Yes, I was running Ubuntu 16.04 in a docker container on CentOS box. I have since rebuilt the boxes with native Ubuntu 16.04. I actually have evaluation access to three of these intel boxes and I tried to run MPI across all three boxes but I'm not sure I have the settings correct as it ran for approx. the same elapsed time as run it on a single box.
$ cat mpi-3host optane30 slots=4 optane29 slots=4 optane28 slots=4 $ mpirun --bind-to socket --hostfile mpi-3host -x ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=14 otbcli_MeanShiftSmoothing -in /u/ror /buildings/data/naip/doqqs/2014/33118/m_3311805_se_11_1_20140513.tif -fout / u/ror/buildings/tmp/test5-smooth.tif -foutpos /u/ror/buildings/tmp/test5- smoothpos.tif -spatialr 24 -ranger 36 -ram 102400 -thres 0.1 -maxiter 100 where all three boxes have identical software installed on them. optane30 is the master and I did an nfs exportfs of /u/ror/buildings and then mounted that on the other two boxes. All the work gets done in the /u/ror/buildings/tmp/ directory. $ lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 56 On-line CPU(s) list: 0-55 Thread(s) per core: 2 Core(s) per socket: 14 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family: 6 Model: 79 Model name: Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz Stepping: 1 CPU MHz: 1845.289 CPU max MHz: 3500.0000 CPU min MHz: 1200.0000 BogoMIPS: 5202.36 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 35840K NUMA node0 CPU(s): 0-13,28-41 NUMA node1 CPU(s): 14-27,42-55 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 aperfmperf eagerfpu pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch epb intel_pt tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm rdseed adx smap xsaveopt cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm arat pln pts Any suggestions on how to work this in a cluster? Thanks, -Steve Performance stats so far: Intel Server Description Elapsed CPU Sec Hours Test 1 -thres 0.001 -maxiter 4 4,521.9 205,217.4 1.26 smoothing 3,747.0 203,160.2 time mpirun -np 4 --bind-to socket otbcli_MeanShiftSmoothing -in /u/ror/buildings/data/naip/doqqs/2014/33118/m_3311805_se_11_1_20140513.tif -fout /u/ror/buildings/tmp/test1-smooth.tif -foutpos /u/ror/buildings/tmp/test1-smoothpos.tif -spatialr 24 -ranger 36 -ram 102400 segmentation 318.1 378.0 time otbcli_LSMSSegmentation -in /u/ror/buildings/tmp/test1-smooth.tif -inpos /u/ror/buildings/tmp/test1-smoothpos.tif -out /u/ror/buildings/tmp/test1-segs.tif -tmpdir /u/ror/buildings/tmp -spatialr 24 -ranger 36 -minsize 128 -tilesizex 1025 -tilesizey 1025 vectorization 456.7 1,679.2 time mpirun -np 4 --bind-to socket otbcli_LSMSVectorization -in /u/ror/buildings/tmp/test1-smooth.tif -inseg /u/ror/buildings/tmp/test1-segs.tif -out /u/ror/buildings/tmp/test1-segments-mpi.shp -tilesizex 1025 -tilesizey 1025 Test 2 -thres 0.001 -maxiter 4 4,318.0 204,090.5 1.20 smoothing 3,746.8 203,418.8 time mpirun -np 4 --bind-to socket otbcli_MeanShiftSmoothing -in /u/ror/buildings/data/naip/doqqs/2014/33118/m_3311805_se_11_1_20140513.tif -fout /u/ror/buildings/tmp/test2-smooth.tif -foutpos /u/ror/buildings/tmp/test2-smoothpos.tif -spatialr 24 -ranger 36 -ram 102400 segmentation 155.1 164.0 time otbcli_LSMSSegmentation -in /u/ror/buildings/tmp/test2-smooth.tif -inpos /u/ror/buildings/tmp/test2-smoothpos.tif -out /u/ror/buildings/tmp/test2-segs.tif -tmpdir /u/ror/buildings/tmp -spatialr 24 -ranger 36 -minsize 128 -tilesizex 1025 -tilesizey 1025 