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Compiling xmipp has hardcoded mpirun with 4 slots #306
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Hi @MohamadHarastani , |
Thanks @DStrelak , I will check it out asap |
Hi @DStrelak ,
These were the line of codes that I edited (starting from this line):
I can't verify if the flag --oversubscribe works with mpiexec This is what I used to test:
Regards |
'--oversubscribe' has been added in MPI 2.1. and e.g. Travis uses version 1.6 |
We can assert the MPI version by parsing 'mpirun --version'. However, we can add the '--oversubscribe' flag to the 'or' string in order to avoid a fail just due to the lack of that flag. We can, alternativelly, put a 'mpi -np 2 ...' . 2 should be always fine, isn't it? |
In theory, yes. I doubt that anybody would be brave enough to use xmipp with less than two cores. |
I thought the same "Who want to run Xmipp with less than 4 cores?" But the answer is "What about the login node in clusters?" Damn! I agree on linking the number of mpi-jobs to the number of cores for the compilation. Indeed, in the hypothetical case than N=1, if
works, it's fine. We are checking that mpirun works and this prove that. |
Can we close this issue? |
I think yes. I forced to use only 2 cores, that is the minimum that makes sense... If the problem persist, please, don't hesitate to reopen this to be able to make an more accurate approach. |
No objection.. thank you both @dmaluenda @DStrelak |
Hello again,
I will try to workaround this by commenting this test.. I will reply again here my progress. Regards, |
Hi @MohamadHarastani , |
Thanks @DStrelak for your reply.
We can close this issue and rediscuss a solution if needed (maybe a flag to pass this mpirun test with an error message that shows the option to run with this flag). Regards, |
Hi @MohamadHarastani , |
I agree on a bypassing flag. I vote for an environ var like By the way, note that the whole config-checking can be skipped just by manually stepping the build
(note the mising |
Thanks a lot for this hint. I don't think a flag is necessary in this case. I will try this option soon and comment on the result. |
Should be resolved . |
Hi,
While compiling xmipp on a personal laptop, I faced an error as follows:
"There are not enough slots available in the system to satisfy the 4 slots"
I have exactly 4 mpi slots in the processor (Intel® Core™ i7-4500U CPU @ 1.80GHz × 4 ).
This printing 4 times was only to print a sentence, but it ended up breaking the compilation.
I fixed this issue by replacing '4' by '2' in all the lines 692 to 698 here:
https://github.com/I2PC/xmipp/blob/devel/xmipp#L692
Couldn't we test if mpi runs during the installation another way? or turn the error into a warning?
Cheers
Mohamad
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