MPI - core assignment/core utilization/process manager difficulties

Jesper_Carlson · February 12, 2013, 9:20am

I am having troubles running my Fortran MPI program on a cluster using PBSPro_11.3.0.121723.

When i execut my script (select information shown here)

#PBS -l select=1:ncpus=8

mpirun -n 8 -env I_MPI_DEBUG 5 ./xhpl_intel64

The scheduler allocates 8 cores for my program however if i ssh into the node and use top i can see that 4 mpiprocesses gets a core each and the last 4 processes shares a core. Thus providing very bad performance.

The wierd thing is that when using the Intel MPI library 4.0.0.028 runtime version this does not happen.

And it does not happen when executed from outside the batch queue

Using the Intel MPI library 4.0.1 and up this happens.

I notice that the < 4.0.1 runtime does not complain about

Setting I_MPI_PROCESS_MANAGER=mpd andadding machinefile $PBS_NODEFILE

will let the previously mentionen 8 core execution run close to 100% CPU however.

if i run 1 8 core job, then submits a 16 core job (thus using the first 8 cores on the same node as the first job and the next 8 nodes on another node)

and follows up with another 8 core job, then the last job and the last 8 cores og the 16 core job are placed on the same cores.

Best regards

Jesper

James_T_Intel · February 12, 2013, 4:01pm

Hi Jesper,

Are you using cpuset? What is the most recent version of the Intel® MPI Library that you’ve tested?

Sincerely,
James Tullos
Technical Consulting Engineer
Intel® Cluster Tools

Jesper_Carlson · February 13, 2013, 1:17pm

Hi James,

As far as i can see the pbs system does not use cpuset (it launches pbs_mon not pbs_mon.cpuset).

I have tried libraries

4.0.0.027

4.0.0.028

these worked, however the software intended to run is compiled using a newer MPI library

-----------------

4.0.1.007

4.0.2.003

4.1.0.024

fails.

I have tried with mpd and with hydra

James_T_Intel · February 13, 2013, 4:20pm

Hi Jesper,

Please send me the debug output (I_MPI_DEBUG=5) from 4.1.0.024.

Sincerely,
James Tullos
Technical Consulting Engineer
Intel® Cluster Tools

Jesper_Carlson · February 15, 2013, 9:21am

I submitted the 3 jobs as described above and got the following output - first qstat - then top on the 2 nodes then output.

qstat

489606.pbsserve s2874169 gccm linp_8 124701 1 8 -- 48:00 R 00:00 n041[0]/0*8

489607.pbsserve s2874169 gccm linp_8 124837 2 16 -- 48:00 R 00:00 n041[0]/1*8+n042[0]/0*8

489608.pbsserve s2874169 gccm linp_8 77214 1 8 -- 48:00 R 00:00 n042[0]/1*8

top

[s2874169@n041 ~]$ top

top - 18:46:17 up 38 days, 4:17, 1 user, load average: 8.12, 2.12, 0.71 Tasks: 486 total, 17 running, 467 sleeping, 0 stopped, 2 zombie Cpu(s): 11.6%us, 0.2%sy, 0.0%ni, 88.2%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Mem: 32826988k total, 29043736k used, 3783252k free, 167704k buffers Swap: 8191992k total, 496k used, 8191496k free, 25257036k cached

PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND

124804 s2874169 20 0 112m 12m 2388 R 98.9 0.0 0:45.31 xhpl_intel64_1

124953 s2874169 20 0 113m 13m 2420 R 98.9 0.0 0:37.90 xhpl_intel64_2

124802 s2874169 20 0 112m 12m 2380 R 97.0 0.0 0:45.23 xhpl_intel64_1

124805 s2874169 20 0 112m 12m 2416 R 97.0 0.0 0:45.23 xhpl_intel64_1

124806 s2874169 20 0 112m 12m 2384 R 97.0 0.0 0:45.14 xhpl_intel64_1

124808 s2874169 20 0 112m 12m 2408 R 97.0 0.0 0:45.27 xhpl_intel64_1

124954 s2874169 20 0 113m 13m 2436 R 97.0 0.0 0:37.87 xhpl_intel64_2

124955 s2874169 20 0 113m 13m 2456 R 97.0 0.0 0:37.84 xhpl_intel64_2

124956 s2874169 20 0 113m 13m 2436 R 97.0 0.0 0:37.84 xhpl_intel64_2

124957 s2874169 20 0 113m 13m 2424 R 97.0 0.0 0:37.85 xhpl_intel64_2

124958 s2874169 20 0 113m 13m 2444 R 97.0 0.0 0:37.89 xhpl_intel64_2

124959 s2874169 20 0 113m 13m 2456 R 97.0 0.0 0:37.86 xhpl_intel64_2

124960 s2874169 20 0 1222m 1.1g 2824 R 97.0 3.5 0:37.88 xhpl_intel64_2

124803 s2874169 20 0 112m 12m 2404 R 95.1 0.0 0:45.32 xhpl_intel64_1

124807 s2874169 20 0 112m 12m 2420 R 95.1 0.0 0:45.26 xhpl_intel64_1

124809 s2874169 20 0 1221m 1.1g 2784 R 95.1 3.5 0:45.15 xhpl_intel64_1

125220 s2874169 20 0 17360 1528 904 R 3.8 0.0 0:00.02 top

[s2874169@n042 ~]$ top top - 18:46:34 up 38 days, 3:37, 0 users, load average: 9.61, 2.69, 0.92 Tasks: 480 total, 17 running, 462 sleeping, 0 stopped, 1 zombie Cpu(s): 5.7%us, 0.1%sy, 0.0%ni, 94.1%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Mem: 32826988k total, 27297112k used, 5529876k free, 163004k buffers Swap: 8191992k total, 0k used, 8191992k free, 24774616k cached

PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND

77314 s2874169 20 0 121m 13m 2428 R 83.7 0.0 0:54.96 xhpl_intel64_2

77320 s2874169 20 0 121m 13m 2452 R 83.7 0.0 0:49.40 xhpl_intel64_2

77313 s2874169 20 0 122m 13m 2456 R 82.1 0.0 0:54.95 xhpl_intel64_2

77315 s2874169 20 0 121m 13m 2444 R 82.1 0.0 0:54.99 xhpl_intel64_2

77394 s2874169 20 0 112m 12m 2408 R 82.1 0.0 0:51.32 xhpl_intel64_3

77396 s2874169 20 0 1221m 1.1g 2776 R 82.1 3.5 0:43.57 xhpl_intel64_3

77316 s2874169 20 0 121m 13m 2436 R 80.5 0.0 0:54.94 xhpl_intel64_2

77391 s2874169 20 0 112m 12m 2424 R 66.0 0.0 0:40.98 xhpl_intel64_3

77390 s2874169 20 0 112m 12m 2416 R 56.3 0.0 0:38.42 xhpl_intel64_3

77395 s2874169 20 0 112m 12m 2396 R 41.8 0.0 0:27.30 xhpl_intel64_3

77317 s2874169 20 0 121m 13m 2444 R 40.2 0.0 0:29.60 xhpl_intel64_2

77318 s2874169 20 0 121m 13m 2432 R 40.2 0.0 0:27.78 xhpl_intel64_2

77319 s2874169 20 0 121m 13m 2444 R 40.2 0.0 0:27.77 xhpl_intel64_2

77389 s2874169 20 0 112m 12m 2384 R 40.2 0.0 0:44.89 xhpl_intel64_3

77392 s2874169 20 0 112m 12m 2404 R 40.2 0.0 0:29.10 xhpl_intel64_3

77393 s2874169 20 0 112m 12m 2384 R 38.6 0.0 0:27.18 xhpl_intel64_3

77675 s2874169 20 0 17360 1536 904 R 1.6 0.0 0:00.01 top

xhpl_intel64_1

/export/home/s2874169/intel/impi/4.1.0.024/intel64/bin/mpirun [2] MPI startup(): shm and ofa data transfer modes [4] MPI startup(): shm and ofa data transfer modes [6] MPI startup(): shm and ofa data transfer modes [3] MPI startup(): shm and ofa data transfer modes [0] MPI startup(): shm and ofa data transfer modes [7] MPI startup(): shm and ofa data transfer modes [1] MPI startup(): shm and ofa data transfer modes [5] MPI startup(): shm and ofa data transfer modes [0] MPI startup(): Rank Pid Node name Pin cpu

[0] MPI startup(): 0 124809 n041 {0,1}

[0] MPI startup(): 1 124802 n041 {2,3}

[0] MPI startup(): 2 124803 n041 {4,5}

[0] MPI startup(): 3 124804 n041 {6,7}

[0] MPI startup(): 4 124805 n041 {8,9}

[0] MPI startup(): 5 124806 n041 {10,11}

[0] MPI startup(): 6 124807 n041 {12,13}

[0] MPI startup(): 7 124808 n041 {14,15}

[0] MPI startup(): I_MPI_DEBUG=5 [0] MPI startup(): I_MPI_FABRICS=shm:ofa

xhpl_intel64_2

/export/home/s2874169/intel/impi/4.1.0.024/intel64/bin/mpirun [4] MPI startup(): shm and ofa data transfer modes [10] MPI startup(): shm and ofa data transfer modes [5] MPI startup(): shm and ofa data transfer modes [12] MPI startup(): shm and ofa data transfer modes [6] MPI startup(): shm and ofa data transfer modes [1] MPI startup(): shm and ofa data transfer modes [3] MPI startup(): shm and ofa data transfer modes [7] MPI startup(): shm and ofa data transfer modes [0] MPI startup(): shm and ofa data transfer modes [15] MPI startup(): shm and ofa data transfer modes [9] MPI startup(): shm and ofa data transfer modes [2] MPI startup(): shm and ofa data transfer modes [13] MPI startup(): shm and ofa data transfer modes [8] MPI startup(): shm and ofa data transfer modes [11] MPI startup(): shm and ofa data transfer modes [14] MPI startup(): shm and ofa data transfer modes [0] MPI startup(): Rank Pid Node name Pin cpu

[0] MPI startup(): 0 124960 n041 {0,1}

[0] MPI startup(): 1 124953 n041 {2,3}

[0] MPI startup(): 2 124954 n041 {4,5}

[0] MPI startup(): 3 124955 n041 {6,7}

[0] MPI startup(): 4 124956 n041 {8,9}

[0] MPI startup(): 5 124957 n041 {10,11}

[0] MPI startup(): 6 124958 n041 {12,13}

[0] MPI startup(): 7 124959 n041 {14,15}

[0] MPI startup(): 8 77313 n042 {0,1}

[0] MPI startup(): 9 77314 n042 {2,3}

[0] MPI startup(): 10 77315 n042 {4,5}

[0] MPI startup(): 11 77316 n042 {6,7}

[0] MPI startup(): 12 77317 n042 {8,9}

[0] MPI startup(): 13 77318 n042 {10,11}

[0] MPI startup(): 14 77320 n042 {12,13}

[0] MPI startup(): 15 77319 n042 {14,15}

[0] MPI startup(): I_MPI_DEBUG=5 [0] MPI startup(): I_MPI_FABRICS=shm:ofa

xhpl_intel64_3

/export/home/s2874169/intel/impi/4.1.0.024/intel64/bin/mpirun [2] MPI startup(): shm and ofa data transfer modes [3] MPI startup(): shm and ofa data transfer modes [0] MPI startup(): shm and ofa data transfer modes [1] MPI startup(): shm and ofa data transfer modes [6] MPI startup(): shm and ofa data transfer modes [7] MPI startup(): shm and ofa data transfer modes [5] MPI startup(): shm and ofa data transfer modes [4] MPI startup(): shm and ofa data transfer modes [0] MPI startup(): Rank Pid Node name Pin cpu

