Is there a way to do a single read() in non-blocking mode on a pipe/terminal/etc, the way I can do it on a socket with recv(MSG_DONTWAIT)?
The reason I need that is because I cannot find any guarantee that a read() on a file-descriptor returned as ready for reading by select() or poll() will not block.
I know can make the file descriptor non-blocking with fcntl(fd, F_SETFL, fcntl(fd, F_GETFL) | O_NONBLOCK) but this will change the mode on that file descriptor globally, not just in the calling thread/process. For example:
% perl -MFcntl=F_SETFL,F_GETFL,O_NONBLOCK -e 'fcntl STDIN, F_SETFL, fcntl(STDIN, F_GETFL, 0) | O_NONBLOCK; select undef, undef, undef, undef'
^Z # put it in the background
% cat
cat: -: Resource temporarily unavailable
This will also make the fd non blocking for both reading and writing, which may confuse the hell out of another process doing the opposite on the same fd, as in:
non_blocking_read | filter | blocking_write
One way I think of is to save the file status flags on starting up and SIGCONT, and restore them on exiting and on SIGTSTP (just the way it's done with the termios settings), but this is very limited, race-prone, and will leave a mess behind in the case where the program exited abnormally.
Putting a save/restore with fcntl() before/after each read() also feels ugly and dumb, and may have other issues too. The same with an ioctl(FIONREAD) just before the read (which I'm not even sure it will work reliably with any fd; assurances in that direction will be welcome, though).
I would be happy even with system specific (eg. linux or bsd-only) solutions.
For reference, here is a discussion about fixing it in linux; the idea didn't seem to get anywhere, though.
A Linux only solution would be to reopen the file descriptor via
"/dev/stdin"|"/dev/tty"|"/dev/fd/$fd".
C example:
#include <stdlib.h>
#include <unistd.h>
#include <fcntl.h>
#include <unistd.h>
#include <stdio.h>
int main()
{
int fd;
char buf[8];
int flags;
if(0>(fd=open("/dev/stdin", O_RDONLY))) return 1;
if(0>(flags = fcntl(fd,F_GETFL))) return 1;
if(0>(flags = fcntl(fd,F_SETFL,flags|O_NONBLOCK))) return 1;
sleep(3);
puts("reading");
ssize_t nr = read(fd, buf, sizeof(buf));
printf("read=%zd\n", nr);
return 0;
}
Unlike a duplicated file descriptor, a reopened filedescriptor will have independent file status flags.
Related
I have 2 question:
Consider the situation where Alice runs a owned Set-UID program
by Bob. The program wants to read the file contained in / etc / data, readable by
Alice, but by no one else. Can this program access the file?
Consider the situation where a process wants to access a file for reading;
the effective user ID of the process is 3000 and the real user ID is 4000. If the file is readable
for user ID 4000, but not for user ID 3000, this process can access the
file?
These are really the same question, and the answer in both cases is no, unless the program uses setresuid to change its effective UID to its real UID, or it uses setfsuid (Linux-specific) to change its filesystem UID to its real UID. But the program would have to be designed for this scenario; an ordinary program that never manipulates its UID/GID and just accesses files will fail the permission check.
Here is a concrete example of how to answer your part 1 question in code:
#include <stdio.h>
#include <stdlib.h>
#include <sys/types.h>
#include <unistd.h>
static void flipuids(void) {
uid_t r = getuid();
uid_t e = geteuid();
if (setreuid(e, r)) {
perror("failed to flip");
exit(1);
}
}
int main(int argc, char *argv[]) {
printf("euid=%d uid=%d\n", geteuid(), getuid());
flipuids();
printf("euid=%d uid=%d\n", geteuid(), getuid());
FILE *file = fopen("/tmp/alices", "r");
if (file == NULL) {
perror("no reads");
exit(1);
}
flipuids();
printf("euid=%d uid=%d\n", geteuid(), getuid());
fclose(file);
}
If you chmod +s ./uidaccess to make sure that the program has these permissions:
$ ls -l ./uidaccess
-rwsr-sr-x 1 bob bob 17008 Apr 18 09:34 uidaccess
Once the program is run by alice, it is an example of a process operating as described in your part 2 question.
