Workaround for installing on machine with < 4 mpi slots

mcianfrocco commented 4 years ago

Hello -

I'm trying to install scipion / XMIPP into a singularity container. To do this, I am installing everything from my home PC (Mac) on which I have sudo privileges.

Everything goes fine until the MPI testing step. In short, it fails because it only finds 1 CPU for the MPI testing step:

mpirun -np 4 --allow-run-as-root echo ' > This sentence should be printed 4 times if mpi runs fine.'

There are not enough slots available in the system to satisfy the 4 slots that were requested by the application:

echo

Either request fewer slots for your application, or make more slots available for use.

Is there an 'easy' way to get around this? I'm not exactly sure which library it is pulling from. If I knew, I could update the mpirun test command to include --oversubscribe, unless there is another way around this test.

I should say that this container will be run eventually on a computing cluster resource, not on my home PC.

Thank you, Mike

pconesa commented 3 years ago

Hi Mike, is only now I'm aware of this issue. Apologies. Is it still relevant? As far as I know this is a mpi test. It work for us as long as you have 4 CPUs. Maybe the container hade less cores?

azazellochg commented 3 years ago

Currently, in xmipp 3.20.07 ./xmipp script requires 2 cpus (I guess was changed from 4), but --oversubscribe is still missing.

mcianfrocco commented 3 years ago

Hi @pconesa - thanks for checking in. I found a workaround by setting up a virtual machine with 4 CPUs on my laptop even though it only has two CPUs. This satisfied the MPI test.

In the future, it would be an appreciated option.

Mike

pconesa commented 3 years ago

Thanks @mcianfrocco . Please make anote @DStrelak , @dmaluenda

DStrelak commented 3 years ago

scipion-em / scipion-installer

Workaround for installing on machine with < 4 mpi slots #20

mpirun -np 4 --allow-run-as-root echo ' > This sentence should be printed 4 times if mpi runs fine.'