date:20130919

[OMPI users] Fwd: compilation aborted for Handler.cpp (code 2)

2013-09-19 Thread Syed Ahsan Ali

I am trying to compile openmpi-1.6.5 on fc16.x86_64 with icc and ifort
but getting the subject error. config.out and make.out is attached.
Following command was used for configure

 ./configure CC=icc CXX=icpc FC=ifort F77=ifort F90=ifort
--prefix=/home/openmpi_gfortran -enable-mpi-f90 --enable-mpi-f77 |&
tee config.out
Please help/advise.
Thank you and best regards
Ahsan
<>

Re: [OMPI users] openmpi, stdin and qlogic infiniband

2013-09-19 Thread Ralph Castain

All that's true - use of stdin isn't encouraged by any means. However, we do 
support it and I've never heard of an interaction between that support and 
infiniband. They are in totally different sections of the code, and shouldn't 
have any crossover.

What the error is saying is that it can't stat the stdin file descriptor, which 
makes me suspicious that something in the OFED support has tampered with it. 
Not sure why that would happen.

I'll have to defer to someone knowledgeable in that area.


On Sep 19, 2013, at 6:37 AM, Jeff Hammond  wrote:

> See this related post 
> http://lists.mpich.org/pipermail/discuss/2013-September/001452.html.
> 
> The only text in the MPI standard I could find related to stdin is "assuming 
> the MPI implementation supports stdin such that this works", which is not 
> what I'd call a ringing endorsement of the practice of using it.
> 
> Tell the AbInit people that they're wrong for using stdin.  There are lots of 
> cases where it won't work.
> 
> Jeff
> 
> 
> On Thu, Sep 19, 2013 at 6:42 AM, Fabrice Boyrie  
> wrote:
> >
> > Hello
> >
> > I have to compile a program (abinit) reading data from stdin and it
> > doesn't works.
> >
> >
> >   I made a simplified version of the program
> >
> >
> >
> > PROGRAM TESTSTDIN
> >
> >   use mpi
> >   integer ( kind = 4 ) error
> >   integer ( kind = 4 ) id
> >   integer ( kind = 4 ) p
> >   real ( kind = 8 ) wtime
> >   CHARACTER(LEN=255) a
> >   call MPI_Init ( error )
> >   call MPI_Comm_size ( MPI_COMM_WORLD, p, error )
> >   call MPI_Comm_rank ( MPI_COMM_WORLD, id, error )
> >
> >   if ( id == 0 ) then
> > PRINT*, "id0"
> > READ(5,'(A)') a
> >   end if
> >
> >   write ( *, '(a)' ) ' '
> >   write ( *, '(a,i8,a)' ) '  Process ', id, ' says "Hello, world!"'
> >
> >   if ( id == 0 ) then
> > write ( *, '(a)' ) 'READ from stdin'
> > write ( *, '(a)' ) a
> >   end if
> >   call MPI_Finalize ( error )
> >
> >   stop
> > end
> >
> >
> > I've tried openmpi 1.6.5 and 1.7.2
> > The fortran compiler is ifort (tried Version 14.0.0.080 Build 20130728
> > and Version 11.1Build 20100806)
> > (c compiler is gcc, centos 6.x, infiniband stack from qlogic
> > infinipath-libs-3.1-3420.1122_rhel6_qlc.x86_64)
> >
> > Trying with and without infiniband (qlogic card)
> >
> > mpirun -np 8 ./teststdin < /tmp/a
> > forrtl: Bad file descriptor
> > forrtl: severe (108): cannot stat file, unit 5, file /proc/43811/fd/0
> > Image  PCRoutineLine
> > Source
> > teststdin  0040BF48  Unknown   Unknown  Unknown
> >
> >
> >
> >  mpirun -mca mtl ^psm -mca btl self,sm -np 8 ./teststdin < /tmp/a
> >
> >  id0
> >   Process0 says "Hello, world!"
> > READ from stdin
> > zer
> >
> >   Process1 says "Hello, world!"
> > ...
> >
> >
> >
> > Is it a known problem ?
> >
> >  Fabrice BOYRIE
> >
> >
> > ___
> > users mailing list
> > us...@open-mpi.org
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> 
> 
> 
> --
> Jeff Hammond
> jeff.scie...@gmail.com
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] openmpi, stdin and qlogic infiniband

2013-09-19 Thread Fabrice Boyrie

Thanks for your answer I will forward it to an AbInit developper...

