imdclient 0.1.3__py3-none-any.whl → 0.1.4__py3-none-any.whl

imdclient/IMD.py

@@ -50,6 +50,7 @@ class IMDReader(StreamReaderBase):
     ):
         super(IMDReader, self).__init__(filename, **kwargs)
 
+        self._imdclient = None
         logger.debug("IMDReader initializing")
 
         if n_atoms is None:
@@ -125,6 +126,7 @@ class IMDReader(StreamReaderBase):
     def close(self):
         """Gracefully shut down the reader. Stops the producer thread."""
         logger.debug("IMDReader close() called")
-        self._imdclient.stop()
+        if self._imdclient is not None:
+            self._imdclient.stop()
         # NOTE: removeme after testing
         logger.debug("IMDReader shut down gracefully.")

imdclient/IMDClient.py

@@ -46,6 +46,10 @@ class IMDClient:
         IMDFramebuffer will be filled with as many :class:`IMDFrame` fit in `buffer_size` bytes [``10MB``]
     timeout : int, optional
         Timeout for the socket in seconds [``5``]
+    continue_after_disconnect : bool, optional [``None``]
+        If True, the client will attempt to change the simulation engine's waiting behavior to
+        non-blocking after the client disconnects. If False, the client will attempt to change it
+        to blocking. If None, the client will not attempt to change the simulation engine's behavior.
     **kwargs : dict (optional)
         Additional keyword arguments to pass to the :class:`BaseIMDProducer` and :class:`IMDFrameBuffer`
     """
@@ -57,6 +61,7 @@ class IMDClient:
         n_atoms,
         socket_bufsize=None,
         multithreaded=True,
+        continue_after_disconnect=None,
         **kwargs,
     ):
 
@@ -64,6 +69,7 @@ class IMDClient:
         self._conn = self._connect_to_server(host, port, socket_bufsize)
         self._imdsinfo = self._await_IMD_handshake()
         self._multithreaded = multithreaded
+        self._continue_after_disconnect = continue_after_disconnect
 
         if self._multithreaded:
             self._buf = IMDFrameBuffer(
@@ -201,7 +207,9 @@ class IMDClient:
             # /proc/sys/net/core/rmem_default
             # Max (linux):
             # /proc/sys/net/core/rmem_max
-            conn.setsockopt(socket.SOL_SOCKET, socket.SO_RCVBUF, socket_bufsize)
+            conn.setsockopt(
+                socket.SOL_SOCKET, socket.SO_RCVBUF, socket_bufsize
+            )
         try:
             logger.debug(f"IMDClient: Connecting to {host}:{port}")
             conn.connect((host, port))
@@ -292,6 +300,17 @@ class IMDClient:
         self._conn.sendall(go)
         logger.debug("IMDClient: Sent go packet to server")
 
+        if self._continue_after_disconnect is not None:
+            wait_behavior = (int)(not self._continue_after_disconnect)
+            wait_packet = create_header_bytes(
+                IMDHeaderType.IMD_WAIT, wait_behavior
+            )
+            self._conn.sendall(wait_packet)
+            logger.debug(
+                "IMDClient: Attempted to change wait behavior to %s", 
+                not self._continue_after_disconnect 
+            )
+
     def _disconnect(self):
         # MUST disconnect before stopping execution
         # if simulation already ended, this method will do nothing
@@ -499,7 +518,14 @@ class BaseIMDProducer(threading.Thread):
 
 class IMDProducerV2(BaseIMDProducer):
     def __init__(
-        self, conn, buffer, sinfo, n_atoms, multithreaded, error_queue, **kwargs
+        self,
+        conn,
+        buffer,
+        sinfo,
+        n_atoms,
+        multithreaded,
+        error_queue,
+        **kwargs,
     ):
         super(IMDProducerV2, self).__init__(
             conn, buffer, sinfo, n_atoms, multithreaded, error_queue, **kwargs
@@ -713,9 +739,6 @@ class IMDProducerV3(BaseIMDProducer):
                 ).reshape((self._n_atoms, 3)),
             )
 
