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 < To: Bill Knebel < 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" < >> 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: owner-nmusers sg: <x-msg:idssoftware oftware > >> > >> > 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 >> > > >> > >> > >;> > >> > From: >> > Sent: Friday, November 04, 2011 2:12 PM >> > To: Nick Holford >> > Cc: ><x-msg: 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: //692/n.holford ; 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/; >> > >> >