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CPati2
New Contributor III
75 Views

Intel Xeon Phi Thread To Core Mapping

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Hi All,

On Xeon Phi, if I run an application with 32 threads and 64 active cores (max 64*4 threads) then will the system allocate:

1) 1 thread to each core 
2) 4 thread to each core
3) Or, I need to map the threads in the code using affinity or flag like KMP_AFFINITY?

Thanks.

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1 Solution
McCalpinJohn
Black Belt
75 Views

The answer is definitely (3).

The tools available for binding depend on the software you are using.  Binding controls are available from Linux (taskset & numactl for external use, and sched_setaffinity() for inline use), from the OpenMP runtime library (using GNU, OpenMP, or Intel-specific environment variables), from the MPI library (again, different options for different implementations).

It is not always easy to understand the interactions of these mechanisms, and it is sometimes difficult to find all of the relevant environment variables for each of the software layers.  Fortunately, the Intel software usually makes it easy to see what binding is actually being applied, so you can keep fiddling until you get the desired behavior.  For codes using the Intel MPI library, I use "I_MPI_DEBUG=4" (or any higher value), and for codes using the Intel Fortran and/or C compilers (including MPI codes), I add the "verbose" option to the KMP_AFFINITY variable.
 

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6 Replies
James_C_Intel2
Employee
75 Views

If you don't tell the OS what to do, it will do something :-). This is no different from running a two thread code on a machine that can support more than two logicalCPUs.

If you want to control what happens and force a specific binding, then you need to enforce it. If you're using Intel (or LLVM) OpenMP you cn force that by using the  KMP_HW_SUBSET envirable. If not, then taskset may be your friend.

McCalpinJohn
Black Belt
76 Views

The answer is definitely (3).

The tools available for binding depend on the software you are using.  Binding controls are available from Linux (taskset & numactl for external use, and sched_setaffinity() for inline use), from the OpenMP runtime library (using GNU, OpenMP, or Intel-specific environment variables), from the MPI library (again, different options for different implementations).

It is not always easy to understand the interactions of these mechanisms, and it is sometimes difficult to find all of the relevant environment variables for each of the software layers.  Fortunately, the Intel software usually makes it easy to see what binding is actually being applied, so you can keep fiddling until you get the desired behavior.  For codes using the Intel MPI library, I use "I_MPI_DEBUG=4" (or any higher value), and for codes using the Intel Fortran and/or C compilers (including MPI codes), I add the "verbose" option to the KMP_AFFINITY variable.
 

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jimdempseyatthecove
Black Belt
75 Views

You may wish to use KMP_AFFINITY=scatter

*** However, this will distribute software threads distributed amongst cores (or sockets on MP) starting at the base logical processor. IOW, if you have two (multiple) processes (programs), each may be assigned to the same scattered hardware threads.

In addition to KMP_HW_SUBSET (or taskset) you have OMP_PLACES and OMP_PROC_BIND.

See: http://pages.tacc.utexas.edu/~eijkhout/pcse/html/omp-affinity.html

Jim Dempsey

CPati2
New Contributor III
75 Views

Hi James

Cownie, James H (Intel) wrote:

If you don't tell the OS what to do, it will do something :-). This is no different from running a two thread code on a machine that can support more than two logicalCPUs.

System Details:

  • Operating System: CentOS Linux 7 (Core)
  • Kernel: Linux 3.10.0-514.10.2.el7.x86_64
  • Architecture: x86-64 Intel(R) Xeon Phi(TM) CPU 7210 @ 1.30GHz

Hi John

McCalpin, John wrote:

It is not always easy to understand the interactions of these mechanisms, and it is sometimes difficult to find all of the relevant environment variables for each of the software layers.  Fortunately, the Intel software usually makes it easy to see what binding is actually being applied, so you can keep fiddling until you get the desired behavior.  For codes using the Intel MPI library, I use "I_MPI_DEBUG=4" (or any higher value), and for codes using the Intel Fortran and/or C compilers (including MPI codes), I add the "verbose" option to the KMP_AFFINITY variable.

What if I am using standard benchmarks that Intel suggest to run using micprun in this document (page 9)?

Also, validation of whether they are running correctly on the cores is required, hence my question of core utilization which I assume will help me validate threads and where they are running.