-    def __del__(self):
-        logger.debug("IMDProducer: I am being deleted")
-
 
 class IMDFrameBuffer:
     """
@@ -762,7 +785,9 @@ class IMDFrameBuffer:
             raise ValueError("pause_empty_proportion must be between 0 and 1")
         self._pause_empty_proportion = pause_empty_proportion
         if unpause_empty_proportion < 0 or unpause_empty_proportion > 1:
-            raise ValueError("unpause_empty_proportion must be between 0 and 1")
+            raise ValueError(
+                "unpause_empty_proportion must be between 0 and 1"
+            )
         self._unpause_empty_proportion = unpause_empty_proportion
 
         if buffer_size <= 0:
@@ -829,7 +854,9 @@ class IMDFrameBuffer:
                 logger.debug("IMDProducer: Noticing consumer finished")
                 raise EOFError
         except Exception as e:
-            logger.debug(f"IMDProducer: Error waiting for space in buffer: {e}")
+            logger.debug(
+                f"IMDProducer: Error waiting for space in buffer: {e}"
+            )
 
     def pop_empty_imdframe(self):
         logger.debug("IMDProducer: Getting empty frame")
@@ -875,7 +902,9 @@ class IMDFrameBuffer:
             imdf = self._full_q.get()
         else:
             with self._full_imdf_avail:
-                while self._full_q.qsize() == 0 and not self._producer_finished:
+                while (
+                    self._full_q.qsize() == 0 and not self._producer_finished
+                ):
                     self._full_imdf_avail.wait()
 
             if self._producer_finished and self._full_q.qsize() == 0:

imdclient/IMDProtocol.py

@@ -34,6 +34,7 @@ class IMDHeaderType(Enum):
     IMD_BOX = 13
     IMD_VELOCITIES = 14
     IMD_FORCES = 15
+    IMD_WAIT = 16
 
 
 def parse_energy_bytes(data, endianness):

imdclient/data/gromacs/md/gromacs_v3_nst1.mdp

@@ -1,5 +1,5 @@
 title                   = PRODUCTION IN NPT
-ld-seed                 = 1
+ld-seed			= 1
 ; Run parameters
 integrator              = md        ; leap-frog integrator
 nsteps                  = 100    ; 1 * 1000 = 1 ps
@@ -7,9 +7,9 @@ dt                      = 0.001     ; 1 fs
 ; Output control
 nstxout                 = 1      ; save coordinates every 1 fs
 nstvout                 = 1      ; save velocities every 1 fs
-nstfout                 = 1
+nstfout                 = 1      ; save forces every 1 fs
 nstenergy               = 1      ; save energies every 1 fs
-nstlog                  = 10      ; update log file every 1 ps
+nstlog                  = 10     
 ; Center of mass (COM) motion
 nstcomm                 = 10        ; remove COM motion every 10 steps
 comm-mode               = Linear    ; remove only COM translation (liquids in PBC) 

imdclient/tests/base.py

@@ -208,3 +208,49 @@ class IMDv3IntegrationTest:
                     imd_u.trajectory[i - first_frame].forces,
                     atol=1e-03,
                 )
+
+    def test_continue_after_disconnect(
+        self, docker_client, topol, tmp_path, port
+    ):
+        u = mda.Universe(
+            (tmp_path / topol),
+            f"imd://localhost:{port}",
+            continue_after_disconnect=True,
+            # Make sure LAMMPS topol can be read
+            # Does nothing if not LAMMPS
+            atom_style="id type x y z",
+        )
+        # Though we disconnect here, the simulation should continue
+        u.trajectory.close()
+        # Wait for the simulation to finish running
+        time.sleep(45)
+
+        # Now, attempt to reconnect- should fail,
+        # since the simulation should have continued
+        with pytest.raises(IOError):
+            u = mda.Universe(
+                (tmp_path / topol),
+                f"imd://localhost:{port}",
+                atom_style="id type x y z",
+            )
+
+    def test_wait_after_disconnect(self, docker_client, topol, tmp_path, port):
+        u = mda.Universe(
+            (tmp_path / topol),
+            f"imd://localhost:{port}",
+            # Could also use None here- just being explicit
+            continue_after_disconnect=False,
+            # Make sure LAMMPS topol can be read
+            # Does nothing if not LAMMPS
+            atom_style="id type x y z",
+        )
+        u.trajectory.close()
+        # Give the simulation engine
+        # enough time to finish running (though it shouldn't)
+        time.sleep(45)
+
+        u = mda.Universe(
+            (tmp_path / topol),
+            f"imd://localhost:{port}",
+            atom_style="id type x y z",
+        )

