-------- 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/> ;
>> >
>> >