[mpich-discuss] mpiexec.hydra binding for multiple compute nodes

[Kenneth Raffenetti]

Justin,

Try using the "-bind-to core" option instead. It should do exactly what 
you are wanting. See this page with examples for more details 
https://wiki.mpich.org/mpich/index.php/Using_the_Hydra_Process_Manager#Process-core_Binding

Ken

On 05/11/2015 04:48 PM, Justin Chang wrote:
> Hello everyone,
>
> I am working with an HPC machine that has this configuring for a single
> compute node:
>
> Machine (64GB total)
>    NUMANode L#0 (P#0 32GB)
>      Socket L#0 + L3 L#0 (25MB)
>        L2 L#0 (256KB) + L1d L#0 (32KB) + L1i L#0 (32KB) + Core L#0 + PU
> L#0 (P#0)
>        L2 L#1 (256KB) + L1d L#1 (32KB) + L1i L#1 (32KB) + Core L#1 + PU
> L#1 (P#1)
>        L2 L#2 (256KB) + L1d L#2 (32KB) + L1i L#2 (32KB) + Core L#2 + PU
> L#2 (P#2)
>        L2 L#3 (256KB) + L1d L#3 (32KB) + L1i L#3 (32KB) + Core L#3 + PU
> L#3 (P#3)
>        L2 L#4 (256KB) + L1d L#4 (32KB) + L1i L#4 (32KB) + Core L#4 + PU
> L#4 (P#4)
>        L2 L#5 (256KB) + L1d L#5 (32KB) + L1i L#5 (32KB) + Core L#5 + PU
> L#5 (P#5)
>        L2 L#6 (256KB) + L1d L#6 (32KB) + L1i L#6 (32KB) + Core L#6 + PU
> L#6 (P#6)
>        L2 L#7 (256KB) + L1d L#7 (32KB) + L1i L#7 (32KB) + Core L#7 + PU
> L#7 (P#7)
>        L2 L#8 (256KB) + L1d L#8 (32KB) + L1i L#8 (32KB) + Core L#8 + PU
> L#8 (P#8)
>        L2 L#9 (256KB) + L1d L#9 (32KB) + L1i L#9 (32KB) + Core L#9 + PU
> L#9 (P#9)
>      HostBridge L#0
>        PCIBridge
>          PCI 1000:0087
>            Block L#0 "sda"
>        PCIBridge
>          PCI 15b3:1003
>            Net L#1 "eth0"
>            Net L#2 "ib0"
>            OpenFabrics L#3 "mlx4_0"
>        PCIBridge
>          PCI 8086:1521
>            Net L#4 "eth1"
>          PCI 8086:1521
>            Net L#5 "eth2"
>        PCIBridge
>          PCI 102b:0533
>        PCI 8086:1d02
>    NUMANode L#1 (P#1 32GB) + Socket L#1 + L3 L#1 (25MB)
>      L2 L#10 (256KB) + L1d L#10 (32KB) + L1i L#10 (32KB) + Core L#10 +
> PU L#10 (P#10)
>      L2 L#11 (256KB) + L1d L#11 (32KB) + L1i L#11 (32KB) + Core L#11 +
> PU L#11 (P#11)
>      L2 L#12 (256KB) + L1d L#12 (32KB) + L1i L#12 (32KB) + Core L#12 +
> PU L#12 (P#12)
>      L2 L#13 (256KB) + L1d L#13 (32KB) + L1i L#13 (32KB) + Core L#13 +
> PU L#13 (P#13)
>      L2 L#14 (256KB) + L1d L#14 (32KB) + L1i L#14 (32KB) + Core L#14 +
> PU L#14 (P#14)
>      L2 L#15 (256KB) + L1d L#15 (32KB) + L1i L#15 (32KB) + Core L#15 +
> PU L#15 (P#15)
>      L2 L#16 (256KB) + L1d L#16 (32KB) + L1i L#16 (32KB) + Core L#16 +
> PU L#16 (P#16)
>      L2 L#17 (256KB) + L1d L#17 (32KB) + L1i L#17 (32KB) + Core L#17 +
> PU L#17 (P#17)
>      L2 L#18 (256KB) + L1d L#18 (32KB) + L1i L#18 (32KB) + Core L#18 +
> PU L#18 (P#18)
>      L2 L#19 (256KB) + L1d L#19 (32KB) + L1i L#19 (32KB) + Core L#19 +
> PU L#19 (P#19)
>
> If I ran my program with 16 processes, I would have the follow batch script:
>
> #!/bin/bash
> #SBATCH -N 1
> #SBATCH -n 20
> #SBATCH -t 0-09:00
> #SBATCH -o output.txt
>
> mpiexec.hydra -bind-to user:0,1,2,3,4,5,6,7,10,11,12,13,14,15,16,17 -n
> 16 ./my_program <args>
>
> This would give me decent speedup. However, what if I want to use 32
> processes? Since each node only has 20 cores I would need #SBATCH -N 2
> and #SBATCH -n 40. However, I want ranks 0-15 and 16-31 to have the same
> mapping as above but on different compute nodes, so how would I do this?
> Or would the above line work so long as I have a multiple of 16 processes?
>
> Thanks,
>
> --
> Justin Chang
> PhD Candidate, Civil Engineering - Computational Sciences
> University of Houston, Department of Civil and Environmental Engineering
> Houston, TX 77004
> (512) 963-3262
>
>
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