Re: [mpich-discuss] MPI_Comm_Spawn causing zombies of hydra_pmi_proxy

26 Mar 2013

      Just for the record: I guess my zombie problem was caused by ignoring 
return codes unequal zero by using the workaround as described in 
http://lists.mpich.org/pipermail/discuss/2013-February/000429.html .

A dirty fix which allows to ignore non-zero return codes and get rid of 
zombies (caused by spawning processes) is to add something like

     int waitstatus, child_pid;
     while ((child_pid = waitpid(-1, &waitstatus, WNOHANG)) > 0)
     {
         printf("HYDRA: child of pid %d finished\n",child_pid);
     }

at the beginning of function HYDU_create_process in 
src/pm/hydra/utils/launch/launch.c .

Best regards
Silvan

On 21.03.2013 12:31, Silvan Brï¿½ndli wrote:
...
PS: Just some additional information on compilers: so far I used icpc,
when changing it to gcc-4.7.2 I still get the zombies. The only change
in the linked libraries is an additional
libdl.so.2 => /lib64/libdl.so.2
Any hint / idea?
Best regards
Silvan
On 19.03.2013 10:47, Silvan Brï¿½ndli wrote:
...
Dear Pavan,
in the attached example I use mpich3, but still I get the zombies. Is
there something wrong with
- my MPI function calls? (disconnect, finalize)
- my linked libraries? (see below)
Thanks in advance!
Best regards
Silvan
ldd_hi
     linux-vdso.so.1 (0x00007fffa01ff000)
     libmpichcxx.so.10 => /opt/mpich3/lib/libmpichcxx.so.10
(0x00007fdfec0e4000)
     libmpich.so.10 => /opt/mpich3/lib/libmpich.so.10
(0x00007fdfebc6f000)
     libopa.so.1 => /opt/mpich3/lib/libopa.so.1 (0x00007fdfeba6d000)
     libmpl.so.1 => /opt/mpich3/lib/libmpl.so.1 (0x00007fdfeb868000)
     libaio.so.1 => /lib64/libaio.so.1 (0x00007fdfeb666000)
     libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fdfeb449000)
     libm.so.6 => /lib64/libm.so.6 (0x00007fdfeb14e000)
     libstdc++.so.6 =>
/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/libstdc++.so.6
(0x00007fdfeae47000)
     libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fdfeac30000)
     libc.so.6 => /lib64/libc.so.6 (0x00007fdfea882000)
     libdl.so.2 => /lib64/libdl.so.2 (0x00007fdfea67e000)
     libgfortran.so.3 =>
/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/libgfortran.so.3
(0x00007fdfea361000)
     libquadmath.so.0 =>
/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/libquadmath.so.0
(0x00007fdfea12b000)
     /lib64/ld-linux-x86-64.so.2 (0x00007fdfec308000)
     librt.so.1 => /lib64/librt.so.1 (0x00007fdfe9f23000)
ldd_main
     linux-vdso.so.1 (0x00007fffeb1ff000)
     libmpichcxx.so.10 => /opt/mpich3/lib/libmpichcxx.so.10
(0x00007f6fc797e000)
     libmpich.so.10 => /opt/mpich3/lib/libmpich.so.10
(0x00007f6fc7509000)
     libopa.so.1 => /opt/mpich3/lib/libopa.so.1 (0x00007f6fc7307000)
     libmpl.so.1 => /opt/mpich3/lib/libmpl.so.1 (0x00007f6fc7102000)
     libaio.so.1 => /lib64/libaio.so.1 (0x00007f6fc6f00000)
     libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f6fc6ce3000)
     libm.so.6 => /lib64/libm.so.6 (0x00007f6fc69e8000)
     libstdc++.so.6 =>
/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/libstdc++.so.6
(0x00007f6fc66e1000)
     libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f6fc64ca000)
     libc.so.6 => /lib64/libc.so.6 (0x00007f6fc611c000)
     libdl.so.2 => /lib64/libdl.so.2 (0x00007f6fc5f18000)
     libgfortran.so.3 =>
/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/libgfortran.so.3
(0x00007f6fc5bfb000)
     libquadmath.so.0 =>
/usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/libquadmath.so.0
(0x00007f6fc59c5000)
     /lib64/ld-linux-x86-64.so.2 (0x00007f6fc7ba2000)
     librt.so.1 => /lib64/librt.so.1 (0x00007f6fc57bd000)
