Sorry for wasting your time with an incorrect diagnosis in my previous mail!
I'm running my script using mpirun -mp 4 and using snowfall+Rmpi on
Linux 64bits. I receive the following error, that terminates the run.
Any idea?
I'm able to reproduce the problem with a minimal script (below).
If n < 16371 it completes 9 iterations without problems. Already at
16371 it dies at iteration 7 (with the error below).
This value of n is suspiciously close to 2^14 (16kb). So maybe it is a
configuration problem of my MPI installation. Or it is an undocumented
limitation of snowfall/snow/Rmpi. My real variable size is around
100000, so I prefer not to implement workarounds to sfExport variables
whose size is < 16k.
If you can point me in the right direction will be really helpful.
Thanks!
mario
TERM: Undefined variable.
TERM: Undefined variable.
TERM: Undefined variable.
TERM: Undefined variable.
Loading required package: utils
Loading required package: utils
Loading required package: utils
Loading required package: utils
Library Rmpi loaded.
snowfall 1.70 initialized: parallel execution on 3 CPUs.
Error in unserialize(obj) : unknown input format
Calls: sfExport ... mpi.recv.Robj -> .mpi.unserialize -> unserialize ->
.Call
Execution halted
MPI Application rank 0 exited before MPI_Finalize() with status 1
/users/mvalle/snow/snow/inst/RMPISNOW: line 40: 15028
Terminated R --no-save $*
/users/mvalle/snow/snow/inst/RMPISNOW: line 40: 23906
Terminated R --no-save $*
/users/mvalle/snow/snow/inst/RMPISNOW: line 40: 22094
Terminated R --no-save $*
--- script ------------------------------------
library('Rmpi')
library('snowfall')
sfInit(parallel=TRUE, cpus=3, type="MPI")
for(i in 1:9) {
n <- 20000
logx <- runif(n, 0.02, 0.54)
sfExport("logx")
}
sfStop()
--
Ing. Mario Valle
Data Analysis and Visualization Group |
http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82
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