subject:"\[OMPI users\] Memory allocation error when linking with MPI libraries"

Re: [OMPI users] Memory allocation error when linking with MPI libraries

2010-08-31 Thread Nicolas Deladerriere

Hi,

Thanks Nysal for these details.

I also fixed my memory allocation issue using environment variable
OMPI_MCA_memory_ptmalloc2_disable which is much more easier (at least in my
case) than compiled new openmpi package and install that new package.
The point is that it is a bit complicated to have information about this
variable (seems to be a secret variable !). Actually I have read that it
cannot be used as normal MCA parameter and cannot be set in configuration
file ( http://www.open-mpi.org/community/lists/users/2010/06/13208.php ).

When using this variable, I have added -x OMPI_MCA_memory_ptmalloc2_disable
option to my mpirun command line. Do I really have to do it ?
Is the environment variable (plus -x option if required) is still the only
solution to set this parameter to 1 ?

Regards,
Nicolas



2010/8/15 Nysal Jan 

> >What does it exactly imply to compile with this option ?
> Open MPI's internal malloc library (ptmalloc) will not be built/used. If
> you are using an RDMA capable interconnect such as Infiniband, you will not
> be able to use the "mpi_leave_pinned" feature. mpi_leave_pinned might
> improve performance for applications that reuse/repeatedly send from the
> same buffer. If you are not using such interconnects then there is no impact
> on performance. For more details see the FAQ entries (24-28) -
> http://www.open-mpi.org/faq/?category=openfabrics#large-message-leave-pinned
>
> --Nysal
>
>
>
> On Thu, Aug 12, 2010 at 6:30 PM, Nicolas Deladerriere <
> nicolas.deladerri...@gmail.com> wrote:
>
>> building openmpi with option "--without-memory-manager" fix my problem.
>>
>> What does it exactly imply to compile with this option ?
>> I guess all malloc use functions from libc instead of openmpi one, but
>> does it have an effect on performance or something else ?
>>
>> Nicolas
>>
>> 2010/8/8 Nysal Jan 
>>
>> What interconnect are you using? Infiniband? Use
>>> "--without-memory-manager" option while building ompi in order to disable
>>> ptmalloc.
>>>
>>> Regards
>>> --Nysal
>>>
>>>
>>> On Sun, Aug 8, 2010 at 7:49 PM, Nicolas Deladerriere <
>>> nicolas.deladerri...@gmail.com> wrote:
>>>
 Yes, I'am using 24G machine on 64 bit Linux OS.
 If I compile without wrapper, I did not get any problems.

 It seems that when I am linking with openmpi, my program use a kind of
 openmpi implemented malloc. Is it possible to switch it off in order ot 
 only
 use malloc from libc ?

 Nicolas

 2010/8/8 Terry Frankcombe 

 You're trying to do a 6GB allocate.  Can your underlying system handle
> that?  IF you compile without the wrapper, does it work?
>
> I see your executable is using the OMPI memory stuff.  IIRC there are
> switches to turn that off.
>
>
> On Fri, 2010-08-06 at 15:05 +0200, Nicolas Deladerriere wrote:
> > Hello,
> >
> > I'am having an sigsegv error when using simple program compiled and
> > link with openmpi.
> > I have reproduce the problem using really simple fortran code. It
> > actually does not even use MPI, but just link with mpi shared
> > libraries. (problem does not appear when I do not link with mpi
> > libraries)
> >% cat allocate.F90
> >program test
> >implicit none
> >integer, dimension(:), allocatable :: z
> >integer(kind=8) :: l
> >
> >write(*,*) "l ?"
> >read(*,*) l
> >
> >ALLOCATE(z(l))
> >z(1) = 111
> >z(l) = 222
> >DEALLOCATE(z)
> >
> >end program test
> >
> > I am using openmpi 1.4.2 and gfortran for my tests. Here is the
> > compilation :
> >
> >% ./openmpi-1.4.2/build/bin/mpif90 --showme -g -o testallocate
> > allocate.F90
> >gfortran -g -o testallocate allocate.F90
> > -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/include -pthread
> > -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib
> > -L/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib -lmpi_f90
> > -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl
> > -lutil -lm -ldl -pthread
> >
> > When I am running that test with different length, I sometimes get a
> > "Segmentation fault" error. Here are two examples using two specific
> > values, but error happens for many other values of length (I did not
> > manage to find which values of lenght gives that error)
> >
> >%  ./testallocate
> > l ?
> >16
> >Segmentation fault
> >% ./testallocate
> > l ?
> >20
> >
> > I used debugger with re-compiled version of openmpi using debug flag.
> > I got the folowing error in function sYSMALLOc
> >
> >Program received signal SIGSEGV, Segmentation fault.
> >0x2b70b3b3 in sYSMALLOc (nb=640016, av=0x2b930200)

