SegFault in read function for serial device - c

Question

I'm attempting to interface with a measurement device through serial. I have already created one successful program that works and does what I want, but it doesn't have live user input.
My problem comes from a program I'm creating where I want to make a live serial terminal to interact with the device. In this program I have the user type the commands to the machine and for some commands the machine has to return a 1 or 0. This is where the problem comes. In the live environment, when I read a 1 after a command I get a segfault.
This is the segment that deals with commands that require the machine to send a 1 or 0.
buf = malloc(1);
if (buf == NULL)
{
perror("memory error");
goto fail;
}
...
if (write == 0)
{
for (i = 0; i < read_com.num; i++)
{
if (strcmp(buff, read_com.check[i]) == 0)
{
ret = write_port(fd, buff, strlen(buff));
if (ret < 0)
goto fail;
ret = read_port(fd, buf, 1);
if (ret < 0)
goto fail;
printf("Read success");
write = 1;
break;
}
}
}
This is the read port function where the segfault is occurring
int read_port(int fd, char *buf, const size_t size)
{
ssize_t r;
size_t received;
received = 0;
while (received < size)
{
r = read(fd, buf + received, size - received);
if (r < 0)
{
perror("failed to read from port");
return -1;
}
if (r == 0)
{
break;
}
received += r;
}
return received;
}
All code below:
live.c:
#include "GPIB_prof.h"
#include "serial.h"
#include "commands.h"
#include <string.h>
#include <stdbool.h>
#include <stdlib.h>
#include <stdio.h>
const struct com read_com = {3, {"OPC?;PRES;\r", "OPC?;WAIT;\r", "CORRON;\r"}};
const struct com numc = {3, {"STAR", "STOP", "POIN"}};
int main(int argc, char *argv[])
{
int fd;
int ret;
char *buff;
char *buf;
int i;
bool write = 0;
int fin = 0;
char *numb;
char *rem;
int star;
int stop;
int poin;
char *dat;
int fc = 0;
char *file;
FILE *temp;
FILE *f;
rem = malloc(256);
if (rem == NULL)
{
perror("memory error");
goto fail;
}
numb = malloc(4);
if (numb == NULL)
{
perror("memory error");
goto fail;
}
buff = malloc(256);
if (buff == NULL)
{
perror("memory error");
goto fail;
}
buf = malloc(1);
if (buf == NULL)
{
perror("memory error");
goto fail;
}
file = malloc(5);
if (file == NULL)
{
perror("memory error");
goto fail;
}
if (argc < 3)
{
printf("Usage: %s [serial device] [baud rate]", argv[0]);
goto fail;
}
fd = open_port(argv[1], atoi(argv[2]));
if (fd < 0)
goto fail;
ret = GPIB_conf(fd, 0);
if (ret < 0)
goto fail;
while (fin == 0)
{
write = 0;
scanf("%s", buff);
strcat(buff, "\r");
//if (ret<0) goto fail;
for (i = 0; i < strlen(buff); i++)
{
if (i < 4)
{
numb[i] = buff[i];
}
else
{
rem[i - 4] = buff[i];
}
}
if (strcmp(numb, "OUTP") == 0)
{
ret = write_port(fd, buff, strlen(buff));
if (ret < 0)
goto fail;
write = 1;
ret = read_port(fd, dat, 50 * poin);
if (ret < 0)
goto fail;
else
goto data;
}
if (write == 0)
{
for (i = 0; i < read_com.num; i++)
{
if (strcmp(buff, read_com.check[i]) == 0)
{
ret = write_port(fd, buff, strlen(buff));
if (ret < 0)
goto fail;
ret = read_port(fd, buf, 1);
if (ret < 0)
goto fail;
printf("Read success");
write = 1;
break;
}
}
}
if (write == 0)
{
for (i = 0; i < numc.num; i++)
{
if (strcmp(numb, numc.check[i]) == 0)
{
ret = write_port(fd, buff, strlen(buff));
if (ret < 0)
goto fail;
write = 1;
if (strcmp(numb, "STAR") == 0)
{
star = atoi(rem);
}
else if (strcmp(numb, "STOP") == 0)
{
stop = atoi(rem);
}
else if (strcmp(numb, "POIN") == 0)
{
poin = atoi(rem);
dat = malloc(50 * poin);
if (dat == NULL)
{
perror("memory error");
goto fail;
}
fc++;
}
break;
}
}
if (write == 0)
{
ret = write_port(fd, buff, strlen(buff));
if (ret < 0)
goto fail;
write = 1;
}
}
}
printf("Start freq: %d\nStop freq: %d\n", star, stop);
