I am trying to make two LEDs blink on my Arduino Uno R3 (for learning purposes). I use avr-gcc and avrdude to compile and load my program.
The first one I make blink within a while loop in main. I am trying to use Timer0 to turn the second one on and off.
First, the code that works :
#include <avr/io.h>
#include <util/delay.h>
int main() {
TCCR0B |= (1 << CS02) | (1 << CS00);
TIMSK0 |= (1 << TOIE0);
DDRD = 1 << PD3;
DDRB = 1 << PB5;
PORTB = 0;
while(1) {
PORTD ^= 1 << PD3;
_delay_ms(500);
}
return 0;
}
As expected, this code makes my LED blink on and off, and start again every second. I am also setting up (but not using) the second LED and the timer.
Now, the issues start when I add an interrupt vector:
...
#include <avr/interrupt.h>
volatile uint8_t intrs;
ISR(TIMER0_OVF_vect) {
if (++intrs >= 62) { // meant to execute every second
PORTB ^= (1 << PB5);
intrs = 0;
}
}
int main() {
intrs = 0;
... // old setup
sei();
while(1) { ... }
}
Now, none of the LEDs blink. Even weirder, none of them blink when I remove the sei(). The only way I've found to make the first LED blink again is to comment out the ISR declaration or to mark it ISR_NAKED.
So, what gives?
PS : I use a makefile to compile & load. When I run it, it looks like this:
$ make
avr-gcc -c -Os -DF_CPU=16000000UL -mmcu=atmega328p -Wall -Wextra main.c
avr-gcc -o prog.elf main.o
avr-objcopy -O ihex -R .eeprom prog.elf prog.hex
avrdude -C/etc/avrdude.conf -v -V -carduino -patmega328p -P/dev/ttyACM0 -b115200 -D -Uflash:w:prog.hex
.. # avrdude logs
I use the arduino framework with setup() and loop() functions. It might not be an optimal choice, but it's easier. Timer 0 is used by wiring.c, which is responsible for delay functions (not _delay_ms() which doesn't use interrupts). This can be disabled, as explained in this post or timer 2 can be used instead. In the latter case, your second code works fine. Could it be that you face a similar problem?
Related
I am trying to parallelise a loop using pragma directives in Rcpp. Aside from a warning message during compilation that pragma is not recognised (although this appears to be a non-issue from what I have read), other pragma commands are not working. This is the minimal example I have been using (content of the for-loop is irrelevant):
sourceCpp(code = '
#include <Rcpp.h>
#include <omp.h>
using namespace Rcpp ;
// [[Rcpp::export]]
int test() {
#pragma omp parallel for
int foo = omp_get_num_threads() ;
for(int i = 0; i < 2; i++) {
Rcout << i ;
}
return foo ;
}')
Here is my error:
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-40~1.4/include" -DNDEBUG -I"C:/Users/User/Documents/R/win-library/4.0/Rcpp/include" -I"C:/Users/User/AppData/Local/Temp/RtmpWW0LXx/sourceCpp-x86_64-w64-mingw32-1.0.4.6" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c file2fe83fae2189.cpp -o file2fe83fae2189.o
file2fe83fae2189.cpp:9: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o sourceCpp_90.dll tmp.def file2fe83fae2189.o -LC:/PROGRA~1/R/R-40~1.4/bin/x64 -lR
C:/rtools40/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/8.3.0/../../../../x86_64-w64-mingw32/bin/ld.exe: file2fe83fae2189.o:file2fe83fae2189.cpp:(.text+0x106): undefined reference to `omp_get_num_threads'
collect2.exe: error: ld returned 1 exit status
I am on a Windows machine so the MacOS compiler issue should not apply, and my num_threads call is inside the pragma section. Any ideas on what is going wrong here?
While this stuff can be finicky, you clearly missed the fact that you must inform Rcpp that you want an OpenMP compilation: you do this via the plugin (or in a package, which is what you should probably use anyway, via the src/Makevars or src/Makevars.win variable).
