> On Apr 5, 2015, at 5:58 PM, Lane, William <william.l...@cshs.org> wrote: > > I think some of the Intel Blade systems in the cluster are > dual core, but don't support hyperthreading. Maybe it > would be better to exclude hyperthreading altogether > from submitted OpenMPI jobs?
Yes - or you can add "--hetero-nodes -use-hwthread-cpus --bind-to hwthread" to the cmd line. This tells mpirun that the nodes aren't all the same, and so it has to look at each node's topology instead of taking the first node as the template for everything. The second tells it to use the HTs as independent cpus where they are supported. I'm not entirely sure the suggestion will work - if we hit a place where HT isn't supported, we may balk at being asked to bind to HTs. I can probably make a change that supports this kind of hetero arrangement (perhaps something like bind-to pu) - might make it into 1.8.5 (we are just starting the release process on it now). > > OpenMPI doesn't crash, but it doesn't run the LAPACK > benchmark either. > > Thanks again Ralph. > > Bill L. > > From: users [users-boun...@open-mpi.org] on behalf of Ralph Castain > [r...@open-mpi.org] > Sent: Wednesday, April 01, 2015 8:40 AM > To: Open MPI Users > Subject: Re: [OMPI users] OpenMPI 1.8.2 problems on CentOS 6.3 > > Bingo - you said the magic word. This is a terminology issue. When we say > "core", we mean the old definition of "core", not "hyperthreads". If you want > to use HTs as your base processing unit and bind to them, then you need to > specify --bind-to hwthread. That warning should then go away. > > We don't require a swap region be mounted - I didn't see anything in your > original message indicating that OMPI had actually crashed, but just wasn't > launching due to the above issue. Were you actually seeing crashes as well? > > > On Wed, Apr 1, 2015 at 8:31 AM, Lane, William <william.l...@cshs.org > <mailto:william.l...@cshs.org>> wrote: > Ralph, > > Here's the associated hostfile: > > #openMPI hostfile for csclprd3 > #max slots prevents oversubscribing csclprd3-0-9 > csclprd3-0-0 slots=12 max-slots=12 > csclprd3-0-1 slots=6 max-slots=6 > csclprd3-0-2 slots=6 max-slots=6 > csclprd3-0-3 slots=6 max-slots=6 > csclprd3-0-4 slots=6 max-slots=6 > csclprd3-0-5 slots=6 max-slots=6 > csclprd3-0-6 slots=6 max-slots=6 > csclprd3-0-7 slots=32 max-slots=32 > csclprd3-0-8 slots=32 max-slots=32 > csclprd3-0-9 slots=32 max-slots=32 > csclprd3-0-10 slots=32 max-slots=32 > csclprd3-0-11 slots=32 max-slots=32 > csclprd3-0-12 slots=12 max-slots=12 > csclprd3-0-13 slots=24 max-slots=24 > csclprd3-0-14 slots=16 max-slots=16 > csclprd3-0-15 slots=16 max-slots=16 > csclprd3-0-16 slots=24 max-slots=24 > csclprd3-0-17 slots=24 max-slots=24 > csclprd3-6-1 slots=4 max-slots=4 > csclprd3-6-5 slots=4 max-slots=4 > > The number of slots also includes hyperthreading > cores. > > One more question, would not having defined swap > partitions on all the nodes in the ring cause OpenMPI > to crash? Because no swap partitions are defined > for any of the above systems. > > -Bill L. > > > From: users [users-boun...@open-mpi.org <mailto:users-boun...@open-mpi.org>] > on behalf of Ralph Castain [r...@open-mpi.org <mailto:r...@open-mpi.org>] > Sent: Wednesday, April 01, 2015 5:04 AM > To: Open MPI Users > Subject: Re: [OMPI users] OpenMPI 1.8.2 problems on CentOS 6.3 > > The warning about binding to memory is due to not having numactl-devel > installed on the system. The job would still run, but we are warning you that > we cannot bind memory to the same domain as the core where we bind the > process. Can cause poor performance, but not fatal. I forget the name of the > param, but you can tell us to "shut up" :-) > > The other warning/error indicates that we aren't seeing enough cores on the > allocation you gave us via the hostile to support one proc/core - i.e., we > didn't at least 128 cores in the sum of the nodes you told us about. I take > it you were expecting that there were that many or more? > > Ralph > > > On Wed, Apr 1, 2015 at 12:54 AM, Lane, William <william.l...@cshs.org > <mailto:william.l...@cshs.org>> wrote: > I'm having problems running OpenMPI jobs > (using a hostfile) on an HPC cluster running > ROCKS on CentOS 6.3. I'm running OpenMPI > outside of Sun Grid Engine (i.e. it is not submitted > as a job to SGE). The program being run is a LAPACK > benchmark. The commandline parameter I'm > using to run the jobs is: > > $MPI_DIR/bin/mpirun -np $NSLOTS -bind-to-core -report-bindings --hostfile > hostfile --mca btl_tcp_if_include eth0 --prefix $MPI_DIR > $BENCH_DIR/$APP_DIR/$APP_BIN > > Where MPI_DIR=/hpc/apps/mpi/openmpi/1.8.2/ > NSLOTS=128 > > I'm getting errors of the form and OpenMPI never runs the LAPACK benchmark: > > -------------------------------------------------------------------------- > WARNING: a request was made to bind a process. While the system > supports binding the process itself, at least one node does NOT > support binding memory to the process location. > > Node: csclprd3-0-11 > > This usually is due to not having the required NUMA support installed > on the node. In some Linux distributions, the required support is > contained in the libnumactl and libnumactl-devel packages. > This is a warning only; your job will continue, though performance may be > degraded. > -------------------------------------------------------------------------- > > -------------------------------------------------------------------------- > A request was made to bind to that would result in binding more > processes than cpus on a resource: > > Bind to: CORE > Node: csclprd3-0-11 > #processes: 2 > #cpus: 1 > > You can override this protection by adding the "overload-allowed" > option to your binding directive. > -------------------------------------------------------------------------- > > The only installed numa packages are: > numactl.x86_64 2.0.7-3.el6 > @centos6.3-x86_64-0/$ > > When I search for the available NUMA packages I find: > > yum search numa | less > > Loaded plugins: fastestmirror > Loading mirror speeds from cached hostfile > ============================== N/S Matched: numa > =============================== > numactl-devel.i686 : Development package for building Applications > that use numa > numactl-devel.x86_64 : Development package for building Applications > that use > : numa > numad.x86_64 : NUMA user daemon > numactl.i686 : Library for tuning for Non Uniform Memory Access > machines > numactl.x86_64 : Library for tuning for Non Uniform Memory Access > machines > > Do I need to install additional and/or different NUMA packages in order to > get OpenMPI to work > on this cluster? > > -Bill Lane > IMPORTANT WARNING: This message is intended for the use of the person or > entity to which it is addressed and may contain information that is > privileged and confidential, the disclosure of which is governed by > applicable law. 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