def compile_matlab_script(original_script_name, list_of_lines_to_add, mulitcore_matlab=False, queue_run=False, debug= False, custom_folders_to_compile= []):
############
# create temp matlab script file
temp_dir = tempfile.mkdtemp( prefix=os.path.abspath("./")+"/tmp_")
###################
# Import custom pathdefenitions if available
try: shutil.copy("./pathdef.m", temp_dir+"/pathdef.m")
except: pass
original_script_name = os.path.abspath(original_script_name)
with restore_curr_dir():
os.chdir(temp_dir)
#print os.getcwd()
add_path_track, known_functions = find_all_scripts_paths(original_script_name, [x.strip("addpath('").strip("')") for x in list_of_lines_to_add], set([original_script_name]))
#add_path_track, known_functions = find_all_scripts_paths(original_script_name, [], set([original_script_name]))
#print "\n\n",known_functions
#sys.exit(1)
for each_function in known_functions:
copyedit_script_for_compiling(each_function)
fh_temp = tempfile.NamedTemporaryFile("w", prefix=os.path.abspath("./")+"/tmp_", suffix=".m", delete=False)
#list_of_lines_to_add.append("cd('%s')" % os.path.split(original_script_name)[0])
list_of_lines_to_add.append("addpath('/net/isi-backup/restricted/face/matlab_mydepfun/')")
list_of_lines_to_add.append("file_list = mydepfun('%s', true)" % os.path.split(original_script_name)[1])
#list_of_lines_to_add.append("cd('%s')" % temp_dir)
ENUMERATE_TOOLBOXES = [
"[temporary_files_variable, toolbox_folders] = dependencies.toolboxDependencyAnalysis({%s})" % ", ".join(["'" + os.path.split(x)[-1][:-2] + "'" for x in known_functions if x[-2:]==".m"]),
"mytoolboxList = cell(1,numel(toolbox_folders)*2);",
"cmp = 0;\n",
"for i=1:numel(toolbox_folders)",
"cmp = cmp +1;",
"if strcmp('general', toolbox_folders{i})",
"if numel(toolbox_folders) == 1",
"mytoolboxList = {'-p','matlab'};",
"end",
"else",
"mytoolboxList{cmp} = '-p';",
"cmp = cmp +1;",
"mytoolboxList{cmp} = toolbox_folders{i};",
"end",
"end",
]
list_of_lines_to_add.append("\n".join(ENUMERATE_TOOLBOXES)+"\n")
##############################
# Adding the possibility to compile entire folder structures into the code
add_in_folders_for_compile = [
"".join(["custom_folders_to_compile = {"]+ ["'"+x+"'," for x in custom_folders_to_compile] +["};"]),
"compile_folders = cell(1,numel(custom_folders_to_compile)*2);",
"cmp = 0;",
"for i=1:numel(custom_folders_to_compile)",
"cmp = cmp +1;,",
"compile_folders{cmp} = '-a';",
"cmp = cmp +1;",
"compile_folders{cmp} = custom_folders_to_compile{i};",
"end",
]
list_of_lines_to_add.append("\n".join(add_in_folders_for_compile)+"\n")
###################
# Major change in mcc command -N removes all knowledge of paths. NO TOOLBOXES
###################
#MCC_string = "mcc( '-m', '-N', '-v', '-R', '-nosplash', '-R', '-nodisplay', '-R', '-nojvm', "
MCC_string = "mcc( '-m', '-N', mytoolboxList{1:numel(mytoolboxList)}, compile_folders{1:numel(compile_folders)},'-v', '-R', '-nosplash', '-R', '-nodisplay', '-R', '-nojvm', "
if not mulitcore_matlab: MCC_string = MCC_string + "'-R', '-singleCompThread', "
MCC_string = MCC_string + "'%s', file_list{1:numel(file_list)-1})" % os.path.split(original_script_name)[1]
list_of_lines_to_add.append(MCC_string)
list_of_lines_to_add.append("exit")
fh_temp.write(";\n".join(list_of_lines_to_add)+";\n")
temp_name = fh_temp.name
fh_temp.close()
#if debug:
# print "\n\n\n\n\n", temp_name, "\n\n\n\n\n"
# sys.exit(1)
############
# prepare run_cmd
fgu217_queue = 'nice -19 qrsh -cwd -q fgu217.q -v BASH_ENV="~/.bashrc" -now n'
matlab_run_cmd = '/net/isi-software/tools/matlab2011b/bin/matlab -nosplash -nodisplay' # -nojvm'
single_core = '-singleCompThread'
curr_script_to_run = '-r "%s; exit"' % (os.path.split(fh_temp.name)[1][:-2])
curr_run_str_list = []
if queue_run: curr_run_str_list.append(fgu217_queue)
curr_run_str_list.append(matlab_run_cmd)
if not mulitcore_matlab: curr_run_str_list.append(single_core)