vectorization 416.1 507.7 time otbcli_LSMSVectorization -in /u/ror/buildings/tmp/test2-smooth.tif -inseg /u/ror/buildings/tmp/test2-segs.tif -out /u/ror/buildings/tmp/test2-segments.shp -tilesizex 1025 -tilesizey 1025 Test 3 -thres 0.1 -maxiter 100 4,256.2 203,771.0 1.18 smoothing 3,747.1 203,180.5 time mpirun -np 4 --bind-to socket otbcli_MeanShiftSmoothing -in /u/ror/buildings/data/naip/doqqs/2014/33118/m_3311805_se_11_1_20140513.tif -fout /u/ror/buildings/tmp/test3-smooth.tif -foutpos /u/ror/buildings/tmp/test3-smoothpos.tif -spatialr 24 -ranger 36 -ram 102400 -thres 0.1 -maxiter 100 segmentation 167.7 178.8 time otbcli_LSMSSegmentation -in /u/ror/buildings/tmp/test3-smooth.tif -inpos /u/ror/buildings/tmp/test3-smoothpos.tif -out /u/ror/buildings/tmp/test3-segs.tif -tmpdir /u/ror/buildings/tmp -spatialr 24 -ranger 36 -minsize 128 -tilesizex 1025 -tilesizey 1025 vectorization 341.4 411.7 time otbcli_LSMSVectorization -in /u/ror/buildings/tmp/test3-smooth.tif -inseg /u/ror/buildings/tmp/test3-segs.tif -out /u/ror/buildings/tmp/test3-segments.shp -tilesizex 1025 -tilesizey 1025 Test 4 ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=14 3,871.2 151,724.4 1.08 smoothing 3,131.0 150,921.2 time mpirun -np 4 --bind-to socket otbcli_MeanShiftSmoothing -in /u/ror/buildings/data/naip/doqqs/2014/33118/m_3311805_se_11_1_20140513.tif -fout /u/ror/buildings/tmp/test4-smooth.tif -foutpos /u/ror/buildings/tmp/test4-smoothpos.tif -spatialr 24 -ranger 36 -ram 102400 -thres 0.1 -maxiter 100 segmentation 184.3 195.1 time otbcli_LSMSSegmentation -in /u/ror/buildings/tmp/test4-smooth.tif -inpos /u/ror/buildings/tmp/test4-smoothpos.tif -out /u/ror/buildings/tmp/test4-segs.tif -tmpdir /u/ror/buildings/tmp -spatialr 24 -ranger 36 -minsize 128 -tilesizex 1025 -tilesizey 1025 vectorization 555.9 608.1 time otbcli_LSMSVectorization -in /u/ror/buildings/tmp/test4-smooth.tif -inseg /u/ror/buildings/tmp/test4-segs.tif -out /u/ror/buildings/tmp/test4-segments.shp -tilesizex 1025 -tilesizey 1025 Test 1 -thres 0.1 -maxiter 100 (Native Ubuntu) 6,238.1 157,528.8 1.73 smoothing 5,571.6 156,831.6 mpirun -np 4 --bind-to socket otbcli_MeanShiftSmoothing -in /u/ror/buildings/data/naip/doqqs/2014/33118/m_3311805_se_11_1_20140513.tif -fout /u/ror/buildings/tmp/test1-smooth.tif -foutpos /u/ror/buildings/tmp/test1-smoothpos.tif -spatialr 24 -ranger 36 -ram 102400 -thres 0.1 -maxiter 100 segmentation 157.5 157.4 otbcli_LSMSSegmentation -in /u/ror/buildings/tmp/test1-smooth.tif -inpos /u/ror/buildings/tmp/test1-smoothpos.tif -out /u/ror/buildings/tmp/test1-segs.tif -tmpdir /u/ror/buildings/tmp -spatialr 24 -ranger 36 -minsize 128 -tilesizex 1025 -tilesizey 1025 vectorization 509.1 539.7 otbcli_LSMSVectorization -in /u/ror/buildings/tmp/test1-smooth.tif -inseg /u/ror/buildings/tmp/test1-segs.tif -out /u/ror/buildings/tmp/test1-segments.shp -tilesizex 1025 -tilesizey 1025 Test 5 3-Server MPI on Ubuntu 3,722.5 149,495.6 1.03 smoothing 3,081.3 148,862.0 mpirun --bind-to socket --hostfile mpi-3host -x ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=14 otbcli_MeanShiftSmoothing -in /u/ror/buildings/data/naip/doqqs/2014/33118/m_3311805_se_11_1_20140513.tif -fout /u/ror/buildings/tmp/test5-smooth.tif -foutpos /u/ror/buildings/tmp/test5-smoothpos.tif -spatialr 24 -ranger 36 -ram 102400 -thres 0.1 -maxiter 100 segmentation 169.1 123.8 otbcli_LSMSSegmentation -in /u/ror/buildings/tmp/test5-smooth.tif -inpos /u/ror/buildings/tmp/test5-smoothpos.tif -out /u/ror/buildings/tmp/test5-segs.tif -tmpdir /u/ror/buildings/tmp -spatialr 24 -ranger 36 -minsize 128 -tilesizex 1025 -tilesizey 1025 vectorization 472.1 509.8 otbcli_LSMSVectorization -in /u/ror/buildings/tmp/test5-smooth.tif -inseg /u/ror/buildings/tmp/test5-segs.tif -out /u/ror/buildings/tmp/test5-segments.shp -tilesizex 1025 -tilesizey 1025 On Tuesday, May 23, 2017 at 4:00:37 AM UTC-4, remicres wrote: > > Hi Stephen, > > >> Thanks, I have this more or less working. I have not set the env variable >> ITK_GLOBAL_DEFAULT_NUMBER_OF_ >> THREADS but I will try that, I seem to be getting about 4 times that many >> threads running. >> > > If you do not adjust the correct number of threads, you could have more > threads than cpus, which will lead to poor performance (The goal is to have > 1 thread on 1 cpu, virtually speaking). > > > >> Below are various problems I've run into. Some of these might be code >> bugs, or config issues, or who knows what :) >> >> I get an error with --bind-to socket >> >> mpirun -np 4 --bind-to socket otbcli_MeanShiftSmoothing -in /u/ror/ >> buildings/data/naip/doqqs/2014/33118/m_3311805_se_11_1_20140513.tif -fout >> /u/ror/buildings/tmp/test1-smooth.tif -foutpos /u/ror/buildings/tmp/test1 >> -smoothpos.tif -spatialr 24 -ranger 36 -ram 102400 >> Unexpected end of /proc/mounts line `overlay / overlay >> rw,seclabel,relatime,lowerdir=/var/lib/docker/overlay2/l/JPC7E5F4RB77LOK22ETL5FMEPN:/var/lib/docker/overlay2/l/DM3Q73J52BCAIEZVAQZGAMXLCX:/var/lib/docker/overlay2/l/WC5LQTPG4RBGOUEZ7KBJZLUB2R:/var/lib/docker/overlay2/l/BESSO2WOBICH2P4GSVX7VSCGG6:/var/lib/docker/overlay2/l/FMSJDZMFK67RHOIIZOLKOICAHI:/var/lib/docker/overlay2/l/U7AFHXIVI6KAKUO2VJMZWLQOHH:/var/lib/docker/overlay2/l/EIRHWP2GOK3F2PH7SHY4FK6J6P,upperdir=/var/lib/docker/overlay2/73d138b0a2dadf534a9d9c7d2ed894484515bfe3d2f1807a2b8' >> -------------------------------------------------------------------------- >> WARNING: Open MPI tried to bind a process but failed. This is a >> warning only; your job will continue, though performance may >> be degraded. >> >> Local host: optane30 >> Application name: /usr/bin/otbcli_MeanShiftSmoothing >> Error message: failed to bind memory >> Location: odls_default_module.c:639 >> >> -------------------------------------------------------------------------- >> >> >> > From your logs, I feel that you are using a virtual environment (docker?). > First impression is that MPI fails to bind processes in this environment. > However I never used MPI in such configuration. > > >> But the job runs to completion. When I try to run otbcli_LSMSVectorization >> under mpi it fails. The same command runs fine without mpi. If this >> command shouldn't run under mpi, you might want to add a check and report >> to the user, or just internally disable mpi. >> > > Indeed, LSMSVectorization does not currently support MPI. > You are absolutely right, we need to add something to prevent the use of > applications which can't work with MPI. > > Thank you for these useful feedbacks, we will take care of improving the > MPI feature, plus providing more doc! > Rémi > > -- -- Check the OTB FAQ at http://www.orfeo-toolbox.org/FAQ.html You received this message because you are subscribed to the Google Groups "otb-users" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/otb-users?hl=en --- You received this message because you are subscribed to the Google Groups "otb-users" group. 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