Gmxapi 50

.travis.yml

@@ -29,6 +29,8 @@ matrix:
       - GMX_THREAD_MPI=ON
       - gmxapi_DIR=$HOME/gromacs
       - GROMACS_DIR=$HOME/gromacs
+      - GROMACS_TAG=devel
+# Todo: GROMACS_TAG=devel needs to be fixed before merging to a release branch.
 
 # It is clearly a bad idea to have the development branch of a project requiring the development branch
 # of another project in the primary build recipe. We either need to build and test development and master
@@ -40,11 +42,11 @@ before_install:
   - apt list --installed
   - test -n $CC  && unset CC
   - test -n $CXX && unset CXX
-  - wget https://github.com/kassonlab/gromacs-gmxapi/archive/master.zip
-  - unzip master.zip
+  - wget https://github.com/kassonlab/gromacs-gmxapi/archive/$GROMACS_TAG.zip
+  - unzip $GROMACS_TAG.zip
 
 install:
-  - pushd gromacs-gmxapi-master
+  - pushd gromacs-gmxapi-$GROMACS_TAG
   - mkdir build
   - pushd build
   - cmake -DCMAKE_INSTALL_PREFIX=$HOME/gromacs -DGMX_FFT_LIBRARY=fftpack -DGMX_GPU=OFF -DGMX_OPENMP=OFF -DGMX_SIMD=None -DGMX_USE_RDTSCP=OFF -DGMX_MPI=$GMX_MPI -DGMX_THREAD_MPI=$GMX_THREAD_MPI ..

CMakeLists.txt

@@ -5,8 +5,42 @@ cmake_minimum_required(VERSION 3.4.3)
 #list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
 
 # Sets the PROJECT_VERSION variable, as well...
-project(gmxpy VERSION 0.0.5)
+project(gmxpy VERSION 0.0.6)
+
+# If the user is not in a virtual environment and is not a privileged user and has not specified an install locatoin
+# for the Python module (GMXAPI_INSTALL_PATH), this option causes the automatic install location to query the user
+# site-packages directory instead of using the default site-packages directory for the interpreter.
+option(GMXAPI_USER_INSTALL "Override the default site-packages directory with the user-specific Python packages directory.\
+(Do not use with virtual environments.)")
+# Since a user may have multiple virtual environments with different Python interpreters, it is generally confusing to
+# have a package for a virtual environment installed in the user's default user site-packages directory.
+
+unset(PYTHONINTERP_FOUND)
+unset(PYTHONLIBS_FOUND)
+find_package(PythonInterp)
+if (PYTHONINTERP_FOUND)
+    message(STATUS "Found Python interpreter: ${PYTHON_EXECUTABLE}")
+    find_package(PythonLibs)
+    if (PYTHONLIBS_FOUND)
+        if (GMXAPI_USER_INSTALL)
+            execute_process(COMMAND ${PYTHON_EXECUTABLE} -m site --user OUTPUT_VARIABLE GMXAPI_DEFAULT_SITE_PACKAGES OUTPUT_STRIP_TRAILING_WHITESPACE)
+            message(STATUS "Python user site-packages directory is ${GMXAPI_DEFAULT_SITE_PACKAGES}")
+        else()
+            execute_process(COMMAND ${PYTHON_EXECUTABLE} -c "import sys; import os; print(os.path.abspath(os.path.join(sys.prefix, 'lib', 'python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}', 'site-packages')))" OUTPUT_VARIABLE GMXAPI_DEFAULT_SITE_PACKAGES OUTPUT_STRIP_TRAILING_WHITESPACE)
+            message(STATUS "Python site-packages directory is ${GMXAPI_DEFAULT_SITE_PACKAGES}")
+        endif()
+    else()
+        message(FATAL "Found Python interpreter ${PYTHON_EXECUTABLE} but this Python installation does not have developer tools."
+                "Set PYTHON_EXECUTABLE to the Python interpreter that was installed with a working Python.h header file.")
+    endif()
+else()
+    message(FATAL "Could not find Python interpreter. Set CMake flag -DPYTHON_EXECUTABLE=/path/to/python to hint.")
+endif()
+
+
+set(GMXAPI_INSTALL_PATH ${GMXAPI_DEFAULT_SITE_PACKAGES}/gmx CACHE PATH "Path to Python module install location (site-packages).")
+
 
 add_subdirectory(pybind11)
 
-add_subdirectory(src/gmx/core)
+add_subdirectory(src/gmx)

setup.py

@@ -26,7 +26,7 @@
 from setuptools.command.test import test as TestCommand
 
 #import gmx.version
-__version__ = '0.0.5'
+__version__ = '0.0.6'
 
 extra_link_args=[]
 
