That is what I did for the gpu case where I was running with 2 mpi processes per node since I had 2 gpus per node. But if that is not really the right way to be doing this, I'll be happy to learn of a better way. Note that for the CPU case in the runPetscProb_2 script I use a different binding. Anyway, if there is a better way to do this, I'll be happy to learn and try the better way. Also, this is recent work that has been done in a hurry because of trying to get ready for this new machine coming in. I probably need to go back and revisit the details to make sure I understand the binding I am really getting. Jed Brown writes:
Hmm, I'll look more carefully, but I think your binding is incorrect.
numactl -l --cpunodebind=$OMPI_COMM_WORLD_LOCAL_RANK ex2 $KSP_ARGS
NUMA node numbering is different from MPI ranks.
On Fri, Feb 24, 2012 at 12:11, Nystrom, William D <[email protected]> wrote:
Hi Jed,
Attached is a gzipped tarball of the stuff I used to run these two test problems with numactl. Actually, I hacked them a bit this morning because I was running them in our test framework for doing acceptance testing of new systems. But the scripts in the tarball should give you all the info you need. There is a top level script called runPetsc that just invokes mpirun from openmpi and calls the wrapper scripts for using numactl. You could actually dispense with the top level script and just invoke the mpirun commands yourself. I include it as an easy way to document what I did. The runPetscProb_1 script runs petsc on the gpus using numactl to control the affinities of the gpus to the cpu numa nodes. The runPetscProb_2 script runs petsc on the cpus using numactl. Note that both of those wrapper scripts are using openmpi variables. I'm not sure how one would do the same thing with another flavor of mpi. But I imagine it is possible. Also, I'm not sure if there are other more elegant ways to run with numactl than using the wrapper script approach. Perhaps there is but this is what we have been doing.
I've also included a Perl script called numa-maps that is useful for actually checking the affinities that you get while running in order to make sure that numactl is doing what you think it is doing. I'm not sure where this script comes from. I find it on some systems and not on others.
I've also include logs with the output of cpuinfo, nvidia-smi and uname -a to answer any questions you had about the system I was running on.
Finally, I've included runPetscProb_1.log and runPetscProb_2.log which contains the log_summary output for my latest runs on the gpu and cpu respectively. Using numactl reduced the runtime for the gpu case as well but not as much as for the cpu case. So the final result was that running the same problem while using all of the gpu resources on a node was about 2.5x times faster than using all of the cpu resources on the same number of nodes.
Let me know if you need more any more info. I'm planning to use this stuff to help test a new gpu cluster that we have just started acceptance testing on. It has the same basic hardware as the testbed cluster for these results but has 308 nodes. That should be interesting and fun.
Thanks,
Dave
-- Dave Nystrom LANL HPC-5 Phone: 505-667-7913 Email: [email protected] Smail: Mail Stop B272 Group HPC-5 Los Alamos National Laboratory Los Alamos, NM 87545
------------------------------ *From:* [email protected] [[email protected]] on behalf of Jed Brown [[email protected]] *Sent:* Thursday, February 23, 2012 10:43 PM
*To:* For users of the development version of PETSc *Cc:* Dave Nystrom
*Subject:* Re: [petsc-dev] Understanding Some Parallel Results with PETSc
On Thu, Feb 23, 2012 at 23:41, Dave Nystrom <[email protected]>wrote:
I could also send you my mpi/numactl command lines for gpu and cpu when I am back in the office.
Yes, please.