subject:"Re\: \[OMPI users\] 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

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

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