Facebook Twitter YouTube Flickr Google Plus

School of Engineering and Computer Science
248 Dodge Hall of Engineering
2200 N. Squirrel Road
Rochester, MI 48309-4401 (map)

Dean's Office: (248) 370-2217
Academic Advising: (248) 370-2201
SECSDean@oakland.edu

  Instagram

Technology Office
CTO HOME
SERVERS
TUTORIALS
RESOURCES
AND FORMS

SECS Computer Technology Office


The Computer Technology Office (CTO) provides technical support for the computing resources in the School of Engineering and Computer Science. The University as a whole offers a wide variety of technological services to students and faculty. As a member of the School of Engineering and Computer Science, we offer an additional set of services in an effort to meet the specific needs of engineering students and faculty. 


Account Creation and Management

In order to access these services you must first have or request a SECS account. The username for this account will be the part of your university email address before the '@' symbol. Your password is independent of your other university passwords. If you are having difficulty logging in, consider resetting your password.

Contact Information

Phone Number: (248) 370-2216
Dodge Hall of Engineering room 153
Monday - Friday 8:00am - 5:00pm

Walk-ins are welcome.

General contact email: help@secs.oakland.edu
To create a ticket: secs@oakland.edu

Submitting A Ticket


To submit a ticket to the CTO Help-desk e-mail to
secs@oakland.edu. This will let us know that you would like a ticket created and we will add you into the queue. This will in turn send you a ticket allowing you to view its status.

The tickets will be handled based on the order received and priority level. The priority level is set by the System Administrator based on a variety of factors one of which is number of individuals impacted by the ticket being completed. The tickets priority may be changed if a similar request by another party is submitted. 

Important note: The educational needs of SECS students always comes first.



Viewing A Ticket

When a ticket is created an e-mail is sent to the individual. In the e-mail you receive there will be a link taking you to the login page of our Ticket Management System. To login, use your netID (your netID is the same as logging into your OU email). To view a ticket, you must be a customer in our Ticketing System. To become a customer simply email us at secs@oakland.edu with "New Customer" as the subject.  To check your place in queue, reply to the tickets email that was sent to you with "status?" in the body of the email.



Edit tab Direct link

Servers

General Purpose Linux Servers

We are in the process of updating our General purpose Linux computing environment. We will keep both environments up at the same time for a while. The transition schedule will be posted here. The new servers run Scientific Linux and require VPN access when connecting from off campus. 

When your SECS account is created, you are given a shell account on all of our Linux servers. The intended use of the General Purpose Linux Servers are to:

  1. Provide educational access to the installed software
  2. Give students the opportunity to work in a Linux environment
  3. Run long running or computationally intensive jobs.

Available Servers

beatles.secs.oakland.edu is intended to load balance and will give you the Linux server that will offer the most free resources.

If you wish to log into a specific server you will want to log into:

  • ringo.secs.oakland.edu
  • harrison.secs.oakland.edu

legacy servers are still currently available:

  • login.secs.oakland.edu
  • janus.secs.oakland.edu
  • pandora.secs.oakland.edu

Accessing the Servers

There are several methods for logging into these servers. 

IMPORTANT: For off-campus access to these servers you MUST first be logged into the SECS VPN

Transferring files to and from the servers

Our Linux environment mounts the SECS Network drive as your home directory. View the "Accessing your network drive" section on the SECS Network Drives page for more information about transferring files.

IMPORTANT: For off-campus access to these servers you MUST first be logged into the SECS VPN

Software

  • Matlab
  • Comsol
  • Netbeans
  • Eclipse
  • Libre Office
  • Cadence
*Multiple versions may be available.

back to top

Environments

  • Java
  • Python
  • gcc
  • Latex
*Multiple versions may be available.

Specialized Linux Servers

^Back to Top^




The GPU server is a Scientific Linux 6.3 server with three Nvidia Tesla® GPUs running the CUDA® software

Logging in

To log into the GPU server, use either ssh or the NX client to log into the server:

  • gpu.secs.oakland.edu

Using CUDA®  

All CUDA® related software is located in /APPS/cuda

To use the CUDA® SDK you have two options:

  • Run /APPS/cuda/SDK.run
    • At "Enter install path (default ~/NVIDIA_GPU_Computing_SDK):"  Press Enter
    • At "Enter CUDA install path (default /APPS/cuda):"  Press Enter
  • Download newest SDK from here to your home directory and run it as above.

