Singularity images does not work with SLURM

[NoelAraujo]

I tried to run a singularity container inside a HPC cluster, my goal is to run accross many nodes. However, and I cannot even create one process. The lines below are how I submit my job:

(...)
#SBATCH --nodes=1     
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=2
#SBATCH --partition=slow

(...)
srun singularity exec \
     --bind=/scratch:/scratch \
     --bind=/var/spool/slurm:/var/spool/slurm \
     work.simg /opt/julia/bin/julia julia_parallel_test.jl

work.simg is my singularity image, that on my computer I am sure that everything works fine.
/opt/julia/bin/julia is the executable path inside the image
julia_parallel_test.jl is the most simple code that I come up:

using ClusterManagers
addprocs_slurm(2, nodes=1, partition="slow")
@everywhere println("process: $(myid()) on host $(gethostname())")

The message the concern us is here:

nested task error: IOError: could not spawn `srun -J julia-31840 -n 2 -o /home/u770885/Noel/./julia-31840-16189562422-%4t.out -D /home/u770885/Noel --partition=slow --nodes=1 /opt/julia/bin/julia --worker=hPfJL8h1rY8YWH7D`: no such file or directory (ENOENT)

The complete error is in the end.

What I think is happening is that : ClusterManagers.jl wants to run /opt/julia/bin/julia over the Node, and not on my singularity image. First of all, am I right ? Second, does anybody has a simple solution ?

Thank you for your attention.

---

Error launching Slurm job:
ERROR: LoadError: TaskFailedException
Stacktrace:
 [1] wait
   @ ./task.jl:317 [inlined]
 [2] addprocs_locked(manager::SlurmManager; kwargs::Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:nodes, :partition), Tuple{Int64, String}}})
   @ Distributed /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Distributed/src/cluster.jl:497
 [3] addprocs(manager::SlurmManager; kwargs::Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:nodes, :partition), Tuple{Int64, String}}})
   @ Distributed /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Distributed/src/cluster.jl:444
 [4] #addprocs_slurm#14
   @ ~/.julia/packages/ClusterManagers/Mq0H0/src/slurm.jl:100 [inlined]
 [5] top-level scope
   @ ~/Noel/julia_parallel_test.jl:2

    nested task error: IOError: could not spawn `srun -J julia-31840 -n 2 -o /home/u770885/Noel/./julia-31840-16189562422-%4t.out -D /home/u770885/Noel --partition=slow --nodes=1 /opt/julia/bin/julia --worker=hPfJL8h1rY8YWH7D`: no such file or directory (ENOENT)
    Stacktrace:
     [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Vector{Any})
       @ Base ./process.jl:99
     [2] #637
       @ ./process.jl:112 [inlined]
     [3] setup_stdios(f::Base.var"#637#638"{Cmd}, stdios::Vector{Any})
       @ Base ./process.jl:196
     [4] _spawn
       @ ./process.jl:111 [inlined]
     [5] open(cmds::Cmd, stdio::Base.DevNull; write::Bool, read::Bool)
       @ Base ./process.jl:370
     [6] open (repeats 2 times)
       @ ./process.jl:361 [inlined]
     [7] launch(manager::SlurmManager, params::Dict{Symbol, Any}, instances_arr::Vector{Distributed.WorkerConfig}, c::Condition)
       @ ClusterManagers ~/.julia/packages/ClusterManagers/Mq0H0/src/slurm.jl:55
     [8] (::Distributed.var"#39#42"{SlurmManager, Condition, Vector{Distributed.WorkerConfig}, Dict{Symbol, Any}})()
       @ Distributed ./task.jl:406
in expression starting at /home/u770885/Noel/julia_parallel_test.jl:2
srun: error: c2: task 0: Exited with exit code 1

[kescobo]

Not certain, but I think this might be a limitation with singularity / SLURM, and not with ClusterManagers.jl

I recently tried to use a python package from inside a singularity container that submits SLURM jobs, and long story short, the cluster environment was such that there was no way to get the container to be able to see the necessary components in order to actually call sbatch or srun.

[kescobo]

(...)
#SBATCH --nodes=1     
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=2
#SBATCH --partition=slow

(...)
srun singularity exec \
     --bind=/scratch:/scratch \
     --bind=/var/spool/slurm:/var/spool/slurm \
     work.simg /opt/julia/bin/julia julia_parallel_test.jl

Wait, are you calling srun from inside your sbatch script? That seems a bit weird - typically, your script would have the #SBATCH lines, and then be normal shell, so eg you'd have my_script.sh:

(...)
#SBATCH --nodes=1     
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=2
#SBATCH --partition=slow

singularity exec \
     --bind=/scratch:/scratch \
     --bind=/var/spool/slurm:/var/spool/slurm \
     work.simg /opt/julia/bin/julia julia_parallel_test.jl

and then run sbatch my_script.sh

[kescobo]

Or alternatively,

srun --nodes 1 --ntasks-per-node=1 --cpus-per-task=2 --partition=slow \
    singularity exec \
     --bind=/scratch:/scratch \
     --bind=/var/spool/slurm:/var/spool/slurm \
     work.simg /opt/julia/bin/julia julia_parallel_test.jl

[NoelAraujo]

OK, no easy solution, looks like we have to sit and wait untl Singularity community to improve its features.

Regarding srun singularity exec \, it was not my idea, I just used an example provided by the cluster staff.

[kescobo]

I just used an example provided by the cluster staff.

Interesting :thinking:. Is your julia script (julia_parallel_test.jl) also trying to spawn srun commands? Seems like nesting calls to the scheduler could be part of the problem, but it's hard to know without knowing more about the cluster architecture.

But based on my experience, I think this is a limitation with singularity rather than with ClusterManagers.jl, so I'll close this for now - I'm happy to keep the conversation going on discourse, slack or zulip if you want to start a thread, feel free to tag me.