Hi Ken, Same result using hwloc-bind (which is a relief because if that didn't agree with /proc/pid/status I would have been unpleasantly surprised!) The most curious thing is that if I set socket:3 I get the exact binding I want! Perhaps my interpretation of --ppn 2 bind-to socket is incorrect. For two socket machines: If I use --bind-to socket I expect one rank on one socket, and the other on the other socket. If I use --bind-to socket:1 I expect both ranks on the same socket. If I use --bind-to socket:2 I expect one rank on each socket (ie the same as --bind-to socket for a two socket machine) Please let me know if that's incorrect. Here's trying various socket counts - using hwloc and looking at /proc/$$/status --bind-to socket - I expect each rank to get it's own socket - but that doesn't happen hydra-3.0.4/mpiexec.hydra --prepend-pattern "%h.%r " --ppn=2 --launcher=ssh --host=jericho101 --bind-to socket utils/get_affinity 2> /dev/null jericho101.0 Affinity from /proc/$$/status : 00ff00ff 0-7,16-23 jericho101.1 Affinity from /proc/$$/status : 00ff00ff 0-7,16-23 jericho101.1 Affinity from hwloc-bind --get : 0x00ff00ff jericho101.0 Affinity from hwloc-bind --get : 0x00ff00ff socket:1 - both processes bound to the same socket. This is what I expect socket:1 to do. hydra-3.0.4/mpiexec.hydra --prepend-pattern "%h.%r " --ppn=2 --launcher=ssh --host=jericho101 --bind-to socket:1 utils/get_affinity jericho101.0 Affinity from /proc/$$/status : 00ff00ff 0-7,16-23 jericho101.1 Affinity from /proc/$$/status : 00ff00ff 0-7,16-23 jericho101.0 Affinity from hwloc-bind --get : 0x00ff00ff jericho101.1 Affinity from hwloc-bind --get : 0x00ff00ff socket:2 - I end up with the same binding as socket and socket:1 hydra-3.0.4/mpiexec.hydra --prepend-pattern "%h.%r " --ppn=2 --launcher=ssh --host=jericho101 --bind-to socket:2 utils/get_affinity jericho101.0 Affinity from /proc/$$/status : 00ff00ff 0-7,16-23 jericho101.1 Affinity from /proc/$$/status : 00ff00ff 0-7,16-23 jericho101.0 Affinity from hwloc-bind --get : 0x00ff00ff jericho101.1 Affinity from hwloc-bind --get : 0x00ff00ff socket:3 - this gets strange - this is the affinity I want! hydra-3.0.4/mpiexec.hydra --prepend-pattern "%h.%r " --ppn=2 --launcher=ssh --host=jericho101 --bind-to socket:3 utils/get_affinity jericho101.0 Affinity from /proc/$$/status : 00ff00ff 0-7,16-23 jericho101.1 Affinity from /proc/$$/status : ff00ff00 8-15,24-31 jericho101.0 Affinity from hwloc-bind --get : 0x00ff00ff jericho101.1 Affinity from hwloc-bind --get : 0xff00ff00 I was originally was asked to look at this because of bad runtimes on faster hardware - fixing the affinity fixed the performance problem. For the test case I was using binding each process to a socket gave me 8% better performance so it's definitely worth working on. Let me know what I can do to help - I don't mind gdbing into mpiexec or something or shoving prints into the code. Also a probably silly question - Does hydra_pmi_proxy figure out and set the affinity? That seems the logical place. I should also note that the other machine where --bind-to socket, socket:1 does the right thing seems to do the wrong thing at socket:2 Of course this all assumes I'm interpreting that socket option correctly. hydra-3.0.4/mpiexec.hydra --prepend-pattern "%h.%r " --ppn=2 --launcher=ssh --host=abrams211a --bind-to socket utils/get_affinity abrams211a.0 Affinity from /proc/$$/status : 00555555 0,2,4,6,8,10,12,14,16,18,20,22 abrams211a.1 Affinity from /proc/$$/status : 00aaaaaa 1,3,5,7,9,11,13,15,17,19,21,23 abrams211a.0 Affinity from hwloc-bind --get : 0x00555555 abrams211a.1 Affinity from hwloc-bind --get : 0x00aaaaaa mpiexec.hydra --prepend-pattern "%h.%r " --ppn=2 --launcher=ssh --host=abrams211a --bind-to socket:1 utils/get_affinity abrams211a.0 Affinity from /proc/$$/status : 00555555 0,2,4,6,8,10,12,14,16,18,20,22 abrams211a.1 Affinity from /proc/$$/status : 00aaaaaa 1,3,5,7,9,11,13,15,17,19,21,23 abrams211a.0 Affinity from hwloc-bind --get : 0x00555555 abrams211a.1 Affinity from hwloc-bind --get : 0x00aaaaaa hydra-3.0.4/mpiexec.hydra --prepend-pattern "%h.%r " --ppn=2 --launcher=ssh --host=abrams211a --bind-to socket:2 utils/get_affinity abrams211a.0 Affinity from /proc/$$/status : 00555555 0,2,4,6,8,10,12,14,16,18,20,22 abrams211a.1 Affinity from /proc/$$/status : 00555555 0,2,4,6,8,10,12,14,16,18,20,22 abrams211a.0 Affinity from hwloc-bind --get : 0x00555555 abrams211a.1 Affinity from hwloc-bind --get : 0x00555555 On 09/18/2013 01:50 AM, Ken Raffenetti wrote:
Hi Bill,
I'm not seeing any obvious problems. However, in my own testing, I found a situation where the grep method you used was unreliable. Can you try using "hwloc-bind --get" instead and see if the results differ?
