Developer Guide

  • 2021.1
  • 12/04/2020
  • Public Content
Contents

Problem: MPI limitation for Docker*

 
Problem
The command fails with the following message:
[root@n1 /]# I_MPI_DEBUG=12 mpirun -n 2 -ppn 1 -env I_MPI_PIN_DOMAIN socket IMB-MPI1 bcast impi_shm_heap_init(): mbind failed (p=0x7f3078b0e000, size=536870912) impi_shm_heap_init(): mbind failed (p=0x7f9b808bc000, size=536870912)
Cause
MPI has limitation on the dev/shm area. It should be not less than 4Gb for 2 sockets node. By default, the Docker* container set 64Mb, which is not enough.
Solution
  1. Make sure the problem is in small size of shm area:
    $df -h /dev/shm [root@n1 /]# df -h /dev/shm Filesystem Size Used Avail Use% Mounted on shm 4.0G 0 4.0G 0% /dev/shm
  2. If it is true, restart Docker using the following command:
    --shm-size=4gb docker run --shm-size=4gb …
 

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