taskReproducible paper template - Tasks: task #15361, Tips, guide-lines, FAQs

 
 

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task #15361: Tips, guide-lines, FAQs

Submitted by:  Boud Roukema <boud>
Submitted on:  Wed 07 Aug 2019 09:40:18 PM UTC  
 
Should Start On:  Wed 07 Aug 2019 12:00:00 AM UTC Should be Finished on:  Wed 07 Aug 2019 12:00:00 AM UTC
Category:  None Priority:  1 - Later
Status:  None Privacy:  Public
Percent Complete:  0% Assigned to:  None
Open/Closed:  Open Effort:  0.00

Thu 08 Aug 2019 12:56:30 AM UTC, comment #1: 

This is a good point! Once we make a webpage/documentation we should add a "Tips" or "Guidelines" section which can be very useful for beginners.

Many people are SUPER-interested in properly organizing their research analysis steps using something like this template. But they need guidance/tips on how to effectively do so. Afterall, as natural scientists, we are not well trained in software egineering tools: many don't even know Git (but fall in love it once they learn it!).

Because of this, even at this early stage, based on my experience with new adopters of this template, I felt that its necessary to add a Tips for designing your project in the `README-hacking.md.

So indeed, I feel we really need to add a section with useful tips on using various software reproducibly.

Since the discussion seemed to be more about adding documentation with tips/FAQs for using software reproducibly, I changed the tile of this task.

Let's use this task to share any tips we find based on experience (like the one you just reported). This way, we won't loose the good points until that a special page is setup for this job.

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Wed 07 Aug 2019 09:40:18 PM UTC, original submission:  

Quoting https://www.open-mpi.org/doc/v2.0/man1/mpirun.1.php#sect22

> The Open MPI team strongly advises against executing mpirun as the root user. MPI applications should be run as regular (non-root) users.
>
> Reflecting this advice, mpirun will refuse to run as root by default. To override this default, you can add the --allow-run-as-root option to the mpirun command line.


Apparently mpich allows the user to run as root without complaining - which is an example of why openmpi is probably a more thorough community developed implementation. There are other mpi implementations too - I've no idea how many others are as careful as openmpi.

When we start preparing documentation, we could add a comment for those users who do everything as root ("noone else but me uses my computer") or those who do things in a chroot gaol. I didn't quite see where package-specific documentation would make sense, so I'm posting this here so it doesn't get forgotten.

However, I'm not fully sure about this being worth documenting - if we try documenting every possible mistake, including those easily found by duckduckgoing or qwanting, then we'll be wasting time doing what other groups/networks already do better. People should look for info in the place they expect (and preferably without totalitarian search engines). E.g. we're not going to distribute tutorials in C or fortran or shell.

Comment: In preparing Debian binary executables, chroot is normally used, since the idea is to simulate a root user installing libraries and so on. So --allow-run-as-root is enabled during after building the mpgrafic binary, so that a minimal reproducible "science run" can be tested. (An alternative could be to create a dummy user, run user-level tests, and then rm the dummy user.)

Boud Roukema <boud>
Project Member

 

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    Date Changed by Updated Field Previous Value => Replaced by
    2019-08-08 makhlaghi Summarympi FAQ - openmpi refuses to run as root => Tips, guide-lines, FAQs

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