define nproc in _one_ place (#66)

* define nproc in _one_ place

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docs/tutorials/download_data.sh

@@ -1,7 +1,7 @@
-# This script can be used to download all data sets used for 
-# this manuscript. The first few variables here can be toggled 
-# to determine which data sets to download. Note that the 
-# simulated DHFR data is NOT available publicly for download 
+# This script can be used to download all data sets used for
+# this manuscript. The first few variables here can be toggled
+# to determine which data sets to download. Note that the
+# simulated DHFR data is NOT available publicly for download
 # and must be requested from the authors.
 
 HEWL_DATA=true # 84 GB on SBGrid

docs/tutorials/tutorial_README.rst

@@ -19,8 +19,8 @@ these tutorials are stored on SBGrid, and can be downloaded using the following
    cd 1117 ; shasum -c files.sha
 
 These tutorials are tested most recently with version 3.17.0 of DIALS.
-To reproduce a python environment for analyzing these data, you can 
-install DIALS (see `DIALS`_) and use the YAML file specified 
+To reproduce a python environment for analyzing these data, you can
+install DIALS (see `DIALS`_) and use the YAML file specified
 :download:`here <manuscript_env.yaml>`.
 
 All referenced scripts can be downloaded :download:`here for PDZ2 <pdz2/pdz2_scripts.tar.gz>` and :download:`here for HEWL <hewl/hewl_scripts.tar.gz>`.

examples/pipeline.sh

@@ -11,6 +11,7 @@
 #SBATCH --time=1:00:00
 
 FILE_INPUT_TEMPLATE="PATH/TO/DATA/e080_###.mccd"
+NPROC=8
 
 # Import data
 # You may need to change some of these values to match your data set
@@ -23,7 +24,7 @@ dials.import geometry.scan.oscillation=0,1 \
 
 # Get a monochromatic geometry model
 laue.find_spots imported.expt \
-    spotfinder.mp.nproc=8 \
+    spotfinder.mp.nproc=$NPROC \
     spotfinder.threshold.dispersion.gain=0.35 \
     spotfinder.filter.max_separation=10 \
     lookup.mask="pixels.mask"
@@ -39,34 +40,32 @@ laue.index imported.expt strong.refl \
 laue.sequence_to_stills monochromatic.*
 
 # Polychromatic pipeline
-N=12 # Max multiprocessing
 laue.optimize_indexing stills.* \
     output.experiments="optimized.expt" \
     output.reflections="optimized.refl" \
     output.log="laue.optimize_indexing.log" \
     wavelengths.lam_min=0.95 \
     wavelengths.lam_max=1.15 \
     reciprocal_grid.d_min=1.4 \
-    nproc=$N
+    nproc=$NPROC
 
-N=8 # Max multiprocessing
 laue.refine optimized.* \
     output.experiments="poly_refined.expt" \
     output.reflections="poly_refined.refl" \
     output.log="laue.poly_refined.log" \
-    nproc=$N
+    nproc=$NPROC
 
 laue.predict poly_refined.* \
     output.reflections="predicted.refl" \
     output.log="laue.predict.log" \
     wavelengths.lam_min=0.95 \
     wavelengths.lam_max=1.15 \
     reciprocal_grid.d_min=1.4 \
-    nproc=$N
+    nproc=$NPROC
 
 laue.integrate poly_refined.expt predicted.refl \
     output.filename="integrated.mtz" \
     output.log="laue.integrate.log" \
-    nproc=$N
+    nproc=$NPROC
 
 # This is where laue_dials ends. The output file integrated.mtz can be merged in careless and refined in phenix to get a model