I'm trying to create a shared MPI COMM between two executables which are both started independently, e.g.
mpiexec -n 1 ./exe1
mpiexec -n 1 ./exe2
I use MPI_Open_port to generate port details and write these to a file in exe1 and then read with exe2. This is followed by MPI_Comm_connect/MPI_Comm_accept and then send/recv communication (minimal example below).
My question is: can we write port information to file in this way, or is the MPI_Publish_name/MPI_Lookup_name required for MPI to work as in this, this and this? As supercomputers usually share a file system, this file based approach seems simpler and maybe avoids establishing a server.
It seems this should work according to the MPI_Open_Port documentation in the MPI 3.1 standard,
port_name is essentially a network address. It is unique within the communication universe to which it belongs (determined by the implementation), and may be used by any client within that communication universe. For instance, if it is an internet (host:port) address, it will be unique on the internet. If it is a low level switch address on an IBM SP, it will be unique to that SP
In addition, according to documentation on the MPI forum:
The following should be compatible with MPI: The server prints out an address to the terminal, the user gives this address to the client program.
MPI does not require a nameserver
A port_name is a system-supplied string that encodes a low-level network address at which a server can be contacted.
By itself, the port_name mechanism is completely portable ...
Writing the port information to file does work as expected, i.e creates a shared communicator and exchanges information using MPICH (3.2) but hangs at the MPI_Comm_connect/MPI_Comm_accept line when using OpenMPI versions 2.0.1 and 4.0.1 (on my local workstation running Ubuntu 12.04 but eventually needs to work on a tier 1 supercomputer). I have raised as an issue here but welcome a solution or workaround in the meantime.
Further Information
If I use the MPMD mode with OpenMPI,
mpiexec -n 1 ./exe1 : -n 1 ./exe2
this works correctly, so must be an issue with allowing the jobs to share ompi_global_scope as in this question. I've also tried adding,
MPI_Info info;
MPI_Info_create(&info);
MPI_Info_set(info, "ompi_global_scope", "true");
with info passed to all commands, with no success. I'm not running a server/client model as both codes run simultaneously so sharing a URL/PID from one is not ideal, although I cannot get this to work even using the suggested approach, which for OpenMPI 2.0.1,
mpirun -n 1 --report-pid + ./OpenMPI_2.0.1 0
1234
mpirun -n 1 --ompi-server pid:1234 ./OpenMPI_2.0.1 1
gives,
ORTE_ERROR_LOG: Bad parameter in file base/rml_base_contact.c at line 161
This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
pmix server init failed
--> Returned value Bad parameter (-5) instead of ORTE_SUCCESS
and with OpenMPI 4.0.1,
mpirun -n 1 --report-pid + ./OpenMPI_4.0.1 0
1234
mpirun -n 1 --ompi-server pid:1234 ./OpenMPI_4.0.1 1
gives,
ORTE_ERROR_LOG: Bad parameter in file base/rml_base_contact.c at line 50
...
A publish/lookup server was provided, but we were unable to connect
to it - please check the connection info and ensure the server
is alive:
Using 4.0.1 means the error should not be related to this bug in OpenMPI.
