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Subject: Re: [OMPI users] openmpi 1.3.1: bind() failed: Permission denied (13)
From: Jerome BENOIT (ml.jgmbenoit_at_[hidden])
Date: 2009-04-02 14:41:41


-------- Original Message --------
Subject: Re: [OMPI users] openmpi 1.3.1: bind() failed: Permission denied (13)
Date: Fri, 03 Apr 2009 02:41:01 +0800
From: Jerome BENOIT <ml.jgmbenoit_at_[hidden]>
Reply-To: ml.jgmbenoit_at_[hidden]
To: Dirk Eddelbuettel <edd_at_[hidden]>
CC: ml.jgmbenoit_at_[hidden]
References: <49CE5244.2000607_at_[hidden]> <CF5D8E90-17CA-4B60-AE85-2BC2EE318AED_at_[hidden]> <49D4EF88.6060506_at_[hidden]> <18901.114.820349.347227_at_ron.nulle.part>

Hello List,

so let me precise:

I submitted on a SLURM box the attached C source phello.c via sbatch with the attached script phello.sh

mpicc -o phello phello.c
sbatch phello.sh

I have set no MCA parameter, and the firewalls are off, and the kernels (2.6.16) were built with no Security feature.

I have also attached the error output.

Thanks in advance,
Jerome

Dirk Eddelbuettel wrote:
> On 3 April 2009 at 01:02, Jerome BENOIT wrote:
> | Hello List,
> |
> | I am trying to fix the following issue (with firewall off):
> |
> | [green][[32664,1],5][../../../../../../ompi/mca/btl/tcp/btl_tcp_component.c:596:mca_btl_tcp_component_create_listen] bind() failed: Permission denied (13)
> |
> | I have tried with new kernel without security features, but without success.
> |
> | Any hint to solve this issue is welcome.
>
> Look five lines below where Jeff told you to provide _complete_ information.
> How are we to guess what you did from a one-line error?
>
> Dirk
> |
> | Jeff Squyres wrote:
> | > Can you supply all the information listed here:
> | >
> | > http://www.open-mpi.org/community/help/
> | >
> | > We need to know exactly how you are invoking mpirun, what MCA parameters
> | > have been set, etc.
> | >
> | >
> | > On Mar 28, 2009, at 12:37 PM, Jerome BENOIT wrote:
> | >
> | >> Hello List,
> | >>
> | >> I have just tried the current SVN Debian package:
> | >> it does not work even without firewall
> | >>
> | >> Please find in attachement my test files and the associated outputs.
> | >>
> | >> hth,
> | >> Jerome
> | >>
> | >> Manuel Prinz wrote:
> | >> > Am Freitag, den 27.03.2009, 20:34 +0800 schrieb Jerome BENOIT:
> | >> >> I have just tried the Sid package (1.3-2), but it does not work
> | >> properly
> | >> >> (when the firewall are off)
> | >> >
> | >> > Though this should work, the version in Sid is broken in other
> | >> respects.
> | >> > I do not recommend using it.
> | >> >
> | >> >> I have just read that the current stable version for OpenMPI is now
> | >> 1.3.1:
> | >> >> I will give it a try once it will be packaged in Sid.
> | >> >
> | >> > I'm the Open MPI maintainer in Debian and am planning to upload a fixed
> | >> > version soon, possible around middle of next week. (It has to be
> | >> > coordinated with the release team.) There is a working version availble
> | >> > in SVN (try "debcheckout openmpi"). You can either build it yourself or
> | >> > I could build it for you. You can mail me in private if you'd like
> | >> me to
> | >> > do so. Please not that installing the new version will break other
> | >> > MPI-related Debian packages. I can explain you the details in private
> | >> > mail since I think this is off-topic for the list.
> | >> >
> | >> > Best regards
> | >> > Manuel
> | >> >
> | >> > _______________________________________________
> | >> > users mailing list
> | >> > users_at_[hidden]
> | >> > http://www.open-mpi.org/mailman/listinfo.cgi/users
> | >> >
> | >>
> | >> --
> | >> Jerome BENOIT
> | >> jgmbenoit_at_mailsnare_dot_net
> | >>
> | >> // `phello.c' MPI C file
> | >> //
> | >> // last major modification 2003/01/05
> | >> // last minor modification 2009/03/27
> | >> //
> | >>
> | >> // mpicc -o phello phello.c
> | >> // mpirun -np 5 phello
> | >>
> | >> #include <unistd.h>
> | >> #include <stdio.h>
> | >> #include <mpi.h>
> | >>
> | >> int main(int narg, char *args[]){
> | >> int rank,size;
> | >> char ProcessorName[MPI_MAX_PROCESSOR_NAME];
> | >> int ProcessorNameLength;
> | >>
> | >> MPI_Init(&narg,&args);
> | >>
> | >> MPI_Comm_rank(MPI_COMM_WORLD,&rank);
> | >> MPI_Comm_size(MPI_COMM_WORLD,&size);
> | >>
> | >> MPI_Get_processor_name(ProcessorName,&ProcessorNameLength);
> | >> sleep(11);
> | >> fprintf(stdout,
> | >> "Hello world! I am %d of %d and my name is `%s'\n",
> | >> rank,size,
> | >> ProcessorName);
> | >>
> | >> MPI_Finalize();
> | >>
> | >> return 0; }
> | >>
> | >> //
> | >> // End of file `phello.c'.
> | >>
> | >> <phello.sh>[green][[7042,1],6][../../../../../../ompi/mca/btl/tcp/btl_tcp_component.c:596:mca_btl_tcp_component_create_listen]
> | >> bind() failed: Permission denied (13)
> | >> [green][[7042,1],5][../../../../../../ompi/mca/btl/tcp/btl_tcp_component.c:596:mca_btl_tcp_component_create_listen]
> | >> bind() failed: Permission denied (13)