imdclient/tests/conftest.py

@@ -1,42 +1,3 @@
 """
 Global pytest fixtures
 """
-
-
-# Command line arguments for 'test_manual.py'
-def pytest_addoption(parser):
-    parser.addoption(
-        "--topol_path_arg",
-        action="store",
-        default=None,
-    )
-    parser.addoption(
-        "--traj_path_arg",
-        action="store",
-        default=None,
-    )
-    parser.addoption(
-        "--first_frame_arg", action="store", type=int, default=None
-    )
-
-
-def pytest_generate_tests(metafunc):
-    # This is called for every test. Only get/set command line arguments
-    # if the argument is specified in the list of test "fixturenames".
-    topol = metafunc.config.option.topol_path_arg
-    traj = metafunc.config.option.traj_path_arg
-    first_frame = metafunc.config.option.first_frame_arg
-
-    if all(
-        arg in metafunc.fixturenames
-        for arg in ["topol_path_arg", "traj_path_arg", "first_frame_arg"]
-    ):
-        if topol is None or traj is None or first_frame is None:
-            raise ValueError(
-                "Must pass all three of '--topol_path_arg <path/to/topology>', "
-                + "'--traj_path_arg <path/to/trajectory>', "
-                + "'--first_frame_arg <first traj frame to compare to IMD>"
-            )
-        metafunc.parametrize("topol_path_arg", [topol])
-        metafunc.parametrize("traj_path_arg", [traj])
-        metafunc.parametrize("first_frame_arg", [first_frame])

imdclient/tests/datafiles.py

@@ -8,7 +8,22 @@ Use as ::
 
 """
 
-__all__ = ["LAMMPS_IN", "LAMMPS_TOPOL", "GROMACS_TRAJ", "GROMACS_MDP"]
+__all__ = [
+    "LAMMPS_TOPOL",
+    "LAMMPS_IN_NST_1",
+    "LAMMPS_IN_NST_8",
+    "GROMACS_TRAJ",
+    "GROMACS_MDP",
+    "GROMACS_TOP" "LAMMPS_IN_NST_1",
+    "GROMACS_GRO",
+    "GROMACS_MDP_NST_1",
+    "GROMACS_MDP_NST_8",
+    "NAMD_TOPOL",
+    "NAMD_CONF_NST_1",
+    "NAMD_CONF_NST_8",
+    "NAMD_PARAMS",
+    "NAMD_PSF",
+]
 
 from importlib import resources
 from pathlib import Path

imdclient/tests/hpc_testing/gromacs/README.md

@@ -0,0 +1,112 @@
+# Manual validation of different compiler options for GROMACS using ASU's SOL
+
+### Running tests
+
+To validate all IMDv3 output (time, integration step, dt, box, positions, velocities, and forces)
+against TRR output with a simple sample simulation, first ensure you're using a 
+python environment which has the testing requirements of IMDClient installed.
+
+If not already installed, do:
+```bash
+conda env create -n imdclient-test -f devtools/conda-envs/test_env.yaml -y
+conda activate imdclient-test
+```
+
+Equivalently, on ASU's Sol, do:
+```bash
+module load mamba
+# Only needed for MPI builds
+module load openmpi/4.1.5
+conda env create -n imdclient-test -f devtools/conda-envs/test_env.yaml -y
+source activate imdclient-test
+```
+
+Then, to run the tests, do:
+```bash
+cd imdclient/tests/hpc_testing/gromacs
+chmod +x validate_gmx.sh
+
+./validate_gmx.sh \
+    --gmx_binary /path/to/gmx
+```
+
+Or, for MPI builds,
+```bash
+./validate_gmx.sh \
+    --gmx_binary /path/to/gmx \
+    --mpi
+```
+
+To validate against your own simulation files, see `validate_gmx.sh` for 
+command line arguments.
+
+### Compiling on ASU's Sol supercomputer
+
+Allocate a GPU node on SOL and clone in https://gitlab.com/ljwoods2/gromacs.git
+
+After cloning, do:
+```bash
+git checkout imd-v3
+module load cmake/3.30.2
+module load gcc-12.1.0-gcc-11.2.0
+moudle load cuda-12.6.1-gcc-12.1.0
+module load openmpi/4.1.5
+
+mkdir -p build_gpu
+cd build_gpu
+
+cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=CUDA -DGMX_MPI=ON
+make -j 4
+make install
+source /your/installation/prefix/here/bin/GMXRC
+```
+<!-- 
+After GROMACS has been built, change into the directory containing this file.
+
+To test on one node, run this in the shell (assuming there are 4 cores available):
+```bash
+/home/ljwoods2/workspace/gromacs/build_mpi/bin/gmx grompp \
+    -f gmx_gpu_test.mdp \
+    -c struct.gro \
+    -p gmx_gpu_test.top \
+    -imd struct_imd.gro \
+    -o gmx_gpu_test.tpr \
+    -maxwarn 1
+
+/home/ljwoods2/workspace/gromacs/build_mpi/bin/gmx mdrun \
+    -s gmx_gpu_test.tpr \
+    -o gmx_gpu_test.trr \
+    -imdwait \
+    -ntmpi 2 \
+    -ntomp 2
+```
+To test on multiple nodes, run this in the shell (assuming there are 4 nodes and 16 cores available, with 1 GPU on each node):
+
+```bash
+module load openmpi/4.1.5
+
+/home/ljwoods2/workspace/gromacs/build_mpi/bin/mpirun \
+    -np 4 \
+    gmx_mpi mdrun \
+    -s gmx_gpu_test.tpr \
+    -o gmx_gpu_test.trr \
+    -imdwait \
+    -ntomp 4 \
+    -gpu_id 0
+```
+
+And in a different shell (from the same directory), run the following commands:
+
+```bash
+module load mamba
+# Environment containing IMDClient
+source activate imdclient-test
+
+mkdir tmp_test
+
+python imdclient/tests/test_manual.py \
+    --topol_arg imdclient/tests/hpc_testing/gromacs/struct.gro \
+    --traj_arg imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.trr \
+    --first_frame_arg 0 \
+    --tmp_path tmp_test
+``` -->

imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.mdp

@@ -0,0 +1,58 @@
+title                   = PRODUCTION IN NPT
+ld-seed			= 1
+; Run parameters
+integrator              = md        ; leap-frog integrator
+nsteps                  = 1000    ; 1 * 1000 = 1 ps
+dt                      = 0.001     ; 1 fs
+; Output control
+nstxout                 = 10      ; save coordinates every 10 fs
+nstvout                 = 10      ; save velocities every 10 fs
+nstfout                 = 10
+nstenergy               = 10      ; save energies every 10 fs
+nstlog                  = 10      ; update log file every 10 fs
+; Center of mass (COM) motion
+nstcomm                 = 10        ; remove COM motion every 10 steps
+comm-mode               = Linear    ; remove only COM translation (liquids in PBC) 
+; Bond parameters
+continuation            = yes       ; first dynamics run
+constraint_algorithm    = lincs     ; holonomic constraints
+constraints             = all-bonds ; all bonds lengths are constrained
+lincs_iter              = 1         ; accuracy of LINCS
+lincs_order             = 4         ; also related to accuracy
+; Nonbonded settings
+cutoff-scheme           = Verlet    ; Buffered neighbor searching
+ns_type                 = grid      ; search neighboring grid cells
+nstlist                 = 10        ; 10 fs, largely irrelevant with Verlet
+rcoulomb                = 1.0       ; short-range electrostatic cutoff (in nm)
+rvdw                    = 1.0       ; short-range van der Waals cutoff (in nm)
+DispCorr                = EnerPres  ; account for cut-off vdW scheme
+; Electrostatics
+coulombtype             = PME       ; Particle Mesh Ewald for long-range electrostatics
+pme_order               = 4         ; cubic interpolation
+fourierspacing          = 0.12      ; grid spacing for FFT
+; Temperature coupling is on
+tcoupl                  = Nose-Hoover       ; good for production, after equilibration
+; we define separate thermostats for the solute and solvent (need to adapt)
+; see default groups defined by Gromacs for your system or define your own (make_ndx)
+tc-grps                 = Protein  SOL      ; the separate groups for the thermostats
+tau-t                   = 1.0      1.0      ; time constants for thermostats (ps)
+ref-t                   = 300      300      ; reference temperature for thermostats (K)
+; Pressure coupling is off
+pcoupl                  = Parrinello-Rahman ; good for production, after equilibration
+tau-p                   = 2.0               ; time constant for barostat (ps)
+compressibility         = 4.5e-5            ; compressibility (1/bar) set to water at ~300K
+ref-p                   = 1.0               ; reference pressure for barostat (bar)
+; Periodic boundary conditions
+pbc                     = xyz       ; 3-D PBC
+; Velocity generation
+gen_vel                 = no
+IMD-group               = System
+IMD-nst                 = 10
+IMD-version             = 3
+IMD-time                = yes
+IMD-box                 = yes
+IMD-coords              = yes
+IMD-unwrap              = no
+IMD-vels                = yes
+IMD-forces              = yes
+IMD-energies            = yes