Re: [OMPI users] Memory allocation error when linking with MPI libraries

2010-08-15 Thread Nysal Jan

>What does it exactly imply to compile with this option ?
Open MPI's internal malloc library (ptmalloc) will not be built/used. If you
are using an RDMA capable interconnect such as Infiniband, you will not be
able to use the "mpi_leave_pinned" feature. mpi_leave_pinned might improve
performance for applications that reuse/repeatedly send from the same
buffer. If you are not using such interconnects then there is no impact on
performance. For more details see the FAQ entries (24-28) -
http://www.open-mpi.org/faq/?category=openfabrics#large-message-leave-pinned

--Nysal


On Thu, Aug 12, 2010 at 6:30 PM, Nicolas Deladerriere <
nicolas.deladerri...@gmail.com> wrote:

> building openmpi with option "--without-memory-manager" fix my problem.
>
> What does it exactly imply to compile with this option ?
> I guess all malloc use functions from libc instead of openmpi one, but does
> it have an effect on performance or something else ?
>
> Nicolas
>
> 2010/8/8 Nysal Jan 
>
> What interconnect are you using? Infiniband? Use
>> "--without-memory-manager" option while building ompi in order to disable
>> ptmalloc.
>>
>> Regards
>> --Nysal
>>
>>
>> On Sun, Aug 8, 2010 at 7:49 PM, Nicolas Deladerriere <
>> nicolas.deladerri...@gmail.com> wrote:
>>
>>> Yes, I'am using 24G machine on 64 bit Linux OS.
>>> If I compile without wrapper, I did not get any problems.
>>>
>>> It seems that when I am linking with openmpi, my program use a kind of
>>> openmpi implemented malloc. Is it possible to switch it off in order ot only
>>> use malloc from libc ?
>>>
>>> Nicolas
>>>
>>> 2010/8/8 Terry Frankcombe 
>>>
>>> You're trying to do a 6GB allocate.  Can your underlying system handle
 that?  IF you compile without the wrapper, does it work?

 I see your executable is using the OMPI memory stuff.  IIRC there are
 switches to turn that off.


