From 175c3a6f9f8b0596f2a9344b98e900aaf59de03b Mon Sep 17 00:00:00 2001
From: David Hendriks <davidhendriks93@gmail.com>
Date: Fri, 8 Nov 2019 15:42:47 +0000
Subject: [PATCH] Busy with loading the shared lib. got some errors about
buffered_printf
---
TODO.org | 19 +-
binary_c_python.c | 2 -
.../custom_logging_functions.py | 226 ++++++++++++++++++
binaryc_python_utils/example_perl.pm | 95 --------
binaryc_python_utils/functions.py | 2 -
binaryc_python_utils/logging_functions.py | 0
custom_logging.c | 18 ++
testing.py | 24 ++
8 files changed, 281 insertions(+), 105 deletions(-)
create mode 100644 binaryc_python_utils/custom_logging_functions.py
delete mode 100644 binaryc_python_utils/example_perl.pm
delete mode 100644 binaryc_python_utils/logging_functions.py
create mode 100644 custom_logging.c
create mode 100644 testing.py
diff --git a/TODO.org b/TODO.org
index 4357237b5..9fec89639 100644
--- a/TODO.org
+++ b/TODO.org
@@ -131,14 +131,21 @@ I get this error when I am using the master version of binary_c with either bran
That went very deep haha. alot of memory allocation stuff
-*** TODO Make sure this works with the last major release of binaryc
+*** DONE Make sure this works with the last major release of binaryc
+ CLOSED: [2019-11-08 Fri 15:00]
*** DONE Finish testing a simpler case (see other repo)
CLOSED: [2019-11-08 Fri 09:37]
-*** TODO Make master master work
-*** TODO Sync master with david_branch
-*** TODO make tag of old master branch for future reference
-*** TODO finish today
-
+*** DONE Make master master work
+ CLOSED: [2019-11-08 Fri 15:00]
+*** DONE Sync master with david_branch
+ CLOSED: [2019-11-08 Fri 15:00]
+*** DONE make tag of old master branch for future reference
+ CLOSED: [2019-11-08 Fri 15:00]
+*** TODO Implement the autogeneration of the library
+*** TODO Load all the things with the c-types
+*** TODO Implement new function for run_binary_with_custom_logging
+*** TODO Make new c function run_binary_with_custom_logging
+*** TODO Put in some new tests in the python test api
** General:
*** DONE Get a more reliable way of loading the default values (running a ./tbse echo or something?)
CLOSED: [2019-10-29 Tue 17:44]
diff --git a/binary_c_python.c b/binary_c_python.c
index e09c5d3dd..a44f974b1 100644
--- a/binary_c_python.c
+++ b/binary_c_python.c
@@ -286,5 +286,3 @@ static PyObject* binary_c_return_arglines(PyObject *self, PyObject *args)
return return_string;
}
-
-
diff --git a/binaryc_python_utils/custom_logging_functions.py b/binaryc_python_utils/custom_logging_functions.py
new file mode 100644
index 000000000..49919e6b9
--- /dev/null
+++ b/binaryc_python_utils/custom_logging_functions.py
@@ -0,0 +1,226 @@
+import os
+import textwrap
+import subprocess
+import socket
+
+# Functions for the automatic logging of stuff
+def autogen_C_logging_code(logging_dict):
+ # See example_perl.pm autologging
+ """
+ Function that autogenerates PRINTF statements for binaryc
+
+ Input:
+ dictionary where the key is the header of that logging line and items which are lists of parameters that will be put in that logging line
+
+ example: {'MY_STELLAR_DATA':
+ [
+ 'model.time',
+ 'star[0].mass',
+ 'model.probability',
+ 'model.dt'
+ ']}
+ """
+
+ # Check if the input is of the correct form
+ if not type(logging_dict)==dict:
+ print("Error: please use a dictionary as input")
+ return None
+
+ code = ''
+ # Loop over dict keys
+ for key in logging_dict:
+ logging_dict_entry = logging_dict[key]
+
+ # Check if item is of correct type:
+ if type(logging_dict_entry)==list:
+
+ # Construct print statement
+ code += 'Printf("{}'.format(key)
+ code += ' {}'.format('%g '*len(logging_dict_entry))
+ code = code.strip()
+ code += '\\n"'
+
+ # Add format keys
+ for param in logging_dict_entry:
+ code += ',((double)stardata->{})'.format(param)
