Two implementations of a popen3() function in POSIX/C providing stdin, stdout, and stderr (http://blog.mikebourgeous.com/2011/06/12/programmatic-process-control-in-c-popen3/)

popen3_2007.c

/*
 * This implementation of popen3() was created in 2007 for an experimental
 * mpg123 frontend and is based on a popen2() snippet found online.  This
 * implementation may behave in unexpected ways if stdin/stdout/stderr have
 * been closed or modified.  No warranty of its correctness, security, or
 * usability is given.  My modifications are released into the public domain,
 * but if used in an open source application, attribution would be appreciated.
 * 
 * Mike Bourgeous
 * https://github.com/mike-bourgeous
 * http://www.mikebourgeous.com/
 */
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <fcntl.h>

/*
 * popen3()
 *
 * Runs the specified command line using a shell (SECURITY WARNING: don't put
 * user-provided input here, to avoid shell expansion), opening pipes for
 * stdin, stdout, and stderr.  If NULL is specified for a given fd, that stream
 * will be discarded.
 *
 * It is recommended to set nonblock_in to zero, nonblock_outerr to nonzero.
 */
pid_t popen3(const char *command, int *fp_in, int *fp_out, int *fp_err, int nonblock_in, int nonblock_outerr) /* {{{ */
{
#define POPEN3_READ 0
#define POPEN3_WRITE 1

	// Based on popen2() from http://snippets.dzone.com/posts/show/1134,
	// where it was listed as freeware.  Modifications by Mike Bourgeous.
	// https://gist.github.com/1022231
	
	int p_stdin[2], p_stdout[2], p_stderr[2];
	pid_t pid;

	/* Open the three pipes */
	if(pipe(p_stdin) != 0 || pipe(p_stdout) != 0 || pipe(p_stderr) != 0) {
		perror("popen3: unable to open pipes for I/O");
		return -1;
	}

	/* Set the pipes to nonblocking IO if requested (a good idea for single-threaded apps) */
	if(nonblock_in) {
		fcntl(p_stdin[POPEN3_WRITE], F_SETFL, fcntl(p_stdin[POPEN3_WRITE], F_GETFL) | O_NONBLOCK);
	}
	if(nonblock_outerr) {
		fcntl(p_stdout[POPEN3_READ], F_SETFL, fcntl(p_stdout[POPEN3_READ], F_GETFL) | O_NONBLOCK);
		fcntl(p_stderr[POPEN3_READ], F_SETFL, fcntl(p_stderr[POPEN3_READ], F_GETFL) | O_NONBLOCK);
	}

	pid = fork();

	if (pid < 0) {
		/* An error occurred */
		return pid;
	} else if (pid == 0) {
		/* This is the child process */

		// Close the parent-side half of the pipes
		close(p_stdin[POPEN3_WRITE]);
		close(p_stderr[POPEN3_READ]);
		close(p_stdout[POPEN3_READ]);

		// Replace the real stdin/stdout/stderr with the pipes created above
		dup2(p_stdin[POPEN3_READ], fileno(stdin));
		dup2(p_stderr[POPEN3_WRITE], fileno(stderr)); // stderr is first in case err is redirected to out (i.e. with 2>&1)
		dup2(p_stdout[POPEN3_WRITE], fileno(stdout));

		execl("/bin/sh", "sh", "-c", command, (char *)NULL);
		perror("popen3: execl failed");
		exit(1);
	}

	/* This is the parent process */

	if(fp_in == NULL) {
		/* fp_in was null - the caller doesn't want to write to stdin */
		close(p_stdin[POPEN3_WRITE]);
	} else {
		/* Give the caller the file number for stdin */
		*fp_in = p_stdin[POPEN3_WRITE];
	}

	if(fp_out == NULL) {
		/* fp_out was null - the caller doesn't want to read from stdout */
		close(p_stdout[POPEN3_READ]);
	} else {
		/* Give the caller the file number for stdout */
		*fp_out = p_stdout[POPEN3_READ];
	}

	if(fp_err == NULL) {
		/* fp_err was null - the caller doesn't want to read from stderr */
		close(p_stderr[POPEN3_READ]);
	} else {
		/* Give the caller the file number for stderr */
		*fp_err = p_stderr[POPEN3_READ];
	}