free(rem);
free(numb);
free(buff);
free(buf);
free(file);
free(dat);
return 0;
data:
ret = sprintf(file, "data%d", fc);
if (ret < 0)
goto fail;
temp = fopen(file, "w+");
if (temp == NULL)
{
perror("failed to open file");
fclose(temp);
goto fail;
}
fclose(temp);
ret = remove(file);
if (ret != 0)
{
perror("failed to remove file");
goto fail;
}
f = fopen(file, "w");
if (f == NULL)
{
perror("failed to open file");
fclose(f);
goto fail;
}
for (i = 0; i < (50 * poin); i++)
{
ret = fprintf(f, "%c", dat[i]);
if (ret < 0)
{
fclose(f);
goto fail;
}
}
fclose(f);
fin++;
fail:
free(rem);
free(numb);
free(buff);
free(buf);
free(file);
free(dat);
return -1;
}
serial.c:
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <fcntl.h>
#include <errno.h>
#include <termios.h>
#include <stdint.h>
#include <unistd.h>
#include "serial.h"
#include "GPIB_prof.h"
struct termios options;
int open_port(const char *dev, uint32_t baud)
{
int fd;
int ret;
char *baud_f;
struct termios opt;
baud_f = malloc(8 * sizeof(char));
if (baud_f == NULL)
{
perror("memory error");
goto fail;
}
fd = open(dev, O_RDWR, 0777);
if (fd < 0)
{
perror(dev);
goto fail;
}
ret = tcflush(fd, TCIOFLUSH);
if (ret)
{
perror("tcgetattr failed");
goto fail;
}
opt.c_cflag = (opt.c_cflag & ~CSIZE) | CS8;
opt.c_cflag &= ~IGNBRK;
opt.c_lflag = 0;
opt.c_oflag = 0;
opt.c_cc[VTIME] = 5;
opt.c_cc[VMIN] = 1;
opt.c_iflag &= ~(IXON | IXOFF | IXANY);
opt.c_cflag |= (CLOCAL | CREAD);
opt.c_cflag &= ~(PARENB | PARODD);
opt.c_cflag |= 0;
opt.c_cflag &= ~CSTOPB;
ret = sprintf(baud_f, "B%d", baud);
if (ret < 0)
{
perror("memory error");
goto fail;
}
baud = (uintptr_t)baud_f;
cfsetospeed(&opt, baud);
cfsetispeed(&opt, baud);
ret = tcsetattr(fd, TCSANOW, &opt);
if (ret)
{
perror("tcsetarre failed");
goto fail;
}
free(baud_f);
return fd;
fail:
free(baud_f);
close(fd);
return -1;
}
int read_port(int fd, char *buf, const size_t size)
{
ssize_t r;
size_t received;
received = 0;
while (received < size)
{
r = read(fd, buf + received, size - received);
if (r < 0)
{
perror("failed to read from port");
return -1;
}
if (r == 0)
{
break;
}
received += r;
}
return received;
}
int write_port(int fd, const char *buf, const size_t size)
{
ssize_t res;
res = write(fd, buf, size);
if (res != (ssize_t)size)
{
perror("failed to write to port");
return -1;
}
usleep(size * 100);
return 0;
}
int GPIB_conf(int fd, int profile)
{
int ret;
switch (profile)
{
case 0:
ret = def(fd);
if (ret < 0)
goto fail;
}
return 0;
fail:
return -1;
}
serial.h
#ifndef _SERIAL_H_
#define _SERIAL_H_
#include <stdint.h>
#include <stddef.h>
#include "GPIB_prof.h"
int open_port (const char *dev, uint32_t baud);
int read_port (int fd, char *buf, size_t size);
int write_port (int fd, const char *buf, size_t size);
int GPIB_conf (int fd, int profile);
#endif
commands.h:
#ifndef _COMMANDS_H_
#define _COMMANDS_H_
struct com
{
const int num;
const char *check[];
};
#endif
GPIB_prof.c:
#include "GPIB_prof.h"
#include "serial.h"
int def(int fd)
{
int ret;
ret = write_port(fd, "++mode 1\r", 9);
if (ret < 0)
goto fail;
ret = write_port(fd, "++addr 16\r", 10);
if (ret < 0)
goto fail;
ret = write_port(fd, "++eoi 0\r", 8);
if (ret < 0)
goto fail;
ret = write_port(fd, "++eot_enable 1\r", 15);
if (ret < 0)
goto fail;
ret = write_port(fd, "++eot_char 13\r", 14);
if (ret < 0)
goto fail;
ret = write_port(fd, "++ifc\r", 6);
if (ret < 0)
goto fail;
ret = write_port(fd, "++auto 1\r", 9);
if (ret < 0)
goto fail;
return 0;
fail:
return -1;
}
GPIB_prof.h:
#ifndef _PROFILE_H_
#define _PROFILE_H_
int def(int fd);
#endif

Answer 1

Caveat: This may not be a total solution as there are many compiler warnings for possibly uninitialized variables, etc.
