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Compilation

Variable unitialized warnings during compilation of Rosetta 3.5

Category: 
Compilation

I am getting a lot of "unitialized" warnings during compilation of rosetta 3.5. See examples below (there is a lot more). I am using Ubuntu 14.04 amd64. I have gcc 4.8 and 4.7 installed. I am compiling with ./scons.py -j1 mode=release cxx_ver=4.7 bin.

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rosetta default and mpi @ same tree?

Category: 
Compilation

Hi there,
Will rosetta default and mpi compilations coexists in the same directory tree?
I usually test flags with rosetta default to check things before launch the mpi process. However, I've experienced some weird behaviors after installing the last version 2014.35. Looks like something stupid but it's worth to check.
Best,
Fred

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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:

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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

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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)

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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

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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

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