[Darshan-users] undefined reference to __wrap_printf
Phil Carns
carns at mcs.anl.gov
Fri Jul 21 15:05:38 CDT 2017
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
>>>>
>>>>
>>>>
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>>>> <https://lists.mcs.anl.gov/mailman/listinfo/darshan-users>
>>>
>>>
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>>
>>
>>
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