[mpich-discuss] can't MPI_Abort a program due to deadlock at pthread_mutex_lock
Jim Dinan
dinan at mcs.anl.gov
Wed Jan 2 10:25:38 CST 2013
Jeff,
Pthread_cancel is unsafe in any context where the cancelled thread can
hold a mutex needed by other threads. This looks to me like a bad
programming practice (e.g. you will also likely leak memory, since you
can't free MPI objects allocated by the thread from inside of a
cancellation handler), not an MPICH-specific problem; there are safer
ways to cancel/cleanup threads.
Do you have a good case for why such functionality is needed?
~Jim.
On 1/2/13 9:49 AM, Jeff Hammond wrote:
> I wrote a program that calls MPI from a pthread. MPI_THREAD_MULTIPLE
> is used. I cancel and then join the pthread back into the main
> program. After I do this, any calls to MPI, including MPI_Abort (see
> first gdb+source below) and MPI_Barrier (see second gdb+source below)
> deadlock on pthread_mutex_lock.
>
> I can understand that canceling the thread while it is holding the MPI
> pthread mutex is a bad idea, but I'm not sure this is an incorrect
> program. Is pthread_cancel using signals? I recall that MPICH
> functions are not guaranteed to be signal-safe.
>
> Is it possible to implement MPI_Abort such that acquisition of the MPI
> mutex is not required in order to allow deadlocked programs to
> terminate? It seems rather unfortunate that MPI_Abort does not
> perform the desired action here. Obviously, I can use abort(), but on
> some implementations, this will leave the system resources in a dirty
> state.
>
> I know a bunch of ways to work around this, but it would be helpful to
> understand exactly what the problem is. I wonder if there is a way to
> modify MPICH such that the mutex is released when a thread holding it
> is cancelled.
>
> Is it possible for MPICH to provide an MPIX call or otherwise document
> an internal, MPICH-specific function to clear the MPI mutex? I could
> resolve this problem if I could merely call MPIX_Mutex_force_unlock()
> and let the program terminate as desired.
>
> Thanks,
>
> Jeff
>
> $ make
> mpicc -g -O0 -Wall -std=gnu99 -c bug.c -o bug.o
> mpicc -g -O0 -Wall -std=gnu99 safemalloc.o bug.o -lm -o bug.x
> rm bug.o
>
> ======== stuck in abort/finalize ========
>
> $ gdb ./bug.x
> GNU gdb 6.3.50-20050815 (Apple version gdb-1752) (Sat Jan 28 03:02:46 UTC 2012)
> Copyright 2004 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General Public License, and you are
> welcome to change it and/or distribute copies of it under certain conditions.
> Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB. Type "show warranty" for details.
> This GDB was configured as "x86_64-apple-darwin"...Reading symbols for
> shared libraries ...... done
>
> warning: Could not find object file
> "/Users/jhammond/eclipse/OSPRI/trunk/tests/devices/mpi-pt/bug.o" - no
> debug information available for "bug.c".
>
>
> (gdb) run
> Starting program:
> /Users/jhammond/eclipse/OSPRI/trunk/tests/devices/mpi-pt/bug.x
> Reading symbols for shared libraries +++++........................ done
> test done except for pthread shutdown
> 0: Progress
> all done
>
> ^C
> Program received signal SIGINT, Interrupt.
> 0x00007fff912fdbf2 in __psynch_mutexwait ()
> (gdb) bt
> #0 0x00007fff912fdbf2 in __psynch_mutexwait ()
> #1 0x00007fff8c80a1a1 in pthread_mutex_lock ()
> #2 0x000000010004912b in MPIU_Thread_CS_enter_lockname_recursive_impl_ ()
> #3 0x0000000100048d64 in MPI_Abort ()
> #4 0x0000000100000cc0 in main ()
> (gdb) quit
> The program is running. Exit anyway? (y or n) y
>
> $ cat bug.c
> #include <stdio.h>
> #include <stdlib.h>
> #include <unistd.h>
> #include <string.h>
> #include <assert.h>
> #include <limits.h>
> #include <pthread.h>
>
> #include <mpi.h>
>
> #define DEBUG
>
> pthread_t Progress_thread;
>
> static void * Progress_function(void * dummy)
> {
> int rank;
> MPI_Comm_rank(MPI_COMM_WORLD, &rank);
>
> while (1)
> {
> #ifdef DEBUG
> printf("%d: Progress \n", rank);
> #endif
> MPI_Probe(MPI_ANY_SOURCE, MPI_ANY_TAG, MPI_COMM_WORLD,
> MPI_STATUS_IGNORE);
> //usleep(500);
> }
>
> return NULL;
> }
>
> int main(int argc, char * argv[])
> {
> int rc;
> int rank, size;
> int provided;
>
> MPI_Init_thread(&argc, &argv, MPI_THREAD_MULTIPLE, &provided);
> if (provided!=MPI_THREAD_MULTIPLE) MPI_Abort(MPI_COMM_WORLD, 1);
>
> MPI_Comm_rank(MPI_COMM_WORLD, &rank);
> MPI_Comm_size(MPI_COMM_WORLD, &size);
>
> rc = pthread_create(&Progress_thread, NULL, &Progress_function, NULL);
> if (rc!=0) MPI_Abort(MPI_COMM_WORLD, rc);
>
> MPI_Barrier(MPI_COMM_WORLD);
>
> printf("test done except for pthread shutdown \n");
> fflush(stdout);
>
> MPI_Barrier(MPI_COMM_WORLD);
>
> rc = pthread_cancel(Progress_thread);
> if (rc!=0) MPI_Abort(MPI_COMM_WORLD, rc);
>
> void * rv;
> rc = pthread_join(Progress_thread, &rv);
> if (rc!=0) MPI_Abort(MPI_COMM_WORLD, rc);
>
> printf("all done \n");
> fflush(stdout);
>
> MPI_Abort(MPI_COMM_SELF, 2);
> MPI_Finalize();
>
> return 0;
> }
>
> ======== stuck in barrier ========
>
> $ gdb ./bug.x
> GNU gdb 6.3.50-20050815 (Apple version gdb-1752) (Sat Jan 28 03:02:46 UTC 2012)
> Copyright 2004 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General Public License, and you are
> welcome to change it and/or distribute copies of it under certain conditions.
> Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB. Type "show warranty" for details.
> This GDB was configured as "x86_64-apple-darwin"...Reading symbols for
> shared libraries ...... done
>
> warning: Could not find object file
> "/Users/jhammond/eclipse/OSPRI/trunk/tests/devices/mpi-pt/bug.o" - no
> debug information available for "bug.c".
>
>
> (gdb) run
> Starting program:
> /Users/jhammond/eclipse/OSPRI/trunk/tests/devices/mpi-pt/bug.x
> Reading symbols for shared libraries +++++........................ done
> before pthread shutdown
> 0: Progress
> after pthread shutdown
> ^C
> Program received signal SIGINT, Interrupt.
> 0x00007fff912fdbf2 in __psynch_mutexwait ()
> (gdb) bt
> #0 0x00007fff912fdbf2 in __psynch_mutexwait ()
> #1 0x00007fff8c80a1a1 in pthread_mutex_lock ()
> #2 0x000000010000f7eb in MPIU_Thread_CS_enter_lockname_recursive_impl_ ()
> #3 0x000000010000f4f7 in MPI_Barrier ()
> #4 0x0000000100000c4d in main ()
> (gdb) quit
> The program is running. Exit anyway? (y or n) y
> Jeffs-MacBook-Pro:mpi-pt jhammond$ cat bug.c
> #include <stdio.h>
> #include <stdlib.h>
> #include <unistd.h>
> #include <string.h>
> #include <assert.h>
> #include <limits.h>
> #include <pthread.h>
>
> #include <mpi.h>
>
> #define DEBUG
>
> pthread_t Progress_thread;
>
> static void * Progress_function(void * dummy)
> {
> int rank;
> MPI_Comm_rank(MPI_COMM_WORLD, &rank);
>
> while (1)
> {
> #ifdef DEBUG
> printf("%d: Progress \n", rank);
> #endif
> MPI_Probe(MPI_ANY_SOURCE, MPI_ANY_TAG, MPI_COMM_WORLD,
> MPI_STATUS_IGNORE);
> //usleep(500);
> }
>
> return NULL;
> }
>
> int main(int argc, char * argv[])
> {
> int rc;
> int rank, size;
> int provided;
>
> MPI_Init_thread(&argc, &argv, MPI_THREAD_MULTIPLE, &provided);
> if (provided!=MPI_THREAD_MULTIPLE) MPI_Abort(MPI_COMM_WORLD, 1);
>
> MPI_Comm_rank(MPI_COMM_WORLD, &rank);
> MPI_Comm_size(MPI_COMM_WORLD, &size);
>
> rc = pthread_create(&Progress_thread, NULL, &Progress_function, NULL);
> if (rc!=0) MPI_Abort(MPI_COMM_WORLD, rc);
>
> MPI_Barrier(MPI_COMM_WORLD);
>
> printf("before pthread shutdown \n");
> fflush(stdout);
>
> MPI_Barrier(MPI_COMM_WORLD);
>
> rc = pthread_cancel(Progress_thread);
> if (rc!=0) MPI_Abort(MPI_COMM_WORLD, rc);
>
> void * rv;
> rc = pthread_join(Progress_thread, &rv);
> if (rc!=0) MPI_Abort(MPI_COMM_WORLD, rc);
>
> printf("after pthread shutdown \n");
> fflush(stdout);
>
> MPI_Barrier(MPI_COMM_WORLD);
>
> printf("before MPI Abort/Finalize \n");
> fflush(stdout);
>
> MPI_Abort(MPI_COMM_SELF, 2);
> MPI_Finalize();
>
> printf("after MPI Abort/Finalize \n");
> fflush(stdout);
>
> return 0;
> }
>
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