Dear all,
I have a large dataset of randomly generated weighed sample for which I
wish to compute a kernel density estimate.
I have used the "np" package successfully for smaller datasets, however
for the larger ones, they take too long when
using the cross validation options for bandwidth selection ("cv.ls" or
"cv.ml"). Of course, they are much quicker with "normal-reference".
To speed things up, I tried to use the "npRmpi" package. I had a lot of
trouble installing it - but after appealing to google and finding the
following page:
http://webappl.blogspot.co.uk/2012/01/install-rmpi-with-mpich2-environment.html
npRmpi was finally installed (basically I just added the flags "-lmpl
-lopa" to the definition of PKG_LIBS in the configure script, and in the
R CMD INSTALL call, I passed the configure.args as the correct paths to
my MPICH2 installation).
However, when I call the "mpi.spawn.Rslaves(nslaves=1)" command, I get
the following errors:
##
> mpi.spawn.Rslaves(nslaves=1)
*** caught segfault ***
address 0x2df0c9f, cause 'memory not mapped'
Traceback:
1: .Call("mpi_comm_spawn", as.character(slave),
as.character(slavearg), as.integer(nslaves), as.integer(info),
as.integer(root), as.integer(intercomm), PACKAGE = "npRmpi")
2: mpi.comm.spawn(slave = system.file("Rslaves.sh", package =
"npRmpi"), slavearg = arg, nslaves = nslaves, info = 0, root =
root, intercomm = intercomm)
3: mpi.spawn.Rslaves(nslaves = 1)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
##
I also installed Rmpi (I installed Rmpi before npRmpi, and in a similar
fashion), and calling the same function "mpi.spawn.Rslaves" gives the
following error:
[mpiexec@manet.somewhere.group] match_arg
(/home/userspace/plwm2/CPP/mpich2-1.4.1p1_gcc4.6.2/src/pm/hydra/utils/args/args.c:122):
unrecognized argument pmi_args
[mpiexec@manet.somewhere.group] HYDU_parse_array
(/home/userspace/plwm2/CPP/mpich2-1.4.1p1_gcc4.6.2/src/pm/hydra/utils/args/args.c:140):
argument matching returned error
[mpiexec@manet.somewhere.group] parse_args
(/home/userspace/plwm2/CPP/mpich2-1.4.1p1_gcc4.6.2/src/pm/hydra/ui/mpich/utils.c:1387):
error parsing input array
[mpiexec@manet.somewhere.group] HYD_uii_mpx_get_parameters
(/home/userspace/plwm2/CPP/mpich2-1.4.1p1_gcc4.6.2/src/pm/hydra/ui/mpich/utils.c:1438):
unable to parse user arguments
Please help!!!
Thanks.
Peter
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