> | >> --------------------------------------------------------------------------
> | >>
> | >> At least one pair of MPI processes are unable to reach each other for
> | >> MPI communications. This means that no Open MPI device has indicated
> | >> that it can be used to communicate between these processes. This is
> | >> an error; Open MPI requires that all MPI processes be able to reach
> | >> each other. This error can sometimes be the result of forgetting to
> | >> specify the "self" BTL.
> | >>
> | >> Process 1 ([[7042,1],2]) is on host: violet
> | >> Process 2 ([[7042,1],5]) is on host: green
> | >> BTLs attempted: self sm tcp
> | >>
> | >> Your MPI job is now going to abort; sorry.
> | >> --------------------------------------------------------------------------
> | >>
> | >> --------------------------------------------------------------------------
> | >>
> | >> It looks like MPI_INIT failed for some reason; your parallel process is
> | >> likely to abort. There are many reasons that a parallel process can
> | >> fail during MPI_INIT; some of which are due to configuration or
> | >> environment
> | >> problems. This failure appears to be an internal failure; here's some
> | >> additional information (which may only be relevant to an Open MPI
> | >> developer):
> | >>
> | >> PML add procs failed
> | >> --> Returned "Unreachable" (-12) instead of "Success" (0)
> | >> --------------------------------------------------------------------------
> | >>
> | >> *** An error occurred in MPI_Init
> | >> *** before MPI was initialized
> | >> *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> | >> [violet:12941] Abort before MPI_INIT completed successfully; not able
> | >> to guarantee that all other processes were killed!
> | >> *** An error occurred in MPI_Init
> | >> *** before MPI was initialized
> | >> *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> | >> [green:13026] Abort before MPI_INIT completed successfully; not able
> | >> to guarantee that all other processes were killed!
> | >> --------------------------------------------------------------------------
> | >>
> | >> mpirun has exited due to process rank 2 with PID 12941 on
> | >> node violet exiting without calling "finalize". This may
> | >> have caused other processes in the application to be
> | >> terminated by signals sent by mpirun (as reported here).
> | >> --------------------------------------------------------------------------
> | >>
> | >> *** An error occurred in MPI_Init
> | >> *** before MPI was initialized
> | >> *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> | >> [blue:15300] Abort before MPI_INIT completed successfully; not able to
> | >> guarantee that all other processes were killed!
> | >> *** An error occurred in MPI_Init
> | >> *** before MPI was initialized
> | >> *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> | >> [indigo:12605] Abort before MPI_INIT completed successfully; not able
> | >> to guarantee that all other processes were killed!
> | >> *** An error occurred in MPI_Init
> | >> *** before MPI was initialized
> | >> *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> | >> [red:12874] Abort before MPI_INIT completed successfully; not able to
> | >> guarantee that all other processes were killed!
> | >> *** An error occurred in MPI_Init
> | >> *** An error occurred in MPI_Init
> | >> *** before MPI was initialized
> | >> *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> | >> [orange:14888] Abort before MPI_INIT completed successfully; not able
> | >> to guarantee that all other processes were killed!
> | >> *** before MPI was initialized
> | >> *** An error occurred in MPI_Init
> | >> *** An error occurred in MPI_Init
> | >> *** before MPI was initialized
> | >> *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> | >> *** before MPI was initialized
> | >> [yellow:11441] Abort before MPI_INIT completed successfully; not able
> | >> to guarantee that all other processes were killed!
> | >> *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> | >> *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
> | >> [orange:14887] Abort before MPI_INIT completed successfully; not able
> | >> to guarantee that all other processes were killed!
> | >> [yellow:11440] Abort before MPI_INIT completed successfully; not able
> | >> to guarantee that all other processes were killed!
> | >> [violet:12932] 8 more processes have sent help message
> | >> help-mca-bml-r2.txt / unreachable proc
> | >> [violet:12932] Set MCA parameter "orte_base_help_aggregate" to 0 to
> | >> see all help / error messages
> | >> [violet:12932] 8 more processes have sent help message
> | >> help-mpi-runtime / mpi_init:startup:internal-failure
> | >>
> | >> /local/benoit
> | >> /scratch/benoit
> | >> /local/benoit
> | >> /local/benoit/FAKEROOT
> | >>
> | >> <ATT8008991.txt>
> | >
> | >
> | _______________________________________________
> | users mailing list
> | users_at_[hidden]
> | http://www.open-mpi.org/mailman/listinfo.cgi/users
>