CPati2
New Contributor III
75 Views

Hi James,

Cownie, James H (Intel) wrote:

If you want to control what happens and force a specific binding, then you need to enforce it. If you're using Intel (or LLVM) OpenMP you cn force that by using the  KMP_HW_SUBSET envirable. If not, then taskset may be your friend.

I did a small experiment:

Benchmark: micprun -k linpack -p "--omp_num_threads 192 --matrix_size 40960 --num_rep 1"
Validation: turbostat

Using above approach, it seems the 192 threads were equally distributed to all the available physical and virtual (threads) cores. Each core got 3 threads. I am validating this based on the "%Busy" column in below log. Same observation is valid for 16/32/64/128/256 threads. 

Is my intuition that threads are distributed equally among all the available resources correct? May be the linkpack benchmark has flag that is taking care of this, but I don't have the source used by micprun to validate the coding methodology used.

Log:

     CPU Avg_MHz   %Busy Bzy_MHz TSC_MHz     SMI  CPU%c1  CPU%c6 CoreTmp  PkgTmp Pkg%pc3 Pkg%pc6 PkgWatt RAMWatt   PKG_%   RAM_%
       -     975   75.01    1300    1300       0   24.99    0.00      34      36    0.00    0.00  119.19   10.29    0.00    0.00
       0    1299   99.90    1300    1300       0    0.10    0.00      33      36    0.00    0.00  119.19   10.29    0.00    0.00
      64    1299   99.90    1300    1300       0    0.10
     128    1299   99.90    1300    1300       0    0.10
     192     199   15.34    1300    1300       0   84.66
       1    1299   99.90    1300    1300       0    0.10    0.00      33
      65    1299   99.90    1300    1300       0    0.10
     129    1299   99.90    1300    1300       0    0.10
     193       1    0.08    1301    1300       0   99.92
       2    1299   99.90    1300    1300       0    0.10    0.00      32
      66    1299   99.90    1300    1300       0    0.10
     130    1299   99.90    1300    1300       0    0.10
     194       1    0.08    1334    1300       0   99.92
       3    1299   99.90    1300    1300       0    0.10    0.00      32
      67    1299   99.90    1300    1300       0    0.10
     131    1299   99.90    1300    1300       0    0.10
     195       2    0.15    1301    1300       0   99.85
       4    1299   99.90    1300    1300       0    0.10    0.00      31
      68    1299   99.90    1300    1300       0    0.10
     132    1299   99.90    1300    1300       0    0.10
     196       1    0.04    1303    1300       0   99.96
       5    1299   99.90    1300    1300       0    0.10    0.00      31
      69    1299   99.90    1300    1300       0    0.10
     133    1299   99.90    1300    1300       0    0.10
     197       1    0.06    1279    1300       0   99.94
       6    1299   99.90    1300    1300       0    0.10    0.00      32
      70    1299   99.90    1300    1300       0    0.10
     134    1299   99.90    1300    1300       0    0.10
     198       1    0.05    1298    1300       0   99.95
       7    1299   99.90    1300    1300       0    0.10    0.00      32
      71    1299   99.90    1300    1300       0    0.10
     135    1299   99.90    1300    1300       0    0.10
     199       6    0.47    1300    1300       0   99.53
       8    1299   99.90    1300    1300       0    0.10    0.00      33
      72    1299   99.90    1300    1300       0    0.10
     136    1299   99.90    1300    1300       0    0.10
     200       1    0.07    1297    1300       0   99.93
       9    1299   99.90    1300    1300       0    0.10    0.00      34
      73    1299   99.90    1300    1300       0    0.10
     137    1299   99.90    1300    1300       0    0.10
     201       1    0.06    1298    1300       0   99.94
      10    1299   99.90    1300    1300       0    0.10    0.00      33
      74    1299   99.90    1300    1300       0    0.10
     138    1299   99.90    1300    1300       0    0.10
     202       1    0.05    1303    1300       0   99.95
      11    1299   99.90    1300    1300       0    0.10    0.00      33
      75    1299   99.90    1300    1300       0    0.10
     139    1299   99.90    1300    1300       0    0.10
     203       0    0.04    1301    1300       0   99.96
      12    1298   99.90    1300    1300       0    0.10    0.00      31
      76    1298   99.90    1300    1300       0    0.10
