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numa_set_interleave_mask problem #26

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iosmers opened this issue Dec 17, 2020 · 2 comments
Open

numa_set_interleave_mask problem #26

iosmers opened this issue Dec 17, 2020 · 2 comments

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@iosmers
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iosmers commented Dec 17, 2020 •
edited

Hi,xiaowei, I'm trying to run pagerank on scale16_s.bin, which from here from issue #6 , but I get a segment fault, it looks like following. I think the numa_set_interleave_mask() function which was called in your init() function in file core/graph.hpp:174 causes this problem, because when I comment out this line code, the program run correctly , get no error and print the result.

Here is detail information:
OS:Ubuntu 18.04
gcc version: 7.5.0
opemmp version : Open MPI 2.1.1 (Language: C++)
slurm version: 17.11.2
cpu infomation:

Architecture:        x86_64
CPU op-mode(s):      32-bit, 64-bit
Byte Order:          Little Endian
CPU(s):              24
On-line CPU(s) list: 0-23
Thread(s) per core:  2
Core(s) per socket:  6
Socket(s):           2
NUMA node(s):        2
Vendor ID:           GenuineIntel
CPU family:          6
Model:               62
Model name:          Intel(R) Xeon(R) CPU E5-2620 v2 @ 2.10GHz
Stepping:            4
CPU MHz:             1200.597
CPU max MHz:         2600.0000
CPU min MHz:         1200.0000
BogoMIPS:            4200.13
Virtualization:      VT-x
L1d cache:           32K
L1i cache:           32K
L2 cache:            256K
L3 cache:            15360K
NUMA node0 CPU(s):   0-5,12-17
NUMA node1 CPU(s):   6-11,18-23
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 pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm cpuid_fault epb pti ssbd ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid fsgsbase smep erms xsaveopt dtherm ida arat pln pts md_clear flush_l1d

I use this command,
srun -N 2 ./toolkits/pagerank ./data/scale16_s.bin 65536 20

I have 1 node named ca33 as control machine and 2 nodes named ca97 and ca100 for computing, I get this error.

WARNING: There is at least non-excluded one OpenFabrics device found,
but there are no active ports detected (or Open MPI was unable to use
them). This is most certainly not what you wanted. Check your
cables, subnet manager configuration, etc. The openib BTL will be
ignored for this job.
Local host: ca97

[ca100:15129] *** Process received signal ***
[ca100:15129] Signal: Segmentation fault (11)
[ca100:15129] Signal code: Address not mapped (1)
[ca100:15129] Failing at address: (nil)
[ca100:15129] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12980)[0x7f8e3c1c9980]
[ca100:15129] [ 1] /usr/lib/x86_64-linux-gnu/libnuma.so.1(numa_bitmask_equal+0xd)[0x7f8e3d0b592d]
[ca100:15129] [ 2] /usr/lib/x86_64-linux-gnu/libnuma.so.1(numa_set_interleave_mask+0x13)[0x7f8e3d0b64e3]
[ca100:15129] [ 3] /home/yinwei/dev/GeminiGraph/./toolkits/pagerank(+0xd2f9)[0x5582c2c632f9]
[ca100:15129] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f8e3bde7bf7]
[ca100:15129] [ 5] /home/yinwei/dev/GeminiGraph/./toolkits/pagerank(+0xd8ba)[0x5582c2c638ba]
[ca100:15129] *** End of error message ***
[ca97:17078] *** Process received signal ***
[ca97:17078] Signal: Segmentation fault (11)
[ca97:17078] Signal code: Address not mapped (1)
[ca97:17078] Failing at address: (nil)
[ca97:17078] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12980)[0x7f0c137b7980]
[ca97:17078] [ 1] /usr/lib/x86_64-linux-gnu/libnuma.so.1(numa_bitmask_equal+0xd)[0x7f0c146a392d]
[ca97:17078] [ 2] /usr/lib/x86_64-linux-gnu/libnuma.so.1(numa_set_interleave_mask+0x13)[0x7f0c146a44e3]
[ca97:17078] [ 3] /home/yinwei/dev/GeminiGraph/./toolkits/pagerank(+0xd2f9)[0x55739a4a72f9]
[ca97:17078] [ 4] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x7f0c133d5bf7]
[ca97:17078] [ 5] /home/yinwei/dev/GeminiGraph/./toolkits/pagerank(+0xd8ba)[0x55739a4a78ba]
[ca97:17078] *** End of error message ***
srun: error: ca100: task 1: Segmentation fault
srun: error: ca97: task 0: Segmentation fault (core dumped)

when I comment out this line core/graph.hpp:174, make and run again, it will get no error. i don't know why.

