There are two points here 1. slurm(stepd) is unable to put the processes in the (null) cgroup. at first glance, this looks more of a slurm jus configuration 2. the MPI process forking. though this has a much better support than in the past, that might not always work, especially with fast interconnects. since you are running on a single node, you should be fine. simply export OMPI_MCA_mpi_warn_on_fork=0 before invoking srun, in order to silence this message.
Cheers, Gilles On Monday, June 20, 2016, Ahmed Rizwan <rizwan.ah...@aalto.fi <javascript:_e(%7B%7D,'cvml','rizwan.ah...@aalto.fi');>> wrote: > Dear MPI users, > > I am getting the errors below while submitting/executing following script, > > #!/bin/sh > #SBATCH -p short > #SBATCH -J layers > #SBATCH -n 12 > #SBATCH -N 1 > #SBATCH -t 01:30:00 > #SBATCH --mem-per-cpu=2500 > #SBATCH --exclusive > #SBATCH --mail-type=END > #SBATCH --mail-user=rizwan.ah...@aalto.fi > #SBATCH -o output_%j.out > #SBATCH -e errors_%j.err > > srun --mpi=pmi2 gpaw-python layers.py > > -------------------------------------------------------------------------- > slurmstepd: error: task/cgroup: unable to add task[pid=126453] to memory > cg '(null)' > slurmstepd: error: task/cgroup: unable to add task[pid=80379] to memory cg > '(null)' > slurmstepd: error: task/cgroup: unable to add task[pid=124258] to memory > cg '(null)' > slurmstepd: error: task/cgroup: unable to add task[pid=124259] to memory > cg '(null)' > slurmstepd: error: task/cgroup: unable to add task[pid=124261] to memory > cg '(null)' > slurmstepd: error: task/cgroup: unable to add task[pid=124266] to memory > cg '(null)' > slurmstepd: error: task/cgroup: unable to add task[pid=124264] to memory > cg '(null)' > slurmstepd: error: task/cgroup: unable to add task[pid=124262] to memory > cg '(null)' > slurmstepd: error: task/cgroup: unable to add task[pid=124260] to memory > cg '(null)' > slurmstepd: error: task/cgroup: unable to add task[pid=124265] to memory > cg '(null)' > slurmstepd: error: task/cgroup: unable to add task[pid=124263] to memory > cg '(null)' > -------------------------------------------------------------------------- > An MPI process has executed an operation involving a call to the > "fork()" system call to create a child process. Open MPI is currently > operating in a condition that could result in memory corruption or > other system errors; your MPI job may hang, crash, or produce silent > data corruption. The use of fork() (or system() or other calls that > create child processes) is strongly discouraged. > > The process that invoked fork was: > > Local host: pe38 (PID 80379) > MPI_COMM_WORLD rank: 1 > > If you are *absolutely sure* that your application will successfully > and correctly survive a call to fork(), you may disable this warning > by setting the mpi_warn_on_fork MCA parameter to 0. > -------------------------------------------------------------------------- > > Is this error fatal or should it be ignored? Thanks > Regards, > Rizwan >