 On Fri, 2010-08-06 at 15:05 +0200, Nicolas Deladerriere wrote:
 > Hello,
 >
 > I'am having an sigsegv error when using simple program compiled and
 > link with openmpi.
 > I have reproduce the problem using really simple fortran code. It
 > actually does not even use MPI, but just link with mpi shared
 > libraries. (problem does not appear when I do not link with mpi
 > libraries)
 >% cat allocate.F90
 >program test
 >implicit none
 >integer, dimension(:), allocatable :: z
 >integer(kind=8) :: l
 >
 >write(*,*) "l ?"
 >read(*,*) l
 >
 >ALLOCATE(z(l))
 >z(1) = 111
 >z(l) = 222
 >DEALLOCATE(z)
 >
 >end program test
 >
 > I am using openmpi 1.4.2 and gfortran for my tests. Here is the
 > compilation :
 >
 >% ./openmpi-1.4.2/build/bin/mpif90 --showme -g -o testallocate
 > allocate.F90
 >gfortran -g -o testallocate allocate.F90
 > -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/include -pthread
 > -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib
 > -L/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib -lmpi_f90
 > -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl
 > -lutil -lm -ldl -pthread
 >
 > When I am running that test with different length, I sometimes get a
 > "Segmentation fault" error. Here are two examples using two specific
 > values, but error happens for many other values of length (I did not
 > manage to find which values of lenght gives that error)
 >
 >%  ./testallocate
 > l ?
 >16
 >Segmentation fault
 >% ./testallocate
 > l ?
 >20
 >
 > I used debugger with re-compiled version of openmpi using debug flag.
 > I got the folowing error in function sYSMALLOc
 >
 >Program received signal SIGSEGV, Segmentation fault.
 >0x2b70b3b3 in sYSMALLOc (nb=640016, av=0x2b930200)
 > at malloc.c:3239
 >3239set_head(remainder, remainder_size | PREV_INUSE);
 >Current language:  auto; currently c
 >(gdb) bt
 >#0  0x2b70b3b3 in sYSMALLOc (nb=640016,
 > av=0x2b930200) at malloc.c:3239
 >#1  0x2b70d0db in opal_memory_ptmalloc2_int_malloc
 > (av=0x2b930200, bytes=64) at malloc.c:4322
 >#2  0x2b70b773 in opal_memory_ptmalloc2_malloc
 > (bytes=64) at malloc.c:3435
 >#3  0x2b70a665 in opal_memory_ptmalloc2_malloc_hook
 > (sz=64, caller=0x2bf8534d) at hooks.c:667
 >#4  0x2bf8534d in _gfortran_internal_free ()
 > from /usr/lib64/libgfortran.so.1
 >#5  0x00400bcc in MAIN__ () at allocate.F90:11
 >#6  0x00400c4e in main ()
 >(gdb) display
 >(gdb) list
 >3234  if ((unsigned long)(size) >= (unsigned long)(nb +
 > MINSIZE)) {
 >

Re: [OMPI users] Memory allocation error when linking with MPI libraries

2010-08-12 Thread Nicolas Deladerriere

building openmpi with option "--without-memory-manager" fix my problem.

What does it exactly imply to compile with this option ?
I guess all malloc use functions from libc instead of openmpi one, but does
it have an effect on performance or something else ?

