Merge pull request #112 from keisukefukuda/fix-misc

misc fix

.gitignore

@@ -3,3 +3,7 @@ versions
 *.pyc
 pylib
 dist
+.idea
+*.egg-info
+.pytest_cache
+

.travis.yml

@@ -4,10 +4,6 @@ sudo: false
 
 dist: trusty
 
-cache:
-    directories:
-     - /home/travis/mpi
-
 env:
   - PIP_VER=19.0.3 TEST_SHELL_CMD=bash  LANG=C
   - PIP_VER=18.0   TEST_SHELL_CMD=zsh   LANG=C

mpienv/command/describe.py

@@ -0,0 +1,23 @@
+# coding: utf-8
+
+import argparse
+
+from mpienv import mpienv
+
+
+parser = argparse.ArgumentParser(
+    prog='mpienv describe',
+    description='Describe a registered MPI')
+parser.add_argument('name', metavar='name', type=str,
+                    help='Name of an MPI installation')
+
+
+def main():
+    args = parser.parse_args()
+
+    # Create a link
+    mpienv.describe(args.name)
+
+
+if __name__ == "__main__":
+    main()

mpienv/command/restore.py

@@ -0,0 +1,21 @@
+# coding: utf-8
+
+import argparse
+
+from mpienv import mpienv
+
+
+parser = argparse.ArgumentParser(
+    prog='mpienv refresh',
+    description='Restore the status')
+
+
+def main():
+    args = parser.parse_args()  # NOQA
+
+    # Create a link
+    mpienv.restore()
+
+
+if __name__ == "__main__":
+    main()

mpienv/command/use.py

@@ -3,19 +3,33 @@
 import argparse
 
 from mpienv import mpienv
+import sys
 
 parser = argparse.ArgumentParser(
     prog='mpienv use', description='Set the specific MPI environment.')
 parser.add_argument('-p', '--mpi4py', action="store_true",
                     dest="mpi4py", default=False,
-                    help="Also switch mpi4py library")
+                    help="Activate mpi4py library for "
+                         "the current python (default)")
+parser.add_argument('--no-mpi4py', action='store_true',
+                    dest='no_mpi4py', default=False,
+                    help="Do not activate mpi4py library")
 parser.add_argument('name', type=str,
                     help="MPI name to use")
 
 
 def main():
     args = parser.parse_args()
-    mpienv.use(args.name, mpi4py=args.mpi4py)
+
+    if args.mpi4py and args.no_mpi4py:
+        sys.stderr.write("mpienv: Error: both of --mpi4py "
+                         "and --no-mpi4py are specified.")
+        exit(1)
+
+    if args.mpi4py:
+        sys.stderr.write("mpienv: Info: --mpi4py is ON by default.\n")
+
+    mpienv.use(args.name, no_mpi4py=args.no_mpi4py)
 
 
 if __name__ == "__main__":

mpienv/core.py

@@ -214,10 +214,18 @@ def is_installed(self, mpiexec):
         return None
 
     def get_current_name(self):
-        try:
-            return next(name for name, mpi in self.items() if mpi.is_active)
-        except StopIteration:
-            raise UnknownMPI()
+        if 'DEFAULT' in self.config2 and 'active' in self.config2['DEFAULT']:
+            name = self.config2['DEFAULT']['active']
+
+            # Check
+            if not self.get_mpi_from_name(name).is_active:
+                sys.stderr.write("mpienv: Error: Internal status is "
+                                 "inconsistent. Please hit 'mpienv use' "
+                                 "command to refresh the status.\n")
+                exit(1)
+            return name
+        else:
+            raise RuntimeError("No MPI is activated.")
 
     def add(self, target, name=None):
         # `target` is expected to be an mpiexec command or its prefix
@@ -253,7 +261,7 @@ def add(self, target, name=None):
                 exit(-1)
 
         if name in self.config2:
-            sys.stderr.write("{} is already registered.".format(name))
+            sys.stderr.write("{} is already registered.\n".format(name))
         else:
             self.config2.add_section(name)
             self.config2[name]['name'] = name
@@ -294,7 +302,7 @@ def rename(self, name_from, name_to):
         if mpi4py.is_installed():
             mpi4py.rename(name_to)
 
-    def use(self, name, mpi4py=False):
+    def use(self, name, no_mpi4py=False):
         mpi = self.get_mpi_from_name(name)
 
         if isinstance(mpi, BrokenMPI):
@@ -310,13 +318,32 @@ def use(self, name, mpi4py=False):
                              "".format(name))
             exit(-1)
 
-        mpi.use(name, mpi4py=mpi4py)
+        mpi.use(name, no_mpi4py=no_mpi4py)
 
     def exec_(self, cmds, **kwargs):
-        name = self.get_current_name()
+        try:
+            name = self.get_current_name()
+        except RuntimeError:
+            sys.stderr.write("mpienv: Error: No MPI is currently activated.\n")
         mpi = self.get_mpi_from_name(name)
         mpi.exec_(cmds, **kwargs)
 
