tMerge branch 'master' of github.com:anders-dc/sphere - sphere - GPU-based 3D d… | |
git clone git://src.adamsgaard.dk/sphere | |
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LICENSE | |
--- | |
commit 7626d19392ecba63c4b2e5f4d419e8423d7a90a0 | |
parent f8c44ac1a8fcdc4d6d1112db0cc1467597912e69 | |
Author: Anders Damsgaard <[email protected]> | |
Date: Mon, 11 Aug 2014 10:16:44 +0200 | |
Merge branch 'master' of github.com:anders-dc/sphere | |
Diffstat: | |
A python/diffusivity-c_grad_p=0.01.sh | 49 +++++++++++++++++++++++++++++… | |
A python/diffusivity-c_grad_p=0.1.sh | 49 +++++++++++++++++++++++++++++… | |
A python/diffusivity-c_grad_p=0.5.sh | 49 +++++++++++++++++++++++++++++… | |
A python/diffusivity-c_phi=0.1.sh | 49 +++++++++++++++++++++++++++++… | |
A python/diffusivity-c_phi=0.5.sh | 49 +++++++++++++++++++++++++++++… | |
A python/diffusivity-starter.py | 53 ++++++++++++++++++++++++++++++ | |
6 files changed, 298 insertions(+), 0 deletions(-) | |
--- | |
diff --git a/python/diffusivity-c_grad_p=0.01.sh b/python/diffusivity-c_grad_p=… | |
t@@ -0,0 +1,49 @@ | |
+#!/bin/sh | |
+#PBS -N diffusivity-c_grad_p=0.01 | |
+#PBS -l nodes=1:ppn=3 | |
+#PBS -l walltime=1920:00:00 | |
+#PBS -q qfermi | |
+#PBS -M [email protected] | |
+#PBS -m abe | |
+ | |
+# Grendel CUDA | |
+source /com/gcc/4.6.4/load.sh | |
+CUDAPATH=/com/cuda/5.5.22 | |
+export PATH=$HOME/bin:$PATH | |
+export PATH=$CUDAPATH/bin:$PATH | |
+export LD_LIBRARY_PATH=$CUDAPATH/lib64:$CUDAPATH/lib:$LD_LIBRARY_PATH | |
+ | |
+# Manually installed Python modules | |
+export PYTHONPATH=$HOME/.local/lib/python:$PYTHONPATH | |
+export PYTHONPATH=$HOME/.local/lib64/python:$PYTHONPATH | |
+ | |
+# Manually installed Python | |
+#export PATH=/home/adc/.local/bin:$PATH | |
+ | |
+# Shared Python2.7 | |
+PYTHON=/com/python/2.7.6 | |
+export PYTHONPATH=$PYTHON/lib:$PYTHONPATH | |
+export PATH=$PYTHON/bin:$PATH | |
+ | |
+echo "`whoami`@`hostname`" | |
+echo "Start at `date`" | |
+ | |
+ORIGDIR=/home/adc/code/sphere | |
+#WORKDIR=/scratch/$PBS_JOBID | |
+WORKDIR=$ORIGDIR | |
+ | |
+#cp -r $ORIGDIR/* $WORKDIR | |
+ | |
+cd $WORKDIR | |
+nvidia-smi | |
+rm CMakeCache.txt | |
+cmake . && make | |
+cd python | |
+python diffusivity-starter.py 0 1.0 0.01 10.0e3 20.0e3 & | |
+python diffusivity-starter.py 1 1.0 0.01 40.0e3 60.0e3 & | |
+python diffusivity-starter.py 2 1.0 0.01 80.0e3 120.0e3 & | |
+wait | |
+ | |
+#cp $WORKDIR/output/* $ORIGDIR/output/ | |
+ | |
+echo "End at `date`" | |
diff --git a/python/diffusivity-c_grad_p=0.1.sh b/python/diffusivity-c_grad_p=0… | |
