[Beowulf] Scaling issues on Xeon E5-2680

[Peter St. John]

I come from the math side, not the electronics side, so this may be an
ill-posed question, but could you try running the job with 12 cores on just
one node, then with 6 cores on each of two nodes? I'm thinking, the 24 core
version may get assigned to more nodes than your 12 core, and it's
communication between nodes that slows it down, e.g. for a job that doesn't
require so much memory as inter-process communication.
Peter

On Sun, Feb 28, 2016 at 11:01 AM, Jon Tegner <tegner at renget.se> wrote:

> Thanks!
>
> 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 \
>         --with-verbs
>
> 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)?
>
> Thanks!
>
> /jon
>
>
> 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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