Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts

0001 [exec5:10861] [[59432,0],5] odls:default:fork binding child [[59432,1],6] to cpus 0001 Hope that helps clear up the confusion! Please say it does, my head hurts... Chris -- Dr Chris Jewell Department of Statistics University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 7615 0778

Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts

ly different to what I had before, but our cluster is busier today :-) Chris -- Dr Chris Jewell Department of Statistics University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 7615 0778

Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts

] [[23443,0],6] odls:default:fork binding child [[23443,1],7] to cpus 0001 [exec1:30779] [[23443,0],5] odls:default:fork binding child [[23443,1],6] to cpus 0001 [exec3:12818] [[23443,0],3] odls:default:fork binding child [[23443,1],4] to cpus 0001 . C -- Dr Chris Jewell Department of Statistics University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 7615 0778

Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts

cluster.stats.local: PE_HOSTFILE shows slots=1 [exec4:17384] ras:gridengine: exec1.cluster.stats.local: PE_HOSTFILE shows slots=1 [exec4:17384] ras:gridengine: exec5.cluster.stats.local: PE_HOSTFILE shows slots=1 Chris -- Dr Chris Jewell Department of Statistics University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 7615 0778

Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts

t then I guess we're into the realm of setting allocation_rule. Is it going to be worth looking at creating a patch for this? I don't know much of the internals of SGE -- would it be hard work to do? I've not that much time to dedicate towards it, but I could put some effort in if necessary... Chris -- Dr Chris Jewell Department of Statistics University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 7615 0778

Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts

for the 2nd job? > > --td That's exactly it. Each MPI process needs to be bound to 1 processor in a way that reflects GE's slot allocation scheme. C -- Dr Chris Jewell Department of Statistics University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 7615 0778

Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts

currently... Cheers, Chris -- Dr Chris Jewell Department of Statistics University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 7615 0778

Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts

are using a version that > predates the change. > > Thanks > Ralph Hi Ralph, I'm using OMPI version 1.4.2. I can upgrade and try it out if necessary. Is there anything I can give you as potential debug material? Cheers, Chris -- Dr Chris Jewell Department of Statistics U

Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts

.stats.local 1 batch.q@exec2.cluster.stats.local 0,1:0,2 exec5.cluster.stats.local 1 batch.q@exec5.cluster.stats.local 0,1:0,2 So the pe_hostfile still doesn't give an accurate representation of the binding allocation for use by OpenMPI. Question: is there a system file or command that I co

Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts

re allocated where on the cluster, and write an OpenMPI rankfile. Any thoughts on that? Cheers, Chris -- Dr Chris Jewell Department of Statistics University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 7615 0778

Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts

JSV to remove core binding for the MPI jobs (but retain it for serial and SMP jobs). Any more ideas?? Cheers, Chris (PS. Dave: how is my alma mater these days??) -- Dr Chris Jewell Department of Statistics University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 7615 0778

Re: [OMPI users] Error when using OpenMPI with SGE multiple hosts

> > It looks to me like your remote nodes aren't finding the orted executable. I > suspect the problem is that you need to forward the path and ld_library_path > tot he remove nodes. Use the mpirun -x option to do so. Hi, problem sorted. It was actually caused by the system I currently use t

[OMPI users] Error when using OpenMPI with SGE multiple hosts

e suggest either what is wrong, or how I might progress with getting more information? Many thanks, Chris -- Dr Chris Jewell Department of Statistics University of Warwick Coventry CV4 7AL UK Tel: +44 (0)24 7615 0778