t@@ -0,0 +1,49 @@ | |
+#!/bin/sh | |
+#PBS -N diffusivity-c_grad_p=0.1 | |
+#PBS -l nodes=1:ppn=3 | |
+#PBS -l walltime=1920:00:00 | |
+#PBS -q qfermi | |
+#PBS -M [email protected] | |
+#PBS -m abe | |
+ | |
+# Grendel CUDA | |
+source /com/gcc/4.6.4/load.sh | |
+CUDAPATH=/com/cuda/5.5.22 | |
+export PATH=$HOME/bin:$PATH | |
+export PATH=$CUDAPATH/bin:$PATH | |
+export LD_LIBRARY_PATH=$CUDAPATH/lib64:$CUDAPATH/lib:$LD_LIBRARY_PATH | |
+ | |
+# Manually installed Python modules | |
+export PYTHONPATH=$HOME/.local/lib/python:$PYTHONPATH | |
+export PYTHONPATH=$HOME/.local/lib64/python:$PYTHONPATH | |
+ | |
+# Manually installed Python | |
+#export PATH=/home/adc/.local/bin:$PATH | |
+ | |
+# Shared Python2.7 | |
+PYTHON=/com/python/2.7.6 | |
+export PYTHONPATH=$PYTHON/lib:$PYTHONPATH | |
+export PATH=$PYTHON/bin:$PATH | |
+ | |
+echo "`whoami`@`hostname`" | |
+echo "Start at `date`" | |
+ | |
+ORIGDIR=/home/adc/code/sphere | |
+#WORKDIR=/scratch/$PBS_JOBID | |
+WORKDIR=$ORIGDIR | |
+ | |
+#cp -r $ORIGDIR/* $WORKDIR | |
+ | |
+cd $WORKDIR | |
+nvidia-smi | |
+rm CMakeCache.txt | |
+cmake . && make | |
+cd python | |
+python diffusivity-starter.py 0 1.0 0.1 10.0e3 20.0e3 & | |
+python diffusivity-starter.py 1 1.0 0.1 40.0e3 60.0e3 & | |
+python diffusivity-starter.py 2 1.0 0.1 80.0e3 120.0e3 & | |
+wait | |
+ | |
+#cp $WORKDIR/output/* $ORIGDIR/output/ | |
+ | |
+echo "End at `date`" | |
diff --git a/python/diffusivity-c_grad_p=0.5.sh b/python/diffusivity-c_grad_p=0… | |
t@@ -0,0 +1,49 @@ | |
+#!/bin/sh | |
+#PBS -N diffusivity-c_grad_p=0.5 | |
+#PBS -l nodes=1:ppn=3 | |
+#PBS -l walltime=1920:00:00 | |
+#PBS -q qfermi | |
+#PBS -M [email protected] | |
+#PBS -m abe | |
+ | |
+# Grendel CUDA | |
+source /com/gcc/4.6.4/load.sh | |
+CUDAPATH=/com/cuda/5.5.22 | |
+export PATH=$HOME/bin:$PATH | |
+export PATH=$CUDAPATH/bin:$PATH | |
+export LD_LIBRARY_PATH=$CUDAPATH/lib64:$CUDAPATH/lib:$LD_LIBRARY_PATH | |
+ | |
+# Manually installed Python modules | |
+export PYTHONPATH=$HOME/.local/lib/python:$PYTHONPATH | |
+export PYTHONPATH=$HOME/.local/lib64/python:$PYTHONPATH | |
+ | |
+# Manually installed Python | |
+#export PATH=/home/adc/.local/bin:$PATH | |
+ | |
+# Shared Python2.7 | |
+PYTHON=/com/python/2.7.6 | |
+export PYTHONPATH=$PYTHON/lib:$PYTHONPATH | |
+export PATH=$PYTHON/bin:$PATH | |
+ | |
+echo "`whoami`@`hostname`" | |
+echo "Start at `date`" | |
+ | |
+ORIGDIR=/home/adc/code/sphere | |
+#WORKDIR=/scratch/$PBS_JOBID | |
+WORKDIR=$ORIGDIR | |
+ | |
+#cp -r $ORIGDIR/* $WORKDIR | |
+ | |
+cd $WORKDIR | |
