Nancy Wilkens-Diehr

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Forward from 2015-2017 CoSSci - Doug,

The current CoSSCi gateway( DBS120005) which is set to expire 3/13 2017 is an Educational grant so it can be extended at any time. However, this probably should graduate to a Research allocation, the next submission window for Research requests is 3/15-4/15. There are examples for gateway research requests here:

https://portal.xsede.org/group/xup/successful-requests#examples-gateways

Let me know if you have any questions, Ken

On 2/15/17 12:50 PM, Doug White wrote:

  • Nancy (Wilkins-Diehr): 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.
SES140029
Dear Ken,
I've just recovered from a year-long stomach cancer and am back working on my projects (http://socscicompute.ss.uci.edu) but I need the 4/1/17 start (3/13/17) that I wasn't able to request earlier given my illness. As Nancy notes a short gap would not be too serious 'tho I have one class running -- one of my former PhDs -- Ren Feng   -- also teaching this spring. 

Feb 14 2017

Nancy (Wilkins-Diehr): 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.

Dear Ken,

I've just recovered from a year-long stomach cancer and am back working on my projects (http://socscicompute.ss.uci.edu) but I need the 4/1/17 start (3/13/17) that I wasn't able to request earlier given my illness. As Nancy notes a short gap would not be too serious 'tho I have one class running -- one of my former PhDs -- Ren Feng -- also teaching this spring.

Jan 8 2017

Hi Doug,

I still think you need to do more to describe the codes, how much CPU a given run will take, how many runs are expected, how this results in the number of compute hours you are requesting. This can all be based on past data from the previous classes. Which codes are run? How many processors does a code run on? How long are the runs? How many runs are there? This would be used to justify the number of CPU hours you are requesting. You have the data since the gateway time has been well-used in the past.

XSEDE proposals are primarily about the use of the resources and less about the science. How much time are you asking for? Is this going in as an education proposal (50,000 CPU limit on Comet). That would be easier to get.

Take a look at https://portal.xsede.org/successful-requests, there are many examples of good proposals, including gateway proposals. Take a careful look through that whole page. The more time you ask for, the more important justification is. If you’re only asking for 50k, you can get by with less, but I’d still list the code details I describe in paragraph 1.

Nancy

December 2016

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.

Nancy

Doug; FOR 2017 DBS2017UC Complex Social Science.docx

On 12/15/16, 10:19 AM, "Douglas White" <douglas.white@uci.edu> wrote:

   Dear Nancy   
   what do I need to do for http://socscicompute.ss.uci.edu/
   Is there an easy way to keep it going over the long turn?
   thanks and have some great holidays

Stuart Martin - 630-252-0904 smartin@mcs.anl.gov - Eric Blau

Nancy July27 2016 (3

Yes, typically the PI will receive notification prior to the expiration of a grant. Doug’s right, the CPU time costs the research team nothing. It’s a proposal/peer review process for continuing access. I believe dates are posted on the website, but typically 3 months prior to expiration a follow-on proposal would need to be in. There are specific windows when the requests can be submitted. For an April 1 start for example the window is Dec 15 to Jan 15. For July 1, the window is March 15 to April 15. This is the thing to keep an eye on. I believe you can see expiration dates for your awards after logging onto the portal, http://portal.xsede.org.

As I said to Doug, I’ll put in for an extension since the deadline (Jan 15) has already passed for an April 1 allocation start.

Nancy

Nancy Jan27 2016 (2

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.

Nancy

Doug Jan 10 2016

Stu, Eric, Jon, Dao,

I think this (ECSS Summary) looks just fine. Thanks to all for putting it together and glad your health is improving. Bob Sinkovits wasn’t listed as an ECSS staff member, so no need to include anything from him. He was on the 2012-2013 project with Lucas and Rachana.

Really great to see the usage this fall and best of luck with the online book.

Thanks,

Nancy


On 1/8/16, 2:59 PM, TO "Doug White"

Doug, thanks for your very nice note and we’re all sorry to hear about your illness, but pleased to hear about the prognosis and the advances that will make that possible.

Just to be clear, there isn’t any kind of time limit for you leading this project. You can remain as PI for many years, you can continue to request CPU resources for many years. It is only the ECSS component that we need to conclude in December. There is the help desk that can always be used for occasional gateway questions, but we can’t continue to devote staff to the project. In ECSS, we have to limit our support so that we can take on new work.

At this point we were moving forward asking Dr. Bell to get a user portal account so we could get him on the systems and make him the PI because that’s what you requested. But that’s not necessary to continue the compute allocation and it also doesn’t reset the clock on ECSS. Hopefully after the help received to date you, Bahattin and Dr. Bell and perhaps others from UCI can move the gateway forward. Eric and Stu will be wrapping up their work this month.

We do wish you and your team continued success with this very novel, cutting edge gateway and our best to you at the holidays.

