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Compilation

Modify and re-compile a single application in Rosetta

Category: 
Compilation

Hi all,

I would like to make a change to the source code of a particular application - it's a very minor, but necessary, change that should make the application more broadly applicable.

However, having made the change in the .cc file - how would I go about recompiling the code so that it links to the rest of the Rosetta package, or is the simplest way just to recompile the whole package?

Thanks in advance.

wsg

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Build Rosetta in cygwin with scons (Windows7)

Category: 
Compilation

Hello , I have been to trying build Rosetta in cygwin with scons to build large fusion protein.
I know here is not scons and cygwin forum...but I couldn't find recent post in another forum.

I installed scons 2.3.3 from binary(.tar.gz)
and added Path
PATH=cygdrive/c/Python27/Scripts
and
PATH=cygdrive/c/Python27

but I typed below command and got below error

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Build error: FragmentPicker.cc:1406: error: 'j' is not a member of 'basic::options::OptionKeys::frags'

Category: 
Compilation

Hi,

I'm trying to build Rosetta with MPI/boost on a linux system, and am using rosetta_2014.35.57232_bundle.

I'm invoking the build with:

python scons.py -j8 bin mode=release extras=boost,boost_thread,mpi

and the build is failing here:

Post Situation: 

Error installing rosetta2014.35 on Ubuntu14.04

Category: 
Compilation

Hello,

I am trying to install rosetta2014.35 on ubuntu14.04.
I installed the last versions of gcc and clang compilers, namely gcc-4.8 and clang-3.5

I installed the following packages and libraries as reccommanded

sudo apt-get install build-essential
sudo apt-get install zlib1g-dev
sudo apt-get update

and executed the commands

cd main/source/
scons bin mode=release

but unsuccessfully!! I always receive the same error (see below)

Also I updated g++ compilers on tools/build/site.setting. topsail file

Post Situation: 

Rosetta problems: terminate called after throwing an instance of 'std::string'

Category: 
Compilation

Hi, Im new to Rosetta and these forums, but I have a problem running Rosetta. I’ve compiled on a CentOS machine, but I keep getting segmentation faults and crashes,

e.g. I try to run AbinitioRelax.default.linuxgccrelease --help

But it crashes in the midst of output with

rmsd_dump | 2 | R| dump all pdbs for loops that
| | | are below in rmsd
terminate called after throwing an instance of 'std::string'
Abort (core dumped)

Post Situation: 

Error installing MPI, static Rosetta3.5 ubuntu

Category: 
Compilation

Dear developers,
I'd tried to complile and install Roseta3.5 in my Ubuntu Ubuntu 12.04.3 LTS x86_64. My MPI version is MPICH2 Version: 1.4.1p1 and is installed at:
/usr/lib/mpich2/lib/libfmpich.so
/usr/lib/mpich2/lib/libmpichf90.so
/usr/lib/mpich2/lib/libmpl.so
/usr/lib/mpich2/lib/libmpichcxx.so
/usr/lib/mpich2/lib/libmpich.so
/usr/lib/mpich2/lib/libopa.so
At first I tried to compile using this options:
sudo scons bin mode=release cxx=gcc cxx_version=4.6 extras=mpi,static -j4

Post Situation: 

Unit test compilation failure on Rosetta 3.5+ with Intel icpc

Category: 
Compilation

Hello,

I'm attempting a complete build with intel/14.0.1.106 + mvapich2/2.0b compiler and MPI libraries. I'd like to be able to compile and run the unit tests as well as the integration tests to serve as a base level benchmark for performance improvements on our system.

#### Part of my configuration file ############################
cat > site.settings.stampede <<EOF
...snip
import os

Post Situation: 

Help for a Beginner Needed! Installation on Win 8 Computer

Category: 
Compilation

Hi- Being very new to this, I've only had a chance to skim through the forums. I did have a few questions, though. As I'm new to using python and RC, I want to thank whomever for answering for their patience in helping me understand this.

Post Situation: 

external/dbio/sqlite3/sqlite3.c: Errors

Category: 
Compilation

Dear all, I keep having problems compiling Rosetta 3.5 on our university cluster. First, I edited site.settings so scons finds mpicc and mpicxx

import os

settings = {

"site" : {

"prepends" : {

"program_path" : os.environ["PATH"].split(":"),

"include_path" : os.environ["INCLUDE"].split(":"),

"library_path" : os.environ["LD_LIBRARY_PATH"].split(":"),

},

"appends" : {

},

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system requirements (python and scons versions, etc) for Rosetta 2014.3x?

Category: 
Compilation

Hello,

I'm having trouble compiling rosetta 2014.34 on a red hat machine, and it looks like the problem may be with one or more missing features/attributes in one (or more) python modules. What versions of python (and I guess scons) are needed?

Thanks, - Mark

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