[Darshan-users] undefined reference to __wrap_printf

Fri Jul 21 15:19:33 CDT 2017

Hi Phil,

Thanks for the suggestion. I solved this issue finally
by recompiling zlib.

Teng

On Fri, Jul 21, 2017 at 1:05 PM, Phil Carns <carns at mcs.anl.gov> wrote:

> It might be helpful to compare the mpich configure/compile lines between
> your two configurations too, in case there is some difference in mpich
> libraries that is triggering an issue.
>
> thanks,
> -Phil
>
>
> On 07/20/2017 05:35 PM, Shane Snyder wrote:
>
>
> On 07/20/2017 04:19 PM, Shane Snyder wrote:
>
> Hi Teng,
>
> First of all, I actually just got darshan 3.1.4 to properly generate a log
> when using static linking. I'm not sure what was leading to the problem I
> had earlier, but after reconfiguring and rebuilding the library, it works
> for me now. I also confirmed the nightly tests were working correctly --
> the log files were going to another spot that I wasn't expecting, so missed
> them the first time around. You may want to try something similar -- just
> rebuilding everything from scratch and trying again. I've also run into
> this problem in the past whenever I was accidentally pointing to an mpich
> build that defaults to using shared libraries rather than the static ones,
> so that could be another thing to check.
>
> As for the error you are getting with Darshan 3.1.3, I've actually never
> seen someone hit that before. That error would be due to the libz
> compression functions (deflate) returning some sort of error. Not exactly
> sure what could cause that, but is the application opening a really large
> amount of files or something like that? I suppose it's possible the
> compression routines could be running out of memory if there is too much
> log data they are trying to compress, but have never seen that happen
> before. If you aren't already, it might be worth trying a test program that
> does very basic I/O just to confirm that we can get Darshan working. One
> that we frequently use is mpi-io-test -- there is a version of this code in
> the darshan source @ darshan-test/regression/test-cases/src. You could
> try just building that and running it (it doesn't take any command line
> parameters) to see if that works?
>
>
> Oh, actually I just noticed in your emails that you were using
> mpi-io-test? That is pretty bizarre...
>
> What system are you running this on? A cluster? Your own personal machine?
> If possible, you might try running somewhere else so we can confirm the
> issue is some problem with the environment on the system you have been
> using... I can't think of why the deflate routines would fail when running
> something simple like mpi-io-test. But if needed, we could probably get you
> a patch or something that tries to give us more details on the libz error
> you are seeing.
>
> --Shane
>
>
> Thanks,
> --Shane
>
> On 07/20/2017 03:52 PM, Teng Wang wrote:
>
> 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/l
>> ibmpi.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/l
>> ibmpi.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/l
>> ibmpi.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/soft
>> ware_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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