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#Proce... 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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