Ken
----- Original Message -----
From: "Bill Ryder" <[email protected]> To: [email protected] Sent: Monday, September 16, 2013 6:04:45 PM Subject: [mpich-discuss] affinity problems with mpiexec.hydra 3.0.4
Greetings all,
I'm trying set affinity for mybrid MPI/OpenMP tasks.
I want to run two processes on a host, and give one socket to one rank, and the other socket to the other rank.
I have two types of hardware - one works perfectly - the other doesn't.
I first saw the problem using mpiexec.hydra with slurm but I've moved to using ssh to remove some possible variables
I have a trivial script which just greps out /proc/$$/status for the Cpus_allowed mask and Cpus_allowed_list
It's just: echo "`hostname` $PMI_RANK `grep Cpus_allowed /proc/$$/status`"
On the machine that is doing what I want I get:
mpiexec.hydra -ppn 2 -hosts abrams201a --bind-to socket -launcher ssh ./get_mapping abrams201a 0 Cpus_allowed: 00555555 Cpus_allowed_list: 0,2,4,6,8,10,12,14,16,18,20,22 abrams201a 1 Cpus_allowed: 00aaaaaa Cpus_allowed_list: 1,3,5,7,9,11,13,15,17,19,21,23
rank 0 gets one socket, rank 1 gets the other socket. This is what I want
But on my other machine with a different topology I get this:
mpiexec.hydra -ppn 2 -hosts jericho101 --bind-to socket -launcher ssh ./get_mapping
jericho101 0 Cpus_allowed: 00000000,00ff00ff Cpus_allowed_list: 0-7,16-23 jericho101 1 Cpus_allowed: 00000000,00ff00ff Cpus_allowed_list: 0-7,16-23
So each rank is trying to use the same socket.
Similarly if I try to bind to a numanode
mpiexec.hydra -ppn 2 -hosts jericho101 --bind-to numa -launcher ssh ./get_mapping jericho101 1 Cpus_allowed: 00000000,00ff00ff Cpus_allowed_list: 0-7,16-23 jericho101 0 Cpus_allowed: 00000000,00ff00ff Cpus_allowed_list: 0-7,16-23
Or even if I send numa:2
mpiexec.hydra -ppn 2 -hosts jericho101 --bind-to numa:2 -launcher ssh ./get_mapping
jericho101 0 Cpus_allowed: 00000000,00ff00ff Cpus_allowed_list: 0-7,16-23 jericho101 1 Cpus_allowed: 00000000,00ff00ff Cpus_allowed_list: 0-7,16-23
So once again instead of handing a numa node to each process - it's handing the same node to both.
How would I start debugging this?
