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 a limitation on the dev/shm area. It should be not less than 4GB for a node with 2 sockets. By default, the Docker* container set 64MB, which is not enough.

Solution

Make sure the problem is the 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

If it is true, restart Docker using the following command:
```
docker run --shm-size=4gb …
```