On 07.03.2013 17:23, Pavan Balaji wrote:
...
I just tried this with the mpich master and it seems to work correctly,
and there are no zombie processes (though I reduced the number of
iterations to 10000, instead of 200000).  This was a problem in mpich
once upon a time, but that was a few years ago.  Are you using the
latest version of mpich (3.0.2)?
-- Pavan
On 03/07/2013 09:44 AM US Central Time, Silvan Brï¿½ndli wrote:
...
PS: The attached programs are a simplification of my code. They
reproduce the zombie problem. Waiting for the 32k zombies takes a
while... but I expect the same behaviour as with my original code.
Am I missing something when finishing the called program? I just use
MPI_Comm_disconnect and MPI_Finalize.
Best regards
Silvan
main.cpp
#include <mpi.h>;
int main(int argc, char *argv[])
{
   int          myrank;
   int spawnerror;
   int value = 123;
   void *buf = &value;
   MPI_Comm child_comm;
if (MPI_Init(&argc,&argv)!=MPI_SUCCESS)
   {
     printf("MPI_Init failed");
   }
MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
char* hiargv[] = {"23",NULL};
   for(int i = 1; i <= 200000; i++)
   {
     value = i;
     printf("Main before spawn %d\n",i);
     MPI_Comm_spawn("./hi",hiargv, 1, MPI_INFO_NULL, myrank,
MPI_COMM_SELF, &child_comm, &spawnerror);
     MPI_Send(buf, 1, MPI_INTEGER, 0, 1, child_comm);
     MPI_Comm_disconnect(&child_comm);
   }
MPI_Finalize();
   return 0;
}
hi.cpp:
#include <mpi.h>;
int main(int argc, char** argv) {
   MPI_Comm parent;
   MPI_Status status;
   int err;
   int value = -1;
   void* buf= &value;
if (MPI_Init(&argc,&argv)!=MPI_SUCCESS)
   {
     printf("MPI_Init failed");
   }
   MPI_Comm_get_parent(&parent);
   if (parent == MPI_COMM_NULL) printf("No parent!");
MPI_Recv(buf, 1, MPI_INTEGER, 0, MPI_ANY_TAG, parent, &status);
   MPI_Comm_disconnect(&parent);
   err = MPI_Finalize();
   printf("hi finalized %d %d \n",err, value);
   return 0;
}
On 07.03.2013 12:38, Silvan Brï¿½ndli wrote:
...
Dear all,
again I have a question related to spawning processes. I understand
the
situation as follows:
My program A spawns program B. Program B spawns program C1, C2 ...
C10000 ...
Program Cx terminates correctly before Cx+1 is called, however
returning
1 to mpiexec. To handle this I use the workaround as described in
http://lists.mpich.org/pipermail/discuss/2013-February/000429.html
Now it looks like with every Spawn a "hydra_pmi_proxy" is started, the
calling program is mpiexec. When the program Cx is finished this
"hydra_pmi_proxy" remains as a zombie until the programs A, B and
mpiexec are finished. When approx. 32k of those "hydra_pmi_proxy"
exist
I get some problems (too many processes or something similar).
What can I do to finish "hydra_pmi_proxy" while my programs A, B and
mpiexec are still running?
I'm glad about every hint.
Best regards
Silvan
_______________________________________________
discuss mailing list     [email protected]
To manage subscription options or unsubscribe:
https://lists.mpich.org/mailman/listinfo/discuss
_______________________________________________
discuss mailing list     [email protected]
To manage subscription options or unsubscribe:
https://lists.mpich.org/mailman/listinfo/discuss
-- 
Dipl.-Ing. Silvan Brï¿½ndli
Numerische Strukturanalyse mit Anwendungen in der Schiffstechnik (M-10)

Technische Universitï¿½t Hamburg-Harburg
Schwarzenbergstraï¿½e 95c
21073 Hamburg

Tel.  : +49 (0)40 42878 - 6187
Fax.  : +49 (0)40 42878 - 6090
e-mail: [email protected]
www   : http://www.tuhh.de/skf

5th GACM Colloquium on Computational Mechanics
http://www.tu-harburg.de/gacm2013

Silvan Brändli

tags

participants (1)