+nvidia-smi | |
+rm CMakeCache.txt | |
+cmake . && make | |
+cd python | |
+python diffusivity-starter.py 0 1.0 0.5 10.0e3 20.0e3 & | |
+python diffusivity-starter.py 1 1.0 0.5 40.0e3 60.0e3 & | |
+python diffusivity-starter.py 2 1.0 0.5 80.0e3 120.0e3 & | |
+wait | |
+ | |
+#cp $WORKDIR/output/* $ORIGDIR/output/ | |
+ | |
+echo "End at `date`" | |
diff --git a/python/diffusivity-c_phi=0.1.sh b/python/diffusivity-c_phi=0.1.sh | |
t@@ -0,0 +1,49 @@ | |
+#!/bin/sh | |
+#PBS -N diffusivity-c_phi=0.1 | |
+#PBS -l nodes=1:ppn=3 | |
+#PBS -l walltime=1920:00:00 | |
+#PBS -q qfermi | |
+#PBS -M [email protected] | |
+#PBS -m abe | |
+ | |
+# Grendel CUDA | |
+source /com/gcc/4.6.4/load.sh | |
+CUDAPATH=/com/cuda/5.5.22 | |
+export PATH=$HOME/bin:$PATH | |
+export PATH=$CUDAPATH/bin:$PATH | |
+export LD_LIBRARY_PATH=$CUDAPATH/lib64:$CUDAPATH/lib:$LD_LIBRARY_PATH | |
+ | |
+# Manually installed Python modules | |
+export PYTHONPATH=$HOME/.local/lib/python:$PYTHONPATH | |
+export PYTHONPATH=$HOME/.local/lib64/python:$PYTHONPATH | |
+ | |
+# Manually installed Python | |
+#export PATH=/home/adc/.local/bin:$PATH | |
+ | |
+# Shared Python2.7 | |
+PYTHON=/com/python/2.7.6 | |
+export PYTHONPATH=$PYTHON/lib:$PYTHONPATH | |
+export PATH=$PYTHON/bin:$PATH | |
+ | |
+echo "`whoami`@`hostname`" | |
+echo "Start at `date`" | |
+ | |
+ORIGDIR=/home/adc/code/sphere | |
+#WORKDIR=/scratch/$PBS_JOBID | |
+WORKDIR=$ORIGDIR | |
+ | |
+#cp -r $ORIGDIR/* $WORKDIR | |
+ | |
+cd $WORKDIR | |
+nvidia-smi | |
+rm CMakeCache.txt | |
+cmake . && make | |
+cd python | |
+python diffusivity-starter.py 0 0.1 1.0 10.0e3 20.0e3 & | |
+python diffusivity-starter.py 1 0.1 1.0 40.0e3 60.0e3 & | |
+python diffusivity-starter.py 2 0.1 1.0 80.0e3 120.0e3 & | |
+wait | |
+ | |
+#cp $WORKDIR/output/* $ORIGDIR/output/ | |
+ | |
+echo "End at `date`" | |
diff --git a/python/diffusivity-c_phi=0.5.sh b/python/diffusivity-c_phi=0.5.sh | |
t@@ -0,0 +1,49 @@ | |
+#!/bin/sh | |
+#PBS -N diffusivity-c_phi=0.5 | |
+#PBS -l nodes=1:ppn=3 | |
+#PBS -l walltime=1920:00:00 | |
+#PBS -q qfermi | |
+#PBS -M [email protected] | |
+#PBS -m abe | |
+ | |
+# Grendel CUDA | |
+source /com/gcc/4.6.4/load.sh | |
+CUDAPATH=/com/cuda/5.5.22 | |
+export PATH=$HOME/bin:$PATH | |
+export PATH=$CUDAPATH/bin:$PATH | |
+export LD_LIBRARY_PATH=$CUDAPATH/lib64:$CUDAPATH/lib:$LD_LIBRARY_PATH | |
+ | |
+# Manually installed Python modules | |
+export PYTHONPATH=$HOME/.local/lib/python:$PYTHONPATH | |
+export PYTHONPATH=$HOME/.local/lib64/python:$PYTHONPATH | |
+ | |
+# Manually installed Python | |