[0] MPI startup(): 0 77396 n042 {0,1}

[0] MPI startup(): 1 77389 n042 {2,3}

[0] MPI startup(): 2 77390 n042 {4,5}

[0] MPI startup(): 3 77391 n042 {6,7}

[0] MPI startup(): 4 77392 n042 {8,9}

[0] MPI startup(): 5 77393 n042 {10,11}

[0] MPI startup(): 6 77394 n042 {12,13}

[0] MPI startup(): 7 77395 n042 {14,15}

[0] MPI startup(): I_MPI_DEBUG=5 [0] MPI startup(): I_MPI_FABRICS=shm:ofa

James_T_Intel · February 15, 2013, 2:20pm

Hi Jesper,

Please try setting I_MPI_PIN_MODE=mpd and see if that helps.

Sincerely,
James Tullos
Technical Consulting Engineer
Intel® Cluster Tools

Jesper_Carlson · February 18, 2013, 11:46am

Hi James,

I ran a test with I_MPI_PIN_MODE=mpd and it made one of the 8 core executions not run at all.

--------------------------

first 8 core execution pbs error file

########################### Execution Started ############################# JobId:492050.pbsserver UserName:s2874169 GroupName:12874169 ExecutionHost:n041 WorkingDir:/var/spool/PBS/mom_priv ###############################################################################

sched_setaffinity: Invalid argument failed to set pid 0’s affinity.

=>> PBS: job killed: walltime 135 exceeded limit 120

/export/home/s2874169/intel/impi/4.1.0.024/intel64/bin/mpirun: line 1: kill: SIGTERM: invalid signal specification

id: cannot find name for group ID 12874169

########################### Job Execution History #############################

pbs output

Starting job Mon Feb 18 19:51:19 EST 2013

/export/home/s2874169/Variable_Runs/LINPACK

n041

/export/home/s2874169/intel/impi/4.1.0.024/intel64/bin/mpirun

job aborted; reason = mpd disappeared

----------------------------------------------------------------

The 16 core execution

the following was added to the I_MPI_DEBUG output (only showing the new/different parts)

