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	tdo not generate separate binary for porous flow, add exclusive mode flag - sph…
	git clone git://src.adamsgaard.dk/sphere
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	---
	commit 7310210eeea7eaea39afad0b6642866a417ef323
	parent 7e9994c85ea1f10fc5040bb9d7d628bc5b4cc133
	Author: Anders Damsgaard <[email protected]>
	Date: Mon, 28 Jul 2014 09:58:07 +0200

	do not generate separate binary for porous flow, add exclusive mode flag

	Diffstat:
	M python/sphere.py \| 4 ++--
	M src/CMakeLists.txt \| 2 --
	M src/device.cu \| 11 ++++++-----
	M src/main.cpp \| 13 +++++++++++--
	D src/porousflow.cpp \| 83 -----------------------------…
	M src/sphere.cpp \| 15 ++++++++-------
	M src/sphere.h \| 4 +++-

	7 files changed, 30 insertions(+), 102 deletions(-)
	---
	diff --git a/python/sphere.py b/python/sphere.py
	t@@ -3103,10 +3103,10 @@ class sim:
	if (cudamemcheck == True):
	cudamemchk = "cuda-memcheck --leak-check full "
	if (self.fluid == True):
	- binary = "porousflow"
	+ fluidarg = "--fluid "

	cmd = "cd ..; " + valgrindbin + cudamemchk + "./" + binary + " " \
	- + quiet + dryarg + "input/" + self.sid + ".bin " + stdout
	+ + quiet + dryarg + fluidarg + "input/" + self.sid + ".bin " + …
	#print(cmd)
	status = subprocess.call(cmd, shell=True)

	diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
	t@@ -30,8 +30,6 @@ CUDA_ADD_EXECUTABLE(../porosity
	CUDA_ADD_EXECUTABLE(../forcechains
	forcechains.cpp file_io.cpp sphere.cpp device.cu utility.cu utility.cpp
	navierstokes.cpp)
	-CUDA_ADD_EXECUTABLE(../porousflow
	- porousflow.cpp navierstokes.cpp file_io.cpp sphere.cpp device.cu utility.c…

	#ADD_EXECUTABLE(unittests boost-unit-tests.cpp sphere.cpp)
	#TARGET_LINK_LIBRARIES(unittests
	diff --git a/src/device.cu b/src/device.cu
	t@@ -109,12 +109,13 @@ __host__ void DEM::initializeGPU(void)
	}

	device = cudadevice; // store in DEM class
	- cout << " Using CUDA device ID " << cudadevice << " with "
	- << max_ncudacores << " cores." << std::endl;

	- // Comment following line when using a system only containing
	- // exclusive mode GPUs
	- cudaChooseDevice(&cudadevice, &prop);
	+ // Only call cudaChooseDevice if the exlusive mode flag isn't set
	+ if (exclusive_mode != 1) {
	+ cout << " Using CUDA device ID " << cudadevice << " with "
	+ << max_ncudacores << " cores." << std::endl;
	+ cudaChooseDevice(&cudadevice, &prop);
	+ }

	checkForCudaErrors("While initializing CUDA device");
	}
	diff --git a/src/main.cpp b/src/main.cpp
	t@@ -36,6 +36,8 @@ int main(const int argc, const char *argv[])
	int nfiles = 0; // number of input files
	float max_val = 0.0f; // max value of colorbar
	float lower_cutoff = 0.0f;// lower cutoff, particles below won't be render…
	+ int fluid = 0;
	+ int exclusive_mode = 0; // system GPUs are running on exclusive mode

	// Process input parameters
	int i;
	t@@ -54,6 +56,7 @@ int main(const int argc, const char *argv[])
	"-e, --exclusive\t\tset this flag for systems containing\n"
	" \t\tonly exclusive-mode GPUs\n"
	"-n, --dry\t\tshow key experiment parameters and quit\n"
	+ "-f, --fluid\t\tsimulate fluid between particles\n"
	"-r, --render\t\trender input files to images instead of\n"
	" \t\tsimulating the temporal evolution\n"
	"-dc, --dont-check\tdon't check values before running\n"
	t@@ -101,6 +104,12 @@ int main(const int argc, const char *argv[])
	else if (argvi == "-dc" \|\| argvi == "--dont-check")
	checkVals = 0;

	+ else if (argvi == "-f" \|\| argvi == "--fluid")
	+ fluid = 1;
	+
	+ else if (argvi == "-e" \|\| argvi == "--exclusive")
	+ exlusive_mode = 1;
	+
	else if (argvi == "-m" \|\| argvi == "--method") {

	render = 1;
	t@@ -153,7 +162,7 @@ int main(const int argc, const char *argv[])

	// Create DEM class, read data from input binary, check values,
	// init cuda, transfer const mem
	- DEM dem(argvi, verbose, checkVals, dry, 1, 1);
	+ DEM dem(argvi, verbose, checkVals, dry, 1, 1, fluid, exclusive…
	// Render image if requested
	if (render == 1)
	dem.render(method, max_val, lower_cutoff);
	t@@ -165,7 +174,7 @@ int main(const int argc, const char *argv[])
	} else {