Minimal code
#include "mpi.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <unistd.h>
#include <iostream>
#include <fstream>
using namespace std;
int main( int argc, char *argv[] )
{
int num_errors = 0;
int rank, size;
char port1[MPI_MAX_PORT_NAME];
char port2[MPI_MAX_PORT_NAME];
MPI_Status status;
MPI_Comm comm1, comm2;
int data = 0;
char *ptr;
int runno = strtol(argv[1], &ptr, 10);
for (int i = 0; i < argc; ++i)
printf("inputs %d %d %s \n", i,runno, argv[i]);
MPI_Init(&argc, &argv);
MPI_Comm_size(MPI_COMM_WORLD, &size);
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
if (runno == 0)
{
printf("0: opening ports.\n");fflush(stdout);
MPI_Open_port(MPI_INFO_NULL, port1);
printf("opened port1: <%s>\n", port1);
//Write port file
ofstream myfile;
myfile.open("port");
if( !myfile )
cout << "Opening file failed" << endl;
myfile << port1 << endl;
if( !myfile )
cout << "Write failed" << endl;
myfile.close();
printf("Port %s written to file \n", port1); fflush(stdout);
printf("Attempt to accept port1.\n");fflush(stdout);
//Establish connection and send data
MPI_Comm_accept(port1, MPI_INFO_NULL, 0, MPI_COMM_WORLD, &comm1);
printf("sending 5 \n");fflush(stdout);
data = 5;
MPI_Send(&data, 1, MPI_INT, 0, 0, comm1);
MPI_Close_port(port1);
}
else if (runno == 1)
{
//Read port file
size_t chars_read = 0;
ifstream myfile;
//Wait until file exists and is avaialble
myfile.open("port");
while(!myfile){
myfile.open("port");
cout << "Opening file failed" << myfile << endl;
usleep(30000);
}
while( myfile && chars_read < 255 ) {
myfile >> port1[ chars_read ];
if( myfile )
++chars_read;
if( port1[ chars_read - 1 ] == '\n' )
break;
}
printf("Reading port %s from file \n", port1); fflush(stdout);
remove( "port" );
//Establish connection and recieve data
MPI_Comm_connect(port1, MPI_INFO_NULL, 0, MPI_COMM_WORLD, &comm1);
MPI_Recv(&data, 1, MPI_INT, 0, 0, comm1, &status);
printf("Received %d 1\n", data); fflush(stdout);
}
//Barrier on intercomm before disconnecting
MPI_Barrier(comm1);
MPI_Comm_disconnect(&comm1);
MPI_Finalize();
return 0;
}
The 0 and 1 simply specify if this code writes a port file or reads it in the example above. This is then run with,
mpiexec -n 1 ./a.out 0
mpiexec -n 1 ./a.out 1
After reading https://www.quora.com/How-can-I-bypass-the-OS-buffering-during-I-O-in-Linux I want to try to access data on the serial port with the O_DIRECT option, but the only way I can seem to do that is by adding the GNU_SOURCE define but when I tried to execute the program, nothing at all is printed on the screen.
If I remove "#define _GNU_SOURCE" and compile, then the system gives me an error on O_DIRECT.
If I remove the define and the O_DIRECT flag, then incorrect (possibly outdated) data is always read, but the data is printed on the screen.
I still want to use the O_DIRECT flag and be able to see the data, so I feel I need an alternative command to printf and friends, but I don't know how to continue.
I attached the code below:
#define _GNU_SOURCE
#include <stdio.h>
#include <stdlib.h>
#include <fcntl.h>
#include <time.h>
#include <unistd.h>
#include <termios.h>
#define TIMEOUT 5
int main(){
char inb[3]; //our byte buffer
int nread=0; //number bytes read from port
int n; //counter
int iosz=128; //Lets get 128 bytes
int fd=open("/dev/ttyS0", O_NOCTTY | O_RDONLY | O_SYNC | O_DIRECT); //Open port
tcflush(fd,TCIOFLUSH);
for(n=0;n<iosz;n++){
int s=time(NULL); //Start timer for 5 seconds
while (time(NULL)-s < TIMEOUT && nread < 1){
inb[0]='A'; //Fill buffer with bad data
inb[1]='B';
inb[2]='C';
nread=read(fd,(char*)inb,1); //Read ONE byte
tcflush(fd,TCIOFLUSH);
if (nread < 0 || time(NULL)-s >= TIMEOUT){
close(fd); //Exit if read error or timeout
return -1;
}
}
printf("%x:%d ",inb[0] & 0xFF,nread); //Print byte as we receive it
}
close(fd); //program ends so close and exit
printf("\n"); //Print byte as we receive it
return 0;
}
First off, I'm no expert on this topic, just curious about it, so take this answer with a pinch of salt.
