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MPI stall

Submitted by jadolfbr on Thu, 2013-10-10 18:59

Hi all,

Has anyone ever had any problems with the master MPI process stalling as it's cleaning up / giving more work to a slave or a little afterward?

I am running more tests tomorrow, but I have had it stall (While still saying it at 100 % cpu) with its output garbled like this before it just stops communicating with the rest the slaves. Once it stops communicating, all the slaves continue to run, but nothing gets output and the job needs to be cancelled. Also, no error message is reported from MPI or Rosetta. It just silently stops:

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Rosetta 3 - General

Sequence design with mixed fixbb-relax protocol

Submitted by kszczepaniak on Thu, 2013-10-03 08:11

Hello,

I would like to design a protein sequence using a mixed fixbb-relax protocol.

Basically, I want to do something like in this publication: http://www.sciencedirect.com/science/article/pii/S0969212612001517

(The idea is to iterate between fixbb and relax protocols as long as the Rosetta energy difference between models is bigger than 1.0 REU)

Does anybody have an idea how to use RosettaScripts to implement this?

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Rosetta 3 - Applications

Rosetta 3.5 Compiling Error - Mac OSX 10.8.5

Submitted by rnotti on Sun, 2013-09-22 18:09

Hi All,

I'm attempting to build Rosetta3.5 on my Mac and keep running into a compiling error with Calculator.os that terminates the build. Any suggestions would be much appreciated. I've also tried building within Xcode, and the build terminates with a number of similar errors (apparently missing files). I downloaded Rosetta3.5 as a single bundle, by the way.

My command line compiler:
[Ryans-iMac:~/applications/rosetta-3.5/rosetta_source] Ryan% gcc -v
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1

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Rosetta 3 - Build/Install

Error with FlexPepDock

Submitted by aloshbau on Sat, 2013-08-10 11:51

Hello,
I am running FlexPepDock-Refine, and getting the following error:
ERROR: this_pose.total_residue() == residue_packstat_.size()
ERROR:: Exit from: src/protocols/toolbox/pose_metric_calculators/PackstatCalculator.cc line: 164
I think it may have to do with non-Rosetta numbering in the input pdbs...
Can someone explain what variables this error is pointing too?

Edit: I renumbered my PDBs and it is working correctly now. But if anyone wants to explain the code a bit I would still be interested.

Thanks,
Amanda

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Rosetta 3 - Applications

Script for precalculating rotamer energies

Submitted by pachecoj on Tue, 2013-08-06 08:59

FYI,

I've attached a script I've written for pre-processing the rotamer energies and writing out to specific file formats. I am working on discrete optimization of side-chain configuration, which happens outside of Rosetta and requires building the backbone-dependent rotamer library and precalculating all single and pairwise rotamer energies.

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PyRosetta - Scripts

Calculate residue-residue pairwise energies

Submitted by pachecoj on Tue, 2013-07-23 04:51

I am trying to calculate all residue-residue pairwise energies for a given conformation. It doesn't appear that these are stored when the score is computed, and that I need to access them directly for every residue pair. I have a few questions regarding this:

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PyRosetta - General

Please help - mpiCC Error

Submitted by Prasanth Kumar on Wed, 2013-07-17 07:46

I'm trying to install mpi version of rosetta-3.4 in cluster.
I got the error when i did "scons bin mode=release extras=mpi (with and without cxx=icc) ", mpiCC : Command not found

In the cluster there is mpicc, mpicxx. There is NO mpic++, mpiCC.

What should i do now?

How do i install mpiCC without administrative previleges?

Please help me:)

Note:- I'm from non cs background.

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Rosetta 3 - Build/Install

Changing constraints code and compiling

Submitted by Ashafix on Sat, 2013-07-06 05:13

Dear Rosetta community,

after reading a lot of helpful posts I managed to compile Rosetta 3.4 on Ubuntu 11.04 in a virtual machine on Windows 7. It runs without any problems and abinitio folding actually works.
I wanted to add a new constraint function (just to test some weird idea, don't ask), unfortunately I neither speak C++, nor understand how the inner organs of Rosetta work.

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