[Beowulf] software for activating one of many programs but not the others?

Alex Chekholko alex at calicolabs.com
Tue Aug 20 10:40:36 PDT 2019

Hi David,

Unfortunately, over the last 30 years we have not settled on One Software
Packaging Method To Rule Them All.

You mention building from source, and then you mention Docker, and there
are maybe 20 other ways to package software in between.

I'm personally a fan of APT, so your users could just do "apt install

Other examples include RPM or EasyBuild+Lmod or less common tools like
Singularity or Snap/Snappy or Flatpak.


On Tue, Aug 20, 2019 at 10:28 AM David Mathog <mathog at caltech.edu> wrote:

> On a system I am setting up there are a very large number of different
> software packages available.  The sources live in /usr/local/src and a
> small number of the most commonly used ones are installed in
> /usr/local/bin, /usr/local/lib and so forth.  The issue is that any of
> the target end users will only want a couple of these.  If they were all
> fully installed into /usr/local there would be some name conflicts.
> They may also be bringing some of their own versions of these, and while
> $PATH order can help there, it would be best to avoid those possible
> conflicts too.  Users don't have priv's to modify /usr/local, so they
> cannot install/uninstall there themselves.
> So I'm looking for something like
>    setup software_name install
>    setup software_name remove
> which would install/uninstall the packages (perhaps by symlinks) from
>    /usr/local/src/software_name
> under the user's home directory.  The goal is that the setup scripts NOT
> be constructed by hand.  It would have a
>    setup software_name install
> which would emulate a:
>    make install
> and automatically translate it into the appropriate setup commands.
> Some of these packages have hundreds of programs, so anything manual is
> going to be very
> painful.
> Anybody seen a piece of software like this?
> I don't expect this to work in all cases.  Some of these packages hard
> code paths into the binaries and/or scripts.  The only hope for them is
> for the user to do some variant of:
>      cd $HOMEDIR
>      (cd /usr/local/src; tar -cf - software_name) | tar -xf -
>      cd software_name
>      make clean  #pray that it gets everything!!!
>      ./configure --prefix=$HOMEDIR
>      make
>      make install
> There is a file which documents how to build each package, although it
> is nowhere near complete at this time.
> Docker is already available if the user wants to go that route, which
> avoids this whole issue, but at the cost of moving big images around.
> Thanks,
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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