Nancy Dec 9 2015 ==

Dear Colleagues and Friends - I've never had such amazing support in my life and career and want not only to express my appreciation but also am in a position finally to explain what my situation is with the illness I've had since mid-October. Please don't pass this information on, however, unless your confidant is sworn to secrecy -- its not good news to spread since its formerly been treated as a death knell. It's kept me debilitated but until these last two weeks it hasn't been clear what it was precisely. Turns out it is pancreatic cancer of a kind that is now finally curable over a several months of chemo and a new drug that for the first time dissolves the pancreatic matrix that prevents healing, then allows the cancer and its matrix to be removed surgically all at once whence all may be well if the cancer modules haven't spread, which they haven't and hopefully wont as there's no sign that it won't heal to date. All this may go fairly quickly toward the cure, which was impossible even a year ago. Damned uncomfortable however in the meantime. What's below is a miraculous recovery of the project with Duran Bell (UC Irvine) monitoring the team as my three-year limit is up. And thanks to all who have brought this (actually two) projects to completion. After March we’ll simply be supporting the project through allocations and not requiring further help from Argonne who have been so helpful (Marru, Tom, Lukasz, Rachana, Eric and Stuart) as well as XSEDE and ECSS and especially Nancy, Ken, Bob and so many others at SDSC. - Doug

Dec 9th It does look like the allocations are now active again

[ucissg@comet-ln3 ~]$ show_accounts ucissg ID name project used available used_by_proj


ucissg uci125 5152 55000 5152 ucissg uci117 245 54954 4954

Request help Dec 7th

Nancy - will call you today to see whether if I submit the attachment (correct format with Duran Bell as PI, etc) for the Eric's HPC submissions to XSEDE we can get the new allocation there as needed....

Doug,

Bob and I are both on travel. Bob for the XRAC meeting, followed by an extended vacation; me for an XSEDE quarterly. I will try to take a look while here. Much of the meeting is closed laptop. My thought was that the new PI would have to submit. I don’t know of a way to transfer PIs since a submission is supposed to represent a given PIs thoughts. There are folks in charge of the XRAC, who are here, so will try to confer with them.

Nancy

From: Doug White <douglas.white@uci.edu> Date: Monday, December 7, 2015 at 12:31 PM To: Bob Sinkovits <sinkovit@sdsc.edu>, Nancy Wilkins-Diehr <wilkinsn@sdsc.edu> Subject: Fwd: Re: Galaxy/CoSSci

Dear Bob, I needed to draw up a new proposal in the fall (attached) with a new PI for the CoSSci project because the 3 year limit was up (similarly for our project) and had sent it to Nancy a couple of months ago before I got sick.... Can't get ahold of Nancy by phone. Would you take a look -- I can submit to XSEDE if the format looks right and can ask for new allocations.

Need to do the same kind of update for our joint network cohesion project....

thanks

From Nancy

Doug,

Bob and I are both on travel. Bob for the XRAC meeting, followed by an extended vacation; me for an XSEDE quarterly. I will try to take a look while here. Much of the meeting is closed laptop. My thought was that the new PI would have to submit. I don’t know of a way to transfer PIs since a submission is supposed to represent a given PIs thoughts. There are folks in charge of the XRAC, who are here, so will try to confer with them.

Nancy

From: Doug White <douglas.white@uci.edu> Date: Monday, December 7, 2015 at 12:31 PM To: Bob Sinkovits <sinkovit@sdsc.edu>, Nancy Wilkins-Diehr <wilkinsn@sdsc.edu> Subject: Fwd: Re: Galaxy/CoSSci

Dear Bob, I needed to draw up a new proposal in the fall (attached) with a new PI for the CoSSci project because the 3 year limit was up (similarly for our project) and had sent it to Nancy a couple of months ago before I got sick.... Can't get ahold of Nancy by phone. Would you take a look -- I can submit to XSEDE if the format looks right and can ask for new allocations.

Need to do the same kind of update for our project....

We could talk at 858 457 0077 thanks

Nancy Wilkins-Diehr Dec 8, 2015, to: Duran Bell <dbell@uci.edu>, cc: Tolga Boztan <Boztan@uci.edu>, Ken Hackworth <hackwort@psc.edu>, Paul Rodriguez <prodriguez@sdsc.edu>, Marlon Pierce <marpierc@iu.edu> Dec 8, 2015

Dr. Bell,

I understand from Dr. Doug White, cc-ed, that you will be taking over as the principal investigator for the UCI Complex Social Science Gateway (http://socscicompute.ss.uci.edu/). I also understand that Bahattin Oztan, also cc-ed, will serve as allocations manager, controlling access to the supercomputer CPU hours used by the gateway.

I’ve spoken with the head of XSEDE’s allocation process, Ken Hackworth (once again cc-ed) and we have been able to process Doug’s supplemental request for more CPU time on Comet with the following justification provided by Doug.

