• 2019 Update 7
  • 03/31/2020

Problem: MPI limitation for Docker*



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)


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.


  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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Notice revision #20110804