CS-Rosetta

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Chemical-Shift-ROSETTA (CS-Rosetta) is a software package for de novo protein structure generation.

Availability

ResourceCentreDescription
KappaNSCthroughput cluster resource of 26 TFLOPS
MatterNSCcluster resource of 37 TFLOPS dedicated to materials science

Security considerations

This program has considerable security issues that need to be addressed if installed on a multiuser system. It is recommended to set the permissions on the install directory to 700 prior to install and until all issues are solved.

  1. The com/csrosettaInit.com environment initialization script unnecessarily puts . first in $PATH, which means that all shell commands will be checked against matching files in the current working directory before execution, and if a matching executable is found, this program will be run instead. For example, it is trivial to produce a malicious program that sends your personal information and passwords to crackers.org and then executes the actual original program so you will never notice anything has gone wrong. If this program is then named cd, or ls, or ssh, or bruker, or any other command commonly used by NMRPipe users, then if an NMRPipe user happens to use any of these commands in a directory containing such a file, the full list of imaginable bad consequences will ensue and cascade. Notably, NMRPipe does not require or use this setting so it can (and SHOULD) be safely removed from ncom/csrosettaInit.com.

Tips and tricks

  1. CS-Rosetta claims to require using (t)csh shell, but actually doesn't. It requires a handful of environment variables to be set, and these can be trivially copied from the csrosettaInit.com csh script. If your centre provides a module for CS-Rosetta, this likely sets all variables correctly for you, regardless of your shell.
  2. CS-Rosetta claims to require com/csrosettaInit.com to be sourced from the user's ~/.cshrc file, but actually doesn't, so users shouldn't. Especially since sourcing an unmodified com/csrosettaInit.com introduces potential security holes (see #Security considerations above).

Compilation and installation

  1. CS-Rosetta's install.com reads the Rosetta path from stdin, and unnecessarily checks that this path corresponds to a default personal Rosetta install, and refuses to proceed if this is not the case. Comments in the file suggest to "ignore this" and to "manually configure" instead. The information obtained from this test is used mainly to create the com/csrosettaInit.com file, and since you likely want to write your own anyway (see #Security considerations above and point 3 below), a feasible solution is to delete the entire code block and replace it with:
    • set rosetta_version = "3"
    • set rosettaDir = WHATEVER_NOT_USED
    • set rosetta = WHATEVER_NOT_USED
    • set rosettaDB = WHATEVER_NOT_USED
  2. CS-Rosetta uses the ancient g77 fortran compiler which may or may not be present on your system. If not, nnmake will not build and thus cause an error with install.com. nnmake builds well with gfortran so this can be fixed by adding e.g. perl -i -pe 's/F77 = g77/F77 = gfortran/g' make.system just after the line cd {$currentDir}/src/nnmake in the install.com file.
  3. com/csrosettaInit.com unnecessarily sets absolute paths to specific builds of Rosetta executables and utilities. It is sufficient to give only the basename of the executables (e.g. AbinitioRelax, extract_pdbs) and ensure that these are on the $PATH on launch. The database path can for example be set using the $ROSETTA3_DB environment variable. The variables rosetta and rosettaDB are only relevant to very old Rosetta 2.x versions and can be set to anything (e.g. NOT_INSTALLED) as long as Rosetta 3.x is available.

License

License: Free.

