Request support/help for PBS with OpenMPI

mkcolg
Posts: 8023
Joined: Jun 30 2004

Re: Request support/help for PBS with OpenMPI

Post by mkcolg » Thu Aug 08, 2019 1:13 pm

Hi Ron,

This is a bit beyond either my or Chris area of expertise, but Chris is going to reach out to other folks within NVIDIA to see if they might have ideas.

Also, you may see if NASA can get in contact with the NVIDIA Solution Architect (SA) assigned to their account (not sure who it is though). SA's should be better able provide insights into hardware and network issues.

-Mat

cparrott
Posts: 10
Joined: Aug 13 2018

Re: Request support/help for PBS with OpenMPI

Post by cparrott » Thu Aug 08, 2019 2:09 pm

Hi Ron,

Just FYI - we are primarily a compiler development and support organization here, so some of your concerns regarding Open MPI performance may fall a bit outside of our area of experience. However, I have reached out to some other people within NVIDIA who can hopefully help us out with these concerns you have raised here.

One of our Open MPI engineers immediately responded back with two suggestions that I wanted to pass along:

1. He is concerned that your PLEIADES cluster may not be using InfiniBand for the Open MPI transport. Here is what he said:
Reading the thread, this comment is worrying :


« So it turns out the openmpi was in fact detecting the infiniband (I think) as the code does run on multiple nodes (just slow). »


No, this is actually a good sign Infiniband was not detected and he's running on TCP/IP.


This is how you check the openib BTL is there (in Open MPI 1.10.7) and force it to be used :

Code: Select all

$ ompi_info | grep openib
                 MCA btl: openib (MCA v2.0.0, API v2.0.0, Component v1.10.7)
$ mpirun -mca btl openib,smcuda,self ...
And this is for UCX (in Open MPI 4.0.0) :

Code: Select all

$ ompi_info | grep ucx
                 MCA osc: ucx (MCA v2.1.0, API v3.0.0, Component v4.0.0)
                 MCA pml: ucx (MCA v2.1.0, API v2.0.0, Component v4.0.0)
$ mpirun -mca pml ucx ...
2. He also mentioned that the previous support of InfiniBand in Open MPI is deprecated as of Open MPI 4.x, and the Open MPI developers are recommending that everyone switch to using UCX instead, and then building Open MPI against UCX. UCX will manage the InfiniBand transport for Open MPI going forward, rather than having Open MPI manage it directly. Based on their recommendations, we are actually planning to update our bundled Open MPI to a 4.x release and change the configuration to use UCX with the 20.1 release, due in early 2020.

This link provides a good overview of how to build UCX and link Open MPI against it:

https://github.com/openucx/ucx/wiki/Ope ... n-with-UCX

Note that you do not need to clone Open MPI source from their github repo as described in the OpenMPI and OpenSHMEM Installation section. It should work fine with Open MPI 4.0.1, for example. You will need to be sure you are using an up-to-date version of UCX, though.

Hopefully this will give you some ideas to try, going forward.

Good luck,

+chris

cparrott
Posts: 10
Joined: Aug 13 2018

Re: Request support/help for PBS with OpenMPI

Post by cparrott » Thu Aug 08, 2019 2:15 pm

Hi Ron,

Here is a step-by-step guide to configuring Open MPI with UCX that another NVIDIA engineer just passed along to me:
1. Setup UCX
=============


a. Download and build gdrcopy (optional but recommended)
git clone https://github.com/NVIDIA/gdrcopy # (see instructions in https://github.com/NVIDIA/gdrcopy)
cd gdrcopy/
sudo make PREFIX=/usr CUDA=/usr/local/cuda all install
sudo ./insmod.sh


# Copy library .so and header to /usr or wherever you decide GDRCOPY_HOME is
sudo cp libgdrapi.so.1 /usr/lib64/
sudo cp libgdrapi.so /usr/lib64/
sudo cp libgdrapi.so.1.4 /usr/lib64/
sudo cp gdrapi.h /usr/include




b. Download UCX
Either download the latest release here: https://github.com/openucx/ucx/releases or clone master branch
git clone https://github.com/openucx/ucx

* Note on picking the closest HCA to a GPU used by a UCX process:
On multiple-HCA machines, using UCX 1.5.x series is recommended for its GPU-HCA affinity support.
The last known 1.5.x release is here:
wget https://github.com/openucx/ucx/releases ... 5.2.tar.gz
tar xfz ucx-1.5.2.tar.gz
cd ucx-1.5.2

c. Build UCX with cuda-support
UCX_HOME=/usr/local/ucx
CUDA_HOME=/usr/local/cuda
GDRCOPY_HOME=/usr

./autogen.sh # if configure isn't present
sudo apt-get install libnuma-dev # if libnuma-dev isn't installed
./configure --prefix=$UCX_HOME --with-cuda=$CUDA_HOME --with-gdrcopy=$GDRCOPY_HOME --enable-mt
sudo make -j install


# Export paths to access binaries and libraries later
export LD_LIBRARY_PATH=$GDRCOPY_HOME/lib64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$UCX_HOME/lib:$LD_LIBRARY_PATH
export PATH=$UCX_HOME/bin:$PATH




2. Setup OpenMPI
=================


a. Download OpenMPI
Either download the latest release here: https://www.open-mpi.org/software/ompi/v4.0 (recommended)
wget https://download.open-mpi.org/release/o ... 0.1.tar.gz
tar xfz openmpi-4.0.1.tar.gz
cd openmpi-4.0.1


or clone master branch
git clone https://github.com/open-mpi/ompi.git


b. Build OpenMPI with cuda-support
OMPI_HOME=/usr/local/openmpi
./autogen.pl # if configure isn't present
./configure --prefix=$OMPI_HOME --enable-mpirun-prefix-by-default --with-cuda=$CUDA_HOME --with-ucx=$UCX_HOME --with-ucx-libdir=$UCX_HOME/lib --enable-mca-no-build=btl-uct --with-pmix=internal
sudo make -j install


3. Run osu-micro-benchmarks (OMB)
=================================

a. Download OMB
Either from here http://mvapich.cse.ohio-state.edu/benchmarks/ (recommended) or clone
git clone https://github.com/forresti/osu-micro-benchmarks.git


b. Build OMB
MPI_HOME=$OMPI_PREFIX
../configure --enable-cuda --with-cuda-include=$CUDA_HOME/include --with-cuda-libpath=$CUDA_HOME/lib64 CC=$MPI_HOME/bin/mpicc CXX=$MPI_HOME/bin/mpicxx --prefix=$PWD
make -j install

c. Run OMB
export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$UCX_HOME/lib:$LD_LIBRARY_PATH
cat hostfile
hsw210 slots=1 max-slots=1
hsw211 slots=1 max-slots=1
mpirun -np 2 --hostfile $PWD/hostfile --mca pml ucx -x UCX_MEMTYPE_CACHE=n -x UCX_TLS=rc,mm,cuda_copy,gdr_copy,cuda_ipc -x LD_LIBRARY_PATH $PWD/get_local_ompi_rank $PWD/mpi/pt2pt/osu_bw D D
Hope you find this helpful.

+chris

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