Note that I'd rename some variables. You have a global called read. That tends to conflict with the standard read function. (i.e.) don't define functions/variables that conflict with standard functions/variables: caveat emptor.
Here is the compiler output I get for (e.g.) cc -o orig orig.c -Wall -Wextra -O2.
Notably, a number of pointer variables may have uninitialized values. This really should be restructured and the warnings fixed as the code is fragile and the compiler is pointing out things that could easily explain your runtime error(s).
orig.c: In function ‘GPIB_conf’:
orig.c:136:15: warning: unused parameter ‘fd’ [-Wunused-parameter]
GPIB_conf(int fd, int profile)
~~~~^~
orig.c: In function ‘main’:
orig.c:217:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
for (i = 0; i < strlen(buff); i++) {
^
orig.c:325:5: warning: increment of a boolean expression [-Wbool-operation]
fin++;
^~
orig.c: In function ‘open_port’:
orig.c:96:2: warning: ‘fd’ may be used uninitialized in this function [-Wmaybe-uninitialized]
close(fd);
^~~~~~~~~
orig.c: In function ‘main’:
orig.c:295:27: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size 1 [-Wformat-overflow=]
ret = sprintf(file, "data%d", fc);
^~
orig.c:295:22: note: directive argument in the range [0, 2147483647]
ret = sprintf(file, "data%d", fc);
^~~~~~~~
orig.c:295:8: note: ‘sprintf’ output between 6 and 15 bytes into a destination of size 5
ret = sprintf(file, "data%d", fc);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
orig.c:332:2: warning: ‘file’ may be used uninitialized in this function [-Wmaybe-uninitialized]
free(file);
^~~~~~~~~~
orig.c:333:2: warning: ‘dat’ may be used uninitialized in this function [-Wmaybe-uninitialized]
free(dat);
^~~~~~~~~
orig.c:329:2: warning: ‘numb’ may be used uninitialized in this function [-Wmaybe-uninitialized]
free(numb);
^~~~~~~~~~
orig.c:331:2: warning: ‘buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
free(buf);
^~~~~~~~~
orig.c:330:2: warning: ‘buff’ may be used uninitialized in this function [-Wmaybe-uninitialized]
free(buff);
^~~~~~~~~~
orig.c:230:32: warning: ‘poin’ may be used uninitialized in this function [-Wmaybe-uninitialized]
ret = read_port(fd, dat, 50 * poin);
~~~^~~~~~
I had to refactor/nop some of the code to get it to compile without the full definitions in the [missing] .h files. However, these hacks do not account for the warnings above.
#include "GPIB_prof.h"
#include "serial.h"
#include "commands.h"
#include <string.h>
#include <stdbool.h>
#include <stdlib.h>
#include <stdio.h>
#define def(_fd) \
0
struct com {
int num;
char *check[3];
};
const struct com read_com = { 3, {"OPC?;PRES;\r", "OPC?;WAIT;\r", "CORRON;\r"} };
const struct com numc = { 3, {"STAR", "STOP", "POIN"} };
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <fcntl.h>
#include <errno.h>
#include <termios.h>
#include <stdint.h>
#include <unistd.h>
#include "serial.h"
#include "GPIB_prof.h"
struct termios options;
int
open_port(const char *dev, uint32_t baud)
{
int fd;
int ret;
char *baud_f;
struct termios opt;
baud_f = malloc(8 * sizeof(char));
if (baud_f == NULL) {
perror("memory error");
goto fail;
}
fd = open(dev, O_RDWR, 0777);
if (fd < 0) {
perror(dev);
goto fail;
}
ret = tcflush(fd, TCIOFLUSH);
if (ret) {
perror("tcgetattr failed");
goto fail;
}
opt.c_cflag = (opt.c_cflag & ~CSIZE) | CS8;
opt.c_cflag &= ~IGNBRK;
opt.c_lflag = 0;
opt.c_oflag = 0;
opt.c_cc[VTIME] = 5;
opt.c_cc[VMIN] = 1;
opt.c_iflag &= ~(IXON | IXOFF | IXANY);
opt.c_cflag |= (CLOCAL | CREAD);
opt.c_cflag &= ~(PARENB | PARODD);
opt.c_cflag |= 0;
opt.c_cflag &= ~CSTOPB;
ret = sprintf(baud_f, "B%d", baud);