Fabrice BOYRIE

NB: The problems seems specific to my qlogic driver
(QLogicIB-Basic.RHEL6-x86_64.7.1.0.0.58.tgz). 


On Thu, Sep 19, 2013 at 08:37:18AM -0500, Jeff Hammond wrote:
> See this related post
> http://lists.mpich.org/pipermail/discuss/2013-September/001452.html.
> 
> The only text in the MPI standard I could find related to stdin is
> "assuming the MPI implementation supports stdin such that this works",
> which is not what I'd call a ringing endorsement of the practice of using
> it.
> 
> Tell the AbInit people that they're wrong for using stdin.  There are lots
> of cases where it won't work.
> 
> Jeff
> 
> 
> On Thu, Sep 19, 2013 at 6:42 AM, Fabrice Boyrie 
> wrote:
> >
> > Hello
> >
> > I have to compile a program (abinit) reading data from stdin and it
> > doesn't works.
> >
> >
> >   I made a simplified version of the program
> >
> >
> >
> > PROGRAM TESTSTDIN
> >
> >   use mpi
> >   integer ( kind = 4 ) error
> >   integer ( kind = 4 ) id
> >   integer ( kind = 4 ) p
> >   real ( kind = 8 ) wtime
> >   CHARACTER(LEN=255) a
> >   call MPI_Init ( error )
> >   call MPI_Comm_size ( MPI_COMM_WORLD, p, error )
> >   call MPI_Comm_rank ( MPI_COMM_WORLD, id, error )
> >
> >   if ( id == 0 ) then
> > PRINT*, "id0"
> > READ(5,'(A)') a
> >   end if
> >
> >   write ( *, '(a)' ) ' '
> >   write ( *, '(a,i8,a)' ) '  Process ', id, ' says "Hello, world!"'
> >
> >   if ( id == 0 ) then
> > write ( *, '(a)' ) 'READ from stdin'
> > write ( *, '(a)' ) a
> >   end if
> >   call MPI_Finalize ( error )
> >
> >   stop
> > end
> >
> >
> > I've tried openmpi 1.6.5 and 1.7.2
> > The fortran compiler is ifort (tried Version 14.0.0.080 Build 20130728
> > and Version 11.1Build 20100806)
> > (c compiler is gcc, centos 6.x, infiniband stack from qlogic
> > infinipath-libs-3.1-3420.1122_rhel6_qlc.x86_64)
> >
> > Trying with and without infiniband (qlogic card)
> >
> > mpirun -np 8 ./teststdin < /tmp/a
> > forrtl: Bad file descriptor
> > forrtl: severe (108): cannot stat file, unit 5, file /proc/43811/fd/0
> > Image  PCRoutineLine
> > Source
> > teststdin  0040BF48  Unknown   Unknown
>  Unknown
> >
> >
> >
> >  mpirun -mca mtl ^psm -mca btl self,sm -np 8 ./teststdin < /tmp/a
> >
> >  id0
> >   Process0 says "Hello, world!"
> > READ from stdin
> > zer
> >
> >   Process1 says "Hello, world!"
> > ...
> >
> >
> >
> > Is it a known problem ?
> >
> >  Fabrice BOYRIE
> >
> >
> > ___
> > users mailing list
> > us...@open-mpi.org
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> 
> 
> 
> --
> Jeff Hammond
> jeff.scie...@gmail.com

> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] openmpi, stdin and qlogic infiniband

2013-09-19 Thread Jeff Hammond

See this related post
http://lists.mpich.org/pipermail/discuss/2013-September/001452.html.

