Difference between revisions of "Nancy Wilkins-Diehr"

From InterSciWiki
Jump to: navigation, search
Line 20: Line 20:
Eric, thank you for (still) swapping in to help.
Eric, thank you for (still) swapping in to help.

Revision as of 10:24, 23 April 2017

Nancy - ECSS - Rachana - Eric - Stuart Martin - Lukasz - Uram - Ken Hackworth hackwort@psc.edu


  • Doug,
  • First step, let’s get an active Comet allocation. You do that at http://portal.xsede.org. I thought you already went into that, which is where you saw that you could only renew for 6 months. Let’s do that and at least get that far.
  • If I were you I would call Francisco Lopez from UCI on the phone and talk through the variables on the SocSci form and see if he can help debug that aspect. You and he could use Google hangouts and screen share to get to the root of the problem more quickly than with email. Nancy Wilkins-Diehr <wilkinsn@sdsc.edu>
  • Nancy Wilkins-Diehr <wilkinsn@sdsc.edu>

DBS120005UC Complex Social Science.docx

  • April 19, 2017[edit]

CPU_Hours__Total__by_User_2014-03-01_to_2017-03-31_timeseries.png -- Nancy

  • Doug, After consulting with Ken (the expert), we believe all you need to do is submit a renewal request. Log in to http://portal.xsede.org (there are links if you’ve forgotten your password, your username is drwhite). 4/16/2017 Once logged in, hover over “allocations” and click on submit/review request. That should allow you to extend your educational allocation, TG-DBS120005.


Eric, thank you for (still) swapping in to help.

Yes, the allocation is out. Doug, this is the message from Ken Hackworth with directions for renewing the allocation. Take a look at that message. You’ll need to log in to http://portal.xsede.edu with your username drwhite. There is a probably a button if you need to reset the password.

There are two components to the gateway – keeping the server running at UCI and keeping a Comet allocation so that the server can launch jobs on Comet.


On 4/11/17, 1:49 PM, "Blau, Eric B." <blau@mcs.anl.gov> wrote:

   I believe that your allocation on Comet at SDSC has expired, which is why jobs submitted from
   aren’t working.
   From the log at
   galaxy.jobs.runners.cli_shell.rsh INFO 2017-04-11 13:40:51,288 RemoteShell execu
   ting cmd: ssh -oStrictHostKeyChecking=yes -oConnectTimeout=60 comet /usr/bin/sba
   tch /home/ucissg/work/33717/galaxy_33717.sh
   galaxy.jobs.runners.cli ERROR 2017-04-11 13:40:52,825 (33717) submission failed
   galaxy.jobs.runners.cli ERROR 2017-04-11 13:40:52,825 (33717) submission failed
   and, if we check on comet:
   [ucissg@comet-ln2 ~]$ show_accounts
   ID name      project      used     available    used_by_proj
   No accounts found for user ucissg on platform sdsc_comet.
   If I recall correctly, the project identifier may be hardcoded in the galaxy job runner cli code.  But I suspect that if you get a new allocation on Comet (at SDSC), it would be a very simple fix to have http://socscicompute.ss.uci.edu work again.

On Apr 11, 2017, at 3:15 PM, Doug White <douglas.white@uci.edu> wrote: http://intersci.ss.uci.edu/wiki/index.php/Harry_Mangalam_/EricBlau

in the period that I had stomach cancer (now recovered) we lost the online working version of http://socscicompute.ss.uci.edu

can either of you (Harry/Eric) figure out how to recover the http://socscicompute.ss.uci.edu ?

the password for http://socscicompute.ss.uci.edu hasn't changed.

the url is the same but might have been moved (to UCI from its original instance at SDSC where Nancy W-D might have an idea in conjunction with Harry M. about how to recover use of the http://socscicompute.ss.uci.edu (which doesnt work currently)


One can still click on the 2rd,3rd,4th boxes with numeric variables starting eg with one var eg v5 in the 2nd row and three or more variables in the 3rd,4th row vars but the old system doesnt work -- it stopped working while I had the cancer. Any suggestion? At http://socscicompute.ss.uci.edu essentially its a very simple matter of entering these kinds of numbers.

I suspected that if I get a new allocation on Comet, which I did at SDSC, it would be a very simple fix to have my http://socscicompute.ss.uci.edu work again (it ran out of time when I had cancer last year). I did get a new allocation on Comet but dont know what to do next or who to email for help. Question: where do I go for the renewal request?

