[Darshan-users] darshan-2.2.6 incorrectly detects weak symbols

[Kevin Harms]

Myriam,

  ok. I had assumed static linking with this change. I'll have to go back and rethink it. thanks for the debug.

kevin

On May 7, 2013, at 7:26 AM, Myriam Botalla <myriam.botalla at bull.net> wrote:

> Hi Kevin
> Yes I had it! 
> The MPI symbols get different types in the executable and that is why checking the temporary binary could be the issue.
> Here is the output:
> 
> With Intel MPI 
> $ ldd IOR
> 	linux-vdso.so.1 =>  (0x00007fff49dff000)
> 	libdl.so.2 => /lib64/libdl.so.2 (0x000000381a000000)
> 	libm.so.6 => /lib64/libm.so.6 (0x000000381b000000)
> 	libmpi.so.4 => /opt/intel/impi/4.1.0.024/intel64/lib/libmpi.so.4 (0x00007f4c86af8000)
> 	libmpigf.so.4 => /opt/intel/impi/4.1.0.024/intel64/lib/libmpigf.so.4 (0x00007f4c868c8000)
> 	librt.so.1 => /lib64/librt.so.1 (0x000000381b800000)
> 	libpthread.so.0 => /lib64/libpthread.so.0 (0x000000381a800000)
> 	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003820400000)
> 	libc.so.6 => /lib64/libc.so.6 (0x000000381a400000)
> 	/lib64/ld-linux-x86-64.so.2 (0x0000003819c00000)
> $ nm IOR|grep -i "mpi_init"
>                 U MPI_Init
> $
> 	
> 
> With Open MPI
> $ ldd IOR
> 	linux-vdso.so.1 =>  (0x00007fff6b558000)
> 	libm.so.6 => /lib64/libm.so.6 (0x000000381b000000)
> 	libmpi.so.1 => /opt/mpi/bullxmpi/1.2.5.1/lib/libmpi.so.1 (0x00007ff47e698000)
> 	libdl.so.2 => /lib64/libdl.so.2 (0x000000381a000000)
> 	libnuma.so.1 => /usr/lib64/libnuma.so.1 (0x000000381b400000)
> 	librt.so.1 => /lib64/librt.so.1 (0x000000381b800000)
> 	libnsl.so.1 => /lib64/libnsl.so.1 (0x0000003cb8800000)
> 	libutil.so.1 => /lib64/libutil.so.1 (0x0000003cb9000000)
> 	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003820400000)
> 	libpthread.so.0 => /lib64/libpthread.so.0 (0x000000381a800000)
> 	libc.so.6 => /lib64/libc.so.6 (0x000000381a400000)
> 	/lib64/ld-linux-x86-64.so.2 (0x0000003819c00000)
> $ nm IOR|grep -i "mpi_init"
>                 U MPI_Init
> $
> 
> Thanks
> Myriam.
> 
> ________________________________________
> From: Kevin Harms [harms at alcf.anl.gov]
> Sent: Monday, May 06, 2013 5:26 PM
> To: Myriam Botalla
> Cc: darshan-users at lists.mcs.anl.gov
> Subject: Re: [Darshan-users] darshan-2.2.6 incorrectly detects weak symbols
> 
> Myriam,
> 
>  can you link an executable and then give the output of:
>  nm <exe> | grep -i mpi_init
> 
> thanks,
> kevin
> 
> On May 6, 2013, at 8:12 AM, Myriam Botalla <myriam.botalla at bull.net> wrote:
> 
>> Hi Phil,
>> I've just upgraded to darshan-2.2.6 and got a serious limitation to instrumentation.
>> Whether it is Intel MPI or OpenMPI I could not generate any darshan logs.
>> It appears the fix added to check for fake MPI skips over instrumentation on our clusters.
>> 
>> Actually both MPI implementations use the weak symbols:
>> 
>> $ nm /opt/intel/impi/4.1.0.024/intel64/lib/libmpi.so.4|grep -i MPI_Init
>> 0000000000602a74 B I_MPI_Initialized
>> 0000000000068900 T I_MPI_init_dat_regestry_info
>> 00000000001e6300 T MPID_nem_impi_init_shm_configuration
>> 00000000001a87a0 W MPI_Init
>> 00000000001b39d0 W MPI_Init_thread
>> 00000000001a89f0 W MPI_Initialized
>> 00000000001a87a0 T PMPI_Init
>> 00000000001b39d0 T PMPI_Init_thread
>> 00000000001a89f0 T PMPI_Initialized
>> $
>> $ nm /opt/mpi/bullxmpi/1.2.4.1/lib/libmpi.so|grep -i MPI_Init
>> 000000000007b2d0 W MPI_Init
>> 000000000007b4a0 W MPI_Init_thread
>> 000000000007b6b0 W MPI_Initialized
>> 000000000007b2d0 T PMPI_Init
>> 000000000007b4a0 T PMPI_Init_thread
>> 000000000007b6b0 T PMPI_Initialized
>> 0000000000066ab0 T ompi_init_preconnect_mpi
>> 0000000000064980 T ompi_mpi_init
>> 0000000000397358 B ompi_mpi_init_started
>> 0000000000397359 B ompi_mpi_initialized
>> $
>> 
>> Now the test for weak symbols is applied to the temporary binary. Is that the issue?
>> Thanks,
>> Myriam.
>> 
>> _______________________________________________
>> Darshan-users mailing list
>> Darshan-users at lists.mcs.anl.gov
>> https://lists.mcs.anl.gov/mailman/listinfo/darshan-users
> 

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