substitution for runpar in eman2

[Qiangong2]

What was the substitution for runpar in eman2? We have multiple scripts that utilize it and because of that, they are stuck using eman 1.9

[sludtke42]

There is no direct substitution. EMAN1 predates the widespread adoption of MPI. EMAN2 has a more flexible system which can use MPI, non-MPI client-server methods, or threads. While the program "e2parallel.py" handles a lot of the client-side implementation for MPI/threads, it can't easily be used to execute arbitrary programs in parallel. They have to be written specifically for the parallelism system. If you want a generic runpar replacement, MPI has the "mpirun" command

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-------------------------------------------------------------------------------------- Steven Ludtke, Ph.D. ***@***.***> Baylor College of Medicine Charles C. Bell Jr., Professor of Structural Biology Dept. of Biochemistry Deputy Director, Advanced Technical Cores and Molecular Biology Academic Director, CryoEM Core Co-Director CIBR Center On Apr 14, 2023, at 1:18 PM, Kurt ***@***.***> wrote: What was the substitution for runpar in eman2? We have multiple scripts that utilize it and because of that, they are stuck using eman 1.9 — Reply to this email directly, view it on GitHub<#567>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACPKF2VF65OCVIAY53KE7HLXBGIG3ANCNFSM6AAAAAAW6XYAVI>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Qiangong2]

If mpirun is the generic replacement, is it a drop-in replacement? or do specific EMAN configurations need to be changed so that it can support mpirun?

[sludtke42]

Not sure I understand the question. EMAN2 has its own parallelism system which can make use of pthreads or MPI depending on what you request. If you request MPI it will make some use of mpirun internally. I thought you were saying you had some other use for runpar, and needed a replacement for that? The strategy in EMAN2 is described (for users) here: http://eman2.org/Parallel If that doesn't answer the question, please explain the issue in more detail.

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----------------------------------------- Steven Ludtke, ***@***.***

On Apr 14, 2023, at 5:52 PM, Kurt ***@***.***> wrote: If mpirun is the generic replacement, is it a drop-in replacement? or do specific EMAN configurations need to be changed so that it can support mpirun? — Reply to this email directly, view it on GitHub <#567 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACPKF2XYJ2ER2YAVJFKWR5DXBHIL3ANCNFSM6AAAAAAW6XYAVI>. You are receiving this because you commented.