	return pid;
#undef POPEN3_READ
#undef POPEN3_WRITE
} /* }}} */

popen3_2011.c

/*
 * This implementation of popen3() was created from scratch in June of 2011.  It
 * is less likely to leak file descriptors if an error occurs than the 2007
 * version and has been tested under valgrind.  It also differs from the 2007
 * version in its behavior if one of the file descriptor parameters is NULL.
 * Instead of closing the corresponding stream, it is left unmodified (typically
 * sharing the same terminal as the parent process).  It also lacks the
 * non-blocking option present in the 2007 version.
 *
 * No warranty of correctness, safety, performance, security, or usability is
 * given.  This implementation is released into the public domain/CC0, but if used
 * in an open source application, attribution would be appreciated.
 *
 * Mike Bourgeous
 * https://github.com/mike-bourgeous
 * http://www.mikebourgeous.com/
 */
#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
#include <fcntl.h>

/*
 * Sets the FD_CLOEXEC flag.  Returns 0 on success, -1 on error.
 */
static int set_cloexec(int fd)
{
	if(fcntl(fd, F_SETFD, fcntl(fd, F_GETFD) | FD_CLOEXEC) == -1) {
		perror("Error setting FD_CLOEXEC flag");
		return -1;
	}

	return 0;
}

/*
 * Runs command in another process, with full remote interaction capabilities.
 * Be aware that command is passed to sh -c, so shell expansion will occur.
 * Writing to *writefd will write to the command's stdin.  Reading from *readfd
 * will read from the command's stdout.  Reading from *errfd will read from the
 * command's stderr.  If NULL is passed for writefd, readfd, or errfd, then the
 * command's stdin, stdout, or stderr will not be changed.  Returns the child
 * PID on success, -1 on error.
 */
pid_t popen3(char *command, int *writefd, int *readfd, int *errfd)
{
	int in_pipe[2] = {-1, -1};
	int out_pipe[2] = {-1, -1};
	int err_pipe[2] = {-1, -1};
	pid_t pid;

	// 2011 implementation of popen3() by Mike Bourgeous
	// https://gist.github.com/1022231

	if(command == NULL) {
		fprintf(stderr, "Cannot popen3() a NULL command.\n");
		goto error;
	}

	if(writefd && pipe(in_pipe)) {
		perror("Error creating pipe for stdin");
		goto error;
	}
	if(readfd && pipe(out_pipe)) {
		perror("Error creating pipe for stdout");
		goto error;
	}
	if(errfd && pipe(err_pipe)) {
		perror("Error creating pipe for stderr");
		goto error;
	}

	pid = fork();
	switch(pid) {
		case -1:
			// Error
			perror("Error creating child process");
			goto error;

		case 0:
			// Child
			if(writefd) {
				close(in_pipe[1]);
				if(dup2(in_pipe[0], 0) == -1) {
					perror("Error assigning stdin in child process");
					exit(-1);
				}
				close(in_pipe[0]);
			}
			if(readfd) {
				close(out_pipe[0]);
				if(dup2(out_pipe[1], 1) == -1) {
					perror("Error assigning stdout in child process");
					exit(-1);
				}
				close(out_pipe[1]);
			}
			if(errfd) {
				close(err_pipe[0]);
				if(dup2(err_pipe[1], 2) == -1) {
					perror("Error assigning stderr in child process");
					exit(-1);
				}
				close(err_pipe[1]);
			}
			execl("/bin/sh", "/bin/sh", "-c", command, (char *)NULL);
			perror("Error executing command in child process");
			exit(-1);

		default:
			// Parent
			break;
	}

	if(writefd) {
		close(in_pipe[0]);
		set_cloexec(in_pipe[1]);
		*writefd = in_pipe[1];
	}
	if(readfd) {
		close(out_pipe[1]);
		set_cloexec(out_pipe[0]);
		*readfd = out_pipe[0];
	}
	if(errfd) {
		close(err_pipe[1]);
		set_cloexec(out_pipe[0]);
		*errfd = err_pipe[0];
	}

	return pid;

error:
	if(in_pipe[0] >= 0) {
		close(in_pipe[0]);
	}
	if(in_pipe[1] >= 0) {
		close(in_pipe[1]);
	}
	if(out_pipe[0] >= 0) {
		close(out_pipe[0]);
	}
	if(out_pipe[1] >= 0) {
		close(out_pipe[1]);
	}
	if(err_pipe[0] >= 0) {
		close(err_pipe[0]);
	}
	if(err_pipe[1] >= 0) {
		close(err_pipe[1]);
	}

	return -1;
}

Thanks for this code.
Line 127 of popen_2011.c should be "set_cloexec(err_pipe[0]);"