Many thanks, sorry for the bother.

I am at UC Irvine as is http://socscicompute.ss.uci.edu but it originates at SDSC.

Nancy says: Doug, After consulting with Ken (the expert), we believe all you need to do is submit a renewal request.

http://socscicompute.ss.uci.edu SDSC

On 4/5/17, 2:47 PM, "Doug White" <douglas.white@uci.edu> wrote:

   Dear Nancy,
   How would I renew my use of http://socscicompute.ss.uci.edu ?

The SDSC time you are asking for is on Comet. That’s where the job runs. UCI hosts the machine with the gateway server. That server sends jobs to Comet.

Yes, you have to ask for the SDSC time every year. Your time runs out on 3/13. The deadline for getting a request in for 4/1 start was Jan 15. I’m sure I sent a note about that previously. Why don’t you send Ken Hackworth (hackwort@psc.edu), who runs the allocations process a note and ask what the best path forward is? You’re not using a lot of time, but you want to have it available continuously so the gateway isn’t interrupted. I would ask Ken about future deadlines and put them on a calendar with a reminder system.


Ken Hackworth

  • Ken Hackworth (hackwort@psc.edu), who runs the allocations process. Missed Jan 15 2017. When is the next data for a request for startup?
  • Emailed Ken 23rd Feb - when is next time for a request for startup?
For an educational allocation with CoSSci gateway I've attached a 2-page proposal request for 2017.
Could you take a look and advise me on what else is needed? Ok for me to be the PI?
Happy holidays ... Doug
DBS120005UC Complex Social Science.docx
  • Hi Doug,
Hi Doug, fine for you to be the PI on this.

This looks good. What I would also do though is describe the codes that are run and the anticipated CPU use. That’s what is looked at most in these proposals – they aren’t science reviews per se, particularly if the science is already funded. Here we look particularly at the code performance and match to the requested systems. For a small request like this one, that’s less important, but I think it still needs to exist. Here are the codes we plan to run, here are the CPU hours we expect those to consume based on past experience. Each code runs for X length of time on Y processors, that’s why we expect the usage we describe. That kind of thing.

Take a look at https://www.xsede.org/web/guest/winning-proposal too, there are some very good gateway-specific suggestions there.

Happy holidays to you too!


On 12/18/16, 1:43 PM, "Douglas White" <douglas.white@uci.edu> wrote:

   For an educational allocation with CoSSci gateway I've attached a 2-page  proposal request for 2017. Nancy
    Could you take a look and advise me on what else is needed? Ok for me to be the PI? 
   Happy holidays ... Doug

Nancy Dec 1/16 2016, Dao

Hi Doug,

Once a year you need to put in a renewal proposal to keep things going. That’s what everyone who uses XSEDE resources has to do. To see expiration dates, CPU time remaining on the allocation, etc, you’ll want to log in to http://portal.xsede.org. That’s where you can find this information whenever you like. Go to the My XSEDE tab.

Right now the only active allocation you have is an educational allocation for the CoSSCI gateway that expires 3/13/17. You’ll want to get a renewal request in by 1/15/17 for a 4/1/17 start. They’ll be able to extend the current allocation for 2 weeks to cover that short gap. Allocations always occur at quarterly intervals. The schedule is at https://portal.xsede.org/allocation-request-steps#table1.

As of today, you have 54,954 hours allocated on Comet with 51,864 used. You have 5000 hours allocated on Gordon with 0 used.

Dec 15, 2014 thru Jan 15, 2015	April 1, 2014 thru March 31, 2015
Mar 15, 2015 thru Apr 15, 2015	Jul 1, 2015 thru June 30, 2016
Jun 15, 2015 thru Jul 15, 2015	Oct 1, 2015 thru September 30, 2016
Sep 15, 2015 thru Oct 15, 2015	Jan 1, 2016 thru December 31, 2016
Table 2. Allocation Types
Education	for classroom instruction and training courses

Hi all,

I am on leave from the University of California, Irvine until December 12th, 2016. Please send your email related to Social Sciences Computing Support to sscs@uci.edu. If you would like to contact me, please use my other email address

Thank you,

Dear Doug,

First, how are you? I hope very much that you are well. I’m writing to conduct a PI interview. We do these at the conclusion of each 12-month period of ECSS support. I'd like to schedule a 15-minute phone call within the next two weeks to discuss your experience with ECSS support in the project entitled “Extended Collaborative Support for UC Complex Social Science (COSSci) Supercomputer Gateway". The ECSS staff members were Eric Blau and Stu Martin (U Chicago). If the staffers primarily interacted with others in your group, it would be good if they could participate in the call. I have attached the project workplan.

Please let me know the best way to schedule this call, e.g. by sending me a phone number and a set of acceptable times. While I would prefer a conversation, you might choose instead to respond in e-mail to the questions below.

Here are some of the things I would like to discuss:

   How was your working relationship with ECSS staff? Was the staff member knowledgeable? courteous?
      Were there any difficulties (attitude, language, anything else)?
   Was the effort in developing the workplan worthwhile? Did it set expectations appropriately?
   Can you quantify the contribution of the ECSS support- e.g. by saying by how much the code was improved,
      or any other measure you have?
   Had you not had ECSS support, can you estimate how many person months it would have taken
      to get to the same stage that your project achieved with the ECSS support?
   Are the results still in use? Can you point to increased science that resulted from the ECSS support?
   Did the staff member suggest future directions? If so, were they pursued?
   Please characterize your satisfaction with the ECSS support on a scale of 1-5 (5 being best).
   When you talk about this work, do you mention the ECSS support? Did the staff member’s work rise
      to the level of becoming a co-author on publications?
   How would you rate the impact of the ECSS support on your entire project, again on a 1-5 scale?
   In layman’s terms, can you briefly summarize any scientific insights that have emerged from your XSEDE work?
   What capabilities would you have liked to see within XSEDE?
   Do you have any other comments or suggestions for the ECSS program?
   Can we quote you by name?

I look forward to your reply.

Best regards,


Hi Doug,

Great to see you today. Right now your allocation for compute time on Comet is set to expire on 4/5/16. Typically requests for time are due 3 months prior to expiration. So the next writing deadline to shoot for would be 4/15/16 for a 7/1/16 start. After several years of a startup, you would be moving to the peer-reviewed XRAC allocation process. There are quarterly windows during which you can submit XRAC requests.

The main page for the allocation process http://www.xsede.org/allocations. Duran is listed as the PI, so it’d be easiest if he put in the request. If you like though, we could change the PI back to you for this project.

Again, great to see you looking so well today.




http://socscicompute.ss.uci.edu/ and http://SocSciCompute.ss.uci.edu/

Nancy SDSC UCSD - LEG-5118


  • 2004-present Area Director for Science Gateways, TeraGrid
Responsible for implementation of revolutionary community interfaces to NSF's cyberinfrastructure resources
  • 2004-2007 Director of Consulting, Documentation and Training, San Diego Supercomputer Center, UC San Diego
Responsible for supporting thousands of researchers on SDSC and TeraGrid high performance computing systems
  • 2001-2004 Associate Director, Scientific Computing Division, San Diego Supercomputer Center, UC San Diego
Responsible for supporting thousands of researchers on SDSC's high performance computing systems

Direction of five groups within the Scientific Computing Division - Scientific Computing Applications, Scientific Computing Services, Grid Applications, Data Applications, Visualization Services

  • 2002-2004 Co-Chair, User Services working group, NSF TeraGrid project
Responsible for user support across the nine sites in the cutting-edge production scientific grid project
  • 1998-2001 Project Manager, National Partnership for Advanced Computational Infrastructure, San Diego Supercomputer Center, UC San Diego
Project management for multidisciplinary projects spanning 30 institutions with an annual budget of ~$35M.
  • 1998-2003 Chair, Resources Working Group, National Partnership for Advanced Computational Infrastructure, San Diego Supercomputer Center, UC San Diego
Coordinate national HPC activities across four academic institutions.
  • 1993-1998 Associate Staff Programmer/Analyst, Scientific Computing, San Diego Supercomputer Center, General Atomics
Led and participated in providing HPC support services to the national academic research community.
  • 1991-1993 Senior Engineer, Fluid Systems Branch, General Atomics
Evaluated passive decay heat removal concepts for gas-cooled nuclear reactor designs.
  • 1988-1991 Engineer, Aerodynamics Group, General Dynamics Convair Division
Performed computational fluid dynamics (CFD) analysis on a wide range of configurations including wind tunnels, cruise missiles and hypersonic vehicles.

And head contributor of SDSC allocation staff to ACCCR project How to Turn Your Project into a Science Gateway