Anyway, here is a worked example I just derived from an older C++ example I had hanging around.
Code
#include <Rcpp.h>
#include <omp.h>
// [[Rcpp::plugins(openmp)]]
// [[Rcpp::export]]
int foo() {
int th_id, nthreads;
#pragma omp parallel private(th_id)
{
th_id = omp_get_thread_num();
std::ostringstream ss; // allow for better synchronization
ss << "Hello World from thread " << th_id << std::endl;
Rcpp::Rcout << ss.str();
#pragma omp barrier
#pragma omp master
{
nthreads = omp_get_num_threads();
Rcpp::Rcout << "There are " << nthreads << " threads" << std::endl;
}
}
return 0;
}
/*** R
foo()
*/
Output
On my machine with a hyperthreaded six-core cpu:
> Rcpp::sourceCpp("answer.cpp")
> foo()
Hello World from thread 0
Hello World from thread 1
Hello World from thread 8
Hello World from thread 10
Hello World from thread 4
Hello World from thread 9
Hello World from thread 11
Hello World from thread 7
Hello World from thread 3
Hello World from thread 5
Hello World from thread 6
Hello World from thread 2
There are 12 threads
[1] 0
>
I have a strange segmentation fault that doesn't exist when everything is in 1 .c file, but does exist when I put part of the code in a dynamically linked library and link it to a test file. The complete code for the working 1 .c file code is at the bottom, the complete code for the error system with 2 .c and 1 .h file come first.
Here is the error system:
example.h:
#include <stdio.h>
#include <stdlib.h>
typedef struct MYARRAY {
int len;
void* items[];
} MYARRAY;
MYARRAY *collection;
void
mypush(void* p);
example.c:
#include "example.h"
void
mypush(void* p) {
printf("Here %lu\n", sizeof collection);
puts("FOO");
int len = collection->len++;
puts("BAR");
collection->items[len] = p;
}
example2.c:
This is essentially a test file:
#include "example.h"
void
test_print() {
puts("Here1");
mypush("foo");
puts("Here2");
}
int
main() {
collection = malloc(sizeof *collection + (sizeof collection->items[0] * 1000));
collection->len = 0;
puts("Start");
test_print();
puts("Done");
return 0;
}
Makefile:
I link example to example2 here, and run:
example:
#clang -I . -dynamiclib \
-undefined dynamic_lookup \
-o example.dylib example.c
#clang example2.c example.dylib -o example2.o
#./example2.o
.PHONY: example
The output is:
$ make example
Start
Here1
Here 8
FOO
make: *** [example] Segmentation fault: 11
But it should show the full output of:
$ make example
Start
Here1
Here 8
FOO
BAR
Here2
Done
The weird thing is everything works if it is this system:
example.c:
#include <stdio.h>
#include <stdlib.h>
typedef struct MYARRAY {
int len;
void* items[];
} MYARRAY;
MYARRAY *collection;
void
mypush(void* p) {
printf("Here %lu\n", sizeof collection);
puts("FOO");
int len = collection->len++;
puts("BAR");
collection->items[len] = p;
}
void
test_print() {
puts("Here1");
mypush("foo");
puts("Here");
}
int
main() {
collection = malloc(sizeof *collection + (sizeof collection->items[0] * 1000));
collection->len = 0;
puts("ASF");
test_print();
return 0;
}
Makefile:
example:
#clang -o example example.c
#./example
.PHONY: example
Wondering why it's creating a segmentation fault when it is linked like this, and what I am doing wrong.
I have checked otool and with DYLD_PRINT_LIBRARIES=YES and it shows it is importing the dynamically linked libraries, but for some reason it's segmentation faulting when linked but works fine when it isn't linked.