GPU Programming 

Nvidia® Documentation:


The SECS Compute Cluster is a CentOS-based ROCKS cluster suite running on Dell Blade Servers. These servers are connected to a 4gbps fiber link to a Dell AX4 San. There are currently 4 blades online, and 4 more are coming online in the summer of 2012. These blades have 16 GB of RAM each, with dual quad-core Xeon processors (the next 4 bought will be nehalem-based.)

The ROCKS cluster suite consists of several open-source cluster components such as OpenMPI and Sun's GridEngine. It is scalable, in that plugging in additional hardware just works, and any computer plugged into the cluster's switch will automatically become a cluster node.

The cluster uses the GFS filesystem (http://sources.redhat.com/cluster/gfs/) to share files between hosts in the cluster. The main reason we use GFS over protocols like NFS, is the locking mechanism supports concurrent write access by nodes in the cluster, so compute nodes can use files as data transport mechanisms if they wish.

Logging in

The cluster operates using a single head node to provide an interface to the user. The compute nodes aren't intended to be logged into directly.

To log into the cluster, use either ssh or the NX client to log into the server:

head.clust.secs.oakland.edu


Shared Storage

The cluster uses a GFS filesystem to store your home directory, but your SECS home directory (the one that corresponds to your H: drive, and your home directory on login.secs.oakland.edu) is also available for access on the cluter head. The path to your SECS home directory is:

/SECSHomes/<x>/<username>

Where <x> is the first letter of your username, and <username> is your username itself. You can copy files to or from this directory, or you can create a symbolic link from your cluster home directory, like so:

ln -s /SECSHomes/<x>/<username> ~/secshomedir
This will create a symbolic link called "secshomedir" in your cluster home directory that links to your SECS home directory.

It is not a good idea to store things like MPI programs and project files in your SECS home directory, since it is only accessible from the head node, and not each of the compute nodes. That is, if you want a file to be seen by every node in the cluster, store it in your cluster home directory, not the SECS home directory.


MPI

The following languages are supported for MPI programs:

C (mpicc)
C++ (mpic++)
Fortran 77 (mpif77)
Fortran 90 (mpif90)
If you want to write an MPI program in Fortran 77, just compile it like you would a normal F77 application, but use "mpif77" to compile it instead of just "f77".

Here is a short tutorial on creating an MPI program in C that will run in parallel on each node in the cluster.

This code creates a simple ring structure on the nodes in the cluster. That is, each node has a "right" and "left" partner node. The 4th node in the cluster, for instance, talks to node 1 as its "right" node, and node 3 as its "left node. It then sends and receives a megabyte of data between each node in the cluster, then exits.

To compile the code, use the following:

mpicc -o mpi-ring mpi-ring.c
This calls a specialized version of gcc called "mpicc", which will create and link your executable against the MPI libraries.

To run the program, use the following:

mpirun -n 4 -machinefile /etc/machines ./mpi-ring
This should produce output looking something like this:

Process 1 on compute-0-1.local
Process 0 on compute-0-0.local
Process 2 on compute-0-2.local
Process 3 on compute-0-3.local
Process 3 on compute-0-3.local:successfully sent (1048576) bytes to id (0)
Process 1 on compute-0-1.local:successfully sent (1048576) bytes to id (2)
Process 2 on compute-0-2.local:successfully sent (1048576) bytes to id (3)
Process 3 on compute-0-3.local:successfully received (1048576) bytes from id (2)
Process 2 on compute-0-2.local:successfully received (1048576) bytes from id (1)
Process 1 on compute-0-1.local:successfully received (1048576) bytes from id (0)
Process 0 on compute-0-0.local:successfully sent (1048576) bytes to id (1)
Process 0 on compute-0-0.local:successfully received (1048576) bytes from id (3) 

Sun Grid Engine

Sun's grid engine is also installed on the SECS cluster. It can be used as a method for invoking applications like Fluent and Comsol.

