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Compilation

PyRosetta on a HPC

Category: 
Compilation

Hello people,  i have been trying to compile PyRosetta on a HPC (Red Hat 6.4) for several weeks now without success.

I tried many different approaches so i will write the gist of it.  I tried compiling PyRosetta which did not work, then I read i have to compile it from source, so this is what I am trying to do. I uploaded Rosetta to the HPC.

most of the programs are old, so I had to install python3.6.1, Cmake 3.5.9, GCC 5.3.0, and Ninja 1.9.0

Post Situation: 

Scons LIBPATH cannot find library

Category: 
Compilation

SCons is unable to find a shared library (libcloog-isl.so.4).

The build fails immediately with the following error:

/share/apps/NYUAD3/gcc/gcc/4.9.3/el7/libexec/gcc/x86_64-unknown-linux-gnu/4.9.3/cc1plus: error while loading shared libraries: libcloog-isl.so.4: cannot open shared object file: No such file or directory

I confirm that libcloog-isl.so.4 does exist:

Post Situation: 

Error msg while compiling on a new cluster

Category: 
Compilation

Not sure why scons is failing on a new cluster

>./scons.py bin -j16 mode=release extras=mpi

I see en error:

scons: *** Do not know how to make File target `bin' (/usr/projects/xyz/shared/rosetta_3.10_release/main/source/bin). Stop.

rosetta_3.10_release could be easily compiled on my local machine.

Post Situation: 

Build problem "Never include <bits/libio.h> directly; use <stdio.h> instead."

Category: 
Compilation

Hi everyone,

I am trying to build Pyrosetta from source in Ubuntu 18.04 x64, but  I am having a compilation error, as indicated in the title.

Does anyone have a clue about what could be the issue or has a better idea to compile it?

I am using python 2.7.15, rosetta build 2018.33.60351, ninja 1.8.2, cmake 3.12.1 and gcc 4.8, specified with the global variables: CC=gcc-4.8 and CXX=g++-4.8. The error log is:

Post Situation: 

pyrosetta with Parallel Studio XE

Category: 
Compilation

Hi,

I'd like to build pyrosetta with the intel compiler and potentially link against the Intel MKL for use on HPC infrastructure. I saw in the rosetta docs, that rosetta can already be used with the intel compiler on TACC resources:

 https://www.rosettacommons.org/docs/latest/build_documentation/TACC

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reporting bugs? (erraser in rosetta 3.10)

Category: 
Compilation

Hi,

Is this the right place to report bugs that have appeared in erraser?  If not, could someone point me to the correct location?

These appear to be occuring in the rosetta 3.10 release (some in python code, others appearing to be in c++ code); and do not appear in erraser from rosetta 3.7; and occur when using the demo example from https://www.rosettacommons.org/demos/latest/public/erraser/README.

 

Best,

Pete

Post Situation: 

99% success rate in unit test, Will it work?

Category: 
Compilation

I am new to Rosetta and trying to install in my workstation. After installation when I  ran the unit test, and it is showing like a 99% success rate. Is it ok to now run the program or I need to fix the issues? If not can you please help me out to fix that? 

After doing this, 

python test/run.py --mode=debug -j32

I am getting

Post Situation: 

Rosetta-based projects using and licensing

Category: 
Compilation

Dear Rosetta Team,

Is it possible to share a code of my Rosetta-dependent non-profit research project and upload it to a publicly accessible GitHub repository licensed under open source license? Is Rosetta License restricts that?

For example, I have "project" like this:

1. Source files that links to Rosetta headers:

Post Situation: 

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