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mpi.spawn.Rslaves is not needed since orterun is used to create 1 master and 3 slaves. I assume Rprofile in Rmpi is used. Then all slaves are in infinite loop waiting for master instructions. They will not take any...

Simon, There are also some minima-finding functions in GSL that you may want to look into. The source for RcppGSL might help with a fully c++ version. Best, -- Hao Ye hye at ucsd.edu On Dec 23, 2014, at...

As Dirk said, it is a feature of OpenMPI. LAM-MPI doesn't have this issue. I don't think there is a solution on slave sides since mpi.bcast is a blocking call. It might be possible to use...

Jim, Try to alter the behave of error in R. Run at the beginning options(error=quote(assign(".mpi.err", FALSE, envir = .GlobalEnv))) Check Rmpi's Rprofile usage. Hao Jim Gattiker wrote: > I'm having trouble with running R under...

Hi Petre, It sounds like what you want is to curry a function f(x, a) into a function g(x) that will then get passed to your root-finder. See: http://stackoverflow.com/questions/152005/how-can-currying-be...

Hi Whit, Regarding 4), my slurm setting is actually to disable it so users cannot remote login or exec on any remote nodes. It seems slurm/munge take care of authentication and remote executions. Hao PS: in /etc/pam.d...

R cannot find libmpi.so in /usr/lib64/openmpi/1.4-gcc/lib. You have to tell R where to find it. There are two ways to do it: 1. Modify the env var LD_LIBRARY_PATH to include /usr...

Hi ff users and Jens, I am using the ff package and it has been working great. Recently I noticed an unexpected behavior in the ff package -- when I save an ff matrix on one machine to an NFS drive...

Melwin, Rmpi needs to be recompiled for R 2.12.0. I have put a 32bit binary version of Rmpi for R 2.12.0 on my site. So far I have no luck with 64bit Rmpi. Compiling is ok...

Hi Henrik, Thanks for your suggestion. I created a directory with 10 R files and tried the following and measured its time system.time(sourceDirectory("~/fun", modifiedOnly = F)) system.time(sourceDirectory("~/fun", modifiedOnly = T)) But the second line seems to...

Hi Marce, R and Lam on nfs should work. Your errors seem indicating that R cannot find the path to lam lib. Can you make sure LAM is working: try lamboot -v lamnodes lamexec C hostname Any errors will indicate...

Grant, In my own work, I found that input validation is actually significantly easier to do in R. (and even if you did do it in the c++ layer, informative error messages should probably be thrown as exceptions back to...

Hi Dirk, Thank for pointing out additional flags needed in order to compile Rmpi correctly. Those flags can be added in configure.ac once openmpi dir is detected. BTW -DMPI2 flag was missed in your Rmpi since the detection of...

Dear Herve, Thanks very much, the latest version 1.4.8 is online now. Best Regards, Chen Hao On 12 Jul 2016, at 2:39 AM, Herv? Pag?s <hpages at fredhutch.org<mailto:hpages at fredhutch.org>> wrote: Hi...

Hi Duncan, Thanks for your reply. I am not sure what you meant by "tell your C function to use the memory that R sent to it". What R can pass to C is a pointer to an array and...

Hi Ingeborg, Dirk already answered some of your questions so I will not repeat here. I just address some of your issues. Overall OpenMPI is not a friendly MPI environment to work with unless it runs under job or resource...

Hi Jens, Thanks for your prompt and informative answers. ff is a fabulous package and your suggestions helped me solve my problems at hands. As I need to incrementally increase each of several large matrices (about 1000 rows *10000 columns...

To all, Look like the max buffer size in any MPI transfer is restricted to 2^31-1. Whether XLENGTH is used or not will not change it. This is the restriction of MPI-2. MPI-3 will address some...

Hi Simon, Thank for pointing out this XLENGTH and R_xlen_t. I will add them in the next release of Rmpi. However I do run into the following issue. On a debian system with R 3.0.1 (8GB...

Hi David and Dimitris, Thanks for your suggestions. They are very helpful. Jeff On Wed, November 11, 2009 12:12 pm, David Winsemius wrote: > > On Nov 11, 2009, at 10:57 AM, David Winsemius wrote: > > >> >> On Nov 11, 2009, at...