Here is a sample script for submission to sun's grid engine for use in the Fluent application:

#!/bin/bash
#$ -S /bin/bash
# Parallel Fluent Gridengine submit script
# Replace {...} by proper values
#$ -V
#$ -pe fluent_pe 16
#$ -cwd
#$ -o gridengine_output.txt -j y
#$ -e gridengine_error.txt
export FLUENT_ARCH=lnamd64
export FLUENT_INC=/gfs/software/fluent-6.3.26/Fluent.Inc
export PATH=$PATH:/gfs/software/fluent-6.3.26/Fluent.Inc/bin
export LM_LICENSE_FILE=27004@atlas.secs.oakland.edu
cd ~/parallel_process
rm gridengine_output.txt
rm gridengine_error.txt
. $FLUENT_INC/setup.sh
fluent 3d -sge -t$NSLOTS -g -pgmpi -sgepe fluent_pe $NSLOTS -i elbow4.dat >>output 


The values in the comments section near the top of the script are variables passed to the Grid Engine environment. In this case, we are setting the parallel environment to fluent's parallel environment, and the number of parallel executions to 16 (that's 4 per cluster node, with 4 cluster nodes.)

The first lines in the script set up the needed variables for launching fluent, and the last line is the actual script itself, executed by sun's grid engine.

To launch the grid engine task, use the "qsub" command, providing the name of the script as an argument.

For additional tutorials in using Sun's grid engine, including submitting and managing jobs, visit the rocks website on sun's grid engine here:

http://www.rocksclusters.org/roll-documentation/sge/5.2/submitting-batch-jobs.html


The Machines File

Many cluster applications ask you for a machines file that contains the names of all the machines in the cluster. For your convenience, a file has been placed in /etc/machines that contains all the node names in the cluster.


Cluster Applications

The following applications are installed on the cluster and able to run in a parallel mode:
  • Comsol 3.5a
  • FEKO
  • Fluent
These and any future software we install will be placed in the /gfs/software directory on the cluster.



Edit tab Direct link


Using SSH with a X-forwarding (Linux)


If you would like to forward X connections (have GUI programs launched on the remote host launch on your machine), use ssh -Y user@host (see below).So for example, if you want to connect to login, the command would be: $ ssh yourusername@login and from offcampus, you would need the full name $ ssh yourusername@login.secs.oakland.edu Graphical ApplicationsOccasionally, you may want to launch a program over ssh such as Matlab or Firefox that is graphical. If you are using a UNIX/Linux based system, this is easy, since Linux systems use X to display windows.

X11 (Mac)

The recommended Command line method for connecting to a remote server using a Mac would be to use Xquartz. Xquartz is an app that comes standard on all Macs since version 10.5. It can be found in Applications -> Utilities -> X11.app.

Note: If your Mac does not have X11 on it, you can download it from the XQuartz website.

To use X11:

1. Start the application located in your Utilities folder. It will be called either X11 or XQuartz.
2. Type "ssh -Y beatles.secs.oakland.edu"
3. To launch a program, type the to path of the executable followed by an ampersand (&) such as "/APPS/eclipse &". This will open a session of the application but still leave the X11 window available for more commands. You can also run multiple instances of the program by using the ampersand. Some programs already have scripts written for them so you only have to type the name of the program followed by the ampersand. For instance, "matlab &"
4. You can also type "gnome-session" to open up the GUI for that session.
5. When you are done with a program, make sure you kill the process. You an check to make sure it is closed out properly by typing "ps -a".






Edit tab Direct link
Forms
Resources



There are several methods available to access your network drive.
  • From the SECS computer labs it is automatically mapped as drive H:. It is visible by clicking start then computer (or "My Computer" on XP)
  • From home or a laptop you can use an scp client such as Winscp to log into login.secs.oakland.edu
  • From any SECS Linux server your network drive will be mounted as your home directory (cd ~)
  • You can download and upload files to you network drive from a web browser by connecting to the vpn using the "web browser access method"
Helpful Links:

Backup and Recovery

We perform automated daily disk to disk backups keeping files for 6 months. There is no Disaster Recover Guarantee or off site backup. So there is some risk of data loss. If you need to recover data from your network drive please submit a ticket with the file name, location and date of the file(s) you need to recover. 


