Some fixes to the blender pipeline and docs (#213)

* Updated blender devops scripts

* Added debug listener to pulsar animation

* updated docs

bsb/blender/_mixin.py

@@ -139,9 +139,24 @@ def animate():
     pass
 
 
+def print_debug(lvl, cat, msg, i=None, total=None):
+    if cat.startswith("cell_"):
+        return
+    kwargs = {}
+    if i is not None:
+        kwargs["end"] = "\r"
+    print(f"[{cat}] {msg}", **kwargs)
+
+
+def devnull(*args, **kwargs):
+    pass
+
+
 def _pulsar(results, cells, **kwargs):
     import math
 
+    cells = list(cells)
+
     # Frames per second
     fps = kwargs.get("fps", 60)
     # Milliseconds per second
@@ -152,6 +167,9 @@ def _pulsar(results, cells, **kwargs):
     spd = kwargs.get("spike_duration", 5)
     # Afterburner: fade out time after animation
     ab = kwargs.get("afterburn", 30)
+    # Get the listener that deals with progress reports
+    listener_name = kwargs.get("listener", "devnull")
+    listener = globals().get(listener_name, devnull)
     # Spike width: number of frames of rising/falling edge of spike animation
     sw = math.ceil(spd / 2 / mpf)
     # Create the signal processor functions. They calculate cell intensity during anim.
@@ -161,18 +179,18 @@ def _pulsar(results, cells, **kwargs):
     # Set up compositor with a glare node.
     _pulsar_glare()
     # Retrieve cell activity from the given results
-    cell_activity = _pulsar_cell_activity(cells, results)
+    cell_activity = _pulsar_cell_activity(cells, results, listener)
     # Animate the cell keyframes
-    _pulsar_animate(cells, cell_activity, mpf, sw, ab, cap, intensity)
+    _pulsar_animate(cells, cell_activity, mpf, sw, ab, cap, intensity, listener)
 
 
 animate.pulsar = _pulsar
 _crowded_pulsars = ["granule_cell", "glomerulus"]
 
 
-def _pulsar_animate(cells, cell_activity, mpf, sw, ab, cap, intensity):
+def _pulsar_animate(cells, cell_activity, mpf, sw, ab, cap, intensity, listener):
     last_frame = 0
-    for cell in cells:
+    for i, cell in enumerate(cells):
         # Hardcoded granule cell solution, fix later.
         _min = 0.3 if cell.type.name not in _crowded_pulsars else 0.0
         spike_frames = (cell_activity[cell.id] / mpf).astype(int)
@@ -253,13 +271,21 @@ def intensity(i, min=0.3):
     return cap, intensity
 
 
-def _pulsar_cell_activity(cells, results):
+def _pulsar_cell_activity(cells, results, listener):
     cell_activity = {}
-    for cell in cells:
+    for i, cell in enumerate(cells):
+        listener("debug", "cell", f"id: {cell.id}", i=i, total=len(cells))
         if str(cell.id) not in results:
+            listener("warn", "cell_data_not_found", f"No data for {cell.id}")
+            cell_activity[cell.id] = _np.empty(0)
+            continue
+        activity = results[str(cell.id)][()]
+        if not len(activity):
+            listener("info", "cell_silent", f"Cell {cell.id} does not fire.")
             cell_activity[cell.id] = _np.empty(0)
             continue
-        cell_activity[cell.id] = activity = results[str(cell.id)][:, 1]
+        listener("debug", "cell_activity", f"Cell {cell.id} fires {len(activity)} times.")
+        cell_activity[cell.id] = results[str(cell.id)][:, 1]
     return cell_activity
 
 

devops/blender-pipe/jrender.slurm

@@ -1,5 +1,5 @@
 #!/bin/bash -l
-#SBATCH --job-name="Blender"
+#SBATCH --job-name="Blender render"
 #SBATCH --mail-type=ALL
 #SBATCH --time=01:00:00
 #SBATCH --nodes=25
@@ -12,10 +12,5 @@
 
 export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
 
-module swap gcc/8.3.0 gcc/9.3.0
-module load daint-mc
-module load cray-python/3.8.2.1
-module load PyExtensions/python3-CrayGNU-20.08
-module load h5py/2.10.0-CrayGNU-20.08-python3-parallel
-
+source load_blender.sh
 srun python render.py $1 $2

