[Darshan-users] undefined reference to __wrap_printf
Phil Carns
carns at mcs.anl.gov
Fri Jul 21 15:33:54 CDT 2017
Great news- I'm glad it's resolved!
On 07/21/2017 04:19 PM, Teng Wang wrote:
> 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
> <mailto: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 <mailto: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
>>>>> <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 <http://darshan-mk-log-dirs.pl/>
>>>>>
>>>>>
>>>>> 3. Generate wrapper
>>>>>
>>>>> darshan-gen-cc.pl <http://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
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Darshan-users mailing list
>>>>> Darshan-users at lists.mcs.anl.gov
>>>>> <mailto:Darshan-users at lists.mcs.anl.gov>
>>>>> https://lists.mcs.anl.gov/mailman/listinfo/darshan-users
>>>>> <https://lists.mcs.anl.gov/mailman/listinfo/darshan-users>
>>>>
>>>>
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>>>>
>>>
>>>
>>>
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>>
>>
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