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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