Nicolas

2010/8/8 Nysal Jan 

> What interconnect are you using? Infiniband? Use
> "--without-memory-manager" option while building ompi in order to disable
> ptmalloc.
>
> Regards
> --Nysal
>
>
> On Sun, Aug 8, 2010 at 7:49 PM, Nicolas Deladerriere <
> nicolas.deladerri...@gmail.com> wrote:
>
>> Yes, I'am using 24G machine on 64 bit Linux OS.
>> If I compile without wrapper, I did not get any problems.
>>
>> It seems that when I am linking with openmpi, my program use a kind of
>> openmpi implemented malloc. Is it possible to switch it off in order ot only
>> use malloc from libc ?
>>
>> Nicolas
>>
>> 2010/8/8 Terry Frankcombe 
>>
>> You're trying to do a 6GB allocate.  Can your underlying system handle
>>> that?  IF you compile without the wrapper, does it work?
>>>
>>> I see your executable is using the OMPI memory stuff.  IIRC there are
>>> switches to turn that off.
>>>
>>>
>>> On Fri, 2010-08-06 at 15:05 +0200, Nicolas Deladerriere wrote:
>>> > Hello,
>>> >
>>> > I'am having an sigsegv error when using simple program compiled and
>>> > link with openmpi.
>>> > I have reproduce the problem using really simple fortran code. It
>>> > actually does not even use MPI, but just link with mpi shared
>>> > libraries. (problem does not appear when I do not link with mpi
>>> > libraries)
>>> >% cat allocate.F90
>>> >program test
>>> >implicit none
>>> >integer, dimension(:), allocatable :: z
>>> >integer(kind=8) :: l
>>> >
>>> >write(*,*) "l ?"
>>> >read(*,*) l
>>> >
>>> >ALLOCATE(z(l))
>>> >z(1) = 111
>>> >z(l) = 222
>>> >DEALLOCATE(z)
>>> >
>>> >end program test
>>> >
>>> > I am using openmpi 1.4.2 and gfortran for my tests. Here is the
>>> > compilation :
>>> >
>>> >% ./openmpi-1.4.2/build/bin/mpif90 --showme -g -o testallocate
>>> > allocate.F90
>>> >gfortran -g -o testallocate allocate.F90
>>> > -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/include -pthread
>>> > -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib
>>> > -L/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib -lmpi_f90
>>> > -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl
>>> > -lutil -lm -ldl -pthread
>>> >
>>> > When I am running that test with different length, I sometimes get a
>>> > "Segmentation fault" error. Here are two examples using two specific
>>> > values, but error happens for many other values of length (I did not
>>> > manage to find which values of lenght gives that error)
>>> >
>>> >%  ./testallocate
>>> > l ?
>>> >16
>>> >Segmentation fault
>>> >% ./testallocate
>>> > l ?
>>> >20
>>> >
>>> > I used debugger with re-compiled version of openmpi using debug flag.
>>> > I got the folowing error in function sYSMALLOc
>>> >
>>> >Program received signal SIGSEGV, Segmentation fault.
>>> >0x2b70b3b3 in sYSMALLOc (nb=640016, av=0x2b930200)
>>> > at malloc.c:3239
>>> >3239set_head(remainder, remainder_size | PREV_INUSE);
>>> >Current language:  auto; currently c
>>> >(gdb) bt
>>> >#0  0x2b70b3b3 in sYSMALLOc (nb=640016,
>>> > av=0x2b930200) at malloc.c:3239
>>> >#1  0x2b70d0db in opal_memory_ptmalloc2_int_malloc
>>> > (av=0x2b930200, bytes=64) at malloc.c:4322
>>> >#2  0x2b70b773 in opal_memory_ptmalloc2_malloc
>>> > (bytes=64) at malloc.c:3435
>>> >#3  0x2b70a665 in opal_memory_ptmalloc2_malloc_hook
>>> > (sz=64, caller=0x2bf8534d) at hooks.c:667
>>> >#4  0x2bf8534d in _gfortran_internal_free ()
>>> > from /usr/lib64/libgfortran.so.1
>>> >#5  0x00400bcc in MAIN__ () at allocate.F90:11
>>> >#6  0x00400c4e in main ()
>>> >(gdb) display
>>> >(gdb) list
>>> >3234  if ((unsigned long)(size) >= (unsigned long)(nb +
>>> > MINSIZE)) {
>>> >3235remainder_size = size - nb;
>>> >3236remainder = chunk_at_offset(p, nb);
>>> >3237av->top = remainder;
>>> >3238set_head(p, nb | PREV_INUSE | (av != _arena ?
>>> > NON_MAIN_ARENA : 0));
>>> >3239set_head(remainder, remainder_size | PREV_INUSE);
>>> >3240check_malloced_chunk(av, p, nb);
>>> >3241return chunk2mem(p);
>>> >3242  }
>>> >3243
>>> >
>>> >
>>> > I also did the same test in C and I got the same problem.
>>> >
>>> > Does someone has any idea that could help me understand what's going
>>> > on ?
>>> >
>>> > Regards
>>> > Nicolas
>>> >
>>> > ___
>>> > users mailing list
>>> > us...@open-mpi.org
>>> >

Re: [OMPI users] Memory allocation error when linking with MPI libraries

2010-08-08 Thread Nysal Jan

What interconnect are you using? Infiniband? Use  "--without-memory-manager"
option while building ompi in order to disable ptmalloc.

