Thanks for the suggestion. This wiki is actually maintained by the MPICH group at ANL. I'm including their discuss list in this reply. I believe that the biggest improvement to the wiki would be to expand on the syntax accepted by user defined binding. On Fri, Nov 15, 2013 at 1:01 PM, Thiago Quirino - NOAA Federal <[email protected]> wrote:

Thank you so much, Jonathan.

Is it possible to add this information to the Wiki? Though I've searched the net for hours, unfortunately I couldn't find any reference to this. The closest I found regarding disabling internal MVAPICH2 and mpiexec.hydra affinities in favor of external MPI process pinning using taskset or numactl was this:

https://scicomp.jlab.org/docs/node/66

Thank you so much again, Jonathan. Thiago.

On Fri, Nov 15, 2013 at 10:31 AM, Jonathan Perkins <[email protected]> wrote:

...

Hello Thiago. I've confirmed that the following syntax will give you what you're asking for. You'll basically need to specify user binding, replace your commas with pluses, and replace your colons with commas.

[perkinjo@sandy1 install]$ ./bin/mpiexec -n 4 -bind-to user:0+1+2+3,4+5+6+7,8+9+10+11,12+13+14+15 -env MV2_ENABLE_AFFINITY=0 ./cpumask 1111000000000000 0000111100000000 0000000011110000 0000000000001111

On Wed, Nov 13, 2013 at 7:02 PM, Thiago Quirino - NOAA Federal <[email protected]> wrote:

...

Hi, Jonathan.

Using mpiexec.hydra's binding capability, is it possible to assign a CPU range for each MPI task in a node? Suppose I want to spawn 4 MPI tasks per node, where each node has 2 sockets with 8 cores each (total 16 cores). I want task 1 to run on CPU range 0-3, task 2 on CPU range 4-7, task 3 on CPU range 8-11, and task 4 on CPU range 12-15. I used to accomplish this using the MV2_CPU_BINDING variables as follows:

export MV2_CPU_MAPPING=0,1,2,3:4,5,6,7:8,9,10,11:12,13,14,15

Can I accomplish the same binding configuration with mpiexec.hydra's binding capability? I only see socket binding options in the Wiki.

Thanks again, Jonathan. Thiago.

On Tue, Nov 12, 2013 at 1:56 PM, Jonathan Perkins <[email protected]> wrote:

...

Hello Thiago. Perhaps you can try an alternative to MV2_ENABLE_AFFINITY. If you use the hydra process manager (mpiexec.hydra), you can disable the library affinity and use the launcher affinity instead. In this case the other threading levels will be available to you.

Please see

https://wiki.mpich.org/mpich/index.php/Using_the_Hydra_Process_Manager#Proce... for more information on how to use this hydra feature. Also please do not forget to set MV2_ENABLE_AFFINITY to 0.

Please let us know if this helps.

On Fri, Nov 8, 2013 at 6:41 PM, Thiago Quirino - NOAA Federal <[email protected]> wrote:

...

Hi, folks. Quick question about MVAPICH2 and affinity support.

Is it possible to invoke MPI_Init_thread with any mode other than "MPI_THREAD_SINGLE" and still use "MV2_ENABLE_AFFINITY=1"? In my hybrid application I mix MPI with raw Pthreads (not OpenMP). I start 4 MPI tasks in each 16 cores node, where each node has 2 sockets with 8 Sandybridge cores each. Each of the 4 MPI tasks then spawns 4 pthreads for a total of 16 pthreads/node, or 1 pthread/core. Within each MPI task, the MPI calls are serialized among the 4 pthreads, so I can use any MPI_THREAD_* mode, but I don't know which mode will work best. I want to assign each of the 4 MPI tasks in a node a set of 4 cores using MV2_CPU_MAPPING (e.g. export MV2_CPU_MAPPING=0,1,2,3:4,5,6,7:8,9,10,11:12,13,14,15) so that the 4 pthreads spawned by each MPI task can migrate to any processor within its exclusive CPU set of size 4.

Is that possible with modes other than MPI_THREAD_SINGLE? If not, do you foresee any issues with using MPI_THREAD_SINGLE while serializing the MPI calls among the 4 pthreads of each MPI task? That is, is there any advantage to using MPI_THREAD_FUNELLED or MPI_THREAD_SERIALIZED versus MPI_THREAD_SINGLE for serialized calls among pthreads?

Thank you so much, folks. Any help is much appreciated.

Best, Thiago.

--------------------------------------------------- Thiago Quirino, Ph.D. NOAA Hurricane Research Division 4350 Rickenbacker Cswy. Miami, FL 33139 P: 305-361-4503 E: [email protected]

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-- Jonathan Perkins http://www.cse.ohio-state.edu/~perkinjo