+    def restore(self):
+        if 'DEFAULT' in self.config2:
+            try:
+                mpi_name = self.config2['DEFAULT']['active']
+                if 'mpi4py' in self.config2['DEFAULT']:
+                    mpi4py = self.config2['DEFAULT'].getboolean('mpi4py')
+                else:
+                    mpi4py = True
+            except KeyError:
+                return
+            self.use(mpi_name, mpi4py)
+
+    def describe(self, name):
+        mpi = self.get_mpi_from_name(name)
+        mpi.describe()
+
 
 _root_dir = (os.environ.get("MPIENV_ROOT", None) or
              os.path.join(os.path.expanduser('~'), '.mpienv'))

mpienv/mpibase.py

@@ -325,6 +325,7 @@ def exec_(self, cmds, dry_run=False, verbose=False):
             print("tempfile = {}".format(tempfile))
             print("hosts = {}".format(remote_hosts))
 
+        # Generate a proxy shell script that runs user programs
         self._generate_exec_script(tempfile, cmds)
 
         # Copy script file
@@ -333,10 +334,19 @@ def exec_(self, cmds, dry_run=False, verbose=False):
                 check_call(['scp', tempfile, '{}:{}'.format(host, tempfile)])
 
         # Run the mpiexec command
-        args, _ = split_mpi_user_prog(cmds)
+        mpi_args, user_args = split_mpi_user_prog(cmds)
+
+        # Warn if user tries to run python program while --mpi4py is not active
+        if user_args[0].startswith('python'):
+            if not mpienv.mpienv.config2['DEFAULT'].getboolean('mpi4py'):
+                sys.stderr.write("mpienv: Warn: It seems that you are trying"
+                                 " to run a pythohn progrma, but mpi4py is not"
+                                 " ")
+
+        # Execute mpiexec
         mpiexec = self.mpiexec
         if dry_run:
-            print(' '.join([mpiexec] + args + [tempfile]))
+            print(' '.join([mpiexec] + mpi_args + [tempfile]))
             if verbose:
                 print("")
                 print(tempfile)
@@ -345,7 +355,7 @@ def exec_(self, cmds, dry_run=False, verbose=False):
         else:
             sys.stdout.flush()
             sys.stderr.flush()
-            os.execv(mpiexec, [mpiexec] + args + [tempfile])
+            os.execv(mpiexec, [mpiexec] + mpi_args + [tempfile])
 
     def run_cmd(self, cmd, extra_envs):
         envs = os.environ.copy()
@@ -376,25 +386,25 @@ def _generate_path(self):
         return env_path
 
     def _generate_ldlib(self):
-        env_ldlib = os.environ.get('LIBRARY_PATH', '').split(':')
+        env_ldlib = os.environ.get('LD_LIBRARY_PATH', '').split(':')
 
-        # Remove all directory that contains 'mpiexec'
         for dir_name in ['lib', 'lib64']:
             lib_dir = os.path.join(self.prefix, dir_name)
             if os.path.exists(lib_dir):
                 # Remove if lib_is already a part of LD_LIBRARY_PATH
+                # to avoid LD_LIBRARY_PATH is too long.
                 if lib_dir in env_ldlib:
                     env_ldlib.remove(lib_dir)
                 env_ldlib = [lib_dir] + env_ldlib
 
         return env_ldlib
 
-    def use(self, name, mpi4py=False):
+    def use(self, name, no_mpi4py=False):
         # Check if the specified `name` is the same as the current one
         try:
             cur_name = mpienv.mpienv.config2['DEFAULT']['name']
             cur_mpi4py = mpienv.mpienv.config2.getboolean('DEFAULT', 'mpi4py')
-            if cur_name == name and cur_mpi4py == mpi4py:
+            if cur_name == name and cur_mpi4py == (not no_mpi4py):
                 return
         except KeyError:
             pass
@@ -403,7 +413,7 @@ def use(self, name, mpi4py=False):
         env_ldlib = self._generate_ldlib()
 
         mpienv.mpienv.config2['DEFAULT']['active'] = name
-        mpienv.mpienv.config2['DEFAULT']['mpi4py'] = str(mpi4py)
+        mpienv.mpienv.config2['DEFAULT']['mpi4py'] = str(not no_mpi4py)
         mpienv.mpienv.config_save()
 
         print('export PATH={}'.format(':'.join(env_path)))
@@ -414,7 +424,7 @@ def use(self, name, mpi4py=False):
         env['LD_LIBRARY_PATH'] = ':'.join(env_ldlib)
 
         py = MPI4Py(self._conf, name)
-        if mpi4py:
+        if not no_mpi4py:
             if not py.is_installed():
                 py.install(env)
             py.use()
@@ -435,3 +445,13 @@ def remove(self):
             shutil.rmtree(self.prefix)
         else:
             os.remove(os.path.join(self._conf['mpi_dir'], self.name))
+
+    def describe(self):
+        print("Name    : {}".format(self.name))
+        print("Type    : {}".format(self.type_))
+        print("Version : {}".format(self.version))
+        print("Path    : {}".format(self.prefix))
+        self._describe()
+
+    def _describe(self):
+        pass

