IMP Reference Guide
2.6.1
The Integrative Modeling Platform
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Distribute IMP tasks to multiple processors or machines. More...
Distribute IMP tasks to multiple processors or machines.
This module employs a master-slave model; the main (master) IMP process sends the tasks out to one or more slaves. Tasks cannot communicate with each other, but return results to the master. The master can then start new tasks, possibly using results returned from completed tasks. The system is fault tolerant; if a slave fails, any tasks running on that slave are automatically moved to another slave.
To use the module, first create a Manager object. Add one or more slaves to the Manager using its add_slave() method (example slaves are LocalSlave, which simply starts another IMP process on the same machine as the master, and SGEQsubSlaveArray, which starts an array of multiple slaves on a Sun GridEngine cluster). Next, call the get_context() method, which creates and returns a new Context object. Add tasks to the Context with the Context.add_task() method (each task is simply a Python function or other callable object). Finally, call Context.get_results_unordered() to send the tasks out to the slaves (a slave only runs a single task at a time; if there are more tasks than slaves later tasks will be queued until a slave is done with an earlier task). This method returns the results from each task as it completes.
Setup in IMP is often expensive, and thus the Manager.get_context() method allows you to specify a Python function or other callable object to do any setup for the tasks. This function will be run on the slave before any tasks from that context are started (the return values from this function are passed to the task functions). If multiple tasks from the same context are run on the same slave, the setup function is only called once.
Troubleshooting
Several common problems with this module are described below, together with solutions.
/bin/sh: qsub: command not found
, but qsub
works fine from a terminal.qsub
command to submit the SGE job that starts the slaves. Thus, qsub
must be in your system PATH. This may not be the case if you are using a shell script such as imppy.sh
to start IMP. To fix this, modify the shell script to add the directory containing qsub
to the PATH, or remove the setting of PATH entirely.ImportError: No module named IMP.parallel.slave_handler
.imppy.sh
, you need to tell the slaves to do that too. Specify the full command line needed to start a suitable Python interpreter as the 'python' argument when you create the Manager object.socket.error: (110, 'Connection timed out')
.socket.error: (111, 'Connection refused')
.Author(s): Ben Webb
Maintainer: benmwebb
License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
Publications:
Namespaces | |
master_communicator | |
Classes for communicating from the master to slaves. | |
subproc | |
Subprocess handling. | |
util | |
Utilities for the IMP.parallel module. | |
Classes | |
class | Context |
A collection of tasks that run in the same environment. More... | |
class | Error |
Base class for all errors specific to the parallel module. More... | |
class | LocalSlave |
A slave running on the same machine as the master. More... | |
class | Manager |
Manages slaves and contexts. More... | |
class | NetworkError |
Error raised if a problem occurs with the network. More... | |
class | NoMoreSlavesError |
Error raised if all slaves failed, so tasks cannot be run. More... | |
class | RemoteError |
Error raised if a slave has an unhandled exception. More... | |
class | SGEPESlaveArray |
An array of slaves in a Sun Grid Engine system parallel environment. More... | |
class | SGEQsubSlaveArray |
An array of slaves on a Sun Grid Engine system, started with 'qsub'. More... | |
class | Slave |
Representation of a single slave. More... | |
class | SlaveArray |
Representation of an array of slaves. More... | |
Standard module functions | |
All | |
std::string | get_module_version () |
std::string | get_module_name () |
std::string | get_data_path (std::string file_name) |
Return the full path to one of this module's data files. More... | |
std::string | get_example_path (std::string file_name) |
Return the full path to one of this module's example files. More... | |
std::string IMP::parallel::get_data_path | ( | std::string | file_name | ) |
Return the full path to one of this module's data files.
To read the data file "data_library" that was placed in the data
directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.
std::string IMP::parallel::get_example_path | ( | std::string | file_name | ) |
Return the full path to one of this module's example files.
To read the example file "example_protein.pdb" that was placed in the examples
directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.