Martin Henry H. Stevens
2005-Oct-26 14:43 UTC
[R] changing memory limits to speed up lsoda
Hi All, I am running R 2.2.0 on Mac OS 10.4.2, dual G5 processors with 8 Gig RAM. I am running a simulation with lsoda that requires ~378 s to complete one set of time intervals. I need to optimize the parameters, and so need to considerably speed up the simulation. I have tried to figure out how to change the appropriate memory allocation and have search R help and Introductory information and the archives, but connot figure out how to allocate more to the right place. I would greatly appreciate any pointers or tips or leads. Thank you, Hank Stevens Dr. Martin Henry H. Stevens, Assistant Professor 338 Pearson Hall Botany Department Miami University Oxford, OH 45056 Office: (513) 529-4206 Lab: (513) 529-4262 FAX: (513) 529-4243 http://www.cas.muohio.edu/~stevenmh/ http://www.muohio.edu/ecology/ http://www.muohio.edu/botany/ "E Pluribus Unum"
Setzer.Woodrow@epamail.epa.gov
2005-Oct-26 15:03 UTC
[R] changing memory limits to speed up lsoda
Hank,
I don't understand why you think memory is the problem, here. I'd try
writing my model in C or Fortran (there is an example in the odesolve
package). That speeds things up a lot, and is what I do with slow
systems.
R. Woodrow Setzer, Jr.
National Center for Computational Toxicology
US Environmental Protection Agency
Mail Drop B205-01/US EPA/RTP, NC 27711
Ph: (919) 541-0128 Fax: (919) 541-1194
"Martin Henry H.
Stevens"
<HStevens at muohio To
.edu> Woodrow Setzer/RTP/USEPA/US at EPA
cc
10/26/2005 10:45
AM Subject
changing memory limits to speed
up lsoda
Hi Woody,
I sent this to r-help as well. Thanks in advance for any input.
I am running R 2.2.0 on Mac OS 10.4.2, dual G5 processors with 8 Gig
RAM.
I am running a simulation with lsoda that requires ~378 s to complete
one set of time intervals. I need to optimize the parameters, and so
need to considerably speed up the simulation.
I have tried to figure out how to change the appropriate memory
allocation and have search R help and Introductory information and
the archives, but connot figure out how to allocate more to the right
place.
I would greatly appreciate any pointers or tips or leads.
Thank you,
Hank Stevens
Dr. Martin Henry H. Stevens, Assistant Professor
338 Pearson Hall
Botany Department
Miami University
Oxford, OH 45056
Office: (513) 529-4206
Lab: (513) 529-4262
FAX: (513) 529-4243
http://www.cas.muohio.edu/~stevenmh/
http://www.muohio.edu/ecology/
http://www.muohio.edu/botany/
"E Pluribus Unum"
Martin, For my simulations (same hardware with less memory). - Optimize the code : using Narray, avoiding loops - Installed distributed computations (PVM & RPVM tools are very easy to use, many thanks to Simon Urbanek for his help) Hope this will help Best Naji Le 26/10/05 16:43, ????Martin Henry H. Stevens???? <HStevens at muohio.edu> a ??crit??:> Hi All, > I am running R 2.2.0 on Mac OS 10.4.2, dual G5 processors with 8 Gig > RAM. > I am running a simulation with lsoda that requires ~378 s to complete > one set of time intervals. I need to optimize the parameters, and so > need to considerably speed up the simulation. > I have tried to figure out how to change the appropriate memory > allocation and have search R help and Introductory information and > the archives, but connot figure out how to allocate more to the right > place. > I would greatly appreciate any pointers or tips or leads. > Thank you, > Hank Stevens > > > Dr. Martin Henry H. Stevens, Assistant Professor > 338 Pearson Hall > Botany Department > Miami University > Oxford, OH 45056 > > Office: (513) 529-4206 > Lab: (513) 529-4262 > FAX: (513) 529-4243 > http://www.cas.muohio.edu/~stevenmh/ > http://www.muohio.edu/ecology/ > http://www.muohio.edu/botany/ > "E Pluribus Unum" > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html >