The only text in the MPI standard I could find related to stdin is
"assuming the MPI implementation supports stdin such that this works",
which is not what I'd call a ringing endorsement of the practice of using
it.

Tell the AbInit people that they're wrong for using stdin.  There are lots
of cases where it won't work.

Jeff


On Thu, Sep 19, 2013 at 6:42 AM, Fabrice Boyrie 
wrote:
>
> Hello
>
> I have to compile a program (abinit) reading data from stdin and it
> doesn't works.
>
>
>   I made a simplified version of the program
>
>
>
> PROGRAM TESTSTDIN
>
>   use mpi
>   integer ( kind = 4 ) error
>   integer ( kind = 4 ) id
>   integer ( kind = 4 ) p
>   real ( kind = 8 ) wtime
>   CHARACTER(LEN=255) a
>   call MPI_Init ( error )
>   call MPI_Comm_size ( MPI_COMM_WORLD, p, error )
>   call MPI_Comm_rank ( MPI_COMM_WORLD, id, error )
>
>   if ( id == 0 ) then
> PRINT*, "id0"
> READ(5,'(A)') a
>   end if
>
>   write ( *, '(a)' ) ' '
>   write ( *, '(a,i8,a)' ) '  Process ', id, ' says "Hello, world!"'
>
>   if ( id == 0 ) then
> write ( *, '(a)' ) 'READ from stdin'
> write ( *, '(a)' ) a
>   end if
>   call MPI_Finalize ( error )
>
>   stop
> end
>
>
> I've tried openmpi 1.6.5 and 1.7.2
> The fortran compiler is ifort (tried Version 14.0.0.080 Build 20130728
> and Version 11.1Build 20100806)
> (c compiler is gcc, centos 6.x, infiniband stack from qlogic
> infinipath-libs-3.1-3420.1122_rhel6_qlc.x86_64)
>
> Trying with and without infiniband (qlogic card)
>
> mpirun -np 8 ./teststdin < /tmp/a
> forrtl: Bad file descriptor
> forrtl: severe (108): cannot stat file, unit 5, file /proc/43811/fd/0
> Image  PCRoutineLine
> Source
> teststdin  0040BF48  Unknown   Unknown
 Unknown
>
>
>
>  mpirun -mca mtl ^psm -mca btl self,sm -np 8 ./teststdin < /tmp/a
>
>  id0
>   Process0 says "Hello, world!"
> READ from stdin
> zer
>
>   Process1 says "Hello, world!"
> ...
>
>
>
> Is it a known problem ?
>
>  Fabrice BOYRIE
>
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users




--
Jeff Hammond
jeff.scie...@gmail.com

Re: [OMPI users] openmpi, stdin and qlogic infiniband

2013-09-19 Thread Reuti

Hi,

Am 19.09.2013 um 13:42 schrieb Fabrice Boyrie:

> I have to compile a program (abinit) reading data from stdin and it
> doesn't works.
> 
>   I made a simplified version of the program
> 
> 
> I've tried openmpi 1.6.5 and 1.7.2
> The fortran compiler is ifort (tried Version 14.0.0.080 Build 20130728

Using:

openmpi-1.4.5_gcc_4.7.2_shared
openmpi-1.6.5_intel_12.1.5_static
openmpi-1.6.5_intel_13.1.3_static

it's working as intended for me - no Infiniband in the game though.