Regards
--Nysal

On Sun, Aug 8, 2010 at 7:49 PM, Nicolas Deladerriere <
nicolas.deladerri...@gmail.com> wrote:

> Yes, I'am using 24G machine on 64 bit Linux OS.
> If I compile without wrapper, I did not get any problems.
>
> It seems that when I am linking with openmpi, my program use a kind of
> openmpi implemented malloc. Is it possible to switch it off in order ot only
> use malloc from libc ?
>
> Nicolas
>
> 2010/8/8 Terry Frankcombe 
>
> You're trying to do a 6GB allocate.  Can your underlying system handle
>> that?  IF you compile without the wrapper, does it work?
>>
>> I see your executable is using the OMPI memory stuff.  IIRC there are
>> switches to turn that off.
>>
>>
>> On Fri, 2010-08-06 at 15:05 +0200, Nicolas Deladerriere wrote:
>> > Hello,
>> >
>> > I'am having an sigsegv error when using simple program compiled and
>> > link with openmpi.
>> > I have reproduce the problem using really simple fortran code. It
>> > actually does not even use MPI, but just link with mpi shared
>> > libraries. (problem does not appear when I do not link with mpi
>> > libraries)
>> >% cat allocate.F90
>> >program test
>> >implicit none
>> >integer, dimension(:), allocatable :: z
>> >integer(kind=8) :: l
>> >
>> >write(*,*) "l ?"
>> >read(*,*) l
>> >
>> >ALLOCATE(z(l))
>> >z(1) = 111
>> >z(l) = 222
>> >DEALLOCATE(z)
>> >
>> >end program test
>> >
>> > I am using openmpi 1.4.2 and gfortran for my tests. Here is the
>> > compilation :
>> >
>> >% ./openmpi-1.4.2/build/bin/mpif90 --showme -g -o testallocate
>> > allocate.F90
>> >gfortran -g -o testallocate allocate.F90
>> > -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/include -pthread
>> > -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib
>> > -L/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib -lmpi_f90
>> > -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl
>> > -lutil -lm -ldl -pthread
>> >
>> > When I am running that test with different length, I sometimes get a
>> > "Segmentation fault" error. Here are two examples using two specific
>> > values, but error happens for many other values of length (I did not
>> > manage to find which values of lenght gives that error)
>> >
>> >%  ./testallocate
>> > l ?
>> >16
>> >Segmentation fault
>> >% ./testallocate
>> > l ?
>> >20
>> >
>> > I used debugger with re-compiled version of openmpi using debug flag.
>> > I got the folowing error in function sYSMALLOc
>> >
>> >Program received signal SIGSEGV, Segmentation fault.
>> >0x2b70b3b3 in sYSMALLOc (nb=640016, av=0x2b930200)
>> > at malloc.c:3239
>> >3239set_head(remainder, remainder_size | PREV_INUSE);
>> >Current language:  auto; currently c
>> >(gdb) bt
>> >#0  0x2b70b3b3 in sYSMALLOc (nb=640016,
>> > av=0x2b930200) at malloc.c:3239
>> >#1  0x2b70d0db in opal_memory_ptmalloc2_int_malloc
>> > (av=0x2b930200, bytes=64) at malloc.c:4322
>> >#2  0x2b70b773 in opal_memory_ptmalloc2_malloc
>> > (bytes=64) at malloc.c:3435
>> >#3  0x2b70a665 in opal_memory_ptmalloc2_malloc_hook
>> > (sz=64, caller=0x2bf8534d) at hooks.c:667
>> >#4  0x2bf8534d in _gfortran_internal_free ()
>> > from /usr/lib64/libgfortran.so.1
>> >#5  0x00400bcc in MAIN__ () at allocate.F90:11
>> >#6  0x00400c4e in main ()
>> >(gdb) display
>> >(gdb) list
>> >3234  if ((unsigned long)(size) >= (unsigned long)(nb +
>> > MINSIZE)) {
>> >3235remainder_size = size - nb;
>> >3236remainder = chunk_at_offset(p, nb);
>> >3237av->top = remainder;
>> >3238set_head(p, nb | PREV_INUSE | (av != _arena ?
>> > NON_MAIN_ARENA : 0));
>> >3239set_head(remainder, remainder_size | PREV_INUSE);
>> >3240check_malloced_chunk(av, p, nb);
>> >3241return chunk2mem(p);
>> >3242  }
>> >3243
>> >
>> >
>> > I also did the same test in C and I got the same problem.
>> >
>> > Does someone has any idea that could help me understand what's going
>> > on ?
>> >
>> > Regards
>> > Nicolas
>> >
>> > ___
>> > 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
>

Re: [OMPI users] Memory allocation error when linking with MPI libraries

2010-08-08 Thread Nicolas Deladerriere

Yes, I'am using 24G machine on 64 bit Linux OS.
If I compile without wrapper, I did not get any problems.