Experts

No experts have currently registered expertise on this specific subject. List of registered field experts:

  FieldAE FTEGeneral activities
Anders Hast (UPPMAX)UPPMAXVisualisation, Digital Humanities30Software and usability for projects in digital humanities
Anders Sjölander (UPPMAX)UPPMAXBioinformatics100Bioinformatics support and training, job efficiency monitoring, project management
Anders Sjöström (LUNARC)LUNARCGPU computing
MATLAB
General programming
Technical acoustics
50Helps users with MATLAB, General programming, Image processing, Usage of clusters
Birgitte Brydsö (HPC2N)HPC2NParallel programming
HPC
Training, general support
Björn Claremar (UPPMAX)UPPMAXMeteorology, Geoscience100Support for geosciences, Matlab
Björn Viklund (UPPMAX)UPPMAXBioinformatics
Containers
100Bioinformatics, containers, software installs at UPPMAX
Chandan Basu (NSC)NSCComputational science100EU projects IS-ENES and PRACE.
Working on climate and weather codes
Diana Iusan (UPPMAX)UPPMAXComputational materials science
Performance tuning
50Compilation, performance optimization, and best practice usage of electronic structure codes.
Frank Bramkamp (NSC)NSCComputational fluid dynamics100Installation and support of computational fluid dynamics software.
Hamish Struthers (NSC)NSCClimate research80Users support focused on weather and climate codes.
Henric Zazzi (PDC)PDCBioinformatics100Bioinformatics Application support
Jens Larsson (NSC)NSCSwestore
Jerry Eriksson (HPC2N)HPC2NParallel programming
HPC
HPC, Parallel programming
Joachim Hein (LUNARC)LUNARCParallel programming
Performance optimisation
85HPC training
Parallel programming support
Performance optimisation
Johan HellsvikPDCMaterialvetenskap30materials theory, modeling of organic magnetic materials,
Johan Raber (NSC)NSCComputational chemistry50
Jonas Lindemann (LUNARC)LUNARCGrid computing
Desktop environments
20Coordinating SNIC Emerging Technologies
Developer of ARC Job Submission Tool
Grid user documentation
Leading the development of ARC Storage UI
Lunarc Box
Lunarc HPC Desktop
Krishnaveni Chitrapu (NSC)NSCSoftware development
Lars Eklund (UPPMAX)UPPMAXChemistry
Data management
FAIR
Sensitive data
100Chemistry codes, databases at UPPMAX, sensitive data, PUBA agreements
Lars Viklund (HPC2N)HPC2NGeneral programming
HPC
HPC, General programming, installation of software, support, containers
Lilit Axner (PDC)PDCComputational fluid dynamics50
Marcus Lundberg (UPPMAX)UPPMAXComputational science
Parallel programming
Performance tuning
100I help users with productivity, program performance, and parallelisation.
Martin Dahlö (UPPMAX)UPPMAXBioinformatics10Bioinformatic support
Mikael Djurfeldt (PDC)PDCNeuroinformatics100
Mirko Myllykoski (HPC2N)HPC2NParallel programming
GPU computing
Parallel programming, HPC, GPU programming, advanced support
Pavlin Mitev (UPPMAX)UPPMAXComputational materials science100
Pedro Ojeda-May (HPC2N)HPC2NMolecular dynamics
Machine learning
Quantum Chemistry
Training, HPC, Quantum Chemistry, Molecular dynamics, R, advanced support
Peter Kjellström (NSC)NSCComputational science100All types of HPC Support.
Peter Münger (NSC)NSCComputational science60Installation and support of MATLAB, Comsol, and Julia.
Rickard Armiento (NSC)NSCComputational materials science40Maintainer of the scientific software environment at NSC.
Szilard PallPDCMolecular dynamics55Algorithms & methods for accelerating molecular dynamics, Parallelization and acceleration of molecular dynamics on modern high performance computing architectures, High performance computing, manycore and heterogeneous architectures, GPU computing
Thomas Svedberg (C3SE)C3SESolid mechanics
Tom Langborg (NSC)NSCSwestore
Torben Rasmussen (NSC)NSCComputational chemistry100Installation and support of computational chemistry software.
Wei Zhang (NSC)NSCComputational science
Parallel programming
Performance optimisation
code optimization, parallelization.
Weine Olovsson (NSC)NSCComputational materials science90Application support, installation and help
Åke Sandgren (HPC2N)HPC2NComputational science50SGUSI

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