« Previous - Version 14/28 (diff) - Next » - Current version
Anton Vasetenkov, 13.01.2015 00:32


Rosetta-Tips

Installation

При компиляции в Ubuntu 14.10 c OpenMpi возникает ошибка:

src/protocols/wum2/EndPoint.cc:21:42: error: a function call cannot appear in a constant-expression
src/protocols/wum2/EndPoint.cc:21:44: error: template argument 1 is invalid

Антон Васетенков предлагает:
1// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*- 2// vi: set ts=2 noet: 3// 4// (c) Copyright Rosetta Commons Member Institutions. 5// (c) This file is part of the Rosetta software suite and is made available under license. 6// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons. 7// (c) For more information, see http://www.rosettacommons.org. Questions about this can be 8// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu. 9 10/// @file protocols/wum2/EndPoint.cc 11/// @brief Non MPI version of EndPoint 12/// @details This class is required because SingleNode role needs to use an EndPoint that is not MPI dependent (ie just a wrapper for 2 queues) 13/// @author Ken Jung 14 15//anton added this 16#include <boost/cstdint.hpp> 17 18#include <protocols/wum2/EndPoint.hh> 19#include <protocols/wum2/WorkUnit.hh> 20 21namespace protocols { 22namespace wum2 { 23 24//anton commented this 25//EndPoint::EndPoint( boost::function < uint64_t () > role_available_mem ) : role_available_mem_( role_available_mem) {} 26 27//anton added this 28EndPoint::EndPoint( boost::function < boost::uint64_t () > role_available_mem ) : role_available_mem_( role_available_mem) {} 29 30} // wum2 31} // protocols 32

Fragments

Генерация

/home/domain/anur/progs/rosseta/main/source/bin/fragment_picker.default.linuxgccrelease -in:file:fasta 1.fasta -in:file:vall /home/domain/anur/progs/rosseta/tools/fragment_tools/vall.apr24.2008.extended.gz -out::file::frag_prefix pep-1 -frags::frag_sizes 9 5 3

Если последовательность вашего белка идёт не первой цепью, то надо сдвинуть остатки в файле фрагментов:

cp ~/progs/rosseta/demos/protocol_capture/2010/FlexPepDock_AbInitio/scripts/frags/shift.sh .
./shift.sh  pep-1.200.3mers 276 > pep-1.200.shift.3mers

Запуск MPI версии на Lomonosv

Тут используется 48 ядер и module openmpi

sbatch -n 48 -o log.abinitio.n48 -t 3000  ompi /home/users/golovin/progs/rosetta_2013wk40_bundle/main/source/bin/FlexPepDocking.mpi.linuxgccrelease @flags.abinitiore

Опции запуска

https://www.rosettacommons.org/docs/latest/full-options-list.html