It seems that when I am linking with openmpi, my program use a kind of
openmpi implemented malloc. Is it possible to switch it off in order ot only
use malloc from libc ?

Nicolas

2010/8/8 Terry Frankcombe 

> You're trying to do a 6GB allocate.  Can your underlying system handle
> that?  IF you compile without the wrapper, does it work?
>
> I see your executable is using the OMPI memory stuff.  IIRC there are
> switches to turn that off.
>
>
> On Fri, 2010-08-06 at 15:05 +0200, Nicolas Deladerriere wrote:
> > Hello,
> >
> > I'am having an sigsegv error when using simple program compiled and
> > link with openmpi.
> > I have reproduce the problem using really simple fortran code. It
> > actually does not even use MPI, but just link with mpi shared
> > libraries. (problem does not appear when I do not link with mpi
> > libraries)
> >% cat allocate.F90
> >program test
> >implicit none
> >integer, dimension(:), allocatable :: z
> >integer(kind=8) :: l
> >
> >write(*,*) "l ?"
> >read(*,*) l
> >
> >ALLOCATE(z(l))
> >z(1) = 111
> >z(l) = 222
> >DEALLOCATE(z)
> >
> >end program test
> >
> > I am using openmpi 1.4.2 and gfortran for my tests. Here is the
> > compilation :
> >
> >% ./openmpi-1.4.2/build/bin/mpif90 --showme -g -o testallocate
> > allocate.F90
> >gfortran -g -o testallocate allocate.F90
> > -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/include -pthread
> > -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib
> > -L/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib -lmpi_f90
> > -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl
> > -lutil -lm -ldl -pthread
> >
> > When I am running that test with different length, I sometimes get a
> > "Segmentation fault" error. Here are two examples using two specific
> > values, but error happens for many other values of length (I did not
> > manage to find which values of lenght gives that error)
> >
> >%  ./testallocate
> > l ?
> >16
> >Segmentation fault
> >% ./testallocate
> > l ?
> >20
> >
> > I used debugger with re-compiled version of openmpi using debug flag.
> > I got the folowing error in function sYSMALLOc
> >
> >Program received signal SIGSEGV, Segmentation fault.
> >0x2b70b3b3 in sYSMALLOc (nb=640016, av=0x2b930200)
> > at malloc.c:3239
> >3239set_head(remainder, remainder_size | PREV_INUSE);
> >Current language:  auto; currently c
> >(gdb) bt
> >#0  0x2b70b3b3 in sYSMALLOc (nb=640016,
> > av=0x2b930200) at malloc.c:3239
> >#1  0x2b70d0db in opal_memory_ptmalloc2_int_malloc
> > (av=0x2b930200, bytes=64) at malloc.c:4322
> >#2  0x2b70b773 in opal_memory_ptmalloc2_malloc
> > (bytes=64) at malloc.c:3435
> >#3  0x2b70a665 in opal_memory_ptmalloc2_malloc_hook
> > (sz=64, caller=0x2bf8534d) at hooks.c:667
> >#4  0x2bf8534d in _gfortran_internal_free ()
> > from /usr/lib64/libgfortran.so.1
> >#5  0x00400bcc in MAIN__ () at allocate.F90:11
> >#6  0x00400c4e in main ()
> >(gdb) display
> >(gdb) list
> >3234  if ((unsigned long)(size) >= (unsigned long)(nb +
> > MINSIZE)) {
> >3235remainder_size = size - nb;
> >3236remainder = chunk_at_offset(p, nb);
> >3237av->top = remainder;
> >3238set_head(p, nb | PREV_INUSE | (av != _arena ?
> > NON_MAIN_ARENA : 0));
> >3239set_head(remainder, remainder_size | PREV_INUSE);
> >3240check_malloced_chunk(av, p, nb);
> >3241return chunk2mem(p);
> >3242  }
> >3243
> >
> >
> > I also did the same test in C and I got the same problem.
> >
> > Does someone has any idea that could help me understand what's going
> > on ?
> >
> > Regards
> > Nicolas
> >
> > ___
> > 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
>