I don't know if what you're trying to do here (if I'm not looking at it the wrong way it seems to be to bypass the kernel and read directly from the port to userspace) was ever a possibility (you can find some examples, like this one but I could not find anything properly documented) but with recent kernels you should be getting an error running your code, but you're not catching it.
If you add these lines after declaring your port:
...
int fd=open("/dev/ttyS0", O_NOCTTY | O_RDONLY | O_SYNC | O_DIRECT );
if (fd == -1) {
fprintf(stderr, "Error %d opening SERIALPORT : %s\n", errno, strerror(errno));
return 1;
}
tcflush(fd,TCIOFLUSH);
....
When you try to run you'll get: Error 22 opening SERIALPORT : Invalid argument
In my humble and limited understanding, you should be able to get the same effect changing the settings on termios to raw, something like this should do:
struct termios t;
tcgetattr(fd, &t); /* get current port state */
cfmakeraw(&t); /* set port state to raw */
tcsetattr(fd, TCSAFLUSH, &t); /* set updated port state */
There are many good sources for termios, but the only place I could find taht also refers to O_DIRECT (for files) is this one.
I understand that a single MPI job Launches many processes which could be run on multiple nodes.
How do I run multiple threads inside of a given MPI process using MPI_THREAD_MULTIPLE?
I was unable to find enough information in relation to the topic.
Assuming your using OpenMP to run multiple threads
You will write the OpenMP code as you would do with out the MPI. (this statement is over simplified)
When the MPI comes you need to consider how your process will communicate. MPI is not sending messages to individual threads but individual process. For that reason MPI provides four modes of interaction with threads.
MPI_THREAD_SINGLE: Provides only one thread
MPI_THREAD_FUNNELED: Can provide many threads, but only the master thread can make MPI calls. The master thread is the one who call MPI_Init...
MPI_THREAD_SERIALIZED: Can provide many threads, but only one can make MPI calls at a time.
MPI_THREAD_MULTIPE: Can provide many threads, and all of them can make MPI call at any time.
You need to specify the mode you want at MPI_Init, which becomes:
MPI_Init_thread(&argc, &argv, HERE_PUT_THE_MODE_YOU_NEED, PROVIDED_MODE)
Ex:
MPI_Init_thread(&argc, &argv, MPI_THREAD_MULTIPE, &provided)
At the provided field the MPI_Init_thread returns the provided mode. Make sure that you got a mode that your code can cope with it.
Also, avoid the use of MPI_Probe and MPI_IProbe, because they are not thread save. You should use MPI_Mprobe and MPI_Improbe.
Here is a simple 'hello world' example as #ab2050 asked:
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <omp.h>
#include "mpi.h"
int main(int argc, char *argv[]) {
int provided;
int rank;
MPI_Init_thread(&argc, &argv, MPI_THREAD_FUNNELED, &provided);
if (provided != MPI_THREAD_FUNNELED) {
fprintf(stderr, "Warning MPI did not provide MPI_THREAD_FUNNELED\n");
}
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
#pragma omp parallel default(none), \
shared(rank), \
shared(ompi_mpi_comm_world), \
shared(ompi_mpi_int), \
shared(ompi_mpi_char)
{
printf("Hello from thread %d at rank %d parallel region\n",
omp_get_thread_num(), rank);
#pragma omp master
{
char helloWorld[12];
if (rank == 0) {
strcpy(helloWorld, "Hello World");
MPI_Send(helloWorld, 12, MPI_CHAR, 1, 0, MPI_COMM_WORLD);
printf("Rank %d send: %s\n", rank, helloWorld);
}
else {
MPI_Recv(helloWorld, 12, MPI_CHAR, 0, 0, MPI_COMM_WORLD,
MPI_STATUS_IGNORE);
printf("Rank %d received: %s\n", rank, helloWorld);
}
}
}
MPI_Finalize();
return 0;
}
You have to run this code on two process. Because 'MPI_THREAD_FUNNELED' is selected only the master thread makes MPI calls.