Version Control (repository)




This section is for information related to SECS web hosting for clubs, organizations, and departments related to the School of Engineering and Computer Science. If you would like to create a non personal website on our server, you will need to gain approval from a department chair or the Dean's office. For new development project, or site overhaul's we recommend utilizing the University's Content management System (CMS) as an alternative to hosting your site on the SECS web server. The CMS allows for easy editing/updating, as well as providing the consistent Oakland University website look. This site was built using the CMS. The account representative for the SECS is Daniel Bodene (bodene@oakland.edu)  and should be your first point of contact. 

About our Environment
A wide variety of development options are supported. Including PHP, Perl, Css, html, Server side includes, Jquery, mysql, and Java. We have a test and production environment. You can ssh, scp and view your web pages using the test environment. The expected work flow is to upload and edit files in the Test environment, View the changes you have made on the test server, and then when you have completed your testing promote the changes to the production environment.

Adhere to Policy #860 found on http://www.oakland.edu/uts/policies. Do not store personally identifiable information such as G#'s or other confidential data, on the SECS webserver or any other SECS server without gaining approval from a data steward and contacting the CTO.

Uploading and editing files in the Test environment
To upload files to the test environment scp (we recommend winSCP from windows) using test.secs.oakland.edu as your host. You must be on campus or connected to the vpn.

Viewing your changes in the Test environment

You can then view your page in a web browser, by using test.yoursite. So if you site is cse.secs.oakland.edu, then you could view the test version of your site at test.cse.secs.oakland.edu. Again this is only available from on campus or by using the vpn.

Promoting changes from the Test to Production environments

Once you are happy with your changes and would like to promote your site from the test environment to the production environment. An authorized promoter can run a promotion script located in /srv/webScripts/. This script will sync the website directories on the test and production web server. Each site ideally should only have one promoter, who should be someone other then a developer. 

Steps required by Authorized promoter to promote site:
  1. connect to the Oakland university wired network or vpn.
  2. ssh into test.secs.oakland.edu
  3. Steps 3-5 are only required if you do not know the name of your promotion script
  4. navigate to the web scripts directory entering the following command:
    cd /srv/webScripts
  5. view the available command by enter the following command:
     ls
  6. find the command that is for your website. It should start with the word promote. Note the name of your script
  7. Run you command by entering the following command where Site is replaced by the name of your site
     /srv/webScripts/promoteSite.sh

Details: The ownership and permission will not be preserved when moving to the production environment. By default only Apache will be able to read and execute the files in your web directory. If you need more advanced permissions, please contact us. Also please note that the database data and schema will not be promoted. This is expected because test and production data should be different. You can still use phpMyAdmin, in both the test and production environments. If you need a more robust solution please contact us.

<div>We perform automated daily disk to disk backups keeping files for 6 months. There is no Disaster Recover Guarantee or off site backup. So there is some risk of data loss. If you need to recover data from your network drive please&nbsp;<a href="/secs/cto/contact_us">submit a ticket</a>&nbsp;with the file name, location and date of the file(s) you need to recover.&nbsp;</div>

 You can also create a public_html folder in your network drive, that will allow you to host your own website using SECS&nbsp;<a href="/secs/cto/personal_websites">Personal Web Hosting</a>.&nbsp;</div>

^Back to Top^



Edit tab Direct link

AcademicsUndergraduate AdmissionsGraduate AdmissionsOnline ProgramsSchool of MedicineProfessional & Continuing EducationHousingFinancial Aid & ScholarshipsTuitionAbout OUCurrent Student ResourcesAcademic DepartmentsAcademic AdvisingEmergenciesFinancial ServicesGeneral EducationGet InvolvedGraduate StudiesGraduation & CommencementKresge LibraryOU BookstoreRegistrationAthleticsGive to OUGrizzlinkAlumni EngagementCommunity ResourcesDepartment of Music, Theatre & DanceMeadow Brook HallMeadow Brook TheatreOU Art GalleryPawley InstituteGolf and Learning CenterRecreation CenterUniversity Human ResourcesAdministrationCenter for Excellence in Teaching & LearningInstitutional Research & AssessmentInformation TechnologyReport a Behavioral ConcernTrainingAcademic Human Resources
Oakland University | 2200 N. Squirrel Road, Rochester, Michigan 48309-4401 | (248) 370-2100 | Contact OU | OU-Macomb
Coordinate map of Auburn Hills Entrance