[green][[25547,1],6][../../../../../../ompi/mca/btl/tcp/btl_tcp_component.c:596:mca_btl_tcp_component_create_listen] bind() failed: Permission denied (13)
[green][[25547,1],5][../../../../../../ompi/mca/btl/tcp/btl_tcp_component.c:596:mca_btl_tcp_component_create_listen] bind() failed: Permission denied (13)
--------------------------------------------------------------------------
At least one pair of MPI processes are unable to reach each other for
MPI communications. This means that no Open MPI device has indicated
that it can be used to communicate between these processes. This is
an error; Open MPI requires that all MPI processes be able to reach
each other. This error can sometimes be the result of forgetting to
specify the "self" BTL.

  Process 1 ([[25547,1],12]) is on host: violet
  Process 2 ([[25547,1],5]) is on host: green
  BTLs attempted: self sm tcp

Your MPI job is now going to abort; sorry.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

  PML add procs failed
  --> Returned "Unreachable" (-12) instead of "Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[indigo:5078] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[indigo:5081] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[blue:5391] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[green:5033] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[yellow:5069] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
--------------------------------------------------------------------------
mpirun has exited due to process rank 2 with PID 5081 on
node indigo exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[orange:5032] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
*** An error occurred in MPI_Init
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[orange:5033] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[red:5047] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
[indigo:05071] 8 more processes have sent help message help-mca-bml-r2.txt / unreachable proc
[indigo:05071] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[indigo:05071] 7 more processes have sent help message help-mpi-runtime / mpi_init:startup:internal-failure