Tena Sakai wrote:
Thank you, Gus.
I agree with what you say about location of OpenMPI software.
Indeed, /usr/local is nfs-mounted to all cluster nodes, albeit
a bit unfortunate name "local." If/when I have a chance to
Set up machines, I will make local really local to each node.
Regards,
Tena Sakai
tsa...@gallo.ucsf.edu
On 1/12/11 4:20 PM, "Gus Correa" <g...@ldeo.columbia.edu> wrote:
Tena Sakai wrote:
Hi,
On a FAQ page (
http://www.open-mpi.org/faq/?category=running#adding-ompi-to-path),
(under 1. What pre-requisites are necessary for running an Open MPI
job?), I see an example
of LD_LIBRARY_PATH environment variable:
LD_LIBRARY_PATH: /opt/openmpi/lib
When I compiled the source, a directory /usr/local/lib/openmpi was
generated (with many
files in it). Given that, do I set D_LIBRARY_PATH to /usr/local/lib or
do I set
it to /usr/local/lib/openmpi?
Thank you.
Tena Sakai
tsa...@gallo.ucsf.edu
To /usr/local/lib.
I would suggest not using the default /usr/local to install OpenMPI,
since it tends to be really local to the machine where you built OpenMPI.
This will require that you install OpenMPI on all nodes/machines if
you want to run programs across a network.
Instead, a simpler way to get OpenMPI available to all nodes,
although installing only on one of them (say the head node of your
cluster) is to do it in a directory that is shared, typically via NFS.
To do so, use the --prefix=/my/shared/OpenMPI/directory option of
the configure script.
There are FAQs about this too.
Anyway, it may depend on your environment also, whether it is a cluster
with a private subnet (where my suggestion is typically used),
a bunch of separate computers on a LAN (where the suggestion won't work
unless you have a shared NFS directory), or other.
Gus Correa
Hi Tena
Just out of curiosity, this is not really an OpenMPI issue,
and I don't know anything about Rmpi either:
How do you intend to use Rmpi?
Interactively without any resource manager control (Torque,SGI,etc),
as in a standalone PC, although utilizing several hosts via MPI?
Interactively but under resource manager control?
(E.g., Torque has the -I directive for this type of thing,
and I guess other resource managers have similar mechanisms.)
In batch mode, where a full R script runs and eventually exits?
(Which can be with or without a resource manager.)
Maybe it is something else.
Matlab (parallel or not), IDL, etc, just like R[mpi],
bring about the same type of questions for us here.
Gus Correa