Your problem is this, in example.h:
MYARRAY *collection;
Since both main.c and example.c include this file, you end up defining collection twice, which results in undefined behavior. You need to make sure you define each object only once. The details are relatively unimportant since anything can happen with undefined behavior, but what's probably happening is that main.c is allocating memory for one object, but the one example.c is using is still NULL. As mentioned in the comments, since you define collection in main.c your linker is able to build the executable without needing to look for that symbol in the dynamic library, so you don't get a link time warning about it being defined there too, and obviously there'd be no cause for a warning at the time you compile the library.
It works for you when you put everything in one file because obviously then you're not defining anything twice, anymore. The error itself is nothing to do with the fact you're using a dynamic library, although that may have made it harder to detect.
It would be better to define this in example.c and provide a constructor function, there's no need for main() to be able to access it directly. But if you must do this, then define it in example.c and just declare an extern identifier in the header file to tell main.c that the object is defined somewhere else.
I've boiled this down to a simple self-contained example. The main thread enqueues 1000 items, and a worker thread tries to dequeue concurrently. ThreadSanitizer complains that there's a race between the read and the write of one of the elements, even though there is an acquire-release memory barrier sequence protecting them.
#include <atomic>
#include <thread>
#include <cassert>
struct FakeQueue
{
int items[1000];
std::atomic<int> m_enqueueIndex;
int m_dequeueIndex;
FakeQueue() : m_enqueueIndex(0), m_dequeueIndex(0) { }
void enqueue(int x)
{
auto tail = m_enqueueIndex.load(std::memory_order_relaxed);
items[tail] = x; // <- element written
m_enqueueIndex.store(tail + 1, std::memory_order_release);
}
bool try_dequeue(int& x)
{
auto tail = m_enqueueIndex.load(std::memory_order_acquire);
assert(tail >= m_dequeueIndex);
if (tail == m_dequeueIndex)
return false;
x = items[m_dequeueIndex]; // <- element read -- tsan says race!
++m_dequeueIndex;
return true;
}
};
FakeQueue q;
int main()
{
std::thread th([&]() {
int x;
for (int i = 0; i != 1000; ++i)
q.try_dequeue(x);
});
for (int i = 0; i != 1000; ++i)
q.enqueue(i);
th.join();
}
ThreadSanitizer output:
==================
WARNING: ThreadSanitizer: data race (pid=17220)
Read of size 4 at 0x0000006051c0 by thread T1:
#0 FakeQueue::try_dequeue(int&) /home/cameron/projects/concurrentqueue/tests/tsan/issue49.cpp:26 (issue49+0x000000402bcd)
#1 main::{lambda()#1}::operator()() const <null> (issue49+0x000000401132)
#2 _M_invoke<> /usr/include/c++/5.3.1/functional:1531 (issue49+0x0000004025e3)
#3 operator() /usr/include/c++/5.3.1/functional:1520 (issue49+0x0000004024ed)
#4 _M_run /usr/include/c++/5.3.1/thread:115 (issue49+0x00000040244d)
#5 <null> <null> (libstdc++.so.6+0x0000000b8f2f)
Previous write of size 4 at 0x0000006051c0 by main thread:
#0 FakeQueue::enqueue(int) /home/cameron/projects/concurrentqueue/tests/tsan/issue49.cpp:16 (issue49+0x000000402a90)
#1 main /home/cameron/projects/concurrentqueue/tests/tsan/issue49.cpp:44 (issue49+0x000000401187)
Location is global 'q' of size 4008 at 0x0000006051c0 (issue49+0x0000006051c0)
Thread T1 (tid=17222, running) created by main thread at:
#0 pthread_create <null> (libtsan.so.0+0x000000027a67)
#1 std::thread::_M_start_thread(std::shared_ptr<std::thread::_Impl_base>, void (*)()) <null> (libstdc++.so.6+0x0000000b9072)
#2 main /home/cameron/projects/concurrentqueue/tests/tsan/issue49.cpp:41 (issue49+0x000000401168)
SUMMARY: ThreadSanitizer: data race /home/cameron/projects/concurrentqueue/tests/tsan/issue49.cpp:26 FakeQueue::try_dequeue(int&)
==================
ThreadSanitizer: reported 1 warnings
Command line:
g++ -std=c++11 -O0 -g -fsanitize=thread issue49.cpp -o issue49 -pthread
g++ version: 5.3.1
Can anybody shed some light onto why tsan thinks this is a data race?
UPDATE
It seems like this is a false positive. To appease ThreadSanitizer, I've added annotations (see here for the supported ones and here for an example). Note that detecting whether tsan is enabled in GCC via a macro has only recently been added, so I had to manually pass -D__SANITIZE_THREAD__ to g++ for now.
#if defined(__SANITIZE_THREAD__)
#define TSAN_ENABLED
#elif defined(__has_feature)
#if __has_feature(thread_sanitizer)
#define TSAN_ENABLED
#endif
#endif
#ifdef TSAN_ENABLED
#define TSAN_ANNOTATE_HAPPENS_BEFORE(addr) \
AnnotateHappensBefore(__FILE__, __LINE__, (void*)(addr))
#define TSAN_ANNOTATE_HAPPENS_AFTER(addr) \
AnnotateHappensAfter(__FILE__, __LINE__, (void*)(addr))
extern "C" void AnnotateHappensBefore(const char* f, int l, void* addr);
extern "C" void AnnotateHappensAfter(const char* f, int l, void* addr);
#else
#define TSAN_ANNOTATE_HAPPENS_BEFORE(addr)
#define TSAN_ANNOTATE_HAPPENS_AFTER(addr)
#endif
struct FakeQueue
{
int items[1000];
std::atomic<int> m_enqueueIndex;
int m_dequeueIndex;
FakeQueue() : m_enqueueIndex(0), m_dequeueIndex(0) { }
void enqueue(int x)
{
auto tail = m_enqueueIndex.load(std::memory_order_relaxed);
items[tail] = x;
TSAN_ANNOTATE_HAPPENS_BEFORE(&items[tail]);
m_enqueueIndex.store(tail + 1, std::memory_order_release);
}
bool try_dequeue(int& x)
{
auto tail = m_enqueueIndex.load(std::memory_order_acquire);
assert(tail >= m_dequeueIndex);
if (tail == m_dequeueIndex)
return false;
TSAN_ANNOTATE_HAPPENS_AFTER(&items[m_dequeueIndex]);
x = items[m_dequeueIndex];
++m_dequeueIndex;
return true;
}
};
// main() is as before
Now ThreadSanitizer is happy at runtime.
This looks like https://gcc.gnu.org/bugzilla/show_bug.cgi?id=78158. Disassembling the binary produced by GCC shows that it doesn't instrument the atomic operations on O0.
As a workaround, you can either build your code with GCC with -O1/-O2, or get yourself a fresh Clang build and use it to run ThreadSanitizer (this is the recommended way, as TSan is being developed as part of Clang and only backported to GCC).
The comments above are invalid: TSan can easily comprehend the happens-before relation between the atomics in your code (one can check that by running the above reproducer under TSan in Clang).
I also wouldn't recommend using the AnnotateHappensBefore()/AnnotateHappensAfter() for two reasons:
you shouldn't need them in most cases; they denote that the code is doing something really complex (in which case you may want to double-check you're doing it right);
if you make an error in your lock-free code, spraying it with annotations may mask that error, so that TSan won't notice it.
The ThreadSanitizer is not good at counting, it cannot understand that writes to the items always happen before the reads.
The ThreadSanitizer can find that the stores of m_enqueueIndex happen before the loads, but it does not understand that the store to items[m_dequeueIndex] must happen before the load when tail > m_dequeueIndex.
I'm a beginner in C language. I'm trying to operate on EEPROM memory in my ATmega 8 and ATtiny2313.
Based on this tutorial I've created the following codes:
1) writes a number to place 5 in uC's eeprom
#define F_CPU 1000000UL
#include <avr/eeprom.h>
int main()
{
number=5;
eeprom_update_byte (( uint8_t *) 5, number );
while (1);
{
}
}
2) blinks the LED n times, where n is the number read from place 5 in eeprom
#define F_CPU 1000000UL
#include <avr/io.h>
#include <util/delay.h>
#include <avr/eeprom.h>
int main()
{
DDRB=0xFF;
_delay_ms(1000);
int number;
number=eeprom_read_byte (( uint8_t *) 5) ;
for (int i=0; i<number; i++) //blinking 'number' times
{
PORTB |= (1<<PB3);
_delay_ms(100);
PORTB &= (0<<PB3);
_delay_ms(400);
}
while (1);
{
}
}
The second program blinks the led many times, and it's never the amount which is supposed to be in eeprom. What's the problem? This happens in both atmega8 and attiny2313.
EDIT:
Console results after compilation of the first program:
18:01:55 **** Incremental Build of configuration Release for project eeprom ****
make all
Invoking: Print Size
avr-size --format=avr --mcu=attiny2313 eeprom.elf
AVR Memory Usage
Device: attiny2313
Program: 102 bytes (5.0% Full)
(.text + .data + .bootloader)
Data: 0 bytes (0.0% Full)
(.data + .bss + .noinit)
Finished building: sizedummy
18:01:56 Build Finished (took 189ms)
That is one of the every time failures for beginners :-)
If you compile simply with avr-gcc <source> -o <out> you will get the wrong results here, because you need optimization! The write procedure MUST be optimized to fulfil the correct write access! So please use '-Os' or '-O3' for compiling with avr-gcc!
If you have no idea if your problem comes from read or write the eeprom, read your eeprom data with avarice/avrdude or similar tools.
The next pitfall can be, that you erase your eeprom section if you program your flash. So please have a look what your programmer really do! A full chip erase erases the eeprom as well.
Next pitfall: What fuses you have set? You are running with the expected clock rate? Maybe you have programmed internal clock and your outside crystal seems to be working with wrong speed?
Another one: Just have a look for the fuses again! JTAG pins switched off? Maybe you see only JTAG flickering :-)
Please add the compiler and programming commands to your question!
As this is my first post to stackoverflow I want to thank you all for your valuable posts that helped me a lot in the past.
I use MinGW (gcc 4.4.0) on Windows-7(64) - more specifically I use Nokia Qt + MinGW but Qt is not involved in my Question.
I need to find the address and -more important- the length of specific functions of my application at runtime, in order to encode/decode these functions and implement a software protection system.
I already found a solution on how to compute the length of a function, by assuming that static functions placed one after each other in a source-file, it is logical to be also sequentially placed in the compiled object file and subsequently in memory.
Unfortunately this is true only if the whole CPP file is compiled with option: "g++ -O0" (optimization level = 0).
If I compile it with "g++ -O2" (which is the default for my project) the compiler seems to relocate some of the functions and as a result the computed function length seems to be both incorrect and negative(!).
This is happening even if I put a "#pragma GCC optimize 0" line in the source file,
which is supposed to be the equivalent of a "g++ -O0" command line option.
I suppose that "g++ -O2" instructs the compiler to perform some global file-level optimization (some function relocation?) which is not avoided by using the #pragma directive.
Do you have any idea how to prevent this, without having to compile the whole file with -O0 option?
OR: Do you know of any other method to find the length of a function at runtime?
I prepare a small example for you, and the results with different compilation options, to highlight the case.
The Source:
// ===================================================================
// test.cpp
//
// Intention: To find the addr and length of a function at runtime
// Problem: The application output is correct when compiled with: "g++ -O0"
// but it's erroneous when compiled with "g++ -O2"
// (although a directive "#pragma GCC optimize 0" is present)
// ===================================================================
#include <stdio.h>
#include <math.h>
#pragma GCC optimize 0
static int test_01(int p1)
{
putchar('a');
putchar('\n');
return 1;
}
static int test_02(int p1)
{
putchar('b');
putchar('b');
putchar('\n');
return 2;
}
static int test_03(int p1)
{
putchar('c');
putchar('\n');
return 3;
}
static int test_04(int p1)
{
putchar('d');
putchar('\n');
return 4;
}
// Print a HexDump of a specific address and length
void HexDump(void *startAddr, long len)
{
unsigned char *buf = (unsigned char *)startAddr;
printf("addr:%ld, len:%ld\n", (long )startAddr, len);
len = (long )fabs(len);
while (len)
{
printf("%02x.", *buf);
buf++;
len--;
}
printf("\n");
}
int main(int argc, char *argv[])
{
printf("======================\n");
long fun_len = (long )test_02 - (long )test_01;
HexDump((void *)test_01, fun_len);
printf("======================\n");
fun_len = (long )test_03 - (long )test_02;
HexDump((void *)test_02, fun_len);
printf("======================\n");
fun_len = (long )test_04 - (long )test_03;
HexDump((void *)test_03, fun_len);
printf("Test End\n");
getchar();
// Just a trick to block optimizer from eliminating test_xx() functions as unused
if (argc > 1)
{
test_01(1);
test_02(2);
test_03(3);
test_04(4);
}
}
The (correct) Output when compiled with "g++ -O0":
[note the 'c3' byte (= assembly 'ret') at the end of all functions]
======================
addr:4199344, len:37
55.89.e5.83.ec.18.c7.04.24.61.00.00.00.e8.4e.62.00.00.c7.04.24.0a.00.00.00.e8.42
.62.00.00.b8.01.00.00.00.c9.c3.
======================
addr:4199381, len:49
55.89.e5.83.ec.18.c7.04.24.62.00.00.00.e8.29.62.00.00.c7.04.24.62.00.00.00.e8.1d
.62.00.00.c7.04.24.0a.00.00.00.e8.11.62.00.00.b8.02.00.00.00.c9.c3.
======================
addr:4199430, len:37
55.89.e5.83.ec.18.c7.04.24.63.00.00.00.e8.f8.61.00.00.c7.04.24.0a.00.00.00.e8.ec
.61.00.00.b8.03.00.00.00.c9.c3.
Test End
The erroneous Output when compiled with "g++ -O2":
(a) function test_01 addr & len seem correct
(b) functions test_02, test_03 have negative lengths,
and fun. test_02 length is also incorrect.
======================
addr:4199416, len:36
83.ec.1c.c7.04.24.61.00.00.00.e8.c5.61.00.00.c7.04.24.0a.00.00.00.e8.b9.61.00.00
.b8.01.00.00.00.83.c4.1c.c3.
======================
addr:4199452, len:-72
83.ec.1c.c7.04.24.62.00.00.00.e8.a1.61.00.00.c7.04.24.62.00.00.00.e8.95.61.00.00
.c7.04.24.0a.00.00.00.e8.89.61.00.00.b8.02.00.00.00.83.c4.1c.c3.57.56.53.83.ec.2
0.8b.5c.24.34.8b.7c.24.30.89.5c.24.08.89.7c.24.04.c7.04.
======================
addr:4199380, len:-36
83.ec.1c.c7.04.24.63.00.00.00.e8.e9.61.00.00.c7.04.24.0a.00.00.00.e8.dd.61.00.00
.b8.03.00.00.00.83.c4.1c.c3.
Test End
This is happening even if I put a "#pragma GCC optimize 0" line in the source file, which is supposed to be the equivalent of a "g++ -O0" command line option.
I don't believe this is true: it is supposed to be the equivalent of attaching __attribute__((optimize(0))) to subsequently defined functions, which causes those functions to be compiled with a different optimisation level. But this does not affect what goes on at the top level, whereas the command line option does.
If you really must do horrible things that rely on top level ordering, try the -fno-toplevel-reorder option. And I suspect that it would be a good idea to add __attribute__((noinline)) to the functions in question as well.