You are here

Home

Compilation

Unit Tests failing for Rosetta installed with mpi on Ubuntu 16.04

Submitted by abhi_pe_acharya on Mon, 2016-06-13 22:11
Category: 
Compilation

Dear Users,

I have been trying to install and run Rosetta 2016.15 weekly build (with MPI) on a  core i7 system on Ubuntu 16.04. For installation, I used the following command

> python ./scons.py mode=release extras=mpi bin

and compiled the test scripts using:

> python ./scons.py mode=release extras=mpi cat=test

The system already has openmpi-1.10.2. The installation was without any errors. However, when I ran the unit tests, I got numerous errors with a 27% pass statistic.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Build/Install

Rosetta: Clustering

Submitted by sskim on Sat, 2016-06-11 14:44
Category: 
Compilation

Hi,

I have used rosetta protein-protein docking to generate 1000 models, and was hoping to use rosetta clustering to analyze the result. 

I have read that rosetta clustering superimposes models for rmsd calculation by default, and I was hoping to find a way to change this default mode for my models.

Is there a way to turn this default mode off? 

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - General

Pyrosetta build error with anaconda python

Submitted by jasnyderjr on Sun, 2016-05-15 20:45
Category: 
Compilation

Hello:

We are trying to build Pyrosetta from source since we wish to use the Glib's with anaconda python rather that Glibs with the system python.

First I do:

/share/apps/local/anaconda/bin/python DeployPyRosetta.py

then cp BuildPyRosetta.sh to ...../source

cd ....../source

Post Situation: 
Unsolved
Forums: 
PyRosetta - Build/Install

Problems compiling on cluster

Submitted by Jhreed on Mon, 2016-03-14 08:27
Category: 
Compilation

Hello,

I've gotten a fair way through the installation process for the latest weekly build of Rosetta, but have run into an issue.

I start SCons using:

./scons.py -j3 mode=release bin

and everything seems good until about 30 minutes into compiling this happens:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Build/Install

change DOF of NH3 group in N terminus

Submitted by SergeyP on Wed, 2016-02-03 02:22
Category: 
Compilation

Hello everyone!

I am trying to change PHI angle, which associated with the 1H atom in NH3 group (that change also moves 2H and 3H atoms). If I set only this parameter through function set_dof everything works fine. However, if I change bond length of C atom (next to the first CA) and bond length of 1H atom (in NH3 group) even with the same values before setting 1H PHI angle it makes change in PHI angle of sidechain CB atom on same value. This change can be detected by writing a pdb file. Here an example and output (pdbs files are attached).

Post Situation: 
Solved
Forums: 
Rosetta 3 - General

Adding included libries to scons

Submitted by Al52 on Wed, 2016-01-20 16:10
Category: 
Compilation

Hello.

I am running a pilot app which uses a test class that requires the cxx test header. I was able to include the path to the compiler by using the -I parameter. However when I try to use scons to build the pilot app executable I don't know how to get scons to add in the extra -I parameter.

Thank you.

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Build/Install

Intel Compiler - Inaccurate G! step errors

Submitted by dtrudg on Tue, 2016-01-19 07:33
Category: 
Compilation

Hi,

We are trying to get Rosetta setup fo a user here at UT Southwestern, and have downloaded and built the 2015.39 release using the Intel Composer XE 2015 compiler suite, with MVAPICH2 2.1 as the MPI stack. This is the standard compiler/mpi stack we use for a large amount of other software on the cluster. Compilation of Rosetta followed the site settings file distributed for the TACC stampede cluster.

When the user runs a simple test of relax.linuxiccrelease:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Build/Install

Unit tests on a non-Intel CPU

Submitted by yuvals on Sun, 2015-12-27 07:03
Category: 
Compilation

Hello Rosetta forum!

I've been trying to run Rosetta (2015wk39) on an IBM Power8 machine. It has 64-bit PowerPC processors, which, according to our CS department, have been set up to work with little-endian byte ordering. Rosetta compiles fine* but I've been getting failures when running unit-tests.

I've attached the full log, and the epilogue is attached inline at the end of this message. Of all failed tests, I can only find details to the test_rotamer_trials test, which have the following error:

Post Situation: 
Unsolved
Forums: 
Rosetta 3 - Build/Install

Pages

Subscribe to RSS - Compilation