choose any address book. Then you can change it's priority by clicking one of the arrows on the right.
To search for an address, click on the Tools menu and choose Address Book.
Select OSU Online Directory from the list of address books on the left. In the top right search box, enter a name or email address and press enter.
Searches work best when you use only a person's last name, or use the format "lastname, firstname".
To search for an address, click on the Window menu and choose Address Book.
Select OSU Online Directory from the list of address books on the left. In the top right search box, enter a name or email address and press enter.
Searches work best when you use only a person's last name, or use the format "lastname, firstname".
Step 1: Go to exmail.oregonstate.edu and login
Step 2: In the upper right hand corner, click "Options" and then select "See All Options..."
Step 3: In the left hand menu, select "Groups"
You're ready to continue.
Step 0: Go to the groups menu in OWA
Step 1:
Oregon State requires that ONID passwords be changed annually for most users. Once you change your password, there's quite a few places that you'll need to enter your new credentials:
1) For laptops and phones, update your wifi password so that you can connect to OSU_Secure: https://cosine.oregonstate.edu/reconfiguring-wi-fi-after-onid-password-change
2) Update all your email clients with your new password:https://cosine.oregonstate.edu/reconfiguring-email-after-onid-password-change
3) For laptops which you login using your ONID account, plug them into OSU's wired network and login so that they pull your credentials from OSU servers and can re-cache them
As Needed:
4) Login to the VPN
5) Remap your T and Z drives on personally owned computers using your new credentials: http://cosine.oregonstate.edu/faqs/data-storage-access
6) Lastly, any webservices that you've been logging into with your ONID account will need your new credentials. You will be reprompted when you connect to them: exmail.oregonstate.edu, webmail.cosine.oregonstate.edu, Microsoft Federation (for Office365 and a few other things), Banner, Canvas, Box, etc.
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.
Intel or AMD Core 2 Duo processor
2 GB RAM
160GB hard drive
CDRW/DVD combo drive
Intel or AMD Core 2 Duo processor
2 GB RAM (1 DIMM)
80GB hard drive
CDRW/DVD combo drive
802.11b/g wireless
Microsoft Windows 10 Enterprise
-- Windows Operating System
Microsoft Office 2016
-- Word, Excel, Outlook, Access, PowerPoint, OneNote, Publisher, Skype for Business
System Center Endpoint Protection
-- Anti-Virus Software
Google Chrome
-- Web Browser
Mozilla Thunderbird
-- Email Client
Adobe Acrobat 2017
-- Read and edit PDF files
PuTTY SSH
-- Secure Shell Client
FileZilla
-- Transfer files via FTP
7-Zip
-- Archive Extraction and Creation Utility
Microsoft Office 2016
-- Word, Excel, PowerPoint, Outlook, OneNote
Adobe Acrobat 2017
-- Read and edit PDF files
** Additionally, we can install other licensed software if presented with the media and license. Also if you wish to purchase a license for new software, we can purchase it for you at an educational discount, information regarding different software available can be found here
Software not included in the standard build (see Software Installed on a new computer) requires that a license be purchased prior to installation. Most of the often-requested software can be purchased from the university here, however, physical media is usually not included with purchase of the license.
Software is typically installed at the Helpdesk Staff or from the TSS software server.
The university gets discounts on many software packages. Before ordering from the vendor, please check the current discounted price list.
OSU maintains a variety of software licenses which are administered by either the Software License Coordinator (for the software listed below), or by Technology Support Services.
Legal use of all software by OSU departments, faculty, staff and students is essential, so please make sure you are familiar with the license restrictions for any of the software below that is installed on your computer(s).
The majority of the software can be installed via the web, by logging into our server over the campus network, or by checking out a CD/DVD. Due to licensing restrictions, you will be required to fill out the order form for each package to obtain access to download and install the software. Detailed information on each software package and online request forms are available by clicking on the links below.
PLEASE NOTE: Some software vendors listed below do not fully technically support Windows 7. You may be able to install and run the software on Windows 7, but you may not be able to get technical support until they officially support Windows 7. Please consult the vendor web sites for more information on supported platforms. Each software information page will be noted once we confirm they support Windows 7.
For the most current Microsoft Office Home Use Program eligibility requirements, ordering process, and pricing, refer to theTSS Software Licensing Site.
For a list of software that is available on the Virtual Server (Umbrella), please refer to the Virtual Computer Lab Software List.
