RE: CycleCloud BigScience Challenge giving away ~8-hours on 30000 core cluster for research

-------- Original Message -------- Subject: Re: [NMusers] CycleCloud BigScience Challenge giving away ~8-hours on 30000 core cluster for research From: Leonid Gibiansky < [email protected] > Date: Mon, November 14, 2011 11:29 am To: Bill Knebel < [email protected] > Cc: [email protected] , David Foster < [email protected] > We have just published a paper (L Gibiansky, E Gibiansky, R Bauer, in print, should appear in JPP in a week or so) that in particular evaluates parallel computing performance on a single 12-CPU Window 7 workstation. We found out that for the TMDD-QSS model in differential equations, "Use of parallel computations with 4 to 12 processors running on the same computer improved the speed proportionally to the number of processors with the efficiency (for 12 processor run) in the range of 85 to 95% for all methods except BAYES, which had parallelization efficiency of about 70%." Efficiency was defined as 100%*(single CPU run time)/(multiple CPU run time)/(number of processors) Roughly, the model run on 11 processors was 10 times faster than the single-processor run of the same model Leonid -------------------------------------- Leonid Gibiansky, Ph.D. President, QuantPharm LLC web: www.quantpharm.com e-mail: LGibiansky at quantpharm.com tel: (301) 767 5566 On 11/14/2011 9:54 AM, Bill Knebel wrote: > David, > > Some limited benchmarking results are listed at the bottom of this > email. It is also important to remember that there are ways that > cloud-computing helps beyond parallel NONMEM. Cloud-computing allows on > demand, user specific, clusters that can grow and shrink depending on > user requirements. This allows for rapid completion of large bootstrap > processes (500 - 1000 jobs) in the time it takes to run one, > non-parallel job. Users can also evaluate model variants simultaneously > with cluster size being increased or decreased as needed. Users do not > have to worry about competing for resources (compute cores) with other > users because cloud-computing clusters are user and/or project specific. > The performance gains are evident in parallel NONMEM jobs and single > modeling projects, but it is important to look beyond the simple > benefits of individual job/project speed-up and more towards the impact > of cloud-computing on the entire portfolio of modeling and simulation > projects in a given group or company. > > Bill > > > Model 1 - ADVAN6, 1000 subjects, dual linear and non-linear elimination > CoresRuntime (hr) > 180.7 > 816.8 > 168.9 > 246.2 > 483.8 > 962.5 > > Model 2 - ADVAN6 - 70 subjects, PKPD model > CoresRuntime (hr) > 14 hr > 81.1 > 160.66 > 240.4 > 480.31 > > cores = number of compute cores (value of "NODES=" argument in NONMEM > pmn file) > > On Nov 9, 2011, at 9:28 PM, David Foster wrote: > >> I agree with Julia, >> >> Thanks for this Bill, but quantitative benchmarking would be very much >> appreciated. >> >> Regards, >> >> David >> >> >> On 10/11/11 9:55 AM, "Ivashina, Julia" < [email protected] >> <x-msg: //692/ [email protected] >> wrote: >> >> Bill, >> >> This is nice to hear about the speed improvements for NONMEM you >> received. >> >> Could you please describe gains in performance in a qualitative >> manner with model examples you used. >> I think everyone will benefit from such NONMEM 7.2 benchmarking. >> >> I posted a similar question in March but not many responded. >> >> Thanks, >> Julia >> >> -----Original Message----- >> From: [email protected] >> <x-msg: //692/ [email protected] > >> [ mailto: [email protected] ] On Behalf Of Bill Knebel >> Sent: Wednesday, November 09, 2011 5:03 PM >> To: [email protected] <x-msg: //692/ [email protected] > >> Cc: Jason Stowe; Nick Holford; William Bachman >> Subject: Re: [NMusers] CycleCloud BigScience Challenge giving away >> ~8-hours on 30000 core cluster for research >> >> Since there seems to be some questions around cloud-based NONMEM, >> we wanted to share our experience of utilizing parallel NONMEM in >> a cloud-based environment. We use the enterprise-licensed version >> of NONMEM(R) 7.2. to perform modeling and simulation, both serial >> and parallelized, on an AWS cloud infrastructure. Briefly, we used >> a combination of recent MPICH2 libraries, the Sun Grid Engine >> integrated ORTE parallel environment, and StarCluster to deploy >> parallel NONMEM(R) on linux AWS EC2 instances of up to 100 cores >> for estimation (which appears to be the current NONMEM(R) 7.2 >> limit for parallel computing), and a virtually unlimited number of >> cores for simulation or use of other open-source modeling tools >> (R, OpenBUGS). The gains in performance are very real, and >> probably the best we've experienced on any multi-user distributed >> computing infrastructure. >> >> Bill >> >> ~~~~~~~~~~~~~~~~~~~~~~~~ >> Bill Knebel, PharmD, PhD >> Principal Scientist II >> >> Metrum Research Group