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Abinitio isolated

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Abinitio isolated

Hello community,


I have found that I am using Rosetta (C++) only to run Abinitio folding simulations.

Is it possible to isolate just the Abinitio executable from the Rosetta bundle and compile it on its own, rather than keep moving and compiling the entire Rosetta (C++) software?

Post Situation: 
Wed, 2018-04-04 07:36

If you want to compile just a single executable, you can pass the name of the executable on the scons command line instead of the 'bin'. ('bin' means to compile the entire bin/ directory.)  -- I think we have this set up now such that you can either do the full path (e.g. 'bin/AbRelax.linuxgccrelease') or you can do just the stem name of the executable (e.g. 'AbRelax').

That might not net you much in compilation time, though. Most of the time in compiling is of the core libraries, which are shared by all the applications, so there's only a small fraction of the time which you'll save.

Regarding moving executables, that's what the static compiled version is for ('extras=static' on the scons commandline). This will create a single file which can be moved to other computers, absent the rest of the source directory. The entries in the bin/ directory will still be symlinks, though, so you'll have to do something like `ls -l bin/` to figure out the file under the build/ directory which is the actual executable which you'll want to copy.

Note that these static executables are not necessarily completely movable. While they'll have no Rosetta-internal dependencies (aside from the Rosetta database), they will still have system hooks. These are set up to be relatively general, but depending on the systems you're moving from and the one you're moving to, you can sometimes have issues. (For example, if you try to run on an older Linux an executable compiled on a newer Linux you can often get GLIBC version errors. This is unsolvable except for recompiling on the older system.)

Wed, 2018-04-04 08:05

That explains what i need,


thank you very much


on a side note, can Rosetta (C++) work in a GPU?

My university's HPC is out of service for a long time, probably until after summer (something in it exploded), and was thinking of using GPU cloud services temporarly. Would that work?

Wed, 2018-04-04 08:47

Rosetta has extremely limited GPU support, and none of that support is relevant to ab initio.  It will run fine on generic cloud CPU.

Wed, 2018-04-04 09:02