@@ -210,7 +210,7 @@ def build_extension(self, ext):
         if build_gromacs:
             # TODO! We need to distinguish dev branch builds from master branch builds or always build with the
             # master branch of the dependency. For one thing, as is, this line needs to be toggled for every release.
-            gromacs_url = "https://github.com/kassonlab/gromacs-gmxapi/archive/dev_5.zip"
+            gromacs_url = "https://github.com/kassonlab/gromacs-gmxapi/archive/devel.zip"
             gmxapi_DIR = os.path.join(extdir, 'data/gromacs')
             if build_for_readthedocs:
                 extra_cmake_args = ['-DCMAKE_INSTALL_PREFIX=' + gmxapi_DIR,
@@ -248,7 +248,7 @@ def build_extension(self, ext):
             os.makedirs(self.build_temp)
 
         # cmake_args += ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir]
-        cmake_args += ['-DCMAKE_INSTALL_PREFIX=' + extdir]
+        cmake_args += ['-DGMXAPI_INSTALL_PATH=' + extdir]
         # if platform.system() == "Windows":
         #     cmake_args += ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}'.format(cfg.upper(), extdir)]
         try:

src/gmx/CMakeLists.txt

@@ -0,0 +1,30 @@
+file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/gmx/data)
+
+configure_file(__init__.py ${CMAKE_BINARY_DIR}/gmx/ COPYONLY)
+configure_file(context.py ${CMAKE_BINARY_DIR}/gmx/ COPYONLY)
+configure_file(data.py ${CMAKE_BINARY_DIR}/gmx/ COPYONLY)
+configure_file(exceptions.py ${CMAKE_BINARY_DIR}/gmx/ COPYONLY)
+configure_file(fileio.py ${CMAKE_BINARY_DIR}/gmx/ COPYONLY)
+configure_file(status.py ${CMAKE_BINARY_DIR}/gmx/ COPYONLY)
+configure_file(system.py ${CMAKE_BINARY_DIR}/gmx/ COPYONLY)
+configure_file(util.py ${CMAKE_BINARY_DIR}/gmx/ COPYONLY)
+configure_file(workflow.py ${CMAKE_BINARY_DIR}/gmx/ COPYONLY)
+
+configure_file(data/topol.tpr ${CMAKE_BINARY_DIR}/gmx/data/ COPYONLY)
+
+configure_file(version.in ${CMAKE_BINARY_DIR}/gmx/version.py @ONLY)
+
+file(COPY test DESTINATION ${CMAKE_BINARY_DIR}/gmx/)
+
+# Todo: we need a target dependent on these files to force fresh configure / copy and to do python -m compileall
+# for the install target.
+
+install(DIRECTORY ${CMAKE_BINARY_DIR}/gmx/
+        DESTINATION ${GMXAPI_INSTALL_PATH}
+        FILES_MATCHING PATTERN "*.py" PATTERN "*.ini"
+        )
+
+install(DIRECTORY ${CMAKE_BINARY_DIR}/gmx/data
+        DESTINATION ${GMXAPI_INSTALL_PATH})
+
+add_subdirectory(core)

src/gmx/context.py

@@ -9,6 +9,8 @@
 
 __all__ = ['Context', 'DefaultContext']
 
+
+import contextlib
 import os
 import warnings
 import networkx as nx
@@ -24,6 +26,21 @@
 logger = logging.getLogger(__name__)
 logger.info('Importing gmx.context')
 
+# ref http://code.activestate.com/recipes/576620-changedirectory-context-manager/#c3
+# Does this really not already exist in os.path or something?
+@contextlib.contextmanager
+def working_directory(path):
+    """A context manager which changes the working directory to the given
+    path, and then changes it back to its previous value on exit.
+
+    """
+    prev_cwd = os.getcwd()
+    os.chdir(path)
+    try:
+        yield
+    finally:
+        os.chdir(prev_cwd)
+
 class Context(object):
     """ Proxy to API Context provides Python context manager.
 
@@ -588,6 +605,7 @@ def __enter__(self):
         instantiate objects to perform the work. In the first implementation, we kind of muddle things into
         a single pass.
         """
+        self.__cwd = os.getcwd()
         import numpy
         try:
             from mpi4py import MPI
@@ -675,12 +693,6 @@ def update(send, recv, tag=None):
         if workdir_list is None:
             workdir_list = [os.path.join('.', str(i)) for i in range(self.size)]
         self.__workdir_list = list([os.path.abspath(dir) for dir in workdir_list])
-        for dir in self.__workdir_list:
-            if os.path.exists(dir):
-                if not os.path.isdir(dir):
-                    raise exceptions.FileError('{} is not a valid working directory.'.format(dir))
-            else:
-                os.mkdir(dir)
 
