• 2019 Update 7
  • 03/31/2020
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 …
 

Product and Performance Information

1

Intel's compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors. These optimizations include SSE2, SSE3, and SSSE3 instruction sets and other optimizations. Intel does not guarantee the availability, functionality, or effectiveness of any optimization on microprocessors not manufactured by Intel. Microprocessor-dependent optimizations in this product are intended for use with Intel microprocessors. Certain optimizations not specific to Intel microarchitecture are reserved for Intel microprocessors. Please refer to the applicable product User and Reference Guides for more information regarding the specific instruction sets covered by this notice.

Notice revision #20110804