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Compilation

Rosetta remodel on intel Xeon Phi

Category: 
Compilation

Greetings, I am planning to use Rosetta Remodel very soon, and as I am designing a system to do so, I found myself wondering if I could use the xeon phi coprocessor's cores to increase output. I believe it can be done with mpi, but I am uncertain about that, performance and how difficult the setup would be.
Also, about how many RAM is required per core? I remember that certain steps in remodel protocol require quite an amount of RAM, and the Xeon Phi I am trying to get hands on is 8GB for 60 cores.
Any insights is really appreciated.

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Error during scons building

Category: 
Compilation

I've been trying to build the latest weekly release (2016.20), and after starting scons using:

external/scons-local/scons.py -j3 mode=release bin 

from the source directory, everything will be fine for around 2h, but then I get this error:

/usr/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
scons: *** [build/src/release/linux/3.2/64/x86/gcc/4.7/default/libObjexxFCL.so] Error 1
scons: building terminated because of errors.

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Compiling problems in rosetta 2016.20

Category: 
Compilation

Hello, everyone!

I have some problems while compiling rosetta_src_2016.20.58704 source code both in my desktop and cluster.
Compilers: gcc 6.1.1 & gcc 4.9.3
Compiling with make:
./make_project.py all
cd build_release
cmake ./
make -j 8

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Error while loading shared libraries: libcifparse.so

Category: 
Compilation

Hello,

I am trying to install CSRosetta and Rosetta on a computer running Fedora 20, but I keep on getting the following error message:

/home/crowlab/Rosetta/main/source/bin/AbinitioRelax.linuxgccrelease: error while loading shared libraries: libcifparse.so: cannot open shared object file: No such file or directory

We have CBFlib-0.9.5.1-1.fc20 package installed, but the software seems to not recognize it. We are not sure what we should have installed instead.

Thank you in advance for your help.

 

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Unit Tests failing for Rosetta installed with mpi on Ubuntu 16.04

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: 

Rosetta: Clustering

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? 

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