         # Check the session "width" against the available parallelism
         if (self.size > comm_size):
@@ -704,6 +716,13 @@ def update(send, recv, tag=None):
             logger.info("Launching work on rank {}.".format(self.rank))
             # Launch the work for this rank
             self.workdir = self.__workdir_list[self.rank]
+            if os.path.exists(self.workdir):
+                if not os.path.isdir(self.workdir):
+                    raise exceptions.FileError('{} is not a valid working directory.'.format(self.workdir))
+            else:
+                os.mkdir(self.workdir)
+
+            # This session will live in a subdirectory of the working directory
             os.chdir(self.workdir)
             logger.info('rank {} changed directory to {}'.format(self.rank, self.workdir))
             sorted_nodes = nx.topological_sort(graph)
@@ -762,6 +781,7 @@ def __exit__(self, exception_type, exception_value, traceback):
         # \todo Make sure session has ended on all ranks before continuing and handle final errors.
 
         self._session = None
+        os.chdir(self.__cwd)
         return False
 
 def get_context(work=None):

src/gmx/core/CMakeLists.txt

@@ -7,7 +7,7 @@
 # cmake was invoked with `-DCMAKE_PREFIX_PATH=...` pointing to the GROMACS
 # installation directory. We can also check now for a GROMACS_DIR environment
 # variable and provide it with the HINTS option.
-find_package(gmxapi 0.0.5 REQUIRED
+find_package(gmxapi 0.0.6 REQUIRED
              HINTS "$ENV{GROMACS_DIR}"
              )
 
@@ -39,6 +39,8 @@ set_target_properties(pygmx_core PROPERTIES OUTPUT_NAME core)
 #    pygmx_core
 #    PROPERTIES LIBRARY_OUTPUT_DIRECTORY "${PYGMX_DIRECTORY}")
 
+set_target_properties(pygmx_core PROPERTIES LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/gmx)
+
 target_include_directories(pygmx_core PRIVATE
     ${CMAKE_CURRENT_SOURCE_DIR}
     ${CMAKE_CURRENT_BINARY_DIR}
@@ -71,7 +73,6 @@ endif()
 set_target_properties(pygmx_core PROPERTIES INSTALL_RPATH_USE_LINK_PATH TRUE)
 
 install(TARGETS pygmx_core
-        LIBRARY DESTINATION
-        ${CMAKE_INSTALL_PREFIX}
-        ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}
-        RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX})
+        LIBRARY DESTINATION ${GMXAPI_INSTALL_PATH}
+        ARCHIVE DESTINATION ${GMXAPI_INSTALL_PATH}
+        RUNTIME DESTINATION ${GMXAPI_INSTALL_PATH})

src/gmx/core/export_context.cpp

@@ -2,10 +2,13 @@
 // Created by Eric Irrgang on 3/18/18.
 //
 
+#include <iostream>
+#include <zconf.h>
 #include "core.h"
 
 #include "gmxapi/context.h"
 
+#include "gromacs/utility/init.h"
 
 namespace gmxpy
 {
@@ -97,15 +100,21 @@ void setMDArgs(std::vector<std::string>* mdargs, py::dict params)
 void export_context(py::module &m)
 {
     using ::gmxapi::Context;
-    // Export execution context class
-    py::class_<Context, std::shared_ptr<Context>> context(m, "Context");
-    context.def(py::init(), "Create a default execution context.");
-    context.def("setMDArgs", &Context::setMDArgs, "Set MD runtime parameters.");
 
     using MDArgs = std::vector<std::string>;
     py::class_<MDArgs, std::unique_ptr<MDArgs>> mdargs(m, "MDArgs");
     mdargs.def(py::init(), "Create an empty MDArgs object.");
     mdargs.def("set", &setMDArgs, "Assign parameters in MDArgs from Python dict.");
+
+    // Export execution context class
+    py::class_<Context, std::shared_ptr<Context>> context(m, "Context");
+    context.def(py::init(), "Create a default execution context.");
+    context.def("setMDArgs", &Context::setMDArgs, "Set MD runtime parameters.");
+
+    // During the registration of the gmx.core.Context Python type, perform appropriate environment initialization
+    // and deinitialize at module destruction.
+    gmx::init(nullptr, nullptr);
+    m.add_object("_current_context", py::capsule([](){ gmx::finalize(); std::cout << "Shutting down GROMACS" << std::endl; }));
 }
 
 } // end namespace gmxpy::detail

src/gmx/core/export_system.cpp

@@ -32,7 +32,9 @@ void export_system(py::module &m)
     py::class_<System, std::shared_ptr<System> > system(m, "MDSystem");
     system.def(py::init(), "A blank system object is possible, but not useful. Use a helper function.");
     system.def("launch",
-               [](System* system){ return system->launch(); },
+               [](System* system){
+                   return system->launch();
+               },
                "Launch the configured workflow in the default context.");
     system.def("launch",
                 [](System* system, std::shared_ptr<Context> context)

src/gmx/data.py

@@ -18,6 +18,6 @@
     raise exceptions.OptionalFeatureNotAvailableWarning("Need pkg_resources from setuptools package to access gmx package data.")
 