Or am I missing something really obvious
Thanks! ---------
Bill Ryder Weta Digital
A bit more data:
mpiexec.hydra --info HYDRA build details: Version: 3.0.4 Release Date: Wed Apr 24 10:08:10 CDT 2013 CC: cc CXX: F77: F90: Configure options: '--prefix=/tech/apps/mpich/hydra' Process Manager: pmi Launchers available: ssh rsh fork slurm ll lsf sge manual persist Topology libraries available: hwloc Resource management kernels available: user slurm ll lsf sge pbs cobalt Checkpointing libraries available: Demux engines available: poll select
I have hwloc 1.3.1 installed locally on each machine
abrams201a looks like:
Machine (48GB) NUMANode L#0 (P#1 24GB) + Socket L#0 + L3 L#0 (12MB) L2 L#0 (256KB) + L1 L#0 (32KB) + Core L#0 PU L#0 (P#0) PU L#1 (P#12) L2 L#1 (256KB) + L1 L#1 (32KB) + Core L#1 PU L#2 (P#2) PU L#3 (P#14) L2 L#2 (256KB) + L1 L#2 (32KB) + Core L#2 PU L#4 (P#4) PU L#5 (P#16) L2 L#3 (256KB) + L1 L#3 (32KB) + Core L#3 PU L#6 (P#6) PU L#7 (P#18) L2 L#4 (256KB) + L1 L#4 (32KB) + Core L#4 PU L#8 (P#8) PU L#9 (P#20) L2 L#5 (256KB) + L1 L#5 (32KB) + Core L#5 PU L#10 (P#10) PU L#11 (P#22) NUMANode L#1 (P#0 24GB) + Socket L#1 + L3 L#1 (12MB) L2 L#6 (256KB) + L1 L#6 (32KB) + Core L#6 PU L#12 (P#1) PU L#13 (P#13) L2 L#7 (256KB) + L1 L#7 (32KB) + Core L#7 PU L#14 (P#3) PU L#15 (P#15) L2 L#8 (256KB) + L1 L#8 (32KB) + Core L#8 PU L#16 (P#5) PU L#17 (P#17) L2 L#9 (256KB) + L1 L#9 (32KB) + Core L#9 PU L#18 (P#7) PU L#19 (P#19) L2 L#10 (256KB) + L1 L#10 (32KB) + Core L#10 PU L#20 (P#9) PU L#21 (P#21) L2 L#11 (256KB) + L1 L#11 (32KB) + Core L#11 PU L#22 (P#11) PU L#23 (P#23) HostBridge L#0 PCIBridge PCI 8086:10e7 Net L#0 "eth0" PCI 8086:10e7 Net L#1 "eth1" PCIBridge PCI 15b3:6746 Net L#2 "eth2" OpenFabrics L#3 "mlx4_0" PCI 15b3:6746 PCI 15b3:6746 PCI 15b3:6746 PCIBridge PCI 102b:0533 PCI 8086:3a20 Block L#4 "sda"
And jericho101 looks like:
achine (96GB) NUMANode L#0 (P#0 48GB) Socket L#0 + L3 L#0 (20MB) L2 L#0 (256KB) + L1 L#0 (32KB) + Core L#0 PU L#0 (P#0) PU L#1 (P#16) L2 L#1 (256KB) + L1 L#1 (32KB) + Core L#1 PU L#2 (P#1) PU L#3 (P#17) L2 L#2 (256KB) + L1 L#2 (32KB) + Core L#2 PU L#4 (P#2) PU L#5 (P#18) L2 L#3 (256KB) + L1 L#3 (32KB) + Core L#3 PU L#6 (P#3) PU L#7 (P#19) L2 L#4 (256KB) + L1 L#4 (32KB) + Core L#4 PU L#8 (P#4) PU L#9 (P#20) L2 L#5 (256KB) + L1 L#5 (32KB) + Core L#5 PU L#10 (P#5) PU L#11 (P#21) L2 L#6 (256KB) + L1 L#6 (32KB) + Core L#6 PU L#12 (P#6) PU L#13 (P#22) L2 L#7 (256KB) + L1 L#7 (32KB) + Core L#7 PU L#14 (P#7) PU L#15 (P#23) HostBridge L#0 PCIBridge PCI 14e4:168e Net L#0 "eth0" PCI 14e4:168e Net L#1 "eth1" PCI 14e4:168e Net L#2 "eth2" PCI 14e4:168e Net L#3 "eth3" PCI 14e4:168e Net L#4 "eth4" PCI 14e4:168e Net L#5 "eth5" PCI 14e4:168e Net L#6 "eth6" PCI 14e4:168e Net L#7 "eth7" PCIBridge PCI 103c:323b Block L#8 "sda" PCIBridge PCI 102b:0533 NUMANode L#1 (P#1 48GB) + Socket L#1 + L3 L#1 (20MB) L2 L#8 (256KB) + L1 L#8 (32KB) + Core L#8 PU L#16 (P#8) PU L#17 (P#24) L2 L#9 (256KB) + L1 L#9 (32KB) + Core L#9 PU L#18 (P#9) PU L#19 (P#25) L2 L#10 (256KB) + L1 L#10 (32KB) + Core L#10 PU L#20 (P#10) PU L#21 (P#26) L2 L#11 (256KB) + L1 L#11 (32KB) + Core L#11 PU L#22 (P#11) PU L#23 (P#27) L2 L#12 (256KB) + L1 L#12 (32KB) + Core L#12 PU L#24 (P#12) PU L#25 (P#28) L2 L#13 (256KB) + L1 L#13 (32KB) + Core L#13 PU L#26 (P#13) PU L#27 (P#29) L2 L#14 (256KB) + L1 L#14 (32KB) + Core L#14 PU L#28 (P#14) PU L#29 (P#30) L2 L#15 (256KB) + L1 L#15 (32KB) + Core L#15 PU L#30 (P#15) PU L#31 (P#31)
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