     140    1298   99.90    1300    1300       0    0.10
     204       1    0.07    1303    1300       0   99.93
      13    1298   99.90    1300    1300       0    0.10    0.00      31
      77    1298   99.90    1300    1300       0    0.10
     141    1298   99.90    1300    1300       0    0.10
     205       1    0.05    1301    1300       0   99.95
      14    1298   99.90    1300    1300       0    0.10    0.00      33
      78    1298   99.90    1300    1300       0    0.10
     142    1298   99.90    1300    1300       0    0.10
     206       1    0.05    1300    1300       0   99.95
      15    1299   99.90    1300    1300       0    0.10    0.00      33
      79    1299   99.90    1300    1300       0    0.10
     143    1299   99.90    1300    1300       0    0.10
     207       1    0.05    1298    1300       0   99.95
      16    1299   99.90    1300    1300       0    0.10    0.00      32
      80    1299   99.90    1300    1300       0    0.10
     144    1299   99.90    1300    1300       0    0.10
     208       1    0.08    1301    1300       0   99.92
      17    1299   99.90    1300    1300       0    0.10    0.00      32
      81    1299   99.90    1300    1300       0    0.10
     145    1299   99.90    1300    1300       0    0.10
     209       1    0.06    1301    1300       0   99.94
      18    1299   99.90    1300    1300       0    0.10    0.00      31
      82    1299   99.90    1300    1300       0    0.10
     146    1299   99.90    1300    1300       0    0.10
     210       1    0.04    1302    1300       0   99.96
      19    1299   99.90    1300    1300       0    0.10    0.00      31
      83    1299   99.90    1300    1300       0    0.10
     147    1299   99.90    1300    1300       0    0.10
     211       1    0.06    1300    1300       0   99.94
      20    1299   99.90    1300    1300       0    0.10    0.00      32
      84    1299   99.90    1300    1300       0    0.10
     148    1299   99.90    1300    1300       0    0.10
     212       1    0.06    1298    1300       0   99.94
      21    1299   99.90    1300    1300       0    0.10    0.00      32
      85    1299   99.90    1300    1300       0    0.10
     149    1299   99.90    1300    1300       0    0.10
     213       1    0.04    1300    1300       0   99.96
      22    1299   99.90    1300    1300       0    0.10    0.00      31
      86    1299   99.90    1300    1300       0    0.10
     150    1299   99.90    1300    1300       0    0.10
     214       1    0.05    1301    1300       0   99.95
      23    1299   99.90    1300    1300       0    0.10    0.00      32
      87    1299   99.90    1300    1300       0    0.10
     151    1299   99.90    1300    1300       0    0.10
     215       1    0.05    1299    1300       0   99.95
      24    1299   99.90    1300    1300       0    0.10    0.00      32
      88    1299   99.90    1300    1300       0    0.10
     152    1299   99.90    1300    1300       0    0.10
     216       1    0.05    1300    1300       0   99.95
      25    1299   99.90    1300    1300       0    0.10    0.00      32
      89    1299   99.90    1300    1300       0    0.10
     153    1299   99.90    1300    1300       0    0.10
     217       1    0.06    1298    1300       0   99.94
      26    1299   99.90    1300    1300       0    0.10    0.00      32
      90    1299   99.90    1300    1300       0    0.10
     154    1299   99.90    1300    1300       0    0.10
     218       1    0.05    1299    1300       0   99.95
      27    1299   99.90    1300    1300       0    0.10    0.00      32
      91    1299   99.90    1300    1300       0    0.10
     155    1299   99.90    1300    1300       0    0.10
     219       1    0.05    1299    1300       0   99.95
      28    1299   99.90    1300    1300       0    0.10    0.00      32
      92    1299   99.90    1300    1300       0    0.10
     156    1299   99.90    1300    1300       0    0.10
     220       1    0.04    1301    1300       0   99.96
      29    1299   99.90    1300    1300       0    0.10    0.00      32
      93    1299   99.90    1300    1300       0    0.10
     157    1299   99.90    1300    1300       0    0.10
     221       1    0.04    1299    1300       0   99.96
      30    1299   99.90    1300    1300       0    0.10    0.00      33
      94    1299   99.90    1300    1300       0    0.10
