Using OpenMP parallelization on Windows 10

[tanoury1]

Hi,
I am using MDAnalysis on my Windows 10 laptop and was trying to run a clustering method on 4 cores as shown below. However, it only runs on a single core. What am I overlooking?

ces1, details1 = encore.ces([u1], select='index 0:55', clustering_method=clustering_method, ncores=4)

Thank you,
Jerry

[IAlibay]

@tanoury1 how was MDAnalysis installed?

You need to use pip to use OpenMP: https://userguide.mdanalysis.org/stable/installation.html#installation

[IAlibay]

@tanoury1 any further updates on this?

[tanoury1]

Hi Irfan, I tried it on my Linux cluster. I created a conda env for mdanalysis using python 3.7. I then did a pip install of the code. I could not get my job to run in parallel. As for running on my Windows machine, I am waiting for my company’s IT group to install the required C++ libraries so I can install mdanalysis with pip. We have some restrictions that will not allow me to install the required libraries. I’ll update when I get that done. Thanks for checking!! Jerry

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On Sat, Jun 11, 2022 at 4:39 AM Irfan Alibay ***@***.***> wrote: @tanoury1 <https://github.com/tanoury1> any further updates on this? — Reply to this email directly, view it on GitHub <#27>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOA2OYWDOI7ZS5TQULKSBW3VORGDRANCNFSM5XB74ZVA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[tanoury1]

Hi Irfan, I am sorry it has been so long since I replied. My apologies for this. I have not been able to get 'ncores=4' to run the code below on 4 cores on my Windows 10 machine. I am using MDAnalysis version 2.4.3, installed via 'pip install'. Are there some other python libraries I need to install? ces1, details1 = encore.ces([u1], select='bynum 261:317', clustering_method=clustering_method, ncores=4) Best regards, Jerry

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On Sun, May 29, 2022 at 11:23 AM Irfan Alibay ***@***.***> wrote: @tanoury1 <https://github.com/tanoury1> how was MDAnalysis installed? You need to use pip to use OpenMP: https://userguide.mdanalysis.org/stable/installation.html#installation — Reply to this email directly, view it on GitHub <#27>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOA2OYR2YT3BDGOAGJ45P63VMODW3ANCNFSM5XB74ZVA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[mtiberti]

hi, as far as we remember there's no parallelisation on the single method - it only happens when using clustering methods with multiple set of parameters (each set is run independently). In that case this would be the expected behaviour

[orbeckst]

As this is currently expected behavior, I am closing this issue.

If this is a feature request, please open it again or open a new one with details of what you'd want to see.