[Beowulf] Scaling issues on Xeon E5-2680

Jon Tegner tegner at renget.se
Sun Feb 28 08:01:45 PST 2016


we are using openmpi-1.10.2, and I believe bind-to core and socket are 
on by default here. Openmpi is built using

./configure \
         --build=x86_64-redhat-linux-gnu \
         --host=x86_64-redhat-linux-gnu \
         --disable-dependency-tracking \
         --prefix=/remote/soft/OpenMPI/1.10.2 \
         --disable-mpi-profile \
         --enable-shared \
         --with-tm \
         --with-sge \

gcc is used throughout.

Code should be using RDMA. I have verified that infiniband performance 
(using openmpi-1.10.2) is what is to be expected (through 
mpitests-osu_bw and mpitest_osu_latency).

Hugepagesize haven't been touched ("grep Hugepagesize /proc/meminfo" 
gives 2048 kB). Is this something worth changing?

numastat gives

                            node0           node1
numa_hit                 6288694         1193663
numa_miss                      0               0
numa_foreign                   0               0
interleave_hit             66539           66287
local_node               6288301         1126078
other_node                   393           67585

on one of the nodes - but these numbers seems to be fairly 
representative for the nodes. However, haven't used numastat before, and 
maybe it should be used simultaneously as the job is running (which it 
wasn't now)?



On 02/28/2016 04:30 PM, cbergstrom at pathscale.com wrote:
> Do you have CPU affinity enabled? Is this omp + MPI? Which compilers and flags. Give more details about the software stack
>    Original Message
> From: Jon Tegner
> Sent: Sunday, February 28, 2016 22:28
> To: beowulf at beowulf.org
> Subject: [Beowulf] Scaling issues on Xeon E5-2680
> Hi,
> have issues with performance on E5-2680. Each of the nodes have 2 of
> these 12 core CPUs on SuperMicro SuperServer 1028R-WMR (i.e., 24 cores
> on each node).
> For one of our applications (CFD/OpenFOAM) we have noticed that the
> calculation runs faster using 12 cores on 4 nodes compared to when using
> 24 cores on 4 nodes.
> In our environment we also have older AMD hardware (nodes with 4 CPUs
> with 12 cores each), and here we don't see these strange scaling issues.
> System is CentOS-7, and communication is over FDR Infiniband. BIOS is
> recently updated, and hyperthreading is disabled.
> Feel a bit lost here, and any hints on how to proceed with this are
> greatly appreciated!
> Thanks,
> /jon
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