[-1] MPI startup(): Imported environment partly inaccesible. Map=0 Info=c74030

[0] MPI startup(): Rank Pid Node name Pin cpu

[0] MPI startup(): 0 36663 n041 n/a

[0] MPI startup(): 1 36656 n041 n/a

[0] MPI startup(): 2 36657 n041 n/a

[0] MPI startup(): 3 36658 n041 n/a

[0] MPI startup(): 4 36659 n041 n/a

[0] MPI startup(): 5 36660 n041 n/a

[0] MPI startup(): 6 36661 n041 n/a

[0] MPI startup(): 7 36662 n041 n/a

---------------------------------------------------------------

The last 8 core execution

If i use I_MPI_PIN_MODE=mpd but remove I_MPI_PROCESS_MANAGER=mpd

i get

[0] MPI startup(): Rank Pid Node name Pin cpu

[0] MPI startup(): 0 37907 n041 {10,12}

[0] MPI startup(): 1 37908 n041 {11,13}

[0] MPI startup(): 2 37909 n041 {0,1}

[0] MPI startup(): 3 37910 n041 {2,3}

[0] MPI startup(): 4 37911 n041 {4,5}

[0] MPI startup(): 5 37912 n041 {6,7}

[0] MPI startup(): 6 37913 n041 {8,9}

[0] MPI startup(): 7 37914 n041 {10,12}

[0] MPI startup(): I_MPI_DEBUG=5

[0] MPI startup(): I_MPI_FABRICS=shm:ofa

[0] MPI startup(): I_MPI_PIN_MAPPING=8:0 0,1 2,2 4,3 6,4 8,5 10,6 11,7 0

----------

[2] MPI startup(): shm and ofa data transfer modes [10] MPI startup(): shm and ofa data transfer modes [9] MPI startup(): shm and ofa data transfer modes [8] MPI startup(): shm and ofa data transfer modes [0] MPI startup(): shm and ofa data transfer modes [5] MPI startup(): shm and ofa data transfer modes [4] MPI startup(): shm and ofa data transfer modes [1] MPI startup(): shm and ofa data transfer modes [7] MPI startup(): shm and ofa data transfer modes [3] MPI startup(): shm and ofa data transfer modes [6] MPI startup(): shm and ofa data transfer modes [14] MPI startup(): shm and ofa data transfer modes [11] MPI startup(): shm and ofa data transfer modes [15] MPI startup(): shm and ofa data transfer modes [12] MPI startup(): shm and ofa data transfer modes [13] MPI startup(): shm and ofa data transfer modes [0] MPI startup(): Rank Pid Node name Pin cpu

[0] MPI startup(): 0 37984 n041 {0,1}

[0] MPI startup(): 1 37985 n041 {4,5}

[0] MPI startup(): 2 37986 n041 {8,9}

[0] MPI startup(): 3 37987 n041 {10,12}

[0] MPI startup(): 4 37988 n041 {2,3}

[0] MPI startup(): 5 37989 n041 {6,13}

[0] MPI startup(): 6 37990 n041 {7,11}

[0] MPI startup(): 7 37991 n041 {0,1}

[0] MPI startup(): 8 113141 n042 {0,1}

[0] MPI startup(): 9 113142 n042 {2,3}

[0] MPI startup(): 10 113143 n042 {4,5}

[0] MPI startup(): 11 113144 n042 {6,7}

[0] MPI startup(): 12 113145 n042 {8,9}

[0] MPI startup(): 13 113146 n042 {10,11}

[0] MPI startup(): 14 113147 n042 {12,13}

[0] MPI startup(): 15 113148 n042 {14,15}

[0] MPI startup(): I_MPI_DEBUG=5

[0] MPI startup(): I_MPI_FABRICS=shm:ofa

[0] MPI startup(): I_MPI_PIN_MAPPING=8:0 0,1 2,2 4,3 6,4 7,5 8,6 10,7 0

-----------

[1] MPI startup(): shm and ofa data transfer modes [3] MPI startup(): shm and ofa data transfer modes [0] MPI startup(): shm and ofa data transfer modes [7] MPI startup(): shm and ofa data transfer modes [5] MPI startup(): shm and ofa data transfer modes [6] MPI startup(): shm and ofa data transfer modes [4] MPI startup(): shm and ofa data transfer modes [2] MPI startup(): shm and ofa data transfer modes [0] MPI startup(): Rank Pid Node name Pin cpu

[0] MPI startup(): 0 113218 n042 {0,1}

[0] MPI startup(): 1 113219 n042 {4,5}

[0] MPI startup(): 2 113220 n042 {8,9}

[0] MPI startup(): 3 113221 n042 {10,12}

[0] MPI startup(): 4 113222 n042 {2,3}

[0] MPI startup(): 5 113223 n042 {6,13}

[0] MPI startup(): 6 113224 n042 {7,11}

[0] MPI startup(): 7 113225 n042 {0,1}

[0] MPI startup(): I_MPI_DEBUG=5

[0] MPI startup(): I_MPI_FABRICS=shm:ofa

[0] MPI startup(): I_MPI_PIN_MAPPING=8:0 0,1 2,2 4,3 6,4 7,5 8,6 10,7 0

However then the processes seems to share cores, looking at top processes that are normally close to 100 %CPU are now close to 50 or 25

James_T_Intel · February 19, 2013, 10:22pm

Hi Jesper,

Please send the output from the following commands:

[plain]/export/home/s2874169/intel/impi/4.1.0.024/intel64/bin/cpuinfo[/plain]

[plain]env | grep I_MPI[/plain]

Sincerely,
James Tullos
Technical Consulting Engineer
Intel® Cluster Tools

Jesper_Carlson · February 26, 2013, 1:59pm

Hi James,

I am sorry for the late reply, somehow the update email got lost from my outlook view (error 40).

