Normally I'd use mpiexec to run a process on multiple hosts like:
mpiexec -n 8 --hostfile hosts.txt python my_mpi_script.py
where my_mpi_script.py depends on mpi4py.
Supposing I couldn't run mpiexec or mpirun, how would I be able to run my_mpi_script.py on multiple hosts -- would this be possible by changing my script or execution environment?
Edit: I'm working with a system that runs the same command on many hosts. Normally, processes would discover each other on the local network rather than all be spawned by MPI. My current solution involves: checking which host I'm on and running mpiexec on exactly one of the hosts. This doesn't work well due to some networking limitations.
Thanks.
I'm testing a simple MPI program on my desktop (Ubuntu LTS 16.04/ Intel® Core™ i3-6100U CPU # 2.30GHz × 4/ gcc 4.8.5 /OpenMPI 3.0.0) and mpirun won't let me use all of the cores on my machine (4). When I run:
$ mpirun -n 4 ./test2
I get the following error:
--------------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 4 slots
that were requested by the application:
./test2
Either request fewer slots for your application, or make more slots available
for use.
--------------------------------------------------------------------------
But if I run with:
$ mpirun -n 2 ./test2
everything works fine.
I've seen from other answers that I can check the number of processors with
cat /proc/cpuinfo | grep processor | wc -l
and this tells me that I have 4 processors. I'm not interested in oversubscribing, I'd just like to be able to use all my processors. Can anyone help?
Your processor has 4 hyperthreads but only 2 cores (see the specs here).
By default, Open MPI does not run more than one MPI task per core.
You can have Open MPI run up to one MPI task per hyperthread with the following option
mpirun --use-hwthread-cpus ...
FWIW
The command you mentioned reports the number of hyperthreads.
A better way to figure out the topology of a machine is via the lstopo command from the hwloc package.
MPI tasks are not bound on cores nor threads on OS X, so if you are running on a Mac, the --oversubscribe -np 4 would lead to the same result.
To resolve your problem, you can use the --use-hwthread-cpus command line arguments for mpirun, as already pointed out by Gilles Gouaillardet. In this case, Open MPI will treat the thread provided by hyperthreading as the Open MPI processor. Otherwise, it will treat a CPU core as an Open MPI processor, which is the default behavior. When using --use-hwthread-cpus, it will correctly determine the total number of processors available to you, that is, all processors available on all hosts specified in the Open MPI host file. Therefore, you do not need to specify the "-n" parameter. In addition, when using the --use-hwthread-cpus command line parameter, Open MPI refers to the threads provided by hyperthreading as "hardware threads". With this technique, you will not oversubscribe, and if some Open MPI processor will run on a virtual machine, it will use the correct number of threads assigned to that virtual machine. And if your processor has more than two threads per core, as a Xeon Phi (Knights Mill, Knights Landing, etc.), it will take all four threads per core as an Open MPI processor.
Use $ lscpu the number of cores per socket * number of sockets would give you number of physical cores(the ones that you can use for mpi) where as number of cores per socket * number of sockets * threads per core will give you number of logical cores(the one that you get by using the command $ cat /proc/cpuinfo | grep processor | wc -l)
I am trying to submit MPI+openmp code in cluster. I am relatively new in using mpi in general. I am trying to use 2 MPI processes and 16 openmp process for each mpi process. I am using following parameters:
#PBS -l nodes=2:ppn=16
OMP_NUM_THREADS=16
export OMP_NUM_THREADS
mpirun -np 2 --bind-to core --map-by ppr:1:node:pe=16 -x OMP_NUM_THREADS ./exe
But this is returning with an error saying::
Your job has requested more processes than the ppr for
this topology can support:
App: ./exe
Number of procs: 2
PPR: 1:node
Please revise the conflict and try again.
Am I doing something wrong here ?
Thanks in advance.
What exactly is the third parameter in the following MPI command
mpiexec -n 2 cpi
Is it no. of cores? So if I am running on Pentium 4 , shall I make it 1?
-n 2: spawn two processes.
cpi: the executable.
Experiment with what is faster, one or two or more processes. Some codes run best with one process per core, some codes benefit from oversubscription.
I have a program running with MPI (OpenMPI) that is filling the output with many instances of this:
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
Other than that, the program seems to be running fine.
I wonder if there is a way to suppress this kind of messages?
-q didn't done it.