PLEASE NOTE: Once you leave the university, you must remove all site-licensed software from your personal computers. Any valid licenses on your work computers may be transferred to another employee.
Questions? Email Angela O'Neal, the Software License Coordinator, or call 541-737-3848.
// TODO: Simple thing
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:
There are a few good choices SSH and SFTP programs for Windows.
The recommended OSU VPN software can be found on the web at: https://sds.oregonstate.edu/
The Cosine tool for automatically mapping network drives can be downloaded here.
The Cosine tool for automatically mapping network drives can be downloaded here.
The Ricoh copier drivers can be downloaded here.
Certain Microsoft software is provided at no cost by Microsoft's academic alliance program.
The page to login and access the software can be found here.
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.
Join the Cosine HPC mailing list for notifications about software updates and maintenance. Visit http://frontend.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.
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_programSubmit the job
qsub submit.shqstat is used to check the status of jobs on the cluster. By itself it will show a brief overview
qstatTo 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:
| Category | State | SGE Letter Code |
| Pending | pending | qw |
| pending, user hold | qw | |
| pending, system hold | hqw | |
| pending, user and system hold | hqw | |
| pending, user hold, re-queue | hRwq | |
| pending, system hold, re-queue | hRwq | |
| pending, user and system hold, re-queue | hRwq | |
| Running | running | r |
| transferring | t | |
| running, re-submit | Rr | |
| transferring, re-submit | Rt | |
| Suspended | job suspended | s, ts |
| queue suspended | S, tS | |
| queue suspended by alarm | T, tT | |
| all suspended with re-submit | Rs, Rts, RS, RtS, RT RtT | |
| Error | all pending states with error | Eqw, Ehqw, EhRqw |
| Deleted | all running and suspended states with deletion | dr, dt, dRr, dRt, ds, dS, dT, dRs, dRS, dRT |
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
Place the following code into a .sh file (i.e. submit.sh):
Type the following commands, replacing "submit.sh" with the name of your .sh file:
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
module load R
R
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)
Place the following code into a .sh file (i.e. submit.sh):
Type the following commands, replacing "submit.sh" with the name of your .sh file:
Examples for Gaussian can be found on the cluster inside the /cm/shared/examples/g09 folder
Thanks to the new campus agreement with Mathworks, Matlab Distributed Computing Server is available and installed on the Cosine cluster.
In order to use matlab, the module must be loaded
$ module avail matlab
$ module load matlab/R2014b
Interactive Matlab sessions can be run in text-only mode or using the full Matlab GUI:
matlab command will try to start the Matlab desktop GUI using X-Windows, if X is not available, then a text-only session will be startedmatlab -nodisplay.If you want to run a text-only Matlab session, you should:
ssh ...qlogin -pe orte <numberOfCoresRequested>module load matlabmatlab -nodisplay
There are three main categories of non-interactive Matlab SGE jobs that you can run on the cluster:
Array jobs should be used when the job does not require any synchronisation between tasks. The script will be launched multiple times, with a varying index. The index is accessible via the environment variable SGE_TASK_ID.
Typical uses of array jobs would include:
An example can be found on the cluster in:
/cm/shared/examples/matlab/array
Rather than submitting SGE jobs that execute Matlab scripts on the cluster nodes, distributed jobs launch tasks on cluster nodes from within Matlab. Distributed jobs require the cluster to be configured within Matlab, and submission scripts which define how tasks should be launched on cluster nodes. The submission of the jobs is performed via Matlab GUI or command line interface.
In order to distributed jobs, you should:
In order to configure it, start Matlab GUI and then go Parallel -> Manage Cluster Profiles
New Window will pop up. In the new window, click on Add -> Custom -> Generic
New profile will be created. Re-name it to something sensible (you will be referring to it through the code). Lets call it Cosine.
Next, make sure you have provided the following info in the Properties tab (leaving all of the other options as default:
| Main Properties | |
|---|---|
| Description of this cluster: | Cosine HPC |
| Folder where cluster stores job data: | use default (unless you want to specify alternative location) |
| Number of workers available to the cluster: | 32 |
| Root folder of MATLAB installation for workers: | use default |
| Cluster uses MathWorks hosted licensing: | false |
| Submit Functions | |
| Function called when submitting independent jobs: | @independentSubmitFcn |
| Function called when submitting communicating jobs: | @communicatingSubmitFcn |
| Cluster Environment | |
| Cluster nodes' operating system: | Unix |
| Job storage location is accessible from client and cluster nodes: | yes |
| Workers | |
| Range of number of workers to run the job: | [1 32] |
| Jobs and task functions | |
| Function to query cluster about the job state: | @getJobStateFcn |
| Function to manage cluster when you call delete on a job: | @deleteJobFcn |
Note, that once profile has been loaded, you can override the settings from the submission script
Once the profile has been set up click ok. Next select newly created profile, and validate the configuration.