Re: [OMPI users] Memory allocation error when linking with MPI libraries

2010-08-08 Thread Terry Frankcombe

You're trying to do a 6GB allocate.  Can your underlying system handle
that?  IF you compile without the wrapper, does it work?

I see your executable is using the OMPI memory stuff.  IIRC there are
switches to turn that off.


On Fri, 2010-08-06 at 15:05 +0200, Nicolas Deladerriere wrote:
> Hello,
> 
> I'am having an sigsegv error when using simple program compiled and
> link with openmpi.
> I have reproduce the problem using really simple fortran code. It
> actually does not even use MPI, but just link with mpi shared
> libraries. (problem does not appear when I do not link with mpi
> libraries)
>% cat allocate.F90
>program test
>implicit none
>integer, dimension(:), allocatable :: z
>integer(kind=8) :: l
> 
>write(*,*) "l ?"
>read(*,*) l
>
>ALLOCATE(z(l))
>z(1) = 111
>z(l) = 222
>DEALLOCATE(z)
> 
>end program test
> 
> I am using openmpi 1.4.2 and gfortran for my tests. Here is the
> compilation :
> 
>% ./openmpi-1.4.2/build/bin/mpif90 --showme -g -o testallocate
> allocate.F90
>gfortran -g -o testallocate allocate.F90
> -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/include -pthread
> -I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib
> -L/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib -lmpi_f90
> -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl
> -lutil -lm -ldl -pthread
> 
> When I am running that test with different length, I sometimes get a
> "Segmentation fault" error. Here are two examples using two specific
> values, but error happens for many other values of length (I did not
> manage to find which values of lenght gives that error)
> 
>%  ./testallocate
> l ?
>16
>Segmentation fault
>% ./testallocate
> l ?
>20
> 
> I used debugger with re-compiled version of openmpi using debug flag.
> I got the folowing error in function sYSMALLOc
> 
>Program received signal SIGSEGV, Segmentation fault.
>0x2b70b3b3 in sYSMALLOc (nb=640016, av=0x2b930200)
> at malloc.c:3239
>3239set_head(remainder, remainder_size | PREV_INUSE);
>Current language:  auto; currently c
>(gdb) bt
>#0  0x2b70b3b3 in sYSMALLOc (nb=640016,
> av=0x2b930200) at malloc.c:3239
>#1  0x2b70d0db in opal_memory_ptmalloc2_int_malloc
> (av=0x2b930200, bytes=64) at malloc.c:4322
>#2  0x2b70b773 in opal_memory_ptmalloc2_malloc
> (bytes=64) at malloc.c:3435
>#3  0x2b70a665 in opal_memory_ptmalloc2_malloc_hook
> (sz=64, caller=0x2bf8534d) at hooks.c:667
>#4  0x2bf8534d in _gfortran_internal_free ()
> from /usr/lib64/libgfortran.so.1
>#5  0x00400bcc in MAIN__ () at allocate.F90:11
>#6  0x00400c4e in main ()
>(gdb) display
>(gdb) list
>3234  if ((unsigned long)(size) >= (unsigned long)(nb +
> MINSIZE)) {
>3235remainder_size = size - nb;
>3236remainder = chunk_at_offset(p, nb);
>3237av->top = remainder;
>3238set_head(p, nb | PREV_INUSE | (av != _arena ?
> NON_MAIN_ARENA : 0));
>3239set_head(remainder, remainder_size | PREV_INUSE);
>3240check_malloced_chunk(av, p, nb);
>3241return chunk2mem(p);
>3242  }
>3243
> 
> 
> I also did the same test in C and I got the same problem. 
> 
> Does someone has any idea that could help me understand what's going
> on ?
> 
> Regards
> Nicolas
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