The cpuinfo was:

Intel(R) Processor information utility, Version 4.1.0 Build 20120831

===== Processor composition =====

Processor name : Intel(R) Xeon(R) E5-2670 0

Packages(sockets) : 0

Cores : 0

Processors(CPUs) : 0

===== Cache sharing =====

Cache Size Processors

L1 32 KB no sharing

L2 256 KB no sharing

L3 20 MB no sharing

----------------

I tried env | grep I_MPI with a few different mpirun options (changing some I_MPI to see the different thing we have done already)

Initially:

I_MPI_FABRICS=shm:ofa

I_MPI_RDMA_CREATE_CONN_QUAL=0

I_MPI_SUBSTITUTE_INSTALLDIR=/sw/dhi/intel/impi/4.0.3.008

I_MPI_ROOT=/export/home/s2874169/intel/impi/4.1.0.024

----------------

Adding I_MPI_PROCESS_MANAGER=mpd made it show up in the env | grep I_MPI list

Adding I_MPI_PIN_MODE=mpd made it show up in the env | grep I_MPI list

Adding I_MPI_SUBSTITUTE_INSTALLDIR=/export/home/s2874169/intel/impi/4.1.0.024 mad it show up it did not change anything with the performance though.

Jesper_Carlson · February 26, 2013, 2:25pm

Hi James,

Update i forgot to mention that the previous post about cpuinfo and env | grep I_MPI was done in the pbs script.

using ssh to login to one of the nodes and then run cpuinfo i got:

Intel(R) Processor information utility, Version 4.1.0 Build 20120831

===== Processor composition =====

Processor name : Intel(R) Xeon(R) E5-2670 0

Packages(sockets) : 2 Cores : 16

Processors(CPUs) : 16

Cores per package : 8

Threads per core : 1

===== Processor identification =====

Processor Thread Id. Core Id. Package Id.

0 0 0 0

1 0 1 0

2 0 2 0

3 0 3 0

4 0 4 0

5 0 5 0

6 0 6 0

7 0 7 0

8 0 0 1

9 0 1 1

10 0 2 1

11 0 3 1

12 0 4 1

13 0 5 1

14 0 6 1

15 0 7 1

===== Placement on packages =====

Package Id. Core Id. Processors

0 0,1,2,3,4,5,6,7 0,1,2,3,4,5,6,7

1 0,1,2,3,4,5,6,7 8,9,10,11,12,13,14,15

===== Cache sharing =====

Cache Size Processors

L1 32 KB no sharing

L2 256 KB no sharing

L3 20 MB (0,1,2,3,4,5,6,7)(8,9,10,11,12,13,14,15)

----------------------------------------------------------------------

And while just logged in using ssh i got

[s2874169@n041 ~]$ env | grep I_MPI

I_MPI_FABRICS=shm:ofa

I_MPI_RDMA_CREATE_CONN_QUAL=0

I_MPI_SUBSTITUTE_INSTALLDIR=/sw/dhi/intel/impi/4.0.3.008

I_MPI_ROOT=/sw/dhi/intel/impi/4.0.3.008

James_T_Intel · February 28, 2013, 8:05pm

Hi Jesper,

The “env” command I asked you to run simply displays the environment, using “grep I_MPI” reduces it to the Intel® MPI Library specific environment variables. So setting a different environment variable would show in the output. Everything there looks fine. However, the cpuinfo output from within the batch script is very wrong. The output when you are logged in directly is correct. I’ll investigate that and see if I can find out why cpuinfo isn’t reporting anything from a script.

Sincerely,
James Tullos
Technical Consulting Engineer
Intel® Cluster Tools

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