curr_run_str_list.append(curr_script_to_run)
curr_run_cmd = " ".join(curr_run_str_list)
############
# run the script
#print curr_run_cmd
#sys.exit(1)
run_cmd(curr_run_cmd, "running matlab scripts")
#
if debug:
print "\n\n\n\n\n", "./"+os.path.split(original_script_name)[1][:-len(".m")]
print original_script_name[:-len(".m")]
print "\n\n",
print "./run_"+os.path.split(original_script_name)[1][:-len(".m")]+".sh"
print os.path.split(original_script_name)[0]+"/run_"+os.path.split(original_script_name)[1][:-len(".m")]+".sh"
print "\n\n\n\n\n"
sys.exit(1)
#sys.exit(1)
os.rename("./"+os.path.split(original_script_name)[1][:-len(".m")], original_script_name[:-len(".m")])
os.rename("./run_"+os.path.split(original_script_name)[1][:-len(".m")]+".sh", os.path.split(original_script_name)[0]+"/run_"+os.path.split(original_script_name)[1][:-len(".m")]+".sh")
############
# cleanup
os.unlink(temp_name)
os.unlink("./mccExcludedFiles.log")
os.unlink("./readme.txt")
for each_function in known_functions:
#print "./"+os.path.split(each_function)[1]
try: os.unlink("./"+os.path.split(each_function)[1])
except: pass
try: os.unlink("./pathdef.m")
except:pass
os.rmdir(temp_dir)
def run_matlab_script_compiled(original_script_name, list_of_variables, list_of_non_symlink_var = [], mulitcore_matlab=False, queue_run=True, cluster_run=True, debug= False, ):
TEMPORARY_FOLDER_FOLDER = "temp_run_folders/"
try: os.mkdir(TEMPORARY_FOLDER_FOLDER)
except: assert os.path.exists(TEMPORARY_FOLDER_FOLDER)
############
# create temp matlab script file
temp_dir = tempfile.mkdtemp( prefix=os.path.abspath("./"+TEMPORARY_FOLDER_FOLDER)+"/tmp_")
symlink_names = []
for curr_var in list_of_variables:
curr_var_name, curr_var_val = curr_var.split(" = ")
curr_var_val = curr_var_val.strip("'")
fh_out = open(temp_dir+"/"+curr_var_name+".txt", "w")
######################
# Make symbolic links to all directories to prevent 64 char limit in matlab issue
# IS THIS ACUTALLY AN ISSUE?
curr_dir, curr_file_name = os.path.split(curr_var_val)
curr_symlink_name = temp_dir+"/"+curr_var_name
symlink_names.append(curr_symlink_name)
os.symlink(os.path.split(os.path.abspath(curr_var_val))[0], curr_symlink_name)
#
######################
#print os.path.split(curr_var_val)
fh_out.write(curr_var_name+"/"+os.path.split(curr_var_val)[1])
#fh_out.write(os.path.abspath(curr_var_val))
fh_out.close()
############
for curr_var in list_of_non_symlink_var:
curr_var_name, curr_var_val = curr_var.split(" = ")
curr_var_val = curr_var_val.strip("'")
fh_out = open(temp_dir+"/"+curr_var_name+".txt", "w")
fh_out.write(curr_var_val)
fh_out.close()
############
# prepare run_cmd
shutil.copy(os.path.split(original_script_name)[0]+"/run_"+os.path.split(original_script_name)[1][:-len(".m")]+".sh", temp_dir+"/run_"+os.path.split(original_script_name)[1][:-len(".m")]+".sh")
shutil.copy(os.path.split(original_script_name)[0]+"/"+os.path.split(original_script_name)[1][:-len(".m")], temp_dir+"/"+os.path.split(original_script_name)[1][:-len(".m")])
fgu217_queue = 'nice -19 qrsh -cwd -q fgu217.q -v BASH_ENV="~/.bashrc" -now n'
cluster_queue = 'nice -19 qrsh -cwd -q medium_jobs.q -v BASH_ENV="~/.bashrc" -now n'
script_to_run_cmd = temp_dir+"/run_"+os.path.split(original_script_name)[1][:-len(".m")]+".sh /net/isi-software/tools/matlab2011b/"
curr_run_str_list = []
if queue_run:
if cluster_run:
curr_run_str_list.append(cluster_queue)
else:
curr_run_str_list.append(fgu217_queue)
curr_run_str_list.append(script_to_run_cmd)
curr_run_cmd = " ".join(curr_run_str_list)
############
# run the script
if debug:
print curr_run_cmd
sys.exit(1)
with restore_curr_dir():
os.chdir(temp_dir)
#sys.exit(1)
if cluster_run: time.sleep(random.randint(1,7))
run_cmd(curr_run_cmd, "running matlab scripts")
############
# cleanup
for x_files in glob.glob(temp_dir+"/*"):
os.unlink(x_files)
shutil.rmtree(temp_dir)
