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Compilation

Combine flags file with command line arguments?

Category: 
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Membrane
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list

Thanks.

Post Situation: 

Error MPI build rosetta2014.35 on Ubuntu14.04 LTS

Category: 
Compilation

Hello!

Recently, I posted some post about install Rosetta3.5 on cygwin.

Finally, I changed the OS and succeeded to install them on the Ubuntu on Virtual box(Win7)
Normal install was good. and docking protocol was worked(I only checked that exe).
./scons.py -j4 mode=release bin

But,I couldn't MPI install by follow command in another new Virtual machine. The first one hour from the beginning was good but I got some error.
I did all command as superuser

Post Situation: 

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.

Post Situation: 

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

Post Situation: 

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

Post Situation: 

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

Post Situation: 

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: 

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