[Darshan-users] undefined reference to __wrap_printf

[Teng Wang]

Hi Shane,

Thanks for your help on this. I tried v3.1.3 and compiled successfully.
But when I ran the application, there was no *.log generated under the
log directory, and I also got a warning from the application:

 darshan library warning: unable to compress job data


May I know how to fix this?

Thanks,
Teng

On Thu, Jul 20, 2017 at 11:51 AM, Shane Snyder <ssnyder at mcs.anl.gov> wrote:

> Hi Teng,
>
> Thanks for reporting this. This is a really strange issue, but I can
> actually reproduce it, too. I'm going to keep digging and see if I can find
> the problem. Will keep you updated.
>
> The strange thing is that I was able to use version 3.1.4 successfully
> right before making the release available (i.e., the log @
> darshan-test/example-output/mpi-io-test-x86_64-3.1.4.darshan was
> generated using version 3.1.4 with static linking). Also strange is that
> our nightly testing is not catching this issue...
>
> FYI, version 3.1.3 and earlier work fine for me if you really need a quick
> resolution -- version 3.1.4 just fixed a couple of non-critical bugs in
> some darshan log parsing utilities, so there shouldn't be much functionally
> different between the versions.
>
> --Shane
>
>
> On 07/20/2017 12:43 PM, Teng Wang wrote:
>
> Hi,
>
>
> I'm having trouble when trying to statically link
>
> Darshan with mpich3.3 applications following the instructions
>
> here. Could you give me any suggestion on how to fix it?
>
>
> http://www.mcs.anl.gov/research/projects/darshan/docs/darshan-runtime.html
>
>
> Here is my steps:
>
> 1. Compile and install darshan 3.1.4
>
> tar -xvzf darshan-3.1.4.tar.gz
>
> cd darshan-3.1.4/darshan-runtime
>
> ./configure --with-mem-align=8 --with-log-path=<log directory>
> --prefix=<install directory> --with-jobid-env=PBS_JOBID --disable-cuserid
> CC=mpicc
>
> make
>
> make install
>
>
> 2. Create log directory, which successfully create the directory
>
> darshan-mk-log-dirs.pl
>
>
> 3. Generate wrapper
>
> darshan-gen-cc.pl `which mpicc` --output mpicc.darshan
>
>
> 4. Compile application (mpi-io-test.c) using mpicc.darshan
>
> mpicc.darshan mpi-io-test.c -o mpi-io-test
>
>
> After step 4, the following issue happened:
>
> initthread.c:(.text+0xc59d): undefined reference to `__wrap_fprintf'
>
> initthread.c:(.text+0xc5bd): undefined reference to `__wrap_fputs'
>
> /global/homes/t/user/software_install/mpich3.3a-static/lib/
> libmpi.a(lib_libmpi_la-finalize.o): In function `MPIR_Add_finalize':
>
> finalize.c:(.text+0x226e): undefined reference to `__wrap_fputs'
>
> finalize.c:(.text+0x227a): undefined reference to `__wrap_fflush'
>
> finalize.c:(.text+0x2286): undefined reference to `__wrap_fflush'
>
> /global/homes/t/user/software_install/mpich3.3a-static/lib/
> libmpi.a(lib_libmpi_la-util.o): In function `MPIDI_OFI_control_handler':
>
> util.c:(.text+0x17bc4): undefined reference to `__wrap_fprintf'
>
> /global/homes/t/user/software_install/mpich3.3a-static/lib/
> libmpi.a(lib_libmpi_la-ch4_globals.o): In function `MPID_Abort':
>
> ch4_globals.c:(.text+0x38b): undefined reference to `__wrap_fputs'
>
> ch4_globals.c:(.text+0x397): undefined reference to `__wrap_fflush'
>
> ch4_globals.c:(.text+0x3a3): undefined reference to `__wrap_fflush'
>
> /tmp/ccyntLoA.o: In function `main':
>
> mpi-io-test.c:(.text+0x5ae): undefined reference to `__wrap_printf'
>
> mpi-io-test.c:(.text+0x819): undefined reference to `__wrap_printf'
>
> /global/homes/t/user/software_install/mpich3.3a-static/lib/
> libmpi.a(lib_libmpi_la-contextid.o): In function `MPIR_Free_contextid':
>
> contextid.c:(.text+0x1c3f): undefined reference to `__wrap_fputs'
>
> contextid.c:(.text+0x1c4b): undefined reference to `__wrap_fflush'
>
> contextid.c:(.text+0x1c57): undefined reference to `__wrap_fflush'
>
>
>
> mpicc.darshan -show mpi-io-test.c -o mpi-io-test gave:
>
>
> gcc -L/usr/lib64/slurmpmi -L/global/common/cori/
> software/libfabric/1.4.1/gnu/lib mpi-io-test.c -o mpi-io-test
> -L/global/homes/t/user/software_install/darshan/lib -ldarshan -lz
> -Wl,@/global/homes/t/user/software_install/darshan/
> share/ld-opts/darshan-base-ld-opts -I/global/homes/t/user/
> software_install/mpich3.3a-static/include -L/global/homes/t/user/
> software_install/mpich3.3a-static/lib -lmpi -lpmi -lpmi -lpthread
> -lfabric -lrt -lpmi -L/global/homes/t/user/software_install/darshan/lib
> -Wl,--start-group -ldarshan -ldarshan-stubs -Wl,--end-group -lz -lrt
> -lpthread
>
>
> The strange thing is when I do
>
> nm libdarshan.a, it did show the functions (e.g. __wrap_printf) were
> linked to
>
> libdarshan.a.
>
>
> *0000000000002bf0 T __wrap__IO_getc*
>
> *0000000000002d80 T __wrap__IO_putc*
>
> *00000000000030b0 T __wrap___isoc99_fscanf*
>
> *0000000000001990 T __wrap_fclose*
>
> *00000000000011d0 T __wrap_fdopen*
>
> *0000000000001810 T __wrap_fflush*
>
> *0000000000002a60 T __wrap_fgetc*
>
> *0000000000003690 T __wrap_fgets*
>
> *0000000000000db0 T __wrap_fopen*
>
> *0000000000000fc0 T __wrap_fopen64*
>
> *00000000000026b0 T __wrap_fprintf*
>
> *0000000000001c80 T __wrap_fputc*
>
> *0000000000001fa0 T __wrap_fputs*
>
> *00000000000028d0 T __wrap_fread*
>
> *00000000000013d0 T __wrap_freopen*
>
> *00000000000015f0 T __wrap_freopen64*
>
> *00000000000032d0 T __wrap_fscanf*
>
> *0000000000003920 T __wrap_fseek*
>
> *0000000000003a30 T __wrap_fseeko*
>
> *0000000000003b40 T __wrap_fseeko64*
>
> *0000000000003c50 T __wrap_fsetpos*
>
>
> Thanks,
>
> Teng
>
>
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