On Feb 28, 2006, at 8:21 AM, Frans Verster wrote:
> All clusters I (may) have access to have MPICH installed and
> configured,
> but no LAM/MPI, so my question is: How can I install LAM within a job
> (PBS or JDL) and configure it just as MPICH. Eventually I'd like to
> submit a job which first installs LAM, next configures it the same way
> as MPICH, install R and more, and last but not least does the real
> work.
Neither LAM nor MPICH generally requires anything "sys-admin level"
to install. The only trick with either is to make sure all the
binaries and libraries for the one you want to use end up in your
path (and LD_LIBRARY_PATH) before the one you don't want to use. So
a real quick /bin/bash script to build LAM and use it in a PBS job
would be something like the one below. Note that this was written
off the top of my head, not tested at all, and may eat your home
directory:
# set lam version to make script easier
export LAM_VERSION 7.1.1
# download LAM
wget http://www.lam-mpi.org/download/files/lam-${LAM_VERSION}.tar.gz
# untar, build, install
tar xzf lam-${LAM_VERSION}.tar.gz
cd lam-${LAM_VERSION}
./configure --prefix=${HOME}/local
make all install
# setup path
export PATH=${HOME}/local/bin:${PATH}
export LD_LIBRARY_PATH=${HOME}/local/lib:${LD_LIBRARY_PATH}
# install R
# use R
I won't support anything I wrote above, just an example of the steps
you would take. Note, however, that this means you're building LAM
during your batch reservation. This is probably a waste of resources
and will probably greatly irritate the cluster sysadmin when he
figures out what you are doing. A much better way of going about
things is to have a script that runs on the build node (often the
head node) pre-batch submission to do all the builds you need for a
run, then submit the run. That way, you don't spend lots of time
with one node compiling along and the others sitting completely idle.
Brian
--
Brian Barrett
LAM/MPI developer and all around nice guy
Have a LAM/MPI day: http://www.lam-mpi.org/
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