hpc-x

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Encountering shm_open permission denied issues with hpcx

If you are using Nvidia hpc-x and encountering issues like the one below during your MPI Run

shm_open(file_name=/ucx_shm_posix_77de2cf3 flags=0xc2) failed: Permission denied

The error message indicates that the shared memory has no permission to be used,  The permission of /dev/shm is found to be 755, not 777, causing the error. The issue can be resolved after the permission is changed to 777. To change and verify the changes:

% chmod 777 /dev/shm 
% ls -ld /dev/shm
drwxrwxrwx 2 root root 40 Jul  6 15:18 /dev/sh

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Installing and using Mellanox HPC-X Software Toolkit

Overview

Taken from Mellanox HPC-X Software Toolkit User Manual 2.3

Mellanox HPC-X is a comprehensive software package that includes MPI and SHMEM communication libraries. HPC-X includes various acceleration packages to improve both the performance and scalability of applications running on top of these libraries, including UCX (Unified Communication X) and MXM (Mellanox Messaging), which accelerate the underlying send/receive (or put/get) messages. It also includes FCA (Fabric Collectives Accelerations), which accelerates the underlying collective operations used by the MPI/PGAS languages.

Download

https://www.mellanox.com/products/hpc-x-toolkit

Installation

% tar -xvf hpcx-v2.6.0-gcc-MLNX_OFED_LINUX-5.0-1.0.0.0-redhat7.6-x86_64.tbz
% cd hpcx-v2.6.0-gcc-MLNX_OFED_LINUX-5.0-1.0.0.0-redhat7.6-x86_64
% export HPCX_HOME=/usr/local/hpcx-v2.6.0-gcc-MLNX_OFED_LINUX-5.0-1.0.0.0-redhat7.6-x86_64

Loading HPC-X Environment from BASH

HPC-X includes Open MPI v4.0.x. Each Open MPI version has its own module file which can be used to load the desired version

% source $HPCX_HOME/hpcx-init.sh
% hpcx_load
% env | grep HPCX
% mpicc $HPCX_MPI_TESTS_DIR/examples/hello_c.c -o $HPCX_MPI_TESTS_DIR/examples/hello_c
% mpirun -np 2 $HPCX_MPI_TESTS_DIR/examples/hello_c
% oshcc $HPCX_MPI_TESTS_DIR/examples/hello_oshmem_c.c -o $HPCX_MPI_TESTS_DIR/examples/
% hello_oshmem_c
% oshrun -np 2 $HPCX_MPI_TESTS_DIR/examples/hello_oshmem_c
% hpcx_unload

Loading HPC-X Environment from Modules

You can use the already built module files in hpcx.

% module use $HPCX_HOME/modulefiles
% module load hpcx
% mpicc $HPCX_MPI_TESTS_DIR/examples/hello_c.c -o $HPCX_MPI_TESTS_DIR/examples/hello_c
% mpirun -np 2 $HPCX_MPI_TESTS_DIR/examples/hello_c
% oshcc $HPCX_MPI_TESTS_DIR/examples/hello_oshmem_c.c -o $HPCX_MPI_TESTS_DIR/examples/
hello_oshmem_c
% oshrun -np 2 $HPCX_MPI_TESTS_DIR/examples/hello_oshmem_c
% module unload hpcx

Building HPC-X with the Intel Compiler Suite

Do take a look at the Mellanox HPC-X® ScalableHPC Software Toolkit

References:

  1. Mellanox HPC-X Software Toolkit User Manual 2.3
  2. Mellanox HPC-X® ScalableHPC Software Toolkit