+ code += ');\n'
+
+ else:
+ print('Error: please use a list for the list of parameters that you want to have logged')
+ code = code.strip()
+ # print("MADE AUTO CODE\n\n{}\n\n{}\n\n{}\n".format('*'*60, repr(code), '*'*60))
+
+ return code
+
+####################################################################################
+def binary_c_log_code(code):
+ """
+ Function to construct the code to construct the custom logging function
+ # see example_perl.pm binary_c_log_code in perl
+ """
+ custom_logging_function_string = """\
+#pragma push_macro(\"MAX\")
+#pragma push_macro(\"MIN\")
+#undef MAX
+#undef MIN
+#include \"binary_c.h\"
+
+void custom_output_function(struct stardata_t * stardata);
+void custom_output_function(struct stardata_t * stardata)
+{{
+ // struct stardata_t * stardata = (struct stardata_t *)x;
+ {};
+}}
+
+#undef MAX
+#undef MIN
+#pragma pop_macro(\"MIN\")
+#pragma pop_macro(\"MAX\")\
+ """.format(code)
+
+ # print(repr(textwrap.dedent(custom_logging_function_string)))
+ return textwrap.dedent(custom_logging_function_string)
+
+def binary_c_write_log_code(code, filename):
+ """
+ Function to write the generated logging code to a file
+ """
+
+ cwd = os.getcwd()
+
+ filePath = os.path.join(cwd, filename)
+ if os.path.exists(filePath):
+ try:
+ os.remove(filePath)
+ except:
+ print("Error while deleting file {}".format(filePath))
+
+ with open(filePath, 'w') as f:
+ f.write(code)
+
+def from_binary_c_config(config_file, flag):
+ """
+ Function to run the binaryc_config command with flags
+ """
+
+ res = subprocess.check_output('{config_file} {flag}'.format(config_file=config_file, flag=flag),
+ shell=True, stderr=subprocess.STDOUT)
+
+ # convert and chop off newline
+ res = res.decode('utf').rstrip()
+ return res
+
+def return_compilation_dict():
+ """
+ Function to build the compile command for the shared library
+
+ inspired by binary_c_inline_config command in perl
+
+ TODO: this function still has some cleaning up to do wrt default values for the compile command
+ # https://developers.redhat.com/blog/2018/03/21/compiler-and-linker-flags-gcc/
+
+
+ returns:
+ - string containing the command to build the shared library
+ """
+
+ # use binary_c-config to get necessary flags
+ BINARY_C_DIR = os.getenv('BINARY_C')
+ if BINARY_C_DIR:
+ BINARY_C_CONFIG = os.path.join(BINARY_C_DIR, 'binary_c-config')
+ BINARY_C_SRC_DIR = os.path.join(BINARY_C_DIR, 'src')
+ # TODO: build in check to see whether the file exists
+ else:
+ raise NameError('Envvar BINARY_C doesnt exist')
+ return None
+
+ # TODO: make more options for the compiling
+ cc = from_binary_c_config(BINARY_C_CONFIG, 'cc')
+
+ # Check for binary_c
+ BINARY_C_EXE = os.path.join(BINARY_C_DIR, 'binary_c')
+ if not os.path.isfile(BINARY_C_EXE):
+ print("We require binary_c executable; have you built binary_c?")
+ raise NameError('BINARY_C executable doesnt exist')
+
+ # TODO: debug
+ libbinary_c = '-lbinary_c'
+ binclibs = from_binary_c_config(BINARY_C_CONFIG, 'libs')
+ libdirs = "{} -L{}".format(from_binary_c_config(BINARY_C_CONFIG, 'libdirs'), BINARY_C_SRC_DIR)
+ bincflags = from_binary_c_config(BINARY_C_CONFIG, 'cflags')
+ bincincdirs = from_binary_c_config(BINARY_C_CONFIG, 'incdirs')
+
+ # combine
+ binclibs = ' {} {} {}'.format(libdirs, libbinary_c, binclibs)
+
+ # setup defaults:
+ defaults = {
+ 'cc': 'gcc', # default compiler
+ 'ccflags': bincflags,
+ 'ld': 'ld', # 'ld': $Config{ld}, # default linker
+ 'debug': 0,
+ 'inc': '{} -I{}'.format(bincincdirs, BINARY_C_SRC_DIR),
+ # inc => ' '.($Config{inc}//' ').' '.$bincincdirs." -I$srcdir ", # include the defaults plus # GSL and binary_c
+ # 'libname': libname, # libname is usually just binary_c corresponding to libbinary_c.so
+ 'libs': binclibs,
+ }
+
+ # set values with defaults. TODO: make other input possile.
