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Initial MinGW compatibility updates #321

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Merged
BryanRumsey merged 2 commits into from
Oct 5, 2022
Merged

Initial MinGW compatibility updates #321

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52b292d
Initial MinGW compatibility updates
jtcooper10 Aug 28, 2022
e03ca98
Fix MinGW make executable name
jtcooper10 Aug 29, 2022
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5 changes: 4 additions & 1 deletion spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/model.c
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,10 @@ Based on a Matlab program by Bruno Jacob (UCSB)
This program is distributed under the terms of the GNU GENERAL PUBLIC LICENSE Version 3.
See the file LICENSE.txt for details.
***************************************************************************************** */
#include <math.h>
#if defined(WIN32) || defined(_WIN32) || defined(__MINGW32__)
#define _USE_MATH_DEFINES
#endif
#include <cmath>
#include <stdio.h>
#include <stdlib.h>

Expand Down
21 changes: 12 additions & 9 deletions spatialpy/solvers/c_base/ssa_sdpd-c-simulation-engine/src/particle.cpp
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Expand Up @@ -26,7 +26,10 @@ See the file LICENSE.txt for details.

#include <stdlib.h>
#include <stdio.h>
#include <math.h>
#if defined(WIN32) || defined(_WIN32) || defined(__MINGW32__)
#define _USE_MATH_DEFINES
#endif
#include <cmath>
#include <cstdlib>
#include <vector>
#include <queue>
Expand Down Expand Up @@ -84,13 +87,13 @@ namespace Spatialpy{

void Particle::check_particle_nan(){
if(
isnan(x[0]) || !isfinite(x[0]) ||
isnan(x[1]) || !isfinite(x[1]) ||
isnan(x[2]) || !isfinite(x[2]) ||
isnan(v[0]) || !isfinite(v[0]) ||
isnan(v[1]) || !isfinite(v[1]) ||
isnan(v[2]) || !isfinite(v[2]) ||
isnan(rho) || !isfinite(rho) ){
std::isnan(x[0]) || !std::isfinite(x[0]) ||
std::isnan(x[1]) || !std::isfinite(x[1]) ||
std::isnan(x[2]) || !std::isfinite(x[2]) ||
std::isnan(v[0]) || !std::isfinite(v[0]) ||
std::isnan(v[1]) || !std::isfinite(v[1]) ||
std::isnan(v[2]) || !std::isfinite(v[2]) ||
std::isnan(rho) || !std::isfinite(rho) ){
printf("ERROR: nan/inf detected!!!\n");
printf("number of neighbors: %li\n", neighbors.size()) ;
printf("id=%i\n",id);
Expand Down Expand Up @@ -183,7 +186,7 @@ namespace Spatialpy{
// Eq 28 of Drawert et al 2019, Tartakovsky et. al., 2007, JCP
double D_i_j = -2.0*(mass*neighbor->mass)/(mass+neighbor->mass)*(rho+neighbor->rho)/(rho*neighbor->rho) * r2 * wfd / (r2+0.01*h*h);

if(isnan(D_i_j)){
if(std::isnan(D_i_j)){
printf("Got NaN calculating D_i_j for me=%i, neighbor=%i\n",id, neighbor->id);
printf("system->dimension=%i ",system->dimension);
printf("r2=%e ",r2);
Expand Down
67 changes: 38 additions & 29 deletions spatialpy/solvers/solver.py
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Expand Up @@ -470,41 +470,50 @@ def compile(self, debug=False, profile=False):
self.__create_propensity_file(stoich_matrix, dep_graph, file_name=self.prop_file_name)

# Build the solver
for make_exe_location in ["make", "mingw32-make"]:
make_exe = shutil.which("make")
if make_exe is not None:
break
if make_exe is None:
raise SimulationError("Make executable could not be found")
makefile = self.spatialpy_rootdir+'/build/Makefile'
makefile_ann = self.spatialpy_rootdir+'/external/ANN/src/Makefile.spatialpy'
cmd_list = ['cd', self.core_dir, '&&',
'make', '-f' , makefile_ann,
'ROOTINC="' + self.spatialpy_rootinc+'"',
'&&',
'make', 'CORE', '-f', makefile,
'ROOT="' + self.spatialpy_rootparam+'"',
'ROOTINC="' + self.spatialpy_rootinc+'"',
'BUILD='+self.core_dir, '&&'
'cd', self.build_dir, '&&', 'make', '-I', self.core_dir, '-f', makefile,
'ROOT="' + self.spatialpy_rootparam+'"',
'ROOTINC="' + self.spatialpy_rootinc+'"',
'COREDIR="' + self.core_dir + '"',
'MODEL=' + self.prop_file_name, 'BUILD='+self.build_dir]

cmd_ann = [
make_exe, '-d', '-C', self.core_dir, '-f', makefile_ann,
f'ROOTINC={self.spatialpy_rootinc}',
]
cmd_core = [
make_exe, '-d', '-C', self.core_dir, 'CORE', '-f', makefile,
f'ROOT={self.spatialpy_rootparam}',
f'ROOTINC={self.spatialpy_rootinc}',
f'BUILD={self.core_dir}',
]
cmd_build = [
make_exe, '-d', '-C', self.build_dir, '-I', self.core_dir, '-f', makefile,
'ROOT=' + self.spatialpy_rootparam,
'ROOTINC=' + self.spatialpy_rootinc,
'COREDIR=' + self.core_dir,
'MODEL=' + self.prop_file_name, 'BUILD='+self.build_dir
]
if profile:
cmd_list.append('GPROFFLAG=-pg')
cmd_build.append('GPROFFLAG=-pg')
if profile or debug:
cmd_list.append('GDB_FLAG=-g')
cmd = " ".join(cmd_list)
cmd_build.append('GDB_FLAG=-g')
if self.debug_level > 1:
cmd = " && ".join([*cmd_ann, *cmd_core, *cmd_build])
print(f"cmd: {cmd}\n")
try:
with subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, shell=True) as handle:
stdout, _ = handle.communicate()
return_code = handle.wait()
if return_code != 0:
try:
print(stdout.decode("utf-8"))
except Exception:
pass
raise SimulationError(f"Compilation of solver failed, return_code={return_code}")

for cmd_target in [cmd_ann, cmd_core, cmd_build]:
result = subprocess.check_output(cmd_target, stderr=subprocess.STDOUT)
if self.debug_level > 1:
print(stdout.decode("utf-8"))
print(result.stdout.decode("utf-8"))
except subprocess.CalledProcessError as err:
try:
print(err.stdout.decode("utf-8"))
except Exception:
pass
raise SimulationError(f"Compilation of solver failed, return_code={result.return_code}")
except OSError as err:
print(f"Error, execution of compilation raised an exception: {err}")
print(f"cmd = {cmd}")
Expand Down Expand Up @@ -559,7 +568,7 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None,
result = Result(self.model, outfile)
if self.debug_level >= 1:
print(f"Running simulation. Result dir: {outfile}")
solver_cmd = f'cd {outfile};{os.path.join(self.build_dir, self.executable_name)}'
solver_cmd = os.path.join(self.build_dir, self.executable_name)

if number_of_threads is not None:
solver_cmd += " -t " + str(number_of_threads)
Expand All @@ -573,7 +582,7 @@ def run(self, number_of_trajectories=1, seed=None, timeout=None,
start = time.monotonic()
return_code = None
try:
with subprocess.Popen(solver_cmd, shell=True,
with subprocess.Popen(solver_cmd, cwd=outfile, shell=True,
stdout=subprocess.PIPE, stderr=subprocess.STDOUT,
start_new_session=True) as process:
try:
Expand Down