IMP Reference Guide
2.6.1
The Integrative Modeling Platform
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Code that uses the MPI parallel library. More...
Code that uses the MPI parallel library.
To enable this module, you must first install an MPI library and then make sure that the mpic++
binary is in the PATH (e.g. on a RedHat/Fedora system, you may need to run module load mpich
or similar) before you run cmake. (There is no need to build all of IMP with mpic++
- that would force all of IMP to need the MPI library, not just the IMP.mpi module.)
If you want to use OpenMPI, note that the default build on many Linux systems doesn't play nicely with Python (you may see errors like mca: base: component_find: unable to open /usr/lib64/openmpi/lib/openmpi/mca_shmem_sysv: perhaps a missing symbol, or compiled for a different version of Open MPI?
). This can be fixed either by recompiling OpenMPI with the --disable-dlopen
configure flag, or by running import DLFCN as dl; sys.setdlopenflags(dl.RTLD_NOW|dl.RTLD_GLOBAL)
in your Python script before importing IMP.mpi. We also recommend that you use version 1.7 of OpenMPI or older, as the 1.8 release does not appear to work with the mpi4py package that some parts of IMP::pmi use.
Author(s): Max Bonomi
Maintainer: benmwebb
License: LGPL
Publications:
Classes | |
class | ReplicaExchange |
A class to implement Hamiltonian Replica Exchange. 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::mpi::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::mpi::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.