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Re: Guix and openmpi in a container environment
From: |
Todor Kondić |
Subject: |
Re: Guix and openmpi in a container environment |
Date: |
Mon, 27 Jan 2020 10:54:59 +0000 |
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Sunday, 19 January 2020 11:25, Todor Kondić <address@hidden> wrote:
> I am getting mpirun errors when trying to execute a simple
>
> mpirun -np 1 program
>
> (where program is e.g. 'ls') command in a container environment.
>
> The error is usually:
>
> All nodes which are allocated for this job are already filled.
>
> which makes no sense, as I am trying this on my workstation (single socket,
> four cores -- your off-the-shelf i5 cpu) and no scheduling system enabled.
>
> I set up the container with this command:
>
> guix environment -C -N --ad-hoc -m default.scm
>
> where default.scm:
>
> (use-modules (guix packages))
> (specifications->manifest
> `(;; Utilities
> "less"
> "bash"
> "make"
> "openssh"
> "guile"
> "nano"
> "glibc-locales"
> "gcc-toolchain@7.4.0"
> "gfortran-toolchain@7.4.0"
> "python"
> "openmpi"
> "fftw"
> "fftw-openmpi"
> ,@(map (lambda (x) (package-name x)) %base-packages)))
>
> Simply installing openmpi (guix package -i openmpi) in my usual Guix profile
> just works out of the box. So, there has to be some quirk where the openmpi
> container installation is blind to some settings within the usual environment.
For the environment above,
if the mpirun invocation is changed to provide the hostname
mpirun --host $HOSTNAME:4 -np 4 ls
ls is executed in four processes and the output is four times the contents of
the current directory as expected.
Of course, ls is not an MPI program. However, testing this elementary fortran
MPI code,
---
program testrun2
use mpi
implicit none
integer :: ierr
call mpi_init(ierr)
call mpi_finalize(ierr)
end program testrun2
---
fails with runtime errors on any number of processes.
The compilation line was:
mpif90 test2.f90 -o testrun2
The mpirun command:
mpirun --host $HOSTNAME:4 -np 4
Let me reiterate, there is no need to declare the host and its maximal number
of slots in the normal user environment. Also, the runtime errors are gone.
Could it be that the openmpi package needs a few other basic dependencies not
present in the package declaration for the particular case of a single node
(normal PC) machine?
Also, I noted that gfortran/mpif90 ignores "CPATH" and "LIBRARY_PATH" env
variables. I had to specify this explicitly via -I and -L flags to the compiler.