LLC >> 2 Tunxis Road, Suite 112 >> Tariffville, CT 06081 >> >> O: 860.735.7043 >> C: 860.930.1370 >> F: 860.760.6014 >> >> >> On Nov 4, 2011, at 3:06 PM, Bachman, William wrote: >> >> > Cloud computing on a system like this requires an unlimited >> enterprise license for NONMEM. Pricing is available from >> [email protected] <x-msg: //692/ [email protected] >. >> > >> > >> > William J. Bachman, Ph.D. >> > Director, Pharmacometrics R&D >> > Icon Development Solutions >> > 6031 University Blvd., Suite 300 >> > Ellicott City, MD 21043 >> > Office 215-616-8699 >> > [email protected] <x-msg://692/ [email protected] > >> > >> > >> > >> > From: [email protected] >> <x-msg: //692/ [email protected] > >> [ mailto: [email protected] ] On Behalf Of Jason Stowe >> > Sent: Friday, November 04, 2011 2:12 PM >> > To: Nick Holford >> > Cc: [email protected] <x-msg: //692/ [email protected] > >> > Subject: Re: [NMusers] CycleCloud BigScience Challenge giving >> away ~8-hours on 30000 core cluster for research >> > >> > Hi Nick, >> > On Thu, Nov 3, 2011 at 8:59 AM, Nick Holford >> < [email protected] ><x-msg: //692/ [email protected] >> >> wrote: >> > Jason, >> > >> > If I was a winner of your competition how would I go about using >> NONMEM? >> > How do you manage NONMEM licensing on you cloud cluster? >> > What NONMEM license fee would one have to pay for 30000 cores? >> > >> > Nick >> > Hi Nick, >> > Unfortunately, I can't speak to an individuals user's NONMEM >> license. We do have commercial clients running NONMEM on >> CycleCloud clusters at varying scales. A winner with appropriate >> licensing doesn't need to run 8 hours on 30k cores, you could also >> run for 24 hours on 10000 cores, etc. If your license relates to >> compilation vs. execution, or if you have a site-wide license, we >> can't say, so you'll need to look at your license to deal with that. >> > >> > Perhaps someone from Icon could talk about this kind of >> non-profit licensing? >> > >> > Thanks, >> > Jason >> > >> > >> > >> > On 2/11/2011 2:19 p.m., Jason Stowe wrote: >> > Hi all, >> > >> > Long time reader, first time poster. >> > >> > Cycle recently announced that we're giving away the equivalent of >> 8-hrs on a 30000 core CycleCloud HPC cluster for a grand prize >> winner in the CycleCloud BigScience Challenge. Up to five >> finalists will win 4 hours on 3000 core clusters as well. The >> Compute time is to benefit academic and non-profit researchers >> that are doing science which could benefit humanity. >> > >> > Some current applicants are in life sciences and CycleCloud >> currently supports reliable/large-scale clusters running NONMEM >> for Top 5 Pharma, so I wanted to welcome more researchers in the >> NONMEM community to enter. >> > >> > We describe the challenge and why we're excited about it here: >> > http://bit.ly/BigScience >> > >> > The application process is simply answering 4 questions (takes >> less than half an hour): State who you are, what is your research, >> why it is important, and how you currently run computation. The >> applicatiopn is available here: >> > http://cyclecomputing.com/big-science-challenge/overview >> > >> > So far, response has been great, and Inside HPC covered >> descriptions of some of the recent applications we've received: >> > http://insidehpc.com/2011/10/27/24209 / >> > http://blog.cyclecomputing.com / >> > >> > Submissions are due by November 7th, so submit early and we hope >> to help some of you get some BigScience done quickly. >> > >> > Best, >> > Jason >> > >> > -- >> > >> > >> > ================================== >> > Jason A. Stowe >> > cell: 607.227.9686 >> > main: 888.292.5320 >> > >> > http://twitter.com/jasonastowe / >> > http://twitter.com/cyclecomputing / >> > >> > Cycle Computing, LLC >> > Leader in Open Compute Solutions for Clouds, Servers, and Desktops >> > Enterprise Condor Support and Management Tools >> > >> > http://www.cyclecomputing.com < http://www.cyclecomputing.com/> ; >> > http://www.cyclecloud.com < http://www.cyclecloud.com/> ; >> > >> > >> > -- >> > Nick Holford, Professor Clinical Pharmacology >> > Dept Pharmacology& Clinical Pharmacology >> > University of Auckland,85 Park Rd,Private Bag 92019,Auckland,New >> Zealand >> > tel:+64(9)923-6730 fax:+64(9)373-7090 mobile:+64(21)46 23 53 >> > email: [email protected] >> <x-msg: //692/ [email protected] > >> > http://www.fmhs.auckland.ac.nz/sms/pharmacology/holford >> > >> > >> > >> > >> > -- >> > >> > >> > ================================== >> > Jason A. Stowe >> > cell: 607.227.9686 >> > main: 888.292.5320 >> > >> > http://twitter.com/jasonastowe / >> > http://twitter.com/cyclecomputing / >> > >> > Cycle Computing, LLC >> > Leader in Open Compute Solutions for Clouds, Servers, and Desktops >> > Enterprise Condor Support and Management Tools >> > >> > http://www.cyclecomputing.com < http://www.cyclecomputing.com/> ; >> > http://www.cyclecloud.com < http://www.cyclecloud.com/> ; >> > >> >