You can import a profile using either the Cluster Profile Manager or the Matlab parallel.importProfile(filename) command.
parallel.importProfile('/cm/shared/examples/matlab/distributed/Cosine.settings');To import settings from the Cluster Profile Manager, use:
Rather than using a previously defined cluster profile, the cluster details can be configured ad-hoc in a .m script file:
cluster = parallel.cluster.Generic(); cluster.NumWorkers = 32; cluster.JobStorageLocation = '/homes/cosine/helpdesk/matlab/'; cluster.IndependentSubmitFcn = @independentSubmitFcn; cluster.CommunicatingSubmitFcn = @communicatingSubmitFcn; cluster.OperatingSystem = 'unix'; cluster.HasSharedFilesystem = true; cluster.GetJobStateFcn = @getJobStateFcn; cluster.DeleteJobFcn = @deleteJobFcn; cluster.RequiresMathWorksHostedLicensing = false;
To save the cluster definition as a profile for later re-use, use:
cluster.saveAsProfile('Cosine')To load a previously saved cluster definition, use:
cluster = parcluster('Cosine')
If you want to pass additional arguments to the SGE specify the submit function as {@communicatingSubmitFcn, 'list_of_additional_qsub_parameters'}
e.g. to specify that 4GB of memory should be requested, and that emails should be sent to name@domain.name at the beginning and end of the job the submit functions should be specified as:
cluster = parcluster('Cosine'); cluster.CommunicatingSubmitFcn = {@communicatingSubmitFcn, '-l h_vmem=5G -m be -M name@domain.name'}; pp = parpool(cluster); parfor i=1:10 hn = system('hostname'); disp(hn); end ... delete(pp)
Make sure that the options you pass to the qsub command are syntactically correct, otherwise the job will fail (see the qsub man page for the list of available options).
An independent job is defined as follows (from http://www.mathworks.co.uk/help/distcomp/program-independent-jobs.html):
An Independent job is one whose tasks do not directly communicate with each other, that is, the tasks are independent of each other. The tasks do not need to run simultaneously, and a worker might run several tasks of the same job in succession. Typically, all tasks perform the same or similar functions on different data sets in an embarrassingly parallel configuration.
Independent jobs are created using the Matlab createJob() function.
An independent job example:
/cm/shared/examples/matlab/distributed/independent
Note: Matlab will submit the job to SGE without the need to write a submission script:
$ matlab -nodisplay < independent.m
A communicating job is defined as follows (from http://www.mathworks.co.uk/help/distcomp/introduction.html):
Communicating jobs are those in which the workers can communicate with each other during the evaluation of their tasks. A communicating job consists of only a single task that runs simultaneously on several workers, usually with different data. More specifically, the task is duplicated on each worker, so each worker can perform the task on a different set of data, or on a particular segment of a large data set. The workers can communicate with each other as each executes its task. The function that the task runs can take advantage of a worker's awareness of how many workers are running the job, which worker this is among those running the job, and the features that allow workers to communicate with each other.
Communicating jobs are required for:
parfor loops which allow multiple loop iterations to be executed in parallel;spmd blocks which run a single program on multiple data - i.e. the same program runs on all workers with behaviour determined by the varying data on each worker (see here).Communicating jobs are created using the Matlab createCommunicatingJob() function and can have a Type of either pool or spmd:
pool job runs the supplied task on one worker and uses the remaining workers as a pool to execute parfor loops, spmd blocks etc., the total number of workers available for parallel code is therefore one less than the total number of workers;spmd job runs the supplied task on all the workers, with no task fundamentally in control - effectively, an spmd job acts as if the entire task is within an spmd block.Communication beween spmd workers (whether in an spmd job or spmd block) occurs using the lab* functions (see Matlab help). Control of spmd workers is usually exerted by message passing and testing data values (e.g. using the worker with labindex of 1 to control other workers).