mpienv/mpienv_init.py

@@ -1,7 +1,9 @@
 import sys
 
 _template = """
-export MPIENV_ROOT="$HOME/.mpienv"
+if [ -z "${MPIENV_ROOT:-}" ]; then
+    export MPIENV_ROOT="$HOME/.mpienv"
+fi
 PYTHON=__SYS_EXECUTABLE__
 
 if [ -z "${MPIENV_VERSIONS_DIR:-}" ]; then
@@ -39,12 +41,26 @@
                    $PYTHON -m mpienv.command.add $*
             }
             ;;
+        "restore" )
+            {
+                eval "$(env PYTHONPATH=$MPIENV_ROOT:${PYTHONPATH:-} $PYTHON -m mpienv.command.restore $*)"  # NOQA
+                if [ -z "${BASH_VERSION:-}" -a ! -z "${ZSH_VERSION:-}" ]; then
+                    rehash
+                fi
+            }
+            ;;
         "rm" )
             {
                 env PYTHONPATH=$MPIENV_ROOT:${PYTHONPATH:-} \
                     $PYTHON -m mpienv.command.rm "$@"
             }
             ;;
+        "describe" )
+            {
+                env PYTHONPATH=$MPIENV_ROOT:${PYTHONPATH:-} \
+                    $PYTHON -m mpienv.command.describe "$@"
+            }
+            ;;
         "rename" )
             {
                 env PYTHONPATH=$MPIENV_ROOT:${PYTHONPATH:-} \
@@ -92,6 +108,8 @@
             ;;
     esac
 }
+
+mpienv restore
 """
 
 

mpienv/py.py

@@ -70,7 +70,7 @@ def clear(self):
         if newpath == "":
             print("unset PYTHONPATH;")
         else:
-            sys.stderr.write("export PYTHONPATH={}\n".format(newpath))
+            print("export PYTHONPATH={}\n".format(newpath))
 
     def rm(self):
         if os.path.exists(self._pylib_dir):

tests/test_main.sh

@@ -82,6 +82,7 @@ setUp() {
   export MPIENV_ROOT=$TMPDIR/mpienv/
   rm -rf $MPIENV_ROOT |:
   mkdir -p $MPIENV_ROOT
+  rm -rf ~/.mpienv  # Regression test. MPIENV_ROOT is set to /tmp/mpienv in this test script.
 }
 
 tearDown() {
@@ -191,6 +192,7 @@ test_openmpi_info() {
 test_1mpi() {
     # mpienv list
     mpienv autodiscover -q --add ${MPI_PREFIX}
+    rm -rf ~/.mpienv  # Regression test. MPIENV_ROOT is set to /tmp/mpienv in this test script.
 
     mpienv list | grep -q mpich-${MPICH_VER}
     assertTrue "$?"
@@ -320,25 +322,26 @@ test_mpi4py_clear_pypath() {
     assertNull "${PYTHONPATH:-}"
 
     mpienv use ${MPICH}
-    assertNull "${PYTHONPATH:-}"
+    assertNotNull "PYTHONPATH must be set for ${MPICH}" "${PYTHONPATH:-}"
 
     mpienv use --mpi4py ${MPICH}
     assertNotNull "PYTHONPATH must be set for ${MPICH}" "${PYTHONPATH:-}"
 
-    mpienv use ${MPICH}
+    mpienv use --no-mpi4py ${MPICH}
     assertNull "PYTHONPATH must be NULL" "${PYTHONPATH:-}"
 
     mpienv use --mpi4py ${MPICH}
     echo "$PYTHONPATH" | grep ${MPICH}
     assertEquals "PYTHONPATH must contain ${MPICH}" 0 $?
 
     mpienv rename "${MPICH}" mpix
-    mpienv use mpix
-    assertNull "PYTHONPATH must be NULL" "${PYTHONPATH:-}"
 
-    mpienv use --mpi4py mpix
+    mpienv use mpix
     echo "$PYTHONPATH" | grep mpix
     assertEquals "PYTHONPATH must contain mpix" 0 $?
+
+    mpienv use --no-mpi4py mpix
+    assertNull "PYTHONPATH must be NULL" "${PYTHONPATH:-}"
 }
 
 test_mpi4py() {
@@ -410,7 +413,7 @@ test_reg_issue10(){
     mpienv use --mpi4py ${MPICH} # this command should install mpi4py to mpich-3.2
     mpienv rename ${MPICH} mpix # The mpi4py module should be taken over to 'mpix'
 
-    OUT=$(mpienv use --mpi4py mpix 2>&1) # this command should NOT intall mpi4py again
+    OUT=$(mpienv use mpix 2>&1) # this command should NOT intall mpi4py again
 
     # If the `use` command does not run `pip install mpi4py`,
     # which is a correct behavior, E-S should be < 1 [s].