tAdded torqueScript generating function - sphere - GPU-based 3D discrete element method algorithm with optional fluid coupling
(HTM) git clone git://src.adamsgaard.dk/sphere
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---
(DIR) commit 3eacaf0437b573b776d293ca3f56e0c21be94aa3
(DIR) parent 323d03bd4f83dd75223dd4d7f43ae4fcb3882a7b
(HTM) Author: Anders Damsgaard <adc@geo.au.dk>
Date: Thu, 14 Mar 2013 05:25:59 +0100
Added torqueScript generating function
Diffstat:
M python/sphere.py | 60 ++++++++++++++++++++++++++++++--
1 file changed, 58 insertions(+), 2 deletions(-)
---
(DIR) diff --git a/python/sphere.py b/python/sphere.py
t@@ -450,6 +450,38 @@ class Spherebin:
fig.clf()
+ def generateBimodalRadii(self,
+ r_small = 0.005,
+ r_large = 0.05,
+ ratio = 0.2,
+ verbose = True):
+ """ Draw radii from two sizes
+ @param r_small: Radii of small population (float), in ]0;r_large[
+ @param r_large: Radii of large population (float), in ]r_small;inf[
+ @param ratio: Approximate volumetric ratio between the two
+ populations (large/small).
+ """
+ if (r_small >= r_large):
+ raise Exception("r_large should be larger than r_small")
+
+ V_small = V_sphere(r_small)
+ V_large = V_sphere(r_large)
+ nlarge = int(V_small/V_large * ratio * self.np[0]) # ignore void volume
+
+ self.radius[:] = r_small
+ self.radius[0:nlarge] = r_large
+ numpy.random.shuffle(self.radius)
+
+ # Test volumetric ratio
+ V_small_total = V_small * (self.np - nlarge)
+ V_large_total = V_large * nlarge
+ if (abs(V_large_total/V_small_total - ratio) > 1.0e5):
+ raise Exception("Volumetric ratio seems wrong")
+
+ if (verbose == True):
+ print("generateBimodalRadii created " + str(nlarge) + " large particles, and " + str(nlarge-self.np[0]) + " small")
+
+
def initRandomPos(self, g = numpy.array([0.0, 0.0, -9.80665]),
gridnum = numpy.array([12, 12, 36]),
periodic = 1,
t@@ -1155,7 +1187,11 @@ class Spherebin:
def torqueScript(self,
email="adc@geo.au.dk",
email_alerts="ae",
- walltime="8:00:00"):
+ walltime="24:00:00",
+ queue="qfermi",
+ cudapath="/com/cuda/4.0.17/cuda",
+ spheredir="/home/adc/code/sphere",
+ workdir="/scratch"):
'Create job script for the Torque queue manager for the binary'
filename = self.sid + ".sh"
t@@ -1163,7 +1199,27 @@ class Spherebin:
try :
fh = open(filename, "w")
- # write stuff
+ fh.write('#!/bin/sh\n')
+ fh.write('#PBS -N ' + self.sid + '\n')
+ fh.write('#PBS -l nodes=1:ppn=1\n')
+ fh.write('#PBS -l walltime=' + walltime + '\n')
+ fh.write('#PBS -q ' + queue + '\n')
+ fh.write('#PBS -M ' + email + '\n')
+ fh.write('#PBS -m ' + email_alerts + '\n')
+ fh.write('CUDAPATH=' + cudapath + '\n')
+ fh.write('export PATH=$CUDAPATH/bin:$PATH\n')
+ fh.write('export LD_LIBRARY_PATH=$CUDAPATH/lib64:$CUDAPATH/lib:$LD_LIBRARY_PATH\n')
+ fh.write('echo "`whoami`@`hostname`"\n')
+ fh.write('echo "Start at `date`"\n')
+ fh.write('ORIGDIR=' + spheredir + '\n')
+ fh.write('WORKDIR=' + workdir + "/$PBS_JOBID\n")
+ fh.write('cp -r $ORIGDIR/* $WORKDIR\n')
+ fh.write('cd $WORKDIR\n')
+ fh.write('cmake . && make\n')
+ fh.write('./sphere input/' + self.sid + '.bin > /dev/null &\n')
+ fh.write('wait\n')
+ fh.write('cp $WORKDIR/output/* $ORIGDIR/output/\n')
+ fh.write('echo "End at `date`"\n')
finally :
if fh is not None: