AP_HAL_Linux: add O_CLOEXEC in places missing it

By opening with O_CLOEXEC we make sure we don't leak the file descriptor
when we are exec'ing or calling out subprograms. Right now we currently
don't do it so there's no harm, but it's good practice in Linux to have
it.

libraries/AP_HAL_Linux/AnalogIn_IIO.cpp

@@ -35,7 +35,7 @@ void AnalogSource_IIO::init_pins(void)
         strncpy(buf, IIO_ANALOG_IN_DIR, sizeof(buf));
         strncat(buf, AnalogSource_IIO::analog_sources[i], sizeof(buf) - strlen(buf) - 1);
 
-        fd_analog_sources[i] = open(buf, O_RDONLY | O_NONBLOCK);
+        fd_analog_sources[i] = open(buf, O_RDONLY | O_NONBLOCK | O_CLOEXEC);
     }
 }
 

libraries/AP_HAL_Linux/AnalogIn_Navio2.cpp

@@ -27,7 +27,7 @@ void AnalogSource_Navio2::set_channel(uint8_t pin)
         ::close(_fd);
     }
 
-    _fd = ::open(channel_path, O_RDONLY);
+    _fd = ::open(channel_path, O_RDONLY|O_CLOEXEC);
 
     if (_fd < 0) {
         hal.console->printf("%s not opened: %s\n", channel_path, strerror(errno));

libraries/AP_HAL_Linux/CameraSensor.cpp

@@ -30,7 +30,7 @@ bool CameraSensor::set_format(uint32_t width, uint32_t height, uint32_t format)
     struct v4l2_subdev_format fmt;
     int ret, fd;
 
-    fd = open(_device_path, O_RDWR);
+    fd = open(_device_path, O_RDWR | O_CLOEXEC);
     if (fd < 0) {
         return false;
     }

libraries/AP_HAL_Linux/GPIO_BBB.cpp

@@ -29,7 +29,7 @@ void GPIO_BBB::init()
     // Idea taken from https://groups.google.com/forum/#!msg/beagleboard/OYFp4EXawiI/Mq6s3sg14HoJ
 
     uint8_t bank_enable[3] = { 5, 65, 105 };
-    int export_fd = open("/sys/class/gpio/export", O_WRONLY);
+    int export_fd = open("/sys/class/gpio/export", O_WRONLY | O_CLOEXEC);
     if (export_fd == -1) {
         AP_HAL::panic("unable to open /sys/class/gpio/export");
     }
@@ -40,7 +40,7 @@ void GPIO_BBB::init()
 
 
     /* open /dev/mem */
-    if ((mem_fd = open("/dev/mem", O_RDWR|O_SYNC) ) < 0) {
+    if ((mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC)) < 0) {
             printf("can't open /dev/mem \n");
             exit (-1);
     }

libraries/AP_HAL_Linux/GPIO_RPI.cpp

@@ -48,7 +48,7 @@ void GPIO_RPI::init()
     int rpi_version = UtilRPI::from(hal.util)->get_rpi_version();
     uint32_t gpio_address = rpi_version == 1 ? GPIO_BASE(BCM2708_PERI_BASE)   : GPIO_BASE(BCM2709_PERI_BASE);
 
-    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
     if (mem_fd < 0) {
         AP_HAL::panic("Can't open /dev/mem");
     }

libraries/AP_HAL_Linux/OpticalFlow_Onboard.cpp

@@ -342,7 +342,7 @@ void OpticalFlow_Onboard::_run_optflow()
         gyro_rate.z = rate_z;
 
 #ifdef OPTICALFLOW_ONBOARD_RECORD_VIDEO
-        int fd = open(OPTICALFLOW_ONBOARD_VIDEO_FILE, O_CREAT | O_WRONLY
+        int fd = open(OPTICALFLOW_ONBOARD_VIDEO_FILE, O_CLOEXEC | O_CREAT | O_WRONLY
                 | O_APPEND, S_IRUSR | S_IWUSR | S_IRGRP |
                 S_IWGRP | S_IROTH | S_IWOTH);
 	    if (fd != -1) {

libraries/AP_HAL_Linux/RCInput_115200.cpp

@@ -37,7 +37,7 @@ using namespace Linux;
 
 void RCInput_115200::init()
 {
-    fd = open(device_path, O_RDWR | O_NONBLOCK);
+    fd = open(device_path, O_RDWR | O_NONBLOCK | O_CLOEXEC);
     if (fd != -1) {
         struct termios options;
 

libraries/AP_HAL_Linux/RCInput_AioPRU.cpp

@@ -35,7 +35,7 @@ using namespace Linux;
 
 void RCInput_AioPRU::init()
 {
-    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
     if (mem_fd == -1) {
         AP_HAL::panic("Unable to open /dev/mem");
     }

libraries/AP_HAL_Linux/RCInput_Navio2.cpp

@@ -65,7 +65,7 @@ int RCInput_Navio2::open_channel(int channel)
         AP_HAL::panic("[RCInput_Navio2]: not enough memory\n");
     }
 
-    int fd = ::open(channel_path, O_RDONLY);
+    int fd = ::open(channel_path, O_RDONLY|O_CLOEXEC);
 
     free(channel_path);
 

libraries/AP_HAL_Linux/RCInput_PRU.cpp

@@ -27,7 +27,7 @@ using namespace Linux;
 
 void RCInput_PRU::init()
 {
-    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
     if (mem_fd == -1) {
         AP_HAL::panic("Unable to open /dev/mem");
     }

libraries/AP_HAL_Linux/RCInput_RPI.cpp

@@ -109,12 +109,12 @@ Memory_table::Memory_table(uint32_t page_count, int version)
     _phys_pages = (void**)malloc(page_count * sizeof(void*));
     _page_count = page_count;
  
-    if ((fdMem = open("/dev/mem", O_RDWR | O_SYNC)) < 0) {
+    if ((fdMem = open("/dev/mem", O_RDWR | O_SYNC | O_CLOEXEC)) < 0) {
         fprintf(stderr,"Failed to open /dev/mem\n");
         exit(-1);
     }
 
-    if ((file = open("/proc/self/pagemap", O_RDWR | O_SYNC)) < 0) {
+    if ((file = open("/proc/self/pagemap", O_RDWR | O_SYNC | O_CLOEXEC)) < 0) {
         fprintf(stderr,"Failed to open /proc/self/pagemap\n");
         exit(-1);
     }
@@ -216,7 +216,7 @@ void RCInput_RPI::set_physical_addresses(int version)
 //Map peripheral to virtual memory
 void* RCInput_RPI::map_peripheral(uint32_t base, uint32_t len)
 {
-    int fd = open("/dev/mem", O_RDWR);
+    int fd = open("/dev/mem", O_RDWR | O_CLOEXEC);
     void * vaddr;
 
     if (fd < 0) {

libraries/AP_HAL_Linux/RCInput_SBUS.cpp

@@ -38,7 +38,7 @@ using namespace Linux;
 
 void RCInput_SBUS::init()
 {
-    fd = open(device_path, O_RDWR | O_NONBLOCK);
+    fd = open(device_path, O_RDWR | O_NONBLOCK | O_CLOEXEC);
     if (fd != -1) {
         printf("Opened SBUS input %s fd=%d\n", device_path, (int)fd);
         fflush(stdout);
@@ -107,7 +107,7 @@ void RCInput_SBUS::_timer_tick(void)
 #if SBUS_DEBUG_LOG
     static int logfd = -1;
     if (logfd == -1) {
-        logfd = open("sbus.log", O_WRONLY|O_CREAT|O_TRUNC, 0644);
+        logfd = open("sbus.log", O_WRONLY|O_CREAT|O_TRUNC|O_CLOEXEC, 0644);
     }
 #endif
 

libraries/AP_HAL_Linux/RCInput_UART.cpp

@@ -17,7 +17,7 @@ using namespace Linux;
 
 RCInput_UART::RCInput_UART(const char *path)
 {
-    _fd = open(path, O_RDONLY|O_NOCTTY|O_NONBLOCK|O_NDELAY);
+    _fd = open(path, O_RDONLY|O_NOCTTY|O_NONBLOCK|O_NDELAY|O_CLOEXEC);
     if (_fd < 0) {
         AP_HAL::panic("RCInput_UART: Error opening '%s': %s",
                              path, strerror(errno));

libraries/AP_HAL_Linux/RCInput_ZYNQ.cpp

@@ -24,7 +24,7 @@ using namespace Linux;
 
 void RCInput_ZYNQ::init()
 {
-    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+    int mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
     if (mem_fd == -1) {
         AP_HAL::panic("Unable to open /dev/mem");
     }

libraries/AP_HAL_Linux/RCOutput_AioPRU.cpp

@@ -36,7 +36,7 @@ void RCOutput_AioPRU::init()
 
    signal(SIGBUS,catch_sigbus);
 
-   mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+   mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
 
    pwm = (struct pwm*) mmap(0, 0x1000, PROT_READ|PROT_WRITE, MAP_SHARED, mem_fd, RCOUT_PRUSS_RAM_BASE);
    iram = (uint32_t*)mmap(0, 0x2000, PROT_READ|PROT_WRITE, MAP_SHARED, mem_fd, RCOUT_PRUSS_IRAM_BASE);

libraries/AP_HAL_Linux/RCOutput_PRU.cpp

@@ -29,7 +29,7 @@ void RCOutput_PRU::init()
 {
     uint32_t mem_fd;
     signal(SIGBUS,catch_sigbus);
-    mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+    mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
     sharedMem_cmd = (struct pwm_cmd *) mmap(0, 0x1000, PROT_READ|PROT_WRITE,
                                             MAP_SHARED, mem_fd, RCOUT_PRUSS_SHAREDRAM_BASE);
     close(mem_fd);

libraries/AP_HAL_Linux/RCOutput_ZYNQ.cpp

@@ -37,7 +37,7 @@ void RCOutput_ZYNQ::init()
 {
     uint32_t mem_fd;
     signal(SIGBUS,catch_sigbus);
-    mem_fd = open("/dev/mem", O_RDWR|O_SYNC);
+    mem_fd = open("/dev/mem", O_RDWR|O_SYNC|O_CLOEXEC);
     sharedMem_cmd = (struct pwm_cmd *) mmap(0, 0x1000, PROT_READ|PROT_WRITE, 
                                             MAP_SHARED, mem_fd, RCOUT_ZYNQ_PWM_BASE);
     close(mem_fd);

libraries/AP_HAL_Linux/Storage.cpp

@@ -35,7 +35,7 @@ void Storage::_storage_create(void)
 {
     mkdir(STORAGE_DIR, 0777);
     unlink(STORAGE_FILE);
-    int fd = open(STORAGE_FILE, O_RDWR|O_CREAT, 0666);
+    int fd = open(STORAGE_FILE, O_RDWR|O_CREAT|O_CLOEXEC, 0666);
     if (fd == -1) {
         AP_HAL::panic("Failed to create " STORAGE_FILE);
     }
@@ -57,10 +57,10 @@ void Storage::_storage_open(void)
     }
 
     _dirty_mask = 0;
-    int fd = open(STORAGE_FILE, O_RDWR);
+    int fd = open(STORAGE_FILE, O_RDWR|O_CLOEXEC);
     if (fd == -1) {
         _storage_create();
-        fd = open(STORAGE_FILE, O_RDWR);
+        fd = open(STORAGE_FILE, O_RDWR|O_CLOEXEC);
         if (fd == -1) {
             AP_HAL::panic("Failed to open " STORAGE_FILE);
         }
@@ -80,7 +80,7 @@ void Storage::_storage_open(void)
     if (ret != sizeof(_buffer)) {
         close(fd);
         _storage_create();
-        fd = open(STORAGE_FILE, O_RDONLY);
+        fd = open(STORAGE_FILE, O_RDONLY|O_CLOEXEC);
         if (fd == -1) {
             AP_HAL::panic("Failed to open " STORAGE_FILE);
         }
@@ -137,7 +137,7 @@ void Storage::_timer_tick(void)
     }
 
     if (_fd == -1) {
-        _fd = open(STORAGE_FILE, O_WRONLY);
+        _fd = open(STORAGE_FILE, O_WRONLY|O_CLOEXEC);
         if (_fd == -1) {
             return;
         }

libraries/AP_HAL_Linux/ToneAlarm.cpp

@@ -38,9 +38,9 @@ bool ToneAlarm::tune_repeat[TONE_NUMBER_OF_TUNES] = {false,true,false,false,fals
 
 ToneAlarm::ToneAlarm()
 {
-    period_fd = open("/sys/devices/ocp.3/pwm_test_P8_36.12/period",O_WRONLY);
-    duty_fd = open("/sys/devices/ocp.3/pwm_test_P8_36.12/duty",O_WRONLY);
-    run_fd = open("/sys/devices/ocp.3/pwm_test_P8_36.12/run",O_WRONLY);
+    period_fd = open("/sys/devices/ocp.3/pwm_test_P8_36.12/period",O_WRONLY|O_CLOEXEC);
+    duty_fd = open("/sys/devices/ocp.3/pwm_test_P8_36.12/duty",O_WRONLY|O_CLOEXEC);
+    run_fd = open("/sys/devices/ocp.3/pwm_test_P8_36.12/run",O_WRONLY|O_CLOEXEC);
 
     tune_num = -1;                    //initialy no tune to play
     tune_pos = 0;

libraries/AP_HAL_Linux/VideoIn.cpp

@@ -68,7 +68,7 @@ bool VideoIn::open_device(const char *device_path, uint32_t memtype)
 
     _fd = -1;
     _buffers = nullptr;
-    _fd = open(device_path, O_RDWR);
+    _fd = open(device_path, O_RDWR|O_CLOEXEC);
     _memtype = memtype;
     if (_fd < 0) {
         hal.console->printf("Error opening device %s: %s (%d).\n",

libraries/AP_HAL_Linux/qflight/dsp_functions.cpp

@@ -275,7 +275,7 @@ int qflight_UART_open(const char *device, int32_t *_fd)
         return -1;
     }
     struct uartbuf &b = uarts[num_open_uarts];
-    int fd = open(device, O_RDWR | O_NONBLOCK);
+    int fd = open(device, O_RDWR | O_NONBLOCK|O_CLOEXEC);
     if (fd == -1) {
         return -1;
     }