Re: [OMPI users] Problem in remote nodes

2010-03-30 Thread uriz . 49949
I've benn investigating and there is no firewall that could stop TCP traffic in the cluster. With the option --mca plm_base_verbose 30 I get the following output: [itanium1] /home/otro > mpirun --mca plm_base_verbose 30 --host itanium2 helloworld.out [itanium1:08311] mca: base: components_open: Lo

Re: [OMPI users] Problem in remote nodes

2010-03-30 Thread Ralph Castain
Looks to me like you have an error in your cmd line - you aren't specifying the number of procs to run. My guess is that the system is hanging trying to resolve the process map as a result. Try adding "-np 1" to the cmd line. The output indicates it is dropping slurm because it doesn't see a slu

[OMPI users] kernel 2.6.23 vs 2.6.24 - communication/wait times

2010-03-30 Thread openmpi
Hello List, I hope you can help us out on that one, as we are trying to figure out since weeks. The situation: We have a program being capable of slitting to several processes to be shared on nodes within a cluster network using openmpi. We were running that system on "older" cluster hardware (In

Re: [OMPI users] Problem in remote nodes

2010-03-30 Thread Robert Collyer
I've been having similar problems using Fedora core 9. I believe the issue may be with SELinux, but this is just an educated guess. In my setup, shortly after a login via mpi, there is a notation in the /var/log/messages on the compute node as follows: Mar 30 12:39:45 kernel: type=1400 audi

Re: [OMPI users] openMPI on Xgrid

2010-03-30 Thread Cristobal Navarro
i looked at TORQUE and looks good, indeed. i will give it a try for testing i just have some questions, Torque requires moab, but from what i've read on the site you have to buy moab right? im looking for a 100% free solution Cristobal On Mon, Mar 29, 2010 at 3:48 PM, Jody Klymak wrote: > >

Re: [OMPI users] openMPI on Xgrid

2010-03-30 Thread Jody Klymak
On Mar 30, 2010, at 11:12 AM, Cristobal Navarro wrote: i just have some questions, Torque requires moab, but from what i've read on the site you have to buy moab right? I am pretty sure you can download torque w/o moab. I do not use moab, which I think is a higher-level scheduling layer

Re: [OMPI users] openMPI on Xgrid

2010-03-30 Thread Craig Tierney
Jody Klymak wrote: > > On Mar 30, 2010, at 11:12 AM, Cristobal Navarro wrote: > >> i just have some questions, >> Torque requires moab, but from what i've read on the site you have to >> buy moab right? > > I am pretty sure you can download torque w/o moab. I do not use moab, > which I think i

Re: [OMPI users] openMPI on Xgrid

2010-03-30 Thread Gus Correa
Craig Tierney wrote: Jody Klymak wrote: On Mar 30, 2010, at 11:12 AM, Cristobal Navarro wrote: i just have some questions, Torque requires moab, but from what i've read on the site you have to buy moab right? I am pretty sure you can download torque w/o moab. I do not use moab, which I thin

Re: [OMPI users] MPI_Init never returns on IA64

2010-03-30 Thread Shaun Jackman
Hi Jeff, I tested 1.4.2a1r22893, and it does not hang in ompi_free_list_grow. I hadn't noticed that the 1.4.1 installation I was using was configured with --enable-mpi-threads. Could that have been related to this problem? Cheers, Shaun On Mon, 2010-03-29 at 17:00 -0700, Jeff Squyres wrote: > C

Re: [OMPI users] MPI_Init never returns on IA64

2010-03-30 Thread Jeff Squyres
On Mar 30, 2010, at 3:15 PM, Shaun Jackman wrote: > Hi Jeff, > > I tested 1.4.2a1r22893, and it does not hang in ompi_free_list_grow. > > I hadn't noticed that the 1.4.1 installation I was using was configured > with --enable-mpi-threads. Could that have been related to this problem? Yes, very

Re: [OMPI users] Problem in remote nodes

2010-03-30 Thread Robert Collyer
I changed the SELinux config to permissive (log only), and it didn't change anything. Back to the drawing board. Robert Collyer wrote: I've been having similar problems using Fedora core 9. I believe the issue may be with SELinux, but this is just an educated guess. In my setup, shortly aft

[OMPI users] Best way to reduce 3D array

2010-03-30 Thread Cole, Derek E
Hi all, I posted before about doing a domain decomposition on a 3D array in C, and this is sort of a follow up to that. I was able to get the calculations working correctly by performing the calculations on XZ sub-domains for all Y dimensions of the space. I think someone referred to this as a

Re: [OMPI users] Best way to reduce 3D array

2010-03-30 Thread Gus Correa
Hi Derek Great to read that you parallelized the code. Sorry to hear about the OO problems, although I enjoyed to read your characterization of it. :) We also have plenty of that, mostly with some Fortran90 codes that go OOverboard. I think I suggested "YZ-books", i.e., decompose the domain acr

Re: [OMPI users] Best way to reduce 3D array

2010-03-30 Thread Ricardo Reis
If using the master/slace IO model, would it be better to cicle through all the process and each one would write it's part of the array into the file. This file would be open in "stream" mode... like do p=0,nprocs-1 if(my_rank.eq.i)then openfile (append mode) write_to_file

Re: [OMPI users] Best way to reduce 3D array

2010-03-30 Thread Gus Correa
Salve Ricardo Reis! Como vai a Radio Zero? Doesn't this serialize the I/O operation across the processors, whereas MPI_Gather followed by rank_0 I/O may perhaps move the data faster to rank_0, and eventually to disk (particularly when the number of processes is large)? I never thought of your s