-- Reuti


> and Version 11.1Build 20100806)
> (c compiler is gcc, centos 6.x, infiniband stack from qlogic
> infinipath-libs-3.1-3420.1122_rhel6_qlc.x86_64)
> 
> Trying with and without infiniband (qlogic card)
> 
> mpirun -np 8 ./teststdin < /tmp/a
> forrtl: Bad file descriptor
> forrtl: severe (108): cannot stat file, unit 5, file /proc/43811/fd/0
> Image  PCRoutineLine
> Source 
> teststdin  0040BF48  Unknown   Unknown  Unknown
> 
> 
> 
> mpirun -mca mtl ^psm -mca btl self,sm -np 8 ./teststdin < /tmp/a
> 
> id0
>  Process0 says "Hello, world!"
> READ from stdin
> zer   
>   
>   
>  
> 
>  Process1 says "Hello, world!"
> ...
> 
> 
> 
> Is it a known problem ?
> 
> Fabrice BOYRIE
> 
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] Segmentation fault with fresh compilation of 1.7.2

2013-09-19 Thread Matthieu Brucher

Hi,

I tried with the latest nightly (well now it may not be the latest
anymore), and orte-info didn't crash. So I'll try again later with my
app.

thanks,

Matthieu

2013/9/15 Matthieu Brucher :
> I can try later this week, yes.
> Thanks
>
> Le 15 sept. 2013 19:09, "Ralph Castain"  a écrit :
>
>> Could you try the current 1.7.3 nightly tarball instead? I don't see a
>> problem there, and I'm wondering if this is something we already fixed. We
>> will be releasing 1.7.3 shortly and it is mostly complete at this time.
>>
>>
>> On Sep 15, 2013, at 10:43 AM, Matthieu Brucher
>>  wrote:
>>
>> Yes, ompi_info does not crash.
>>
>> Le 15 sept. 2013 18:05, "Ralph Castain"  a écrit :
>>>
>>> No - out of curiosity, does ompi_info work? I'm wondering if this is
>>> strictly an orte-info problem.
>>>
>>> On Sep 15, 2013, at 10:03 AM, Matthieu Brucher
>>>  wrote:
>>>
>>> Just --with-lsf. Perhaps because then it must be launched through lsf?
>>>
>>> Le 15 sept. 2013 18:02, "Ralph Castain"  a écrit :

 I'm not entirely sure - I don't see anything that would cause that
 problem in that location. How did you configure this?


 On Sep 12, 2013, at 3:17 AM, Matthieu Brucher
  wrote:

 > Hi,
 >
 > I compiled OpenMPI on a RHEL6 box with LSF support, but when I run
 > sonthing, it crashes. Also orte-info crashes:
 >
 > Package: Open MPI mbruc...@xxx.com Distribution
 >Open RTE: 1.7.2
 >  Open RTE repo revision: r28673
 >   Open RTE release date: Jun 26, 2013
 >OPAL: 1.7.2
 >  OPAL repo revision: r28673
 >   OPAL release date: Jun 26, 2013
 >Ident string: 1.7.2
 >  Prefix: /xxx/mbrucher/openmpi
 > Configured architecture: x86_64-unknown-linux-gnu
 >  Configure host: xxx.xxx.com
 >   Configured by: mbrucher
 >   Configured on: Thu Sep 12 10:22:06 BST 2013
 >  Configure host: xxx.xxx.com
 >Built by: mbrucher
 >Built on: Thu Sep 12 10:24:59 BST 2013
 >  Built host: xxx.xxx.com
 >  C compiler: gcc
 > C compiler absolute: /usr/bin/gcc
 >  C compiler family name: GNU
 >  C compiler version: 4.4.6
 >  Internal debug support: no
 > Memory profiling support: no
 > Memory debugging support: no
 > libltdl support: yes
 >   Heterogeneous support: no
 > orterun default --prefix: no
 >   MPI_WTIME support: gettimeofday
 > Symbol vis. support: yes
 >   FT Checkpoint support: no (checkpoint thread: no)
 > [abgengcluster:45509] *** Process received signal ***
 > [abgengcluster:45509] Signal: Segmentation fault (11)
 > [abgengcluster:45509] Signal code: Address not mapped (1)
 > [abgengcluster:45509] Failing at address: 0xf8
 > [abgengcluster:45509] [ 0] /lib64/libpthread.so.0() [0x3ffc00f4a0]
 > [abgengcluster:45509] [ 1]
 >
 > /xxx/mbrucher/openmpi/lib/libopen-pal.so.5(opal_libevent2019_event_priority_set+0x6f)
 > [0x2aae84a736ef]
 > [abgengcluster:45509] [ 2]
 > /xxx/mbrucher/openmpi/lib/libopen-rte.so.5(orte_iof_base_open+0x31c)
 > [0x2aae847edfbc]
 > [abgengcluster:45509] [ 3] orte-info(orte_info_open_components+0x71f)
 > [0x406b8f]
 > [abgengcluster:45509] [ 4] orte-info(main+0x93d) [0x40450d]
 > [abgengcluster:45509] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd)
 > [0x3ffb81ecdd]
 > [abgengcluster:45509] [ 6] orte-info() [0x403b09]
 > [abgengcluster:45509] *** End of error message ***
 > Segmentation fault (core dumped)
 >
 > Is there something that I missed?
 >
 > Cheers,
 >
 > Matthieu
 > --
 > Information System Engineer, Ph.D.
 > Blog: http://matt.eifelle.com
 > LinkedIn: http://www.linkedin.com/in/matthieubrucher
 > Music band: http://liliejay.com/
 > ___
 > users mailing list
 > us...@open-mpi.org
 > http://www.open-mpi.org/mailman/listinfo.cgi/users

