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Update libroadrunner setup #406

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9bb3ec4
fix for new .zip bundles
rheiland Feb 8, 2026
0953f6c
fix header path
rheiland Feb 8, 2026
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89 changes: 25 additions & 64 deletions beta/setup_libroadrunner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@
import urllib.request
import os
import sys
import tarfile
import zipfile

def reminder_dynamic_link_path_macos():
Expand All @@ -27,15 +26,12 @@ def reminder_dynamic_link_path_linux():
print("\n* To make this permanent, add this line to the bottom of the respective shell startup file, e.g., .bashrc, .bash_profile, or .zshenv in your home directory.")
print("\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\n")

os_type = platform.system()

# Old:
# if os.path.exists(os.path.join(os.path.dirname(os.path.dirname(__file__)), "addons", "libRoadrunner", "roadrunner")):
os_type = platform.system() # can test that it downloads correct OS .zip by overriding this value

# New: July 2023 - trying to be smarter about deciding whether to (re)download libRR
# NOTE: needs to be tested cross-platform!
if os.path.exists(os.path.join(os.path.dirname(os.path.dirname(__file__)), "addons", "libRoadrunner", "roadrunner","include","rr","C","rrc_api.h")):
print('\nlibroadrunner already installed.\n')
if os.path.exists(os.path.join(os.path.dirname(os.path.dirname(__file__)), "addons", "libRoadrunner", "roadrunner","include","rr","rrc_api.h")):
print('\nNote: libroadrunner is already installed so we will not re-install it. \nIf you want to force a re-install, delete the "roadrunner" directory in /addons/libRoadrunner then re-compile.\n')

# regardless, let's remind the user about the env var requirement!
if os_type.lower() == 'darwin':
Expand All @@ -55,38 +51,30 @@ def reminder_dynamic_link_path_linux():
if os_type.lower() == 'darwin':
reminder_dynamic_link_path_macos()
if "ARM64" in platform.uname().version:
# pass
# print('... for the arm64 processor.')
# url = "https://github.com/PhysiCell-Tools/intracellular_libs/raw/main/ode/libs/macos12_arm64/libroadrunner_c_api.dylib"
rr_file = "roadrunner_macos_arm64.tar.gz"
url = "https://github.com/PhysiCell-Tools/intracellular_libs/raw/main/ode/roadrunner_macos_arm64.tar.gz"
rr_file = "roadrunner_macos_arm64.zip"
url = "https://github.com/PhysiCell-Tools/intracellular_libs/raw/main/ode/roadrunner_macos_arm64.zip"
mac_silicon = True
else:
rr_file = "roadrunner-osx-10.9-cp36m.tar.gz"
url = "https://sourceforge.net/projects/libroadrunner/files/libroadrunner-1.4.18/" + rr_file + "/download"
rr_file = "roadrunner_macos_x86_64.zip"
url = "https://github.com/PhysiCell-Tools/intracellular_libs/raw/main/ode/roadrunner_macos_x86_64.zip"
elif os_type.lower().startswith("win"):
rr_file = "roadrunner-win64-vs14-cp35m.zip"
url = "https://sourceforge.net/projects/libroadrunner/files/libroadrunner-1.4.18/" + rr_file + "/download"
rr_file = "roadrunner_win_x86_64.zip"
url = "https://github.com/PhysiCell-Tools/intracellular_libs/raw/main/ode/roadrunner_win_x86_64.zip"
elif os_type.lower().startswith("linux"):
reminder_dynamic_link_path_linux()
rr_file = "cpplibroadrunner-1.3.0-linux_x86_64.tar.gz"
url = "https://sourceforge.net/projects/libroadrunner/files/libroadrunner-1.3/" + rr_file + "/download"
rr_file = "roadrunner_ubuntu_24.zip"
url = "https://github.com/PhysiCell-Tools/intracellular_libs/raw/main/ode/roadrunner_ubuntu_24.zip"
else:
print("Your operating system seems to be unsupported. Please submit a ticket at https://sourceforge.net/p/physicell/tickets/ ")
sys.exit(1)

print("url=",url)
if mac_silicon:
fname = url.split('/')[-1]
else:
fname = url.split('/')[-2]
fname = url.split('/')[-1]
print("fname=",fname)

