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Compilation

arm64 processor is not supported for new M1 chip

Category: 
Compilation

Hello,

I'm fairly new to dealing with these kinds of software installation and compilation. I want to download the latest release of rosetta on my M1 Macbook air laptop and I've run into the following problem when I try to compile the rosetta bundle in the Rosetta/main/source directory:

source % ./scons.py -j6 mode=release bin

scons: Reading SConscript files ...

Traceback (most recent call last):

  File "/Users/martinfe/Rosetta/main/source/SConstruct", line 183, in main

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error in installing rosetta for use in phenix

Category: 
Compilation

Hi everybody!

I'm trying to install Rosetta (version 3.10) for use in Phenix on Ubuntu 20. No problem with Phenix installation, but when I run "rosetta.build_phenix_interface nproc=2" I got the following:

Substituting phenix.python into build shell scripts
  update_options.sh
  update_ResidueType_enum_files.sh

  Phenix modules found : /home/stefano/programmi/phenix-1.19.1-4122/modules/phenix
False
/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source

Post Situation: 

error in installing rosetta for use in phenix

Category: 
Compilation

Hi everybody!

I'm trying to install Rosetta (version 3.10) for use in Phenix on Ubuntu 20. No problem with Phenix installation, but when I run "rosetta.build_phenix_interface nproc=2" I got the following:

Substituting phenix.python into build shell scripts
  update_options.sh
  update_ResidueType_enum_files.sh

  Phenix modules found : /home/stefano/programmi/phenix-1.19.1-4122/modules/phenix
False
/home/stefano/programmi/rosetta/rosetta_src_2018.33.60351_bundle/main/source

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An error occurred during the installation

Category: 
Compilation

Dear Rosetta Users,

I recentlly downloaded the src version of rosetta 2020.50 and compiled it with scons.py, but there was an error. It seems that the program was pointing towards a wrong directory (the bin version directory) for the generate_database_cache application. I'm attaching the log file. Thank you in advance!

Post Situation: 

slurm not availble

Category: 
Compilation

Good afternoon,

I am attemtpting to compile according to item 1.5.1 at https://csrosetta.chemistry.ucsc.edu/node/1354...

$ module load   python/2.7 slurm openmpi/gcc/64

however slurm is not available. The cluster uses PBSPro. Can anyone suggest a work-around?

Thanks - Dave Morgan Ph.D., Colbert Lab, NDSU 

Post Situation: 

Error in Ubuntu 20.10

Category: 
Compilation

Hi, sorry for disturbing you but  I have problems installing Rosetta.  In Ubuntu 20.10.

I have also tried with clans, but it did not work.  I follow all the classical error list, but still no success. Also I am not sure what is the error. 

Could someone help me, please?

regards

JP

Post Situation: 

Error compiling mpi under Big Sur

Category: 
Compilation

Using updated Xcode and a fresh install of macos Big Sur, I get the following error (below) when compiling using: "./scons.py -j 12 mode=release bin extras=mpi"

 Open-mpi is installed (via homebrew) and if I run "ompi_info" all the info seems correct (see atached .txt). Any suggestions would be appreacited. Thanks!

-Andrew

 

Post Situation: 

Build Error on macOS Big Sur

Category: 
Compilation

Hi,

I am trying to build rosetta 3.12 on macOS Big Sur but I receive the following error:

-----------------------------------------------------------------------------------------------------------------------

In file included from src/apps/public/AbinitioRelax.cc:20:

In file included from src/basic/options/option.hh:17:

In file included from src/utility/options/OptionCollection.hh:21:

Post Situation: 

helical bundle predict

Category: 
Compilation
Structure prediction

Hi everyone,

I'm interested in using the helical_bundle_predict method. In this link (https://www.rosettacommons.org/docs/latest/structure_prediction/helical-bundle-predict) it is described as an application but I cannot understand how to make the system install it. It may have something to do with the fact that it is a pilot application, but still it is not clear to me which files I need to modify in order to install it with scons. 

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Error on rna_denovo_setup.py

Category: 
Compilation

Dear all,

I got this error when I want to use the rna_denovo_setup.py 

>~/tools/rna_tools/bin/rna_denovo_setup.py -fasta fasta -secstruct_file secstruct -no_minimize -tag glycine_riboswitch -working_res 1-159 -native 3p49_native_RNA.pdb -cst_file constraints -staged_constraints -cycles 20000 -ignore_zero_occupancy false -silent helix0.out helix1.out helix2.out helix3.out helix4.out helix5.out helix6.out helix7.out -input_silent_res 2-9 65-72 16-21 26-31 33-35 54-56 39-42 48-51 81-85 155-159 92-97 101-106 108-110 145-147 114-117 139-142

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