     158    1299   99.90    1300    1300       0    0.10
     222       1    0.05    1302    1300       0   99.95
      31    1299   99.90    1300    1300       0    0.10    0.00      33
      95    1299   99.90    1300    1300       0    0.10
     159    1299   99.90    1300    1300       0    0.10
     223       1    0.04    1155    1300       0   99.96
      32    1299   99.90    1300    1300       0    0.10    0.00      32
      96    1299   99.90    1300    1300       0    0.10
     160    1299   99.90    1300    1300       0    0.10
     224       1    0.04    1302    1300       0   99.96
      33    1299   99.90    1300    1300       0    0.10    0.00      32
      97    1299   99.90    1300    1300       0    0.10
     161    1299   99.90    1300    1300       0    0.10
     225       1    0.04    1302    1300       0   99.96
      34    1299   99.90    1300    1300       0    0.10    0.00      32
      98    1299   99.90    1300    1300       0    0.10
     162    1299   99.90    1300    1300       0    0.10
     226       1    0.04    1298    1300       0   99.96
      35    1299   99.90    1300    1300       0    0.10    0.00      32
      99    1299   99.90    1300    1300       0    0.10
     163    1299   99.90    1300    1300       0    0.10
     227       1    0.04    1296    1300       0   99.96
      36    1299   99.90    1300    1300       0    0.10    0.00      31
     100    1299   99.90    1300    1300       0    0.10
     164    1299   99.90    1300    1300       0    0.10
     228       1    0.05    1302    1300       0   99.95
      37    1299   99.90    1300    1300       0    0.10    0.00      31
     101    1299   99.90    1300    1300       0    0.10
     165    1299   99.90    1300    1300       0    0.10
     229       1    0.10    1300    1300       0   99.90
      38    1299   99.90    1300    1300       0    0.10    0.00      32
     102    1299   99.90    1300    1300       0    0.10
     166    1299   99.90    1300    1300       0    0.10
     230       1    0.05    1300    1300       0   99.95
      39    1299   99.90    1300    1300       0    0.10    0.00      32
     103    1299   99.90    1300    1300       0    0.10
     167    1299   99.90    1300    1300       0    0.10
     231       1    0.05    1301    1300       0   99.95
      40    1299   99.90    1300    1300       0    0.10    0.00      32
     104    1299   99.90    1300    1300       0    0.10
     168    1299   99.90    1300    1300       0    0.10
     232       1    0.05    1302    1300       0   99.95
      41    1299   99.90    1300    1300       0    0.10    0.00      32
     105    1299   99.90    1300    1300       0    0.10
     169    1299   99.90    1300    1300       0    0.10
     233       1    0.04    1296    1300       0   99.96
      42    1299   99.90    1300    1300       0    0.10    0.00      32
     106    1299   99.90    1300    1300       0    0.10
     170    1299   99.90    1300    1300       0    0.10
     234       1    0.05    1299    1300       0   99.95
      43    1299   99.90    1300    1300       0    0.10    0.00      32
     107    1299   99.90    1300    1300       0    0.10
     171    1299   99.90    1300    1300       0    0.10
     235       1    0.05    1298    1300       0   99.95
      44    1299   99.90    1300    1300       0    0.10    0.00      31
     108    1299   99.90    1300    1300       0    0.10
     172    1299   99.90    1300    1300       0    0.10
     236       1    0.08    1300    1300       0   99.92
      45    1299   99.90    1300    1300       0    0.10    0.00      31
     109    1299   99.90    1300    1300       0    0.10
     173    1299   99.90    1300    1300       0    0.10
     237       1    0.05    1303    1300       0   99.95
      46    1299   99.90    1300    1300       0    0.10    0.00      31
     110    1299   99.90    1300    1300       0    0.10
     174    1299   99.90    1300    1300       0    0.10
     238       1    0.04    1304    1300       0   99.96
      47    1299   99.90    1300    1300       0    0.10    0.00      31
     111    1299   99.90    1300    1300       0    0.10
     175    1299   99.90    1300    1300       0    0.10
     239       1    0.05    1390    1300       0   99.95
      48    1299   99.90    1300    1300       0    0.10    0.00      32
     112    1299   99.90    1300    1300       0    0.10
