I'm running my script using mpirun -mp 4 and using snowfall+Rmpi on
Linux 64bits. I receive the following error, but apparently without
consequences on the results.
Any idea?
I'm able to reproduce it with a minimal script (below). Seems the
critical issue is the for loop. Without it no error.
Thanks for your help!
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', verbose=FALSE)
library('snowfall', verbose=FALSE)
# Initialize cluster
sfInit(parallel=TRUE, cpus=3, type="MPI")
for(i in 1:2) {
# Prepare fake data
n <- 46000
x <- runif(n, 0.02, 0.54)
logx <- log(x)
sfExport("logx")
# Compute fake function
computeTakens <- function(r0idx) {
if(r0idx == 1) return(NA)
return(1/(logx[r0idx] - sum(logx[1:(r0idx-1)])/(r0idx-1)))
}
res <- sfClusterApplyLB(n:1, computeTakens)
}
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