	// Do not transfer to const. mem after the first file
	- DEM dem(argvi, verbose, checkVals, dry, 1, 0);
	+ DEM dem(argvi, verbose, checkVals, dry, 1, 0, fluid, exclusive…

	// Render image if requested
	if (render == 1)
	diff --git a/src/porousflow.cpp b/src/porousflow.cpp
	t@@ -1,83 +0,0 @@
	-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
	-/* SPHERE source code by Anders Damsgaard Christensen, 2010-12, */
	-/* a 3D Discrete Element Method algorithm with CUDA GPU acceleration. */
	-/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
	-
	-// Licence: GNU Public License (GPL) v. 3. See license.txt.
	-// See doc/sphere-doc.pdf for full documentation.
	-// Compile with GNU make by typing 'make' in the src/ directory.
	-// SPHERE is called from the command line with './sphere_<architecture> projec…
	-
	-
	-// Including library files
	-#include <iostream>
	-#include <string>
	-#include <cstdlib>
	-
	-// Including user files
	-#include "constants.h"
	-#include "datatypes.h"
	-#include "sphere.h"
	-
	-//////////////////
	-// MAIN ROUTINE //
	-//////////////////
	-// The main loop returns the value 0 to the shell, if the program terminated
	-// successfully, and 1 if an error occured which caused the program to crash.
	-int main(const int argc, const char *argv[])
	-{
	- // Default values
	- int verbose = 1;
	- int dry = 0;
	- int nfiles = 0;
	- int darcy = 1;
	-
	- // Process input parameters
	- int i;
	- for (i=1; i<argc; ++i) { // skip argv[0]
	-
	- std::string argvi = std::string(argv[i]);
	-
	- // Display help if requested
	- if (argvi == "-h" \|\| argvi == "--help") {
	- std::cout << argv[0] << ": particle dynamics simulator\n"
	- << "Usage: " << argv[0] << " [OPTION[S]]... [FILE1 ...]\nOptio…
	- << "-h, --help\t\tprint help\n"
	- << "-n, --dry\t\tshow key experiment parameters and quit\n"
	- << std::endl;
	- return 0; // Exit with success
	- }
	-
	- else if (argvi == "-n" \|\| argvi == "--dry")
	- dry = 1;
	-
	- else if (argvi == "-q" \|\| argvi == "--quiet")
	- verbose = 0;
	-
	- // The rest of the values must be input binary files
	- else {
	- nfiles++;
	-
	- if (verbose == 1)
	- std::cout << argv[0] << ": processing input file: " << argvi <<
	- std::endl;
	-
	- // Create DEM class, read data from input binary,
	- // check values, init cuda, transfer const mem, solve Darcy flow
	- DEM dem(argvi, verbose, 1, dry, 1, 1, darcy);
	- if (dry == 0)
	- dem.startTime();
	- }
	- }
	-
	- // Check whether there are input files specified
	- if (!argv[0] \|\| argc == 1 \|\| nfiles == 0) {
	- std::cerr << argv[0] << ": missing input binary file\n"
	- << "See `" << argv[0] << " --help` for more information"
	- << std::endl;
	- return 1; // Return unsuccessful exit status
	- }
	-
	- return 0; // Return successfull exit status
	-}
	-// vim: tabstop=8 expandtab shiftwidth=4 softtabstop=4
	diff --git a/src/sphere.cpp b/src/sphere.cpp
	t@@ -14,13 +14,14 @@
	// Constructor: Reads an input binary, and optionally checks
	// and reports the values
	DEM::DEM(const std::string inputbin,
	- const int verbosity,
	- const int checkVals,
	- const int dry,
	- const int initCuda,
	- const int transferConstMem,
	- const int porousflow)
	-: verbose(verbosity), navierstokes(porousflow)
	+ const int verbosity,
	+ const int checkVals,
	+ const int dry,
	+ const int initCuda,
	+ const int transferConstMem,
	+ const int fluidFlow,
	+ const int exlusive)
	+: verbose(verbosity), navierstokes(fluidFlow), exlusive_mode(exlusive)
	{
	using std::cout;
	using std::cerr;
	diff --git a/src/sphere.h b/src/sphere.h
	t@@ -57,6 +57,7 @@ class DEM {
	int ndevices; // number of CUDA GPUs
	int device; // primary GPU
	int* domain_size; // elements per GPU
	+ int exlusive_mode; // devices are running in exclusive mode (1)


	// DEVICE ARRAYS
	t@@ -296,7 +297,8 @@ class DEM {
	const int dry = 0,
	const int initCuda = 1,
	const int transferConstMem = 1,
	- const int darcyflow = 0);
	+ const int fluidFlow = 0,
	+ const int exclusive = 0);

	// Destructor
	~DEM(void);