"The UC Complex Social Science (CoSSci) that features a Galaxy system now has five databases containing circa 3000 societies and 3000 variables for the Ethnographic Atlas, Standard Cross-Cultural Sample, FGH Fishers, Hunters and Gatherers, Western North American Indians and XC which integrates the other four, and it has provided for a total of 2413 students in an Advances in Sociology Class over the last three years to test and develop models of causal effects on dependent variables in these databases. These not only include independent variables from data codebooks but also – a new and unique feature – the Dow-Eff R code for identifying autocorrelation effects for each specific model that represent human evolutionary effects of the movement of language families, spatial diffusion, and ecology as predictive features of model outcomes separate from the main independent variables. Using 2-stage regression, both sets of features – evolutionary and contemporaneous – can be tested for exogeneity on many different dimensions. Before the Dow-Eff R code executes these analyses, it also imputes missing data, optionally for all observations that match the dependent variable, which makes for very accurate results."

We have added an additional 50,000 CPU hours on Comet to the allocation. The expiration date of April 5, 2016 remains unchanged. As the PI, you’ll receive notifications if the account is low on time and as the expiration date approaches with instructions about what to do.

In order to change the PI in our system over to you, we need you to create an XSEDE user portal account (http://portal.xsede.org). Once you’ve done this, can you reply to those on this list with your portal username and we will make that change?

We’d like to see the gateway move forward, in its use by classes and other users and also in UCI’s ability to support effort for its maintenance. We’re excited by such a novel use of supercomputing resources.

Sincerely,

Nancy

Nancy Wilkins-Diehr Dec 8, 2015

---From Ken Hackworth

All,

I have processed the Comet supplements and the process should be complete in the next 24 hours, this will reactivate the access to the allocations.

Dr. Bell, once you have created your XSEDE portal account we will be able to make the PI change from Doug to you. At that time we will also add Bahattin as the allocation manager for the projects which will allow the complete management of the projects.

If you have any questions or concerns please let me know.

Ken Hackworth
XSEDE Allocations

C.Lance Moxley <help@xsede.org> Dec 8, 2015

You will be contacted via letter or via email after reviews are submitted and a decision has been made.

        At any time you can check the status of your current submission, as well as review past submissions, by logging into:
        https://portal.xsede.org and clicking on the Allocations tab.
        
        For a Startup or Educational proposal, you should expect an answer within two weeks.
        A Supplement or Appeal submission will be considered by the Startup, and thus a response may take up to five weeks.
        
        Please contact allocations@xsede.org with any questions.
        
        Request Title: Extended Collaborative Support for UC Complex Social Science (CoSSci) Supercomputer Gateway
        Request Number: SES140029
        PI Name: Douglas R. White
        Request Type: New
        Allocation Type: Startup
        Uploaded Documents:Progress Report: CoSSci Supplement.pdf

Best Regards, XSEDE Allocations ==This notice has been sent to the PI, all co-PIs, and the Allocation Manager of this request. PI Name: Douglas White PI Organization: University of California, Irvine Request: Extended Collaborative Support for UC Complex Social Science (CoSSci) Supercomputer Gateway Action Type: Supplement Request Number: SES140029 Allocations Admin Comments: Awarded Resources: SDSC Dell Cluster with Intel Haswell Processors (Comet): 50,000.0 SUs

Dear Dr. White

The Startup panel met recently and considered your request. Your request has been recommended for an award.

PIs or their chosen delegate may login to https://portal.xsede.org and use the XSEDE Portal 'Add/Remove User' page to manage users for your new project on any awarded resource.

It could take up to five days for these accounts to be active. For details about the decision and reviewer comments, please go to:

https://portal.xsede.org, login, click on the ALLOCATIONS tab, click on 'Submit/Review Request', and finally, click on button 'Click to Enter or View a Request'.

For questions regarding this decision, please contact help@xsede.org


Sincerely,

             XSEDE Allocations

Dec 8, 2015

This notice has been sent to the PI, all co-PIs, and the Allocation Manager of this request. PI Name: Douglas White PI Organization: University of California, Irvine Request: Extended Collaborative Support for UC Complex Social Science (CoSSci) Supercomputer Gateway Action Type: Supplement Request Number: SES140029 Allocations Admin Comments: Awarded Resources: SDSC Dell Cluster with Intel Haswell Processors (Comet): 50,000.0 SUs

Dear Dr. White

The Startup panel met recently and considered your request. Your request has been recommended for an award.

PIs or their chosen delegate may login to https://portal.xsede.org and use the XSEDE Portal 'Add/Remove User' page to manage users for your new project on any awarded resource.

It could take up to five days for these accounts to be active. For details about the decision and reviewer comments, please go to:

https://portal.xsede.org, login, click on the ALLOCATIONS tab, click on 'Submit/Review Request', and finally, click on button 'Click to Enter or View a Request'.

For questions regarding this decision, please contact help@xsede.org


Sincerely,

             XSEDE Allocations