+ ld = defaults['ld']
+ debug = defaults['debug']
+ inc = defaults['inc'] # = ($ENV{BINARY_GRID2_INC} // $defaults{inc}).' '.($ENV{BINARY_GRID2_EXTRAINC} // '');
+ libs = defaults['libs'] # = ($ENV{BINARY_GRID2_LIBS} // $defaults{libs}).' '.($ENV{BINARY_GRID2_EXTRALIBS}//'');
+ ccflags = defaults['ccflags'] # = $ENV{BINARY_GRID2_CCFLAGS} // ($defaults{ccflags}) . ($ENV{BINARY_GRID2_EXTRACCFLAGS} // '');
+
+ # you must define _SEARCH_H to prevent it being loaded twice
+ ccflags += ' -shared -D_SEARCH_H'
+
+ # ensure library paths to the front of the libs:
+ libs_content = libs.split(' ')
+ library_paths = [el for el in libs_content if el.startswith('-L')]
+ non_library_paths = [el for el in libs_content if (not el.startswith('-L') and not el=='')]
+ libs = "{} {}".format(' '.join(library_paths), ' '.join(non_library_paths))
+
+ print("Building shared library for custom logging with (binary_c.h) at {} on {}\n".format(BINARY_C_SRC_DIR, socket.gethostname()))
+ print("With options:\n\tcc = {cc}\n\tccflags = {ccflags}\n\tld = {ld}\n\tlibs = {libs}\n\tinc = {inc}\n\n".format(
+ cc=cc, ccflags=ccflags, ld=ld, libs=libs, inc=inc)
+ )
+
+ return {
+ 'cc': cc,
+ 'ld': ld,
+ 'ccflags': ccflags,
+ 'libs': libs,
+ 'inc': inc
+ }
+
+def compile_shared_lib(code, sourcefile_name, outfile_name):
+ """
+ Function to write the custom logging code to a file and then compile it.
+ """
+
+ # Write code to file
+ binary_c_write_log_code(code, sourcefile_name)
+
+ # create compilation command
+ compilation_dict = return_compilation_dict()
+
+ # Construct full command
+ command = "{cc} {ccflags} {libs} -o {outfile_name} {sourcefile_name} {inc}".format(
+ cc=compilation_dict['cc'],
+ ccflags=compilation_dict['ccflags'],
+ libs=compilation_dict['libs'],
+ outfile_name=outfile_name,
+ sourcefile_name=sourcefile_name,
+ inc=compilation_dict['inc'])
+
+ # remove extra whitespaces:
+ command = ' '.join(command.split())
+
+ # Execute compilation
+ print('Executing following command:\n{command}'.format(command=command))
+ res = subprocess.check_output('{command}'.format(command=command),
+ shell=True)
+
+ if res:
+ print('Output of compilation command:\n{}'.format(res))
\ No newline at end of file
diff --git a/binaryc_python_utils/example_perl.pm b/binaryc_python_utils/example_perl.pm
deleted file mode 100644
index 58877d2f6..000000000
--- a/binaryc_python_utils/example_perl.pm
+++ /dev/null
@@ -1,95 +0,0 @@
-# Autologging
-# Perl code for autogeneration
-sub autogen_C_logging_code
-{
- # given a hash of arrays of variable names, where the hash
- # key is the header, autogenerate PRINTF statements
- my ($self) = @_;
- my $code = undef;
- if(defined $self->{_grid_options}->{C_auto_logging} &&
- ref $self->{_grid_options}->{C_auto_logging} eq 'HASH'
- )
- {
- $code = '';
-
- foreach my $header (keys %{$self->{_grid_options}->{C_auto_logging}})
- {
- if(ref $self->{_grid_options}->{C_auto_logging}->{$header} eq 'ARRAY')
- {
- $code .= 'PRINTF("'.$header.' ';
- foreach my $x (@{$self->{_grid_options}->{C_auto_logging}->{$header}})
- {
- $code .= '%g ';
- }
- $code .= '\n"';
-
- foreach my $x (@{$self->{_grid_options}->{C_auto_logging}->{$header}})
- {
- $code .= ',((double)stardata->'.$x.')';
- }
- $code .= ');'
- }
- }
- }
- print "MADE AUTO CODE \n\n************************************************************\n\n$code\n\n************************************************************\n";
