Hi again,

I think the problem is solved. Thanks to Gus, I've tried
mpirun -mca mpi_paffinity_alone 1
while running the program, and I've made a quick search on that, it assures that every program works on a specific core I guess.
(correct me if I'm wrong).
I've ran over 20 tests, and now it works fine.

Thanks a lot,

Saygin

On Thu, Aug 12, 2010 at 11:39 AM, Saygin Arkan <saygenius@gmail.com> wrote:
Hi Gus,

1 - first of all, turning off hyper-threading is not an option. And it gives pretty good results if I can find a way to arrange the cores.

2 - Actually Eugene (one of her messages in this thread) had suggested to arrange the slots.
I did and wrote the results, it delivers the cores randomly, nothing changed.
but I haven't checked loadbalance option. -byslot or -bynode is not gonna help.

3 - Could you give me a bit more detail how affinity works? or what it does actually?

Thanks a lot for your suggestions

Saygin


On Wed, Aug 11, 2010 at 6:18 PM, Gus Correa <gus@ldeo.columbia.edu> wrote:
Hi Saygin

You could:

1) turn off hyperthreading (on BIOS), or

2) use the mpirun options (you didn't send your mpirun command)
to distribute the processes across the nodes, cores, etc.
"man mpirun" is a good resource, see the explanations about
the -byslot, -bynode, -loadbalance options.

3) In addition, you can use the mca parameters to set processor affinity
in the mpirun command line "mpirun -mca mpi_paffinity_alone 1 ..."
I don't know how this will play in a hyperthreaded machine,
but it works fine in our dual processor quad-core computers
(not hyperthreaded).

Depending on your code, hyperthreading may not help performance anyway.

I hope this helps,
Gus Correa

Saygin Arkan wrote:
Hello,

I'm running mpi jobs in non-homogeneous cluster. 4 of my machines have the following properties, os221, os222, os223, os224:

vendor_id       : GenuineIntel
cpu family      : 6
model           : 23
model name      : Intel(R) Core(TM)2 Quad  CPU   Q9300  @ 2.50GHz
stepping        : 7
cache size      : 3072 KB
physical id     : 0
siblings        : 4
core id         : 3
cpu cores       : 4
fpu             : yes
fpu_exception   : yes
cpuid level     : 10
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good pni monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr sse4_1 lahf_lm
bogomips        : 4999.40
clflush size    : 64
cache_alignment : 64
address sizes   : 36 bits physical, 48 bits virtual

and the problematic, hyper-threaded 2 machines are as follows, os228 and os229:

vendor_id       : GenuineIntel
cpu family      : 6
model           : 26
model name      : Intel(R) Core(TM) i7 CPU         920  @ 2.67GHz
stepping        : 5
cache size      : 8192 KB
physical id     : 0
siblings        : 8
core id         : 3
cpu cores       : 4
fpu             : yes
fpu_exception   : yes
cpuid level     : 11
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts rep_good pni monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr sse4_1 sse4_2 popcnt lahf_lm ida
bogomips        : 5396.88
clflush size    : 64
cache_alignment : 64
address sizes   : 36 bits physical, 48 bits virtual


The problem is: those 2 machines seem to be having 8 cores (virtually, actualy core number is 4).
When I submit an MPI job, I calculated the comparison times in the cluster. I got strange results.

I'm running the job on 6 nodes, 3 core per node. And sometimes ( I can say 1/3 of the tests) os228 or os229 returns strange results. 2 cores are slow (slower than the first 4 nodes) but the 3rd core is extremely fast.

2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - RANK(0) Printing Times...
2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - os221 RANK(1)    :38 sec
2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - os222 RANK(2)    :38 sec
2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - os224 RANK(3)    :38 sec
2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - os228 RANK(4)    :37 sec
2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - os229 RANK(5)    :34 sec
2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - os223 RANK(6)    :38 sec
2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - os221 RANK(7)    :39 sec
2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - os222 RANK(8)    :37 sec
2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - os224 RANK(9)    :38 sec
2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - os228 RANK(10)    :*48 sec*
2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - os229 RANK(11)    :35 sec
2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - os223 RANK(12)    :38 sec
2010-08-05 14:30:58,926 50672 DEBUG [0x7fcadf98c740] - os221 RANK(13)    :37 sec
2010-08-05 14:30:58,926 50673 DEBUG [0x7fcadf98c740] - os222 RANK(14)    :37 sec
2010-08-05 14:30:58,926 50673 DEBUG [0x7fcadf98c740] - os224 RANK(15)    :38 sec
2010-08-05 14:30:58,926 50673 DEBUG [0x7fcadf98c740] - os228 RANK(16)    :*43 sec*
2010-08-05 14:30:58,926 50673 DEBUG [0x7fcadf98c740] - os229 RANK(17)    :35 sec
TOTAL CORRELATION TIME: 48 sec


or another test:

2010-08-09 15:28:10,947 272904 DEBUG [0x7f27dec27740] - RANK(0) Printing Times...
2010-08-09 15:28:10,947 272904 DEBUG [0x7f27dec27740] - os221 RANK(1)    :170 sec
2010-08-09 15:28:10,947 272904 DEBUG [0x7f27dec27740] - os222 RANK(2)    :161 sec
2010-08-09 15:28:10,947 272904 DEBUG [0x7f27dec27740] - os224 RANK(3)    :158 sec
2010-08-09 15:28:10,947 272904 DEBUG [0x7f27dec27740] - os228 RANK(4)    :142 sec
2010-08-09 15:28:10,947 272904 DEBUG [0x7f27dec27740] - os229 RANK(5)    :*256 sec*
2010-08-09 15:28:10,947 272904 DEBUG [0x7f27dec27740] - os223 RANK(6)    :156 sec
2010-08-09 15:28:10,947 272904 DEBUG [0x7f27dec27740] - os221 RANK(7)    :162 sec
2010-08-09 15:28:10,947 272905 DEBUG [0x7f27dec27740] - os222 RANK(8)    :159 sec
2010-08-09 15:28:10,947 272905 DEBUG [0x7f27dec27740] - os224 RANK(9)    :168 sec
2010-08-09 15:28:10,947 272905 DEBUG [0x7f27dec27740] - os228 RANK(10)    :141 sec
2010-08-09 15:28:10,947 272905 DEBUG [0x7f27dec27740] - os229 RANK(11)    :136 sec
2010-08-09 15:28:10,947 272905 DEBUG [0x7f27dec27740] - os223 RANK(12)    :173 sec
2010-08-09 15:28:10,947 272905 DEBUG [0x7f27dec27740] - os221 RANK(13)    :164 sec
2010-08-09 15:28:10,947 272905 DEBUG [0x7f27dec27740] - os222 RANK(14)    :171 sec
2010-08-09 15:28:10,947 272905 DEBUG [0x7f27dec27740] - os224 RANK(15)    :156 sec
2010-08-09 15:28:10,947 272905 DEBUG [0x7f27dec27740] - os228 RANK(16)    :136 sec
2010-08-09 15:28:10,947 272905 DEBUG [0x7f27dec27740] - os229 RANK(17)    :*250 sec*
2010-08-09 15:28:10,947 272905 DEBUG [0x7f27dec27740] - TOTAL CORRELATION TIME: 256 sec


Do you have any idea? Why it is happening?
I assume that it gives 2 jobs to 2 cores in os229, but actually those 2 are one core.
Do you have any idea? If you have, how can I fix it? because the longest time affects the whole time information. 100 sec delay is too much for 250 sec comparison time,
and it might have finish around 160 sec.



--
Saygin


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