 ___
 users mailing list
 us...@open-mpi.org
 http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>>> ___
>>> users mailing list
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>>>
>>>
>>> ___
>>> users mailing list
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>>
>>

[OMPI users] openmpi, stdin and qlogic infiniband

2013-09-19 Thread Fabrice Boyrie

Hello

I have to compile a program (abinit) reading data from stdin and it
doesn't works.


  I made a simplified version of the program



PROGRAM TESTSTDIN

  use mpi
  integer ( kind = 4 ) error
  integer ( kind = 4 ) id
  integer ( kind = 4 ) p
  real ( kind = 8 ) wtime
  CHARACTER(LEN=255) a
  call MPI_Init ( error )
  call MPI_Comm_size ( MPI_COMM_WORLD, p, error )
  call MPI_Comm_rank ( MPI_COMM_WORLD, id, error )

  if ( id == 0 ) then
PRINT*, "id0"
READ(5,'(A)') a
  end if

  write ( *, '(a)' ) ' '
  write ( *, '(a,i8,a)' ) '  Process ', id, ' says "Hello, world!"'

  if ( id == 0 ) then
write ( *, '(a)' ) 'READ from stdin'
write ( *, '(a)' ) a
  end if
  call MPI_Finalize ( error )

  stop
end


I've tried openmpi 1.6.5 and 1.7.2
The fortran compiler is ifort (tried Version 14.0.0.080 Build 20130728
and Version 11.1Build 20100806)
(c compiler is gcc, centos 6.x, infiniband stack from qlogic
infinipath-libs-3.1-3420.1122_rhel6_qlc.x86_64)

Trying with and without infiniband (qlogic card)

mpirun -np 8 ./teststdin < /tmp/a
forrtl: Bad file descriptor
forrtl: severe (108): cannot stat file, unit 5, file /proc/43811/fd/0
Image  PCRoutineLine
Source 
teststdin  0040BF48  Unknown   Unknown  Unknown



 mpirun -mca mtl ^psm -mca btl self,sm -np 8 ./teststdin < /tmp/a

 id0
  Process0 says "Hello, world!"
READ from stdin
zer 


   

  Process1 says "Hello, world!"
...



Is it a known problem ?

 Fabrice BOYRIE

[OMPI users] Fwd: compilation aborted for Handler.cpp (code 2)

Re: [OMPI users] openmpi, stdin and qlogic infiniband

Re: [OMPI users] openmpi, stdin and qlogic infiniband

Re: [OMPI users] openmpi, stdin and qlogic infiniband

Re: [OMPI users] openmpi, stdin and qlogic infiniband

Re: [OMPI users] Segmentation fault with fresh compilation of 1.7.2

[OMPI users] openmpi, stdin and qlogic infiniband

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