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Phenix-Rosetta integration tests

Submitted by sansari on Wed, 2014-06-18 15:42
Category: 
Phenix / MR Rosetta

Hi there,

I'm a HPC systems administrator trying to setup Phenix and Rosetta for use with MR Rosetta. I find that the MR Rosetta test suite (phenix_regression.wizards.test_command_line_rosetta_quick) fails at test_fixed_model with the following error in Rosetta:

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Rosetta 3 - Build/Install

static version

Submitted by albumns on Sun, 2014-05-11 02:03
Category: 
Compilation

Hello:

I am compiling version 3.5 with command:

scons bin mode=release extras=static extras=mpi -j6

it finished successfully without any errors. However, I found that all the tools are named with ***mpi, such as:

homodimer_design.mpi.linuxgccrelease

I am just wondering, with the command I used, does it also a static compiled version?

thx a lot

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Rosetta 3 - Build/Install

Trouble linking with Xcode/clang 5.1

Submitted by stranges on Tue, 2014-03-11 09:34

Hi all,
Just a heads up. There's a problem linking with the new OSX Command Line Tools and clang version 5.1.
This is with the most recent weekly release 2014 week 04
Any suggestions would be appreciated

Clang version:
clang --version
Apple LLVM version 5.1 (clang-503.0.38) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.1.0
Thread model: posix

Error message

Undefined symbols for architecture x86_64:
"core::io::silent::ProteinSilentStruct_Template::fill_struct(core::pose::Pose const&, std::string)", referenced from:

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Rosetta 3 - Build/Install

error while loading shared libraries: libmpi_cxx.so.1

Submitted by tevang on Fri, 2014-02-28 05:35

Greetings,

I encounter a strange error when I try to run minirosetta on a cluster. Although compilation appears to finish successfully, minirosetta does not find a library that exists. This is how I run it:

module purge
module load OpenMPI/1.4.5-GCC-4.6.3
export PATH=/gpfs/h/lspro220u2/Opt:/gpfs/h/build/eb131021/software/OpenMPI/1.4.5-GCC-4.6.3/bin:$PATH
export LD_LIBRARY_PATH=/gpfs/h/build/eb131021/software/OpenMPI/1.4.5-GCC-4.6.3/lib:$LD_LIBRARY_PATH
export INCLUDE=/gpfs/h/build/eb131021/software/OpenMPI/1.4.5-GCC-4.6.3/include

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Rosetta 3 - Build/Install

Rosetta 3.5 Compiling Error - fedora 20

Submitted by chaperone on Thu, 2014-02-06 02:18

Hi All,

I have been trying to install rosetta on fedora 20 and keep running into a compiling error with EndPoint that terminates the build. Any suggestions would be much appreciated.

localhost 102% uname -a
Linux localhost.localdomain 3.11.10-301.fc20.x86_64

The error I got after command "scons bin mode=release" and successfully building for 30min or so:

scons: Reading SConscript files ...
svn_version.py reports this is a non-version-control release version of Rosetta
scons: done reading SConscript files.
scons: Building targets ...

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Rosetta 3 - Build/Install

make_fragments.pl can't find ForkManager.pm

Submitted by fred on Wed, 2014-01-29 07:42

Hi there,
How can modify make_fragments.pl script so as it finds the necessary Perl modules?

-bash-4.1$ ./make_fragments.pl
Can't locate Parallel/ForkManager.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at ./make_fragments.pl line 1840.
BEGIN failed--compilation aborted at ./make_fragments.pl line 1840.
-bash-4.1$ locate ForkManager.pm

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Rosetta 3 - Build/Install

install in AMD cluster

Submitted by albumns on Wed, 2014-01-15 02:16

Hello:

I am trying to install rosettat-3.5 in a AMD based cluster with command:

scons bin extras=mpi mode=release

but it failed with messages:

-----------------------------------------------------------------
scons: Reading SConscript files ...
Copy("user.options", "user.options.template")
Copy("user.settings", "user.settings.template")
Copy("/home/users/albert/install/rosetta-3.5/src/pilot_apps.src.settings", "/home/users/albert/install/rosetta-3.5/src/pilot_apps.src.settings.template")
Traceback (most recent call last):

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Rosetta 3 - Build/Install

Compiler error - libcore.3.a GeometricSolEnergy

Submitted by Robert on Tue, 2014-01-14 13:36

I'm trying to compile a fresh install and I get this error.

Anyone seen this before?

build/src/release/linux/2.6/64/x86/gcc/4.5/static/libcore.3.a(ContextIndependentGeometricSolEnergy.o): In function `core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::residue_pair_energy_ext(core::conformation::Residue const&, core::conformation::Residue const&, core::scoring::ResPairMinimizationData const&, core::pose::Pose const&, core::scoring::ScoreFunction const&, core::scoring::EMapVector&) const':

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Rosetta 3 - Build/Install

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