[OMPI users] Memory allocation error when linking with MPI libraries

2010-08-06 Thread Nicolas Deladerriere

Hello,

I'am having an sigsegv error when using simple program compiled and link
with openmpi.
I have reproduce the problem using really simple fortran code. It actually
does not even use MPI, but just link with mpi shared libraries. (problem
does not appear when I do not link with mpi libraries)
   % cat allocate.F90
   program test
   implicit none
   integer, dimension(:), allocatable :: z
   integer(kind=8) :: l

   write(*,*) "l ?"
   read(*,*) l

   ALLOCATE(z(l))
   z(1) = 111
   z(l) = 222
   DEALLOCATE(z)

   end program test

I am using openmpi 1.4.2 and gfortran for my tests. Here is the compilation
:

   % ./openmpi-1.4.2/build/bin/mpif90 --showme -g -o testallocate
allocate.F90
   gfortran -g -o testallocate allocate.F90
-I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/include -pthread
-I/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib
-L/s0/scr1/TOMOT_19311_HAL_/openmpi-1.4.2/build/lib -lmpi_f90 -lmpi_f77
-lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl
-pthread

When I am running that test with different length, I sometimes get a
"Segmentation fault" error. Here are two examples using two specific values,
but error happens for many other values of length (I did not manage to find
which values of lenght gives that error)

   %  ./testallocate
l ?
   16
   Segmentation fault
   % ./testallocate
l ?
   20

I used debugger with re-compiled version of openmpi using debug flag. I got
the folowing error in function sYSMALLOc

   Program received signal SIGSEGV, Segmentation fault.
   0x2b70b3b3 in sYSMALLOc (nb=640016, av=0x2b930200) at
malloc.c:3239
   3239set_head(remainder, remainder_size | PREV_INUSE);
   Current language:  auto; currently c
   (gdb) bt
   #0  0x2b70b3b3 in sYSMALLOc (nb=640016, av=0x2b930200) at
malloc.c:3239
   #1  0x2b70d0db in opal_memory_ptmalloc2_int_malloc
(av=0x2b930200, bytes=64) at malloc.c:4322
   #2  0x2b70b773 in opal_memory_ptmalloc2_malloc (bytes=64)
at malloc.c:3435
   #3  0x2b70a665 in opal_memory_ptmalloc2_malloc_hook
(sz=64, caller=0x2bf8534d) at hooks.c:667
   #4  0x2bf8534d in _gfortran_internal_free () from
/usr/lib64/libgfortran.so.1
   #5  0x00400bcc in MAIN__ () at allocate.F90:11
   #6  0x00400c4e in main ()
   (gdb) display
   (gdb) list
   3234  if ((unsigned long)(size) >= (unsigned long)(nb + MINSIZE)) {
   3235remainder_size = size - nb;
   3236remainder = chunk_at_offset(p, nb);
   3237av->top = remainder;
   3238set_head(p, nb | PREV_INUSE | (av != _arena ?
NON_MAIN_ARENA : 0));
   3239set_head(remainder, remainder_size | PREV_INUSE);
   3240check_malloced_chunk(av, p, nb);
   3241return chunk2mem(p);
   3242  }
   3243


I also did the same test in C and I got the same problem.

Does someone has any idea that could help me understand what's going on ?

Regards
Nicolas

Re: [OMPI users] Memory allocation error when linking with MPI libraries

Re: [OMPI users] Memory allocation error when linking with MPI libraries

Re: [OMPI users] Memory allocation error when linking with MPI libraries

Re: [OMPI users] Memory allocation error when linking with MPI libraries

Re: [OMPI users] Memory allocation error when linking with MPI libraries

Re: [OMPI users] Memory allocation error when linking with MPI libraries

[OMPI users] Memory allocation error when linking with MPI libraries

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