parallel invocation of ripple

[Dan Bergeron]

We've been running R/qtl for several months now without any issues
except time.
For our data the ripple step executes for weeks, so clearly we want to
do it in parallel.

We installed SNOW and mpi on our linux cluster (fedora) and added the
n.cluster parameter to our ripple call:

rip1lik <- ripple( mydata,
chr=1,
window=2,
method="likelihood",
error.prob=0.05,
map.function="kosambi",
maxit=100000,
n.cluster = 8 )

The response is:

rip1lik<-
ripple(mydata,chr=1,window=2,method="likelihood",error.prob=0.05,map.function="kosambi",maxit=100000,n.cluster=8)
974 total orders
[mpi...@inquiry.unh.edu] match_arg (./utils/args/args.c:122):
unrecognized argument pmi_args
[mpi...@inquiry.unh.edu] HYDU_parse_array (./utils/args/args.c:140):
argument matching returned error
[mpi...@inquiry.unh.edu] parse_args (./ui/mpich/utils.c:1387): error
parsing input array
[mpi...@inquiry.unh.edu] HYD_uii_mpx_get_parameters (./ui/mpich/
utils.c:1438): unable to parse user arguments

Usage: ./mpiexec [global opts] [exec1 local opts] : [exec2 local
opts] : ...

Global options (passed to all executables):
<and a lot more "usage" information>
----------------------------------------------------------------------
Our first effort had yielded an error message that the software could
not find "libmpl.so.1". Our sysadmin then updated the mpich2
installation to one that includes libmpl.so.1 and we got a little
farther. Has anyone seen this problem before? Are there multiple
versions of mpich2 that are different?

Thanks

[Karl Broman]

I have not seen this problem before.

Week-long jobs running ripple seems unusual to me. I would look for a different approach to what you are trying to do. But that is separate from ./utils/args/args.c problem you are having.

karl

> --
> You received this message because you are subscribed to the Google Groups "R/qtl discussion" group.
> To post to this group, send email to rqtl...@googlegroups.com.
> To unsubscribe from this group, send email to rqtl-disc+...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/rqtl-disc?hl=en.
>