The following variables are specified at OpenMP data scoping place
because is needed by gcc version 6.1.1. Older versions like 4.8 do not require to declare them.
ompi_mpi_comm_world
ompi_mpi_char
I am trying to create a GUI in Qt4 for my tcl based tool. In order to populate widgets I need to execute some tcl commands. I read about QProcess and I am invoking tcl scripts using QProcess and then grabbing their output from stdout.
Suppose I execute 3 commands in tcl then when I query stdout I believe I should see 3 outputs corresponding to each of the three commands, however this is not happening consistently. Behavior is flaky.
As you can see in the main.cpp I am executing multiple commands using runTclCommand() function and in the end executing getData() function to read stdout.
main.cpp:
#include <QApplication>
#include <QProcess>
#include <QDebug>
#include "Tclsh.h"
int main(int argc, char *argv[])
{
QApplication a(argc, argv);
QByteArray out;
Tclsh *tcl = new Tclsh;
tcl->startTclsh();
tcl->runTclCommand("set ::tcl_interactive 1\n");
tcl->runTclCommand("set a 23\n");
tcl->runTclCommand("puts $a\n");
tcl->runTclCommand("set a 40\n");
tcl->runTclCommand("puts $a\n");
// out = idl->getData();
out = tcl->getData();
}
Tclsh.cpp:
#include <QProcessEnvironment>
#include <QProcess>
#include <QDebug>
#include "Tclsh.h"
void Tclsh::startTclsh() {
QString program = "/usr/bin/tclsh8.4";
this->setProcessChannelMode(QProcess::MergedChannels);
this->start(program);
if ( !this->waitForStarted()) {
qDebug()<<"ERROR Starting tclsh";
}
return;
}
void Tclsh::runTclCommand(const char *cmd) {
qDebug()<<"CMD:"<<cmd;
this->write(cmd);
if (!this->waitForBytesWritten()) {
qDebug()<<"Error in writing data";
}
}
QByteArray Tclsh::getData() {
if (!this->waitForReadyRead()) {
qDebug()<<"Error in reading stdout: Ready read signal is not emitted";
}
QByteArray data = this->readAllStandardOutput();
qDebug()<<"DATA:"<<data;
return data;
}
However, sometime I get the following output:
CMD: set ::tcl_interactive 1
CMD: set a 23
CMD: puts $a
CMD: set a 40
CMD: puts $a
DATA: "1
% 23
% 23
% "
And sometimes this:
CMD: set ::tcl_interactive 1
CMD: set a 23
CMD: puts $a
CMD: set a 40
CMD: puts $a
DATA: "1
"
I do not understand why this is happening. I would really appreciate if someone can point me to the error in my approach here.
Thanks,
Newbie
Edit: After some more research, here are my thoughts
According to Qt manual, readyRead signal will be emitted whenever new data is available (as specified by #Frank Osterfeld also, thanks!). It will not wait for complete output data to be available (which is justified since it does not know when will that happen). Hence my approach is not good. What I can do is something like this:
start the process -> wait for process to finish -> read stdout
This will ensure that flaky behavior does not arise as process is already finished when I am reading hence no new data can come.
However, in this proposed approach I am not clear about one thing: Does stdout is specific to a process? I mean can it happen that process which was supposed to read stdout output from process1, can get other stdout data from some other process which happen to write stdout at the same time as process1?
Thanks,
Newbie
I am closing this question. Reading from a channel more than once does not seem to a be a good idea. Instead what I do now is write what I want to write in one go --> close the channel for writing --> then read it back. In that way I get consistent output.