An independent job example:
/cm/shared/examples/matlab/distributed/communication
Note: Matlab will submit the job to SGE without the need to write a submission script:
$ matlab -nodisplay < communication.m
The examples in both the communicating and independent jobs sections submit the job then wait (block) until the job is complete, subsequently extracting the results and deleting the job, i.e.
cluster = parcluster('Cosine'); ijob = createJob(cluster); .... submit(ijob); wait(job, 'finished'); %Wait for the job to finish results = getAllOutputArguments(ijob); %retrieve results ... destroy(job); %destroy the job
In some situations, this might not be desired - e.g. where client is not allowed to run for long times on the submit host. In such cases a non-blocking submit script should be used instead. The only difference to the communicating and independent scrips defined earlier is that a non-blocking job doesn't have the wait and destroy calls.
A non-blocking independent submit script:
/cm/shared/examples/matlab/distributed/independent/independent_noblock.m
A non-blocking communicating submit script:
/cm/shared/examples/matlab/distributed/communication/communication_noblock.m
Once the job has been completed, the results can be fetched programmatically:
cluster = parcluster('Cosine'); job = cluster.findJob('ID',1); job_output = fetchOutputs(job);
The ID used in cluster.findJob('ID', ...) above is the internal Matlab job ID as displayed at the end of the example non-blocking submit scripts, not the SGE job ID.
Once you have finished with it you can delete it using
destroy(job);
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
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.
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: 536Appears 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| HARDWARE | QUEUE ASSIGNMENT | ||||||||||
| NODE | CPU | CORES | RAM (GB) | Network | all.q | di.q | finch.q | gpu.q | lazzati.q | schneider.q | test.q |
| cosine001 | E5-2620 v3 @ 2.40GHz | 24 | 64 | 10 Gbps | 12 | 24 | |||||
| cosine002 | E5-2680 v3 @ 2.50GHz | 48 | 256 | 10 Gbps | 48 | ||||||
| cosine003 | E5-2697 v2 @ 2.70GHz | 48 | 256 | 10 Gbps | 48 | ||||||
| cosine004 | E5-2620 v4 @ 2.10GHz | 32 | 64 | 10 Gbps | 28 | 2 | |||||
| cosine005 | E5-2695 v4 @ 2.10GHz | 72 | 256 | 10 Gbps | 72 | ||||||
| cosine006 | E5-2620 v4 @ 2.10GHz | 16 | 64 | 10 Gbps | 16 | ||||||
| cosine007 | E5-2620 v4 @ 2.10GHz | 16 | 64 | 10 Gbps | 16 | ||||||
| cosine008 | E5-2620 v4 @ 2.10GHz | 16 | 64 | 10 Gbps | 16 | ||||||
| di001 | E5-2680 v3 @ 2.50GHz | 48 | 256 | 10 Gbps | 48 | ||||||
| di002 | E5-2680 v3 @ 2.50GHz | 48 | 256 | 10 Gbps | 48 | ||||||
| di003 | E5-2680 v3 @ 2.50GHz | 48 | 256 | 10 Gbps | 48 | ||||||
| finch001 | E5-2630 v2 @ 2.60GHz | 24 | 128 | 10 Gbps | 12 | 24 | |||||
| lazzati001 | E5-2695 v3 @ 2.30GHz | 48 | 128 | FDR | 56 | ||||||
| lazzati002 | E5-2695 v3 @ 2.30GHz | 48 | 128 | FDR | 56 | ||||||
| lazzati003 | E5-2695 v3 @ 2.30GHz | 48 | 128 | FDR | 56 | ||||||
| lazzati004 | E5-2695 v3 @ 2.30GHz | 48 | 128 | FDR | 56 | ||||||
| schneider001 | E5-2620 @ 2.00 GHz | 24 | 128 | 1 Gbps | 24 | 24 | |||||
| schneider002 | E5-2630 v2 @ 2.60 GHz | 24 | 128 | 1 Gbps | 24 | 24 | |||||
| Totals: | 680 | 2752 | 220 | 144 | 24 | 2 | 224 | 48 | 24 | ||
- Where cores are allocated to more than one queue the investor queues take precedence during scheduling.
GPU Resources
Node cosine004 contains 2 NVIDIA Tesla K40m GPU Computing Accelerators. Each card provides 2880 cores and 12GB of RAM.
How do I connect to VPN for off-campus use?
VPN is a program that you can use in order to access the OSU network from home, just as if you were on-campus.
Once you have established a VPN connection by following instructions on this page you can find instructions on connecting to Cosine's Network drives here.
