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

Submitted by Esbenjannik on Mon, 2014-10-27 02:09
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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Rosetta 3 - Build/Install

Error installing MPI, static Rosetta3.5 ubuntu

Submitted by samuelrpita on Fri, 2014-10-24 11:23
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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Rosetta 3 - Build/Install

Unit test compilation failure on Rosetta 3.5+ with Intel icpc

Submitted by sidio47 on Mon, 2014-09-29 11:52
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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Rosetta 3 - Build/Install

Help for a Beginner Needed! Installation on Win 8 Computer

Submitted by wushufury on Sun, 2014-09-21 14:21
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.

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Rosetta 3 - Build/Install

external/dbio/sqlite3/sqlite3.c: Errors

Submitted by janwp on Sat, 2014-09-20 03:27
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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Rosetta 3 - Build/Install

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

Submitted by megirvin on Wed, 2014-09-03 08:50
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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Rosetta 3 - Build/Install

Install rosetta_2014.30.57114_bundle on ubuntu-14.04.1-desktop-amd64

Submitted by lanselibai on Wed, 2014-09-03 07:55
Category: 
Compilation

Dear Sir or Madam,
I want to install rosetta_2014.30.57114_bundle on my Win 7 PC. After installing VMware Player and ubuntu-14.04.1-desktop-amd64, I tried to follow instructions on

https://www.rosettacommons.org/docs/latest/Build-Documentation.html#Comp...

After "Change directory to main/source" and "./scons.py -j1 bin", I was told:

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Rosetta 3 - Build/Install

compile pyrosetta under redhat 5.9 with g++ 4.1.2 and python 2.7.4

Submitted by coomteng@gmail.com on Sun, 2014-08-31 09:53
Category: 
Compilation

Hi,

the compilation was successful but when I run the TestBindings.py it always shows the following error.

rosetta-3.5/rosetta_source/src/python/bindings/rosetta/core/scoring/methods/__methods_all_at_once_.so: undefined symbol: _ZN4core7scoring7methods15PBLifetimeCache7set_pbpERKSsN7utility7pointer10owning_ptrINS0_25PoissonBoltzmannPotentialEEE

g++ version: 4.1.2 or 4.4.7 the same error.
python version 2.7.4
boost_version: 1.46 or 1.5.6

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PyRosetta - Build/Install

Building with "extra=graphics" on Linux?

Submitted by hansellt on Fri, 2014-08-01 06:09
Category: 
Compilation

I was trying to build Rosetta_2014.22.56873 with "extras=graphics" enabled on Debian linux 7.5

I get a number of errors related to narrowing conversions while building viewers.cc

Apparently "-Werror=narrowing" is set as a flag, and I was wondering what kind of trouble i would be getting my self in for if I just changed that flag and compiled it anyway.

I've attached a listing of the build and the errors received

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Rosetta 3 - Build/Install

rosetta_2014.22.56873: Unknown argument: '-finline-limit=20000'

Submitted by franfdez on Wed, 2014-07-30 02:17
Category: 
Compilation

I am trying to install rosetta_2014.22.56873 on an iMac [OSX 10.8.5; Darwin Ms-iMac.local 12.5.0 Darwin Kernel Version 12.5.0: Sun Sep 29 13:33:47 PDT 2013; root:xnu-2050.48.12~1/RELEASE_X86_64 x86_64] but the compilation failed with the following message:

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