WARNING: There is at least non-excluded one OpenFabrics device found,
but there are no active ports detected (or Open MPI was unable to use
them). This is most certainly not what you wanted. Check your
cables, subnet manager configuration, etc. The openib BTL will be
ignored for this job.
Local host: ca97

edge_data_size:0
unit_size:4
edge_unit_size:8
vertices size is 65536
edges size is 2728272
iterations is 20
delta(0)=1.000000
delta(1)=1.201973
delta(2)=0.299845
delta(3)=0.121878
delta(4)=0.053445
delta(5)=0.023630
delta(6)=0.010217
delta(7)=0.004646
delta(8)=0.001908
delta(9)=0.000956
delta(10)=0.000324
delta(11)=0.000227
delta(12)=0.000150
delta(13)=0.000127
delta(14)=0.000108
delta(15)=0.000092
delta(16)=0.000078
delta(17)=0.000066
delta(18)=0.000056
delta(19)=0.000048
exec_time=0.105598(s)
pr_sum=47355.429527
pr[4]=1348.359586
delta(0)=1.000000
delta(1)=1.201973
delta(2)=0.299845
delta(3)=0.121878
delta(4)=0.053445
delta(5)=0.023630
delta(6)=0.010217
delta(7)=0.004646
delta(8)=0.001908
delta(9)=0.000956
delta(10)=0.000324
delta(11)=0.000227
delta(12)=0.000150
delta(13)=0.000127
delta(14)=0.000108
delta(15)=0.000092
delta(16)=0.000078
delta(17)=0.000066
delta(18)=0.000056
delta(19)=0.000048
exec_time=0.102557(s)
pr_sum=47355.429527
pr[4]=1348.359586
delta(0)=1.000000
delta(1)=1.201973
delta(2)=0.299845
delta(3)=0.121878
delta(4)=0.053445
delta(5)=0.023630
delta(6)=0.010217
delta(7)=0.004646
delta(8)=0.001908
delta(9)=0.000956
delta(10)=0.000324
delta(11)=0.000227
delta(12)=0.000150
delta(13)=0.000127
delta(14)=0.000108
delta(15)=0.000092
delta(16)=0.000078
delta(17)=0.000066
delta(18)=0.000056
delta(19)=0.000048
exec_time=0.107026(s)
pr_sum=47355.429527
pr[4]=1348.359586
delta(0)=1.000000
delta(1)=1.201973
delta(2)=0.299845
delta(3)=0.121878
delta(4)=0.053445
delta(5)=0.023630
delta(6)=0.010217
delta(7)=0.004646
delta(8)=0.001908
delta(9)=0.000956
delta(10)=0.000324
delta(11)=0.000227
delta(12)=0.000150
delta(13)=0.000127
delta(14)=0.000108
delta(15)=0.000092
delta(16)=0.000078
delta(17)=0.000066
delta(18)=0.000056
delta(19)=0.000048
exec_time=0.091182(s)
pr_sum=47355.429527
pr[4]=1348.359586
delta(0)=1.000000
delta(1)=1.201973
delta(2)=0.299845
delta(3)=0.121878
delta(4)=0.053445
delta(5)=0.023630
delta(6)=0.010217
delta(7)=0.004646
delta(8)=0.001908
delta(9)=0.000956
delta(10)=0.000324
delta(11)=0.000227
delta(12)=0.000150
delta(13)=0.000127
delta(14)=0.000108
delta(15)=0.000092
delta(16)=0.000078
delta(17)=0.000066
delta(18)=0.000056
delta(19)=0.000048
exec_time=0.083132(s)
pr_sum=47355.429527
pr[4]=1348.359586
delta(0)=1.000000
delta(1)=1.201973
delta(2)=0.299845
delta(3)=0.121878
delta(4)=0.053445
delta(5)=0.023630
delta(6)=0.010217
delta(7)=0.004646
delta(8)=0.001908
delta(9)=0.000956
delta(10)=0.000324
delta(11)=0.000227
delta(12)=0.000150
delta(13)=0.000127
delta(14)=0.000108
delta(15)=0.000092
delta(16)=0.000078
delta(17)=0.000066
delta(18)=0.000056
delta(19)=0.000048
exec_time=0.077558(s)
pr_sum=47355.429527
pr[4]=1348.359586