devops/blender-pipe/jsequence.slurm

@@ -1,8 +1,7 @@
 #!/bin/bash -l
-#SBATCH --job-name="Render Blender"
+#SBATCH --job-name="Blender seauence"
 #SBATCH --mail-type=ALL
-#SBATCH --mail-user=robin.deschepper93@gmail.com
-#SBATCH --time=00:15:00
+#SBATCH --time=00:45:00
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-core=1
 #SBATCH --ntasks-per-node=1
@@ -13,5 +12,5 @@
 
 export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
 
-source $HOME/load_blender.sh
-srun blender-2.91.0-cacd57b67a15-linux64/blender -b $1 -E CYCLES -P render.py -- $2
+source load_blender.sh
+srun blender -b $1 -E CYCLES -P sequence.py -- $2

devops/blender-pipe/load_blender.sh

@@ -0,0 +1,10 @@
+module load daint-mc Mesa/.18.3.3-CrayGNU-20.08
+module load gcc/9.3.0
+# Multicore stack
+module load daint-mc
+# Python 3 & mpi4py
+module load cray-python/3.8.2.1
+# Cython
+module load PyExtensions/python3-CrayGNU-20.08
+# h5py
+module load h5py/2.10.0-CrayGNU-20.08-python3-parallel

devops/blender-pipe/render.py

@@ -15,23 +15,22 @@
     print("pathinfo:", op.parts, len(op.parts), op.parts[:-1])
     if len(op.parts) > 1:
         Path(os.path.join(*op.parts[:-1])).mkdir(parents=True, exist_ok=True)
-    op.mkdir(exist_ok=False)
 
 print(f"Starting blender {e} job")
 
 subprocess.check_call(
     [
-        "blender-2.90.0-linux64/blender",
+        "blender",
         "-b",
         f,
         "-E",
         e,
         "-o",
         o,
         "-s",
-        rank,
+        str(rank),
         "-j",
-        size,
+        str(size),
         "-a",
     ]
 )

docs/source/guides/blender.rst

@@ -55,13 +55,13 @@ you want or you can continue to use some of the BSB blendins:
   import bpy, bsb.core, h5py, itertools
 
   network = bsb.core.from_hdf5("mynetwork.hdf5")
-  # Blend the network into the current scene
-  network.for_blender().blend("scaffold", bpy.context.scene)
+  # Blend the network into the current scene under the name `scaffold`
+  network.for_blender().blend(bpy.context.scene, "scaffold")
   # Load all cell types
   network.load_populations()
   # Or, if you'd like to use the populations:
   populations = network.get_populations()
-  cells = itertools.chain(p.cells for p in populations)
+  cells = itertools.chain(*(p.cells for p in populations.values()))
   # Use the 'pulsar' animation to animate all cells with the simulation results
   with h5py.File("my_results.hdf5", "r") as f:
     network.animate.pulsar(f, cells)
@@ -82,3 +82,33 @@ you want or you can continue to use some of the BSB blendins:
 	unpopulated versions of your Blender files, run the blendin script, save as another
 	file, render it and make the required changes to the unpopulated version, repeating the
 	process. Optimizations are likely to be added in the future.
+
+Blender HPC workflow
+====================
+
+The ``devops/blender-pipe`` folder contains scripts to facilitate the rendering and
+sequencing of BSB blendfiles on HPC systems. Copy them together to a directory on the HPC
+system and make sure that the ``blender`` command opens Blender. The pipeline contains 2
+steps, ``rendering`` each frame in parallel and ``sequencing`` the rendered images into a
+video.
+
+jrender.slurm
+-------------
+
+The render jobscript uses ``render.py`` to invoke Blender. Each Blender process will be
+tasked with rendering a certain proportion of the frames. ``jrender.slurm`` takes 2
+arguments, the blendfile and the output image folder:
+
+.. code-block:: bash
+
+	sbatch jrender.slurm my_file.blend my_file_imgs
+
+jsequence.slurm
+---------------
+
+The sequencing jobscript stitches together the rendered frames into a video. This has to
+be done in serial on a single node. It takes the blendfile and image folder as arguments:
+
+.. code-block:: bash
+
+	sbatch jsequence.slurm my_file.blend my_file_imgs