Windows and Mac OS X (Pre 10.6)
-- Note: For best compatibility use Firefox or Internet Explorer to connect to sds.oregonstate.edu
Mac OS X and iOS
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.
If you place files in your Z: drive under the public_html directory, those files will be available on the internet at:
http://science.oregonstate.edu/~USERNAME
Where USERNAME is your science username. Please note the ~ before the USERNAME.
If public_html directory does not exist in your Z: drive: Create a new folder— Right click and go to New , then Folder . Name the new folder public_html . Remember, your webpage must be named index.html for the page to show up automactically.
http://www.webmonkey.com/ is a good resource for how to make webpages.
The Cosine Helpdesk will provide secondary support for maintaining content on departmental web sites. However, this is an "as-time-allows" service, and requesters should have the expectation that requests may take weeks to fulfill, depending on the nature of the request and the current Helpdesk workload. Departments would be best served by having a competent individual in the department trained to maintain web site content, and using Helpdesk for this task only as absolutely necessary.
Requests should be submitted through the Helpdesk ticketing system (send a descriptive Email to helpdesk@science.oregonstate.edu) and Helpdesk staff will work on requests as time permits.
For Windows 7 & 8.1:
Press and hold the Windows key + R
Type "cmd" into the search field and hit enter to open the command prompt.
Within the command prompt. Type "ipconfig /all", then hit Enter.
Look for "Ethernet adapter Local Area Connection." Under that category look for "IPv4 Address." If your "IPv4 Address" starts with "128.193.XXX.XXX" and you are located on campus, then the IP is valid.
If the "IPv4 Address" starts with a "169.XXX.XXX.XXX" that means the computer defaulted to an IP address that is invalid.
If your “IP Address” starts with “169.” this means your computer has defaulted to an invalid IP address.
This prompts your computer to request a new IP from the server
Type “ipconfig /all”, then Enter to see if your IP address has refreshed to a valid campus IP (i.e. starts with “128.193”)
If this does not work, restarting your computer may fix the problem
For Windows 7:
Click the Start icon 
Type "cmd" in the search field, then hit Enter
Critical security patches for the Windows operating system are deployed through a system called Automatic Updates. The updates usually patch a hole in the OS which would otherwise allow a computer to be compromised. These patches are vital for a secure network and environment.
All computers on the SCIENCE domain have the same policy on how they check for updates.
The domain policy for automatic updates works like this:
Every 8 hours the client computer checks our update server for new updates. If there are new updates it will download them and prompt you to install them. This comes in the form of a popup notification like this:
From here you can install the updates manually, and if required, restart the computer.
If you do not install the updates manually, then the computer will install the update at 3:00 am every night and if no one is logged on, it will restart if required.
If the computer is logged on, it will prompt you if you wish to restart. If you choose [NO] it will prompt you again every 30 minutes until the computer is restarted.
If the computer is turned off at 3:00 am and there are updates to install then 5 minutes after the system starts up again the updates will be installed, and you will be prompted to restart the computer.
It is recommended to install updates as soon as possible and to restart the computer if required.
In Windows 7, Click on Start then Right Click on "Computer" and select Properties
In Windows 8, Right Click the Windows button and select System
Go To Tools, then click "Internet Options".
In the General Tab, under Browsing history, click on "Delete".
Select what items you want to clear, and select "Delete".
Go to Tools, and select "Delete Browsing History". 
Click "Delete Files" .
Click Yes. 
Go to Tools, and select "Internet Options". 
Click "Delete Files". 
Check the box next to "Delete all offline content", then click OK. 
Go to Tools, and select "Clear Private Data". 
Make sure all boxes are checked, then click "Clear Private Data Now".
OSU_Access is the unsecured campus wireless network. Anybody with an ONID account or a Conference Login can connect.
You can connect to OSU Access using your laptop's wireless connection. If it is set to automatically connect, it may ask you if you really want to connect to it. You may also have to select it from the list of wireless networks, and it may ask you if you really want to connect here as well. In either case select Ok, or Connect.
When you open your browser, you should get a sign-in/registration page. You can choose to either sign in, which is just a temporary 600 minute login, or you can register your computer's MAC address so that you don't have to sign in again. We strongly recommend that customers permanently register their machines.
For instructions on how to permanently register your machine, Click Here.
The OSU Public Wireless network is also called "Access" and it can be used in the following aeas according to this map.
OSU's Wireless connection instructions.
OSU's Wireless connection instructions.
OSU's Wireless connection instructions.
541-737-5574
