2x mpi performance difference between ASRock 2U4N-F/x200 and Supermicro SYS-5038K-i

Per_J_ — Thu, 28 Nov 2019 16:26:19 GMT

Hi,

I have two different Xeon Phi 7210 systems - ASRock 2U4N-F/x200 and Supermicro SYS-5038K-i.

When I run HPL linpack benchmark from Intel they are both around 1700GFlops.

When I run OpenFOAM with mpi the SuperMicro is twice as fast as the ASRock.

137s vs 233s in DDR4 memory and 70s vs 159s in MCDRAM - all are run with I_MPI_PIN_DOMAIN=core and I_MPI_PIN_PROCESSOR_LIST=allcores.

I tried with a clean install on both and with the same system disk in both systems.

Is there a setting I am missing? Or can there be such a performance difference between the two systems?

Best regards,

Per

it also depends on the memory

JJK — Fri, 29 Nov 2019 08:27:53 GMT

it also depends on the memory configuration of the Xeon Phi and which mode you are running in: SNC-2, SNC-4 (recommended), MC-DRAM cached, etc. The output of 'numactl -H' can shed light on this. Post the output of that command for both systems and compare.

Both are in quadrant mode

Per_J_ — Fri, 29 Nov 2019 13:02:11 GMT

Both are in quadrant mode

Supermicro:

MCDRAM is hotpluggable

node 0 size: 98180 MB
node 0 free: 94310 MB
node 1 cpus:
node 1 size: 16384 MB
node 1 free: 16384 MB
node distances:
node 0 1
0: 10 31
1: 31 10

ASRock:

There is no option in BIOS for hotpluggable MCDRAM

node 0 size: 49031 MB
node 0 free: 46869 MB
node 1 cpus:
node 1 size: 16384 MB
node 1 free: 15977 MB
node distances:
node 0 1
0: 10 31
1: 31 10

I will try to put them in SNC-4 mode and run a few more tests

Thanks,

Per_J_ — Fri, 29 Nov 2019 16:20:58 GMT

Thanks,

Now I have run some tests in SNC-4 mode

There was a slight improvement on the run time on both systems 68s vs 155s in MCDRAM but the difference remains.

I also ran IMB-MPI1 benchmark on both system (the outputs are attached). They differ quite a lot data exchange is faster on Supermicro and reduce/scatter/gather is faster on ASRock.

results from numactl -H

ASRock:

available: 8 nodes (0-7)
node 0 cpus: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207
node 0 size: 12167 MB
node 0 free: 11130 MB
node 1 cpus: 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223
node 1 size: 12288 MB
node 1 free: 11571 MB
node 2 cpus: 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
node 2 size: 12288 MB
node 2 free: 11498 MB
node 3 cpus: 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255
node 3 size: 12288 MB
node 3 free: 11270 MB
node 4 cpus:
node 4 size: 4096 MB
node 4 free: 4096 MB
node 5 cpus:
node 5 size: 4096 MB
node 5 free: 4096 MB
node 6 cpus:
node 6 size: 4096 MB
node 6 free: 4096 MB
node 7 cpus:
node 7 size: 4096 MB
node 7 free: 4096 MB
node distances:
node 0 1 2 3 4 5 6 7
0: 10 21 21 21 31 41 41 41
1: 21 10 21 21 41 31 41 41
2: 21 21 10 21 41 41 31 41
3: 21 21 21 10 41 41 41 31
4: 31 41 41 41 10 41 41 41
5: 41 31 41 41 41 10 41 41
6: 41 41 31 41 41 41 10 41
7: 41 41 41 31 41 41 41 10

Supermicro:

available: 8 nodes (0-7)
node 0 cpus: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207
node 0 size: 24452 MB
node 0 free: 22859 MB
node 1 cpus: 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223
node 1 size: 24576 MB
node 1 free: 23583 MB
node 2 cpus: 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239
node 2 size: 24576 MB
node 2 free: 23317 MB
node 3 cpus: 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255
node 3 size: 24576 MB
node 3 free: 23396 MB
node 4 cpus:
node 4 size: 4096 MB
node 4 free: 3964 MB
node 5 cpus:
node 5 size: 4096 MB
node 5 free: 3971 MB
node 6 cpus:
node 6 size: 4096 MB
node 6 free: 3966 MB
node 7 cpus:
node 7 size: 4096 MB
node 7 free: 3974 MB
node distances:
node 0 1 2 3 4 5 6 7
0: 10 21 21 21 31 41 41 41
1: 21 10 21 21 41 31 41 41
2: 21 21 10 21 41 41 31 41
3: 21 21 21 10 41 41 41 31
4: 31 41 41 41 10 41 41 41
5: 41 31 41 41 41 10 41 41
6: 41 41 31 41 41 41 10 41
7: 41 41 41 31 41 41 41 10

topic Both are in quadrant mode in Software Archive

2x mpi performance difference between ASRock 2U4N-F/x200 and Supermicro SYS-5038K-i

it also depends on the memory

Both are in quadrant mode

Thanks,