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Compilation

I used mpirun/mpiexec and it runs same job 32times

Category: 
Compilation

First, I'm sorry for my poor english.

I compiled rosetta applications via mpi options

(/home/ael/Desktop/rosetta_bin_linux_2020.28.61328_bundle/main/source/bin/relax.mpi.linuxgccrelease)

and I tried to use relax application to prepare structure

Then, when i start relax application, my cpus (16cores, 32threads) rus fully and it calculates same calculations 32times

(one output pdbs and 32 scores in .sc file)

how can i solve this problems?

 

Post Situation: 

Compilation problems

Category: 
Compilation
Hi. I have had some problems installing Rosetta 3.12, I have downloaded the source version, the zlib1g-dev package, gcc 9.3.0 and python 3.8.2, my operating system is Ubuntu 20.04.1 LTS. The problem is when I compile rosetta:

if I type: ./scons.py -j 2 mode = release bin ... this is the output from the terminal:

~ / rosetta / main / source $ ./scons.py -j 2 mode = release bin
Post Situation: 

running Rosetta with MPI

Category: 
Compilation

Hello,

I am planning to do four different docking (with 200  structures for one of the partner to capture backbone flexibility) with at least nstruct=500. I need to run it by usening several nodes and processors in our cluster.  I tried to compile MPI  in our cluster, but I got an error attached to this post. Could you please guide me how I can solve the error?

 

 

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How to create an ObjexxFCL FArray?

Category: 
Compilation

    pyrosetta.rosetta.ObjexxFCL is a Python module wrapped by PyBind11 around a C++ wrapper for Fortran, so I expect this matryoshka to be a problem. The documentation says these are being slowly phased out and it is uncommon finding a method that requires a ObjexxFCL FArray as opposed to a vector. However, I wanted to use one...

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clean_pdb not working

Category: 
Compilation

The simple clean_pdb.py does not function.

When I look at the script it is trying to print the wget_cmd command, WHY??

Here is the input and output:

python /home/aserobian/Documents/rosetta/tools/protein_tools/scripts/clean_pdb.py 2n2a AB
  File "/home/aserobian/Documents/rosetta/tools/protein_tools/scripts/clean_pdb.py", line 56
    print wget_cmd
          ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(wget_cmd)?

What is wrong here?

 

Post Situation: 

Questions about alanine scanning in Rosetta

Category: 
Compilation

Hi,

I am using AlaScan.xml to do alanine scanning for my antibody antigen complex, but when I run the script, there was error said “protocols.rosetta_scripts.ParsedProtocol: Mover Docking reports failure!”

 

Following is my script:

<ROSETTASCRIPTS>

       <SCOREFXNS>

              <ScoreFunction name="interface" weights="interface"/>

       </SCOREFXNS>

       <FILTERS>

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Rosetta3.12 installation

Category: 
Compilation

Hi all,

Here is the long text of my rescent Rosetta installation process. I really appreciate if you can read it and help with the problem!

I am trying to install newest Rosetta3.12 on a cluster I am currently working with (RHEL6). The version of gcc on this cluster is gcc 4.4.7 which means I need to install a newer gcc first.

Post Situation: 

Error in building fragment_picker with boost_thread

Category: 
Compilation

Hi all,

I am new to the whole Rosetta community and am asking for some help in compiling Rosetta3.  I have downloaded build Rosetta3.12 build 2020.08.61146 and tried to compile the thread boost version of fragment pick by using

./scons.py mode=release extras=boost_thread bin/fragment_picker.boost_thread.linuxgccrelease -j 20

The error message that I get is:

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Post Situation: 

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