# home = os.path.expanduser("~")
print('libRoadRunner will now be installed into this location:')
# dir_name = os.path.join(home, 'libroadrunner')
dir_name = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'addons', 'libRoadrunner')
print(dir_name + '\n')
print(f'Will create {dir_name} if it does not exist.')
# print(' - Press ENTER to confirm the location')
# print(' - Press CTL-C to abort the installation')
# print(' - Or specify a different location below\n')
Expand Down Expand Up @@ -121,17 +109,8 @@ def reminder_dynamic_link_path_linux():
my_file = os.path.join(dir_name, fname)
print('my_file = ',my_file)

if os_type.lower().startswith("win"):
rrlib_dir = my_file[:-4]
else: # darwin or linux
if mac_silicon:
# idx_end = my_file.rindex('/')
# rrlib_dir = my_file[:idx_end]
rrlib_dir = my_file[:-7]
# rrlib_dir = my_file
else:
rrlib_dir = my_file[:-7]
print('rrlib_dir = ',rrlib_dir)
# rrlib_dir = my_file[:-4] # assume all are .zip
# print('rrlib_dir = ',rrlib_dir)

def download_cb(blocknum, blocksize, totalsize):
readsofar = blocknum * blocksize
Expand All @@ -148,36 +127,18 @@ def download_cb(blocknum, blocksize, totalsize):
urllib.request.urlretrieve(url, my_file, download_cb)

new_dir_name = "roadrunner"
print(f"chdir to {dir_name}")
os.chdir(dir_name)
print('installing (uncompressing) the file...')
if os_type.lower().startswith("win"):
try:
with zipfile.ZipFile(rr_file) as zf:
zf.extractall('.')
os.rename("roadrunner-win64-vs14-cp35m", new_dir_name)
except:
print('error unzipping the file')
exit(1)
else: # Darwin or Linux
try:
print("untarring ",rr_file)
tar = tarfile.open(rr_file)
tar.extractall()
tar.close()
if 'darwin' in os_type.lower():
if mac_silicon:
os.rename("roadrunner_macos_arm64", new_dir_name)
else:
os.rename("roadrunner-osx-10.9-cp36m", new_dir_name)
else:
os.rename("libroadrunner", new_dir_name)
except:
if mac_silicon:
print()
# pass
else:
print('error untarring the file')
exit(1)
try:
with zipfile.ZipFile(rr_file) as zf:
zf.extractall('.') # should create "roadrunner" directory
# rr_dir = rr_file[:-4]
# print(f'renaming dir: {rr_dir} to {new_dir_name}')
# os.rename(rr_dir, new_dir_name)
except:
print('error unzipping the file')
exit(1)

print('Done.\n')

Expand Down
12 changes: 4 additions & 8 deletions sample_projects_intracellular/ode/ode_energy/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -17,12 +17,8 @@ OSFLAG :=
ifeq ($(OS),Windows_NT)
OSFLAG += -D WIN32
OMP_LIB :=
# LIBRR_DIR := C:\Users\heiland\libroadrunner\roadrunner-win64-vs14-cp35m
# LIBRR_LIBS := C:\Users\heiland\libroadrunner\roadrunner-win64-vs14-cp35m/bin
# LIBRR_CFLAGS := -I${LIBRR_DIR}/include/rr/C
# CFLAGS := -march=$(ARCH) -fomit-frame-pointer -fopenmp -m64 -std=c++11 -D ADDON_ROADRUNNER
LIBRR_DIR := .\addons\libRoadrunner\roadrunner
LIBRR_CFLAGS := -I${LIBRR_DIR}\include\rr\C
LIBRR_CFLAGS := -I${LIBRR_DIR}\include\rr
LIBRR_LIBS := ${LIBRR_DIR}\lib
ifeq ($(PROCESSOR_ARCHITECTURE),AMD64)
OSFLAG += -D AMD64
Expand All @@ -37,13 +33,13 @@ else
OMP_LIB :=
# LIBRR_DIR := $(shell pwd)/intracellular_libs/roadrunner
LIBRR_DIR := ./addons/libRoadrunner/roadrunner
LIBRR_CFLAGS := -I${LIBRR_DIR}/include/rr/C
LIBRR_CFLAGS := -I${LIBRR_DIR}/include/rr
LIBRR_LIBS := ${LIBRR_DIR}/lib
endif
ifeq ($(UNAME_S),Darwin)
OSFLAG += -D OSX
LIBRR_DIR := ./addons/libRoadrunner/roadrunner
LIBRR_CFLAGS := -I${LIBRR_DIR}/include/rr/C
LIBRR_CFLAGS := -I${LIBRR_DIR}/include/rr
LIBRR_LIBS := ${LIBRR_DIR}/lib
endif

Expand All @@ -52,7 +48,7 @@ else
# ifeq ($(UNAME_P),x86_64)
# OSFLAG += -D AMD64
# LIBRR_DIR := $(shell pwd)/intracellular_libs/roadrunner
# LIBRR_CFLAGS := -I${LIBRR_DIR}/include/rr/C
# LIBRR_CFLAGS := -I${LIBRR_DIR}/include/rr
# # CFLAGS := -march=$(ARCH) -fomit-frame-pointer -fopenmp -m64 -std=c++11 -D LIBROADRUNNER
# CFLAGS := -march=$(ARCH) -fomit-frame-pointer -fopenmp -m64 -std=c++11 -D ADDON_ROADRUNNER
# endif
Expand Down
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