 if os.path.exists(_tpr_filename) and os.path.isfile(_tpr_filename):
-    tpr_filename = _tpr_filename
+    tpr_filename = os.path.abspath(_tpr_filename)
 else:
     raise exceptions.OptionalFeatureNotAvailableError('Package data file data/topol.tpr not accessible at {}'.format(_tpr_filename))

src/gmx/test/test_mpiarraycontext.py

@@ -15,19 +15,19 @@
 # add the handlers to the logger
 logging.getLogger().addHandler(ch)
 
-import gmx
-import gmx.core
-import os
-# Get a test tpr filename
-from gmx.data import tpr_filename
-
 try:
     from mpi4py import MPI
     withmpi_only = pytest.mark.skipif(not MPI.Is_initialized() or MPI.COMM_WORLD.Get_size() < 2,
                                       reason="Test requires at least 2 MPI ranks, but MPI is not initialized or too small.")
 except ImportError:
     withmpi_only = pytest.mark.skip(reason="Test requires at least 2 MPI ranks, but mpi4py is not available.")
 
+import gmx
+import gmx.core
+import os
+# Get a test tpr filename
+from gmx.data import tpr_filename
+
 class ConsumerElement(gmx.workflow.WorkElement):
     """Simple workflow element to test the shared data resource."""
     def __init__(self, name):
@@ -138,18 +138,19 @@ def launch_test_consumer(rank=None):
 @pytest.mark.usefixtures("cleandir")
 class ArrayContextTestCase(unittest.TestCase):
     def test_basic(self):
-        md = gmx.workflow.from_tpr(tpr_filename)
-        context = gmx.context.ParallelArrayContext(md)
-        with context as session:
-            session.run()
+        # Todo: let Context run work that will fit, even if it is narrower.
+        # md = gmx.workflow.from_tpr(tpr_filename)
+        # context = gmx.context.ParallelArrayContext(md)
+        # with context as session:
+        #     session.run()
 
         md = gmx.workflow.from_tpr([tpr_filename, tpr_filename])
         context = gmx.context.ParallelArrayContext(md)
         with context as session:
             session.run()
             # This is a sloppy way to see if the current rank had work to do.
-            if hasattr(context, "workdir"):
-                rank = context.rank
+            rank = context.rank
+            if rank == 0:
                 output_path = os.path.join(context.workdir, 'traj.trr')
                 assert(os.path.exists(output_path))
                 print("Worker {} produced {}".format(rank, output_path))
@@ -178,11 +179,18 @@ def test_shared_data(self):
         context.work = workspec
 
         # Confirm that oversized width is caught
-        import mpi4py
-        size = mpi4py.MPI.COMM_WORLD.Get_size()
+        from mpi4py import MPI
+        size = MPI.COMM_WORLD.Get_size()
+        rank = MPI.COMM_WORLD.Get_rank()
+        logging.debug("Attempting to launch work with width 3 on rank {}".format(rank))
         if size < width:
             with pytest.raises(gmx.exceptions.UsageError):
-                context.__enter__()
+                with context:
+                    pass
+        # We need to make sure that all ranks in the communicator enter and exit the context. We can probably handle this better.
+        else:
+            with context:
+                pass
 
         # Create a workspec that we expect to be runnable.
         consumer.workspec = None
@@ -196,6 +204,7 @@ def test_shared_data(self):
         context.add_operation(consumer.namespace, consumer.operation, translate_test_consumer)
         context.work = workspec
 
+        logging.debug("Attempting to run session with width {} on rank {}".format(size, rank))
         with context as session:
             session.run()
             assert session.graph.nodes[consumer.name]['check'] == True

src/gmx/test/test_pymd.py

@@ -62,19 +62,6 @@ def test_APIObjectsFromTpr(self):
         apisystem = gmx.core.from_tpr(tpr_filename)
         assert isinstance(apisystem, gmx.core.MDSystem)
         assert hasattr(apisystem, 'launch')
-        session = apisystem.launch()
-        assert hasattr(session, 'run')
-        session.run()
-        # Test rerunability
-        # system = gmx.System()
-        # runner = gmx.runner.SimpleRunner()
-        # runner._runner = apirunner
-        # system.runner = runner
-        # assert isinstance(system, gmx.System)
-        # assert isinstance(system.runner, gmx.runner.Runner)
-        # assert isinstance(system.runner._runner, gmx.core.SimpleRunner)
-        # with gmx.context.DefaultContext(system.runner) as session:
-        #     session.run()
     def test_SystemFromTpr(self):
         system = gmx.System._from_file(tpr_filename)
         system.run()