     176    1299   99.90    1300    1300       0    0.10
     240       1    0.05    1302    1300       0   99.95
      49    1299   99.90    1300    1300       0    0.10    0.00      32
     113    1299   99.90    1300    1300       0    0.10
     177    1299   99.90    1300    1300       0    0.10
     241       1    0.05    1299    1300       0   99.95
      50    1299   99.90    1300    1300       0    0.10    0.00      30
     114    1299   99.90    1300    1300       0    0.10
     178    1299   99.90    1300    1300       0    0.10
     242       1    0.06    1304    1300       0   99.94
      51    1299   99.90    1300    1300       0    0.10    0.00      30
     115    1299   99.90    1300    1300       0    0.10
     179    1299   99.90    1300    1300       0    0.10
     243       1    0.05    1303    1300       0   99.95
      52    1299   99.90    1300    1300       0    0.10    0.00      31
     116    1299   99.90    1300    1300       0    0.10
     180    1299   99.90    1300    1300       0    0.10
     244       1    0.06    1182    1300       0   99.94
      53    1299   99.90    1300    1300       0    0.10    0.00      32
     117    1299   99.90    1300    1300       0    0.10
     181    1299   99.90    1300    1300       0    0.10
     245       1    0.05    1304    1300       0   99.95
      54    1299   99.90    1300    1300       0    0.10    0.00      31
     118    1299   99.90    1300    1300       0    0.10
     182    1299   99.90    1300    1300       0    0.10
     246       1    0.06    1304    1300       0   99.94
      55    1299   99.90    1300    1300       0    0.10    0.00      31
     119    1299   99.90    1300    1300       0    0.10
     183    1299   99.90    1300    1300       0    0.10
     247       1    0.05    1302    1300       0   99.95
      56    1299   99.90    1300    1300       0    0.10    0.00      33
     120    1299   99.90    1300    1300       0    0.10
     184    1299   99.90    1300    1300       0    0.10
     248       1    0.05    1297    1300       0   99.95
      57    1299   99.90    1300    1300       0    0.10    0.00      33
     121    1299   99.90    1300    1300       0    0.10
     185    1299   99.90    1300    1300       0    0.10
     249       6    0.45    1300    1300       0   99.55
      58    1299   99.90    1300    1300       0    0.10    0.00      32
     122    1299   99.90    1300    1300       0    0.10
     186    1299   99.90    1300    1300       0    0.10
     250       1    0.05    1299    1300       0   99.95
      59    1299   99.90    1300    1300       0    0.10    0.00      32
     123    1299   99.90    1300    1300       0    0.10
     187    1299   99.90    1300    1300       0    0.10
     251       1    0.06    1303    1300       0   99.94
      60    1299   99.90    1300    1300       0    0.10    0.00      32
     124    1299   99.90    1300    1300       0    0.10
     188    1299   99.90    1300    1300       0    0.10
     252       1    0.11    1301    1300       0   99.89
      61    1299   99.90    1300    1300       0    0.10    0.00      32
     125    1299   99.90    1300    1300       0    0.10
     189    1299   99.90    1300    1300       0    0.10
     253       3    0.24    1300    1300       0   99.76
      62    1299   99.90    1300    1300       0    0.10    0.00      33
     126    1299   99.90    1300    1300       0    0.10
     190    1299   99.90    1300    1300       0    0.10
     254       1    0.08    1298    1300       0   99.92
      63    1299   99.90    1300    1300       0    0.10    0.00      33
     127    1299   99.90    1300    1300       0    0.10
     191    1299   99.90    1300    1300       0    0.10
     255       9    0.69    1300    1300       0   99.31

 

75 Views

Hi

May be the linkpack benchmark has flag that is taking care of this, but I don't have the source used by micprun to validate the coding methodology used.

Micperf package provides useful help command:

micprun -k linpack -p help

You can dig even deeper as micprun is written in python, I don't recommend it but you can read the code with:

vim `which micprun`

 I case of linpack, micprun just wraps executable provided by MKL.
The KMP_AFFINITY set by micprun is KMP_AFFINITY=compact,1,0

Regards
Sebastian

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