Brian help!!!!!! :-)
If this is the case, my next question is, how do I supply the usual
xgrid options, such as working directory, standard input file, etc?
Or is that simply not possible?
Do I simply have to have some other way (eg ssh) to get files to/
from agent machines, like I would for a batch system like PBS?
It looks like I never implemented those options (shame on me). I've
added that to my to-do list, although I can't give an accurate time-
table for implementation at this point. One thing to note is that
rather than using XGrid's standard input/output forwarding services,
we use Open MPI's services. So if you do:
mpirun -np 2 ./myapp < foo.txt
Under Xgrid with Open MPI, I'm trying to run applications that require more than just reading standard input/output but also the creation and writing of other intermediate files. For an application that like HP Linpack that just reads and writes one file, things work fine. My guess is that this is where things are getting hung up. Below, my application was trying to write out a file called "testrun.nex.run1.p" and failed. The MrBayes application writes out two files for each mpi process.
Initial log likelihoods for run 1:
Chain 1 -- -429.987779
Chain 2 -- -386.761468
Could not open file "testrun.nex.run1.p"
Memory allocation error on at least one processor
Error in command "Mcmc"
There was an error on at least one processor
Error in command "Execute"
Will exit with signal 1 (error) because quitonerror is set to yes
Am I just misunderstanding how to set up Open MPI to work with Xgrid?
Research Computing Consultant