-
- return $code;
-}
-
-Which is used in flexi-grid via this:
-$population->set( C_auto_logging => {
- 'MY_STELLAR_DATA' =>
- [
- 'model.time',
- 'star[0].mass',
- 'model.probability',
- 'model.dt'
- ]
- });
-
-# binary_c_log_code
-sub binary_c_log_code
-{
- my ($code) = @_;
- return "
-#pragma push_macro(\"MAX\")
-#pragma push_macro(\"MIN\")
-#undef MAX
-#undef MIN
-#include \"binary_c.h\"
-
-void custom_output_function(SV * x);
-SV * custom_output_function_pointer(void);
-
-SV * custom_output_function_pointer()
-{
- /*
- * use PTR2UV to convert the function pointer
- * &custom_output_function to an unsigned int,
- * which is then converted to a Perl SV
- */
- return (SV*)newSVuv(PTR2UV(&custom_output_function));
-}
-
-void custom_output_function(SV * x)
-{
- struct stardata_t * stardata = (struct stardata_t *)x;
- $code;
-}
-#undef MAX
-#undef MIN
-#pragma pop_macro(\"MIN\")
-#pragma pop_macro(\"MAX\")
-";
-}
-
-And then to use it via
- $population->set(
- C_logging_code => '
- PRINTF("MY_STELLAR_DATA %g %g %g %g\n",
- stardata->model.time,
- stardata->star[0].mass,
- stardata->model.probability,
- stardata->model.dt);
- '
- );
diff --git a/binaryc_python_utils/functions.py b/binaryc_python_utils/functions.py
index 41ec72081..d12a3e6bf 100644
--- a/binaryc_python_utils/functions.py
+++ b/binaryc_python_utils/functions.py
@@ -134,8 +134,6 @@ def parse_output(output, selected_header):
print('Sorry, didnt find any line matching your header {}'.format(selected_header))
return None
-
-
keys = value_dicts[0].keys()
# Construct final dict.
diff --git a/binaryc_python_utils/logging_functions.py b/binaryc_python_utils/logging_functions.py
deleted file mode 100644
index e69de29bb..000000000
diff --git a/custom_logging.c b/custom_logging.c
new file mode 100644
index 000000000..ef5b587fb
--- /dev/null
+++ b/custom_logging.c
@@ -0,0 +1,18 @@
+#pragma push_macro("MAX")
+#pragma push_macro("MIN")
+#undef MAX
+#undef MIN
+#include "binary_c.h"
+
+void custom_output_function(struct stardata_t * stardata);
+void custom_output_function(struct stardata_t * stardata)
+{
+ // struct stardata_t * stardata = (struct stardata_t *)x;
+ Printf("MY_STELLAR_DATA %g %g\n",((double)stardata->model.time),((double)stardata->star[0].mass));
+Printf("my_sss2 %g %g\n",((double)stardata->model.time),((double)stardata->star[1].mass));;
+}
+
+#undef MAX
+#undef MIN
+#pragma pop_macro("MIN")
+#pragma pop_macro("MAX")
\ No newline at end of file
diff --git a/testing.py b/testing.py
new file mode 100644
index 000000000..688e77020
--- /dev/null
+++ b/testing.py
@@ -0,0 +1,24 @@
+import ctypes
+
+from binaryc_python_utils.custom_logging_functions import autogen_C_logging_code, binary_c_log_code, compile_shared_lib
+
+
+# generate logging lines
+logging_line = autogen_C_logging_code(
+ {
+ 'MY_STELLAR_DATA': ['model.time', 'star[0].mass'],
+ 'my_sss2': ['model.time', 'star[1].mass']
+ }
+)
+
+# Generate code around logging lines
+created_code = binary_c_log_code(logging_line)
+
+#
+compile_shared_lib(created_code, sourcefile_name='custom_logging.c', outfile_name='libcustom_logging.so')
+
+# Loading library
+libmean = ctypes.CDLL("libcustom_logging.so") # loads the shared library
+
+# Get memory adress of function. mimicking a pointer
+mem = ctypes.cast(libmean.custom_output_function, ctypes.c_void_p).value
\ No newline at end of file
--
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