if (ret < 0) {
perror("memory error");
goto fail;
}
baud = (uintptr_t) baud_f;
cfsetospeed(&opt, baud);
cfsetispeed(&opt, baud);
ret = tcsetattr(fd, TCSANOW, &opt);
if (ret) {
perror("tcsetarre failed");
goto fail;
}
free(baud_f);
return fd;
fail:
free(baud_f);
close(fd);
return -1;
}
int
read_port(int fd, char *buf, const size_t size)
{
ssize_t r;
size_t received;
received = 0;
while (received < size) {
r = read(fd, buf + received, size - received);
if (r < 0) {
perror("failed to read from port");
return -1;
}
if (r == 0) {
break;
}
received += r;
}
return received;
}
int
write_port(int fd, const char *buf, const size_t size)
{
ssize_t res;
res = write(fd, buf, size);
if (res != (ssize_t) size) {
perror("failed to write to port");
return -1;
}
usleep(size * 100);
return 0;
}
int
GPIB_conf(int fd, int profile)
{
int ret;
switch (profile) {
case 0:
ret = def(fd);
if (ret < 0)
goto fail;
}
return 0;
fail:
return -1;
}
int
main(int argc, char *argv[])
{
int fd;
int ret;
char *buff;
char *buf;
int i;
bool write = 0;
bool fin = 0;
char *numb;
char *rem;
int star;
int stop;
int poin;
char *dat;
int fc = 0;
char *file;
FILE *temp;
FILE *f;
rem = malloc(256);
if (rem == NULL) {
perror("memory error");
goto fail;
}
numb = malloc(4);
if (numb == NULL) {
perror("memory error");
goto fail;
}
buff = malloc(256);
if (buff == NULL) {
perror("memory error");
goto fail;
}
buf = malloc(1);
if (buf == NULL) {
perror("memory error");
goto fail;
}
file = malloc(5);
if (file == NULL) {
perror("memory error");
goto fail;
}
if (argc < 3) {
printf("Usage: %s [serial device] [baud rate]", argv[0]);
goto fail;
}
fd = open_port(argv[1], atoi(argv[2]));
if (fd < 0)
goto fail;
ret = GPIB_conf(fd, 0);
if (ret < 0)
goto fail;
while (fin == 0) {
write = 0;
scanf("%s", buff);
strcat(buff, "\r");
// if (ret<0) goto fail;
for (i = 0; i < strlen(buff); i++) {
if (i < 4) {
numb[i] = buff[i];
}
else {
rem[i - 4] = buff[i];
}
}
if (strcmp(numb, "OUTP") == 0) {
ret = write_port(fd, buff, strlen(buff));
if (ret < 0)
goto fail;
write = 1;
ret = read_port(fd, dat, 50 * poin);
if (ret < 0)
goto fail;
else
goto data;
}
if (write == 0) {
for (i = 0; i < read_com.num; i++) {
if (strcmp(buff, read_com.check[i]) == 0) {
ret = write_port(fd, buff, strlen(buff));
if (ret < 0)
goto fail;
ret = read_port(fd, buf, 1);
if (ret < 0)
goto fail;
printf("Read success");
write = 1;
break;
}
}
}
if (write == 0) {
for (i = 0; i < numc.num; i++) {
if (strcmp(numb, numc.check[i]) == 0) {
ret = write_port(fd, buff, strlen(buff));
if (ret < 0)
goto fail;
write = 1;
if (strcmp(numb, "STAR") == 0) {
star = atoi(rem);
}
else if (strcmp(numb, "STOP") == 0) {
stop = atoi(rem);
}
else if (strcmp(numb, "POIN") == 0) {
poin = atoi(rem);
dat = malloc(50 * poin);
if (dat == NULL) {
perror("memory error");
goto fail;
}
fc++;
}
break;
}
}
if (write == 0) {
ret = write_port(fd, buff, strlen(buff));
if (ret < 0)
goto fail;
write = 1;
}
}
}
printf("Start freq: %d\nStop freq: %d\n", star, stop);
free(rem);
free(numb);
free(buff);
free(buf);
free(file);
free(dat);
return 0;
data:
ret = sprintf(file, "data%d", fc);
if (ret < 0)
goto fail;
temp = fopen(file, "w+");
if (temp == NULL) {
perror("failed to open file");
fclose(temp);
goto fail;
}
fclose(temp);
ret = remove(file);
if (ret != 0) {
perror("failed to remove file");
goto fail;
}
f = fopen(file, "w");
if (f == NULL) {
perror("failed to open file");
fclose(f);
goto fail;
}
for (i = 0; i < (50 * poin); i++) {
ret = fprintf(f, "%c", dat[i]);
if (ret < 0) {
fclose(f);
goto fail;
}
}
fclose(f);
fin++;
fail:
free(rem);
free(numb);
free(buff);
free(buf);
free(file);
free(dat);
return -1;
}