+#export PATH=/home/adc/.local/bin:$PATH | |
+ | |
+# Shared Python2.7 | |
+PYTHON=/com/python/2.7.6 | |
+export PYTHONPATH=$PYTHON/lib:$PYTHONPATH | |
+export PATH=$PYTHON/bin:$PATH | |
+ | |
+echo "`whoami`@`hostname`" | |
+echo "Start at `date`" | |
+ | |
+ORIGDIR=/home/adc/code/sphere | |
+#WORKDIR=/scratch/$PBS_JOBID | |
+WORKDIR=$ORIGDIR | |
+ | |
+#cp -r $ORIGDIR/* $WORKDIR | |
+ | |
+cd $WORKDIR | |
+nvidia-smi | |
+rm CMakeCache.txt | |
+cmake . && make | |
+cd python | |
+python diffusivity-starter.py 0 0.5 1.0 10.0e3 20.0e3 & | |
+python diffusivity-starter.py 1 0.5 1.0 40.0e3 60.0e3 & | |
+python diffusivity-starter.py 2 0.5 1.0 80.0e3 120.0e3 & | |
+wait | |
+ | |
+#cp $WORKDIR/output/* $ORIGDIR/output/ | |
+ | |
+echo "End at `date`" | |
diff --git a/python/diffusivity-starter.py b/python/diffusivity-starter.py | |
t@@ -0,0 +1,53 @@ | |
+#!/usr/bin/env python | |
+import sphere | |
+import numpy | |
+import sys | |
+ | |
+# launch with: | |
+# $ python diffusivity-starter <DEVICE> <C_PHI> <C_GRAD_P> <DP_1, DP_2, ...> | |
+ | |
+for sigma0_str in sys.argv[4:]: | |
+ | |
+ sigma0 = float(sigma0_str) | |
+ device = int(sys.argv[1]) | |
+ c_phi = float(sys.argv[2]) | |
+ c_grad_p = float(sys.argv[3]) | |
+ | |
+ sim = sphere.sim('diffusivity-relax') | |
+ sim.readlast() | |
+ | |
+ sim.sid = 'permeability-dp=' + str(dp) + '-c_phi=' + str(c_phi) + \ | |
+ '-c_grad_p=' + str(c_grad_p) | |
+ print(sim.sid) | |
+ | |
+ # Checkerboard colors | |
+ x_min = numpy.min(sim.x[:,0]) | |
+ x_max = numpy.max(sim.x[:,0]) | |
+ y_min = numpy.min(sim.x[:,1]) | |
+ y_max = numpy.max(sim.x[:,1]) | |
+ z_min = numpy.min(sim.x[:,2]) | |
+ z_max = numpy.max(sim.x[:,2]) | |
+ color_nx = 6 | |
+ color_ny = 6 | |
+ color_nz = 6 | |
+ for i in range(sim.np): | |
+ ix = numpy.floor((sim.x[i,0] - x_min)/(x_max/color_nx)) | |
+ iy = numpy.floor((sim.x[i,1] - y_min)/(y_max/color_ny)) | |
+ iz = numpy.floor((sim.x[i,2] - z_min)/(z_max/color_nz)) | |
+ sim.color[i] = (-1)**ix + (-1)**iy + (-1)**iz | |
+ | |
+ sim.cleanup() | |
+ sim.adjustUpperWall() | |
+ sim.zeroKinematics() | |
+ sim.consolidate(normal_stress = 10.0e3) | |
+ sim.initFluid(mu = 17.87e-4, p = 1.0e5, hydrostatic = True) | |
+ sim.setFluidBottomNoFlow() | |
+ sim.setFluidTopFixedPressure() | |
+ sim.setDEMstepsPerCFDstep(10) | |
+ sim.setMaxIterations(2e5) | |
+ sim.initTemporal(total = 5.0, file_dt = 0.01, epsilon=0.07) | |
+ sim.run(dry=True) | |
+ sim.run(device=0) | |
+ #sim.writeVTKall() | |
+ sim.visualize('walls') | |
+ sim.visualize('fluid-pressure') |