edge_data_size:0
unit_size:4
edge_unit_size:8
vertices size is 65536
edges size is 2728272
iterations is 20
delta(0)=1.000000
delta(1)=1.201973
delta(2)=0.299845
delta(3)=0.121878
delta(4)=0.053445
delta(5)=0.023630
delta(6)=0.010217
delta(7)=0.004646
delta(8)=0.001908
delta(9)=0.000956
delta(10)=0.000324
delta(11)=0.000227
delta(12)=0.000150
delta(13)=0.000127
delta(14)=0.000108
delta(15)=0.000092
delta(16)=0.000078
delta(17)=0.000066
delta(18)=0.000056
delta(19)=0.000048
exec_time=0.098069(s)
pr_sum=47355.429527
pr[4]=1348.359586
delta(0)=1.000000
delta(1)=1.201973
delta(2)=0.299845
delta(3)=0.121878
delta(4)=0.053445
delta(5)=0.023630
delta(6)=0.010217
delta(7)=0.004646
delta(8)=0.001908
delta(9)=0.000956
delta(10)=0.000324
delta(11)=0.000227
delta(12)=0.000150
delta(13)=0.000127
delta(14)=0.000108
delta(15)=0.000092
delta(16)=0.000078
delta(17)=0.000066
delta(18)=0.000056
delta(19)=0.000048
exec_time=0.113920(s)
pr_sum=47355.429527
pr[4]=1348.359586
delta(0)=1.000000
delta(1)=1.201973
delta(2)=0.299845
delta(3)=0.121878
delta(4)=0.053445
delta(5)=0.023630
delta(6)=0.010217
delta(7)=0.004646
delta(8)=0.001908
delta(9)=0.000956
delta(10)=0.000324
delta(11)=0.000227
delta(12)=0.000150
delta(13)=0.000127
delta(14)=0.000108
delta(15)=0.000092
delta(16)=0.000078
delta(17)=0.000066
delta(18)=0.000056
delta(19)=0.000048
exec_time=0.087034(s)
pr_sum=47355.429527
pr[4]=1348.359586
delta(0)=1.000000
delta(1)=1.201973
delta(2)=0.299845
delta(3)=0.121878
delta(4)=0.053445
delta(5)=0.023630
delta(6)=0.010217
delta(7)=0.004646
delta(8)=0.001908
delta(9)=0.000956
delta(10)=0.000324
delta(11)=0.000227
delta(12)=0.000150
delta(13)=0.000127
delta(14)=0.000108
delta(15)=0.000092
delta(16)=0.000078
delta(17)=0.000066
delta(18)=0.000056
delta(19)=0.000048
exec_time=0.091063(s)
pr_sum=47355.429527
pr[4]=1348.359586
delta(0)=1.000000
delta(1)=1.201973
delta(2)=0.299845
delta(3)=0.121878
delta(4)=0.053445
delta(5)=0.023630
delta(6)=0.010217
delta(7)=0.004646
delta(8)=0.001908
delta(9)=0.000956
delta(10)=0.000324
delta(11)=0.000227
delta(12)=0.000150
delta(13)=0.000127
delta(14)=0.000108
delta(15)=0.000092
delta(16)=0.000078
delta(17)=0.000066
delta(18)=0.000056
delta(19)=0.000048
exec_time=0.093679(s)
pr_sum=47355.429527
pr[4]=1348.359586
delta(0)=1.000000
delta(1)=1.201973
delta(2)=0.299845
delta(3)=0.121878
delta(4)=0.053445
delta(5)=0.023630
delta(6)=0.010217
delta(7)=0.004646
delta(8)=0.001908
delta(9)=0.000956
delta(10)=0.000324
delta(11)=0.000227
delta(12)=0.000150
delta(13)=0.000127
delta(14)=0.000108
delta(15)=0.000092
delta(16)=0.000078
delta(17)=0.000066
delta(18)=0.000056
delta(19)=0.000048
exec_time=0.079862(s)
pr_sum=47355.429527
pr[4]=1348.359586
@iosmers
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iosmers commented Dec 21, 2020

@coolerzxw

@coolerzxw
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Hi @iosmers , have you tried running the program via mpirun with "--bind-to none"?

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