Comments (11)
gllort
commented on August 11, 2024
Hi Jean,
Could you please share the output of the "ldd" and "nm" commands on the
application binary?
Thanks!
-- G.
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emercadal
commented on August 11, 2024
Closed due to inactivity.
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vineetsoni
commented on August 11, 2024
Hello,
I have the same error with Extrae 3.8.3 installed using GCC 10.3.1 on Fedora 33. The configuration command of Extrae is:
../configure --prefix=<path-to-install> --with-papi=/usr --with-binutils=/usr --with-elf=/usr --with-libz=/usr --with-unwind=/usr --with-mpi=<path-to-intelmpi> --enable-posix-clock --without-dyninst --enable-openmpI am testing with the Extrae example of MPI+OMP. The output of ldd pi is:
linux-vdso.so.1 (0x00007ffc92939000)
libmpifort.so.12 => <path-to-intelmpi>/lib/libmpifort.so.12 (0x00007f2bc7585000)
libmpi.so.12 => <path-to-intelmpi>/lib/libmpi.so.12 (0x00007f2bc5e26000)
librt.so.1 => /lib64/librt.so.1 (0x00007f2bc5e03000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f2bc5de1000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f2bc5dd8000)
libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f2bc5d97000)
libc.so.6 => /lib64/libc.so.6 (0x00007f2bc5bcc000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f2bc5bb1000)
libfabric.so.1 => <path-to-intelmpi>/libfabric/lib/libfabric.so.1 (0x00007f2bc596f000)
/lib64/ld-linux-x86-64.so.2 (0x00007f2bc7946000)nm /lib64/libgomp.so.1 has no symbols.
ldd ${EXTRAE_HOME}/lib/libompitrace.so does not have libgomp.so.1 but has:
linux-vdso.so.1 (0x00007fff9338c000)
libmpi.so.12 => <path-to-intelmpi>/lib/libmpi.so.12 (0x00007f1936eeb000)
libpapi.so.6.0 => /usr/lib64/libpapi.so.6.0 (0x00007f1936e5e000)
libunwind.so.8 => /usr/lib64/libunwind.so.8 (0x00007f1936e44000)
libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x00007f1936cb9000)
libdl.so.2 => /usr/lib64/libdl.so.2 (0x00007f1936cb2000)
libz.so.1 => /usr/lib64/libz.so.1 (0x00007f1936c96000)
librt.so.1 => /usr/lib64/librt.so.1 (0x00007f1936c8b000)
libc.so.6 => /usr/lib64/libc.so.6 (0x00007f1936ac0000)
/lib64/ld-linux-x86-64.so.2 (0x00007f193922a000)
libfabric.so.1 => /usr/lib64/libfabric.so.1 (0x00007f19368ab000)
libgcc_s.so.1 => /usr/lib64/libgcc_s.so.1 (0x00007f1936890000)
libpfm.so.4 => /usr/lib64/libpfm.so.4 (0x00007f1936632000)
libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00007f193660e000)
liblzma.so.5 => /usr/lib64/liblzma.so.5 (0x00007f19365e2000)
libm.so.6 => /usr/lib64/libm.so.6 (0x00007f193649c000)
librdmacm.so.1 => /usr/lib64/librdmacm.so.1 (0x00007f193647f000)
libefa.so.1 => /usr/lib64/libefa.so.1 (0x00007f1936475000)
libnl-3.so.200 => /usr/lib64/libnl-3.so.200 (0x00007f1936452000)
libnl-route-3.so.200 => /usr/lib64/libnl-route-3.so.200 (0x00007f19363cd000)
libpsm_infinipath.so.1 => /usr/lib64/libpsm_infinipath.so.1 (0x00007f1936372000)
libpsm2.so.2 => /usr/lib64/libpsm2.so.2 (0x00007f1936307000)
libnuma.so.1 => /usr/lib64/libnuma.so.1 (0x00007f19362f9000)
libibverbs.so.1 => /usr/lib64/libibverbs.so.1 (0x00007f19362d8000)
libinfinipath.so.4 => /usr/lib64/libinfinipath.so.4 (0x00007f19362c5000)
libuuid.so.1 => /usr/lib64/libuuid.so.1 (0x00007f19362bc000)Do you see anything wrong here?
Thanks,
Vineet
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gllort
commented on August 11, 2024
Hi Vineet, this part looks good to me. Can you please check some additional things?
- Is the section 'openmp' in the configuration file 'extrae.xml' set to 'enabled="yes"'?
- Can you post the output of 'nm pi | grep -i gomp'?
- Can you post the full execution output?
Thanks!
-- G.
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vineetsoni
commented on August 11, 2024
Hi German,
Here are the answers:
- Is the section 'openmp' in the configuration file 'extrae.xml' set to 'enabled="yes"'?
<openmp enabled="yes" ompt="no">
<locks enabled="no" />
<taskloop enabled="no" />
<counters enabled="yes" />
</openmp>
- Can you post the output of 'nm pi | grep -i gomp'?
U GOMP_parallel@@GOMP_4.0
- Can you post the full execution output?
Extrae: WARNING! omp_get_thread_num_real is a NULL pointer. Did the initialization of this module trigger? Retrying initialization...
Welcome to Extrae 3.8.3
Extrae: Detected GOMP version is 4.5
Extrae: Detected and hooked OpenMP runtime: [GNU GOMP]
Extrae: OMP_NUM_THREADS set to 4
Extrae: Parsing the configuration file (../extrae.xml) begins
Extrae: Tracing package is located on /home/vsoni/tools/install/extrae-3.8.3
Extrae: Generating intermediate files for Paraver traces.
Extrae: MPI routines will collect HW counters information.
Extrae: OpenMP routines will collect HW counters information.
Extrae: WARNING! omp_get_thread_num_real is a NULL pointer. Did the initialization of this module trigger? Retrying initialization...
Extrae: WARNING! omp_get_thread_num_real is a NULL pointer. Did the initialization of this module trigger? Retrying initialization...
Extrae: WARNING! You have ended executing Extrae's omp_get_thread_num weak symbol! That's likely to happen when you load the tracing library for OpenMP, but your application is not compiled/linked against OpenMP.
Extrae: WARNING! omp_get_thread_num_real is a NULL pointer. Did the initialization of this module trigger? Retrying initialization...
Extrae: WARNING! You have ended executing Extrae's omp_get_thread_num weak symbol! That's likely to happen when you load the tracing library for OpenMP, but your application is not compiled/linked against OpenMP.
Extrae: WARNING! omp_get_thread_num_real is a NULL pointer. Did the initialization of this module trigger? Retrying initialization...
Extrae: WARNING! You have ended executing Extrae's omp_get_thread_num weak symbol! That's likely to happen when you load the tracing library for OpenMP, but your application is not compiled/linked against OpenMP.
It continues printing these messages and never seems to actually start/end the computation.
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gllort
commented on August 11, 2024
Hi Vineet, can you please also share the execution script where the LD_PRELOAD variable is set? Thanks!
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vineetsoni
commented on August 11, 2024
Here's the trace.sh:
#!/bin/bash
source /home/vsoni/tools/install/extrae-3.8.3/etc/extrae.sh
export OMP_NUM_THREADS=4
export EXTRAE_CONFIG_FILE=../extrae.xml
export LD_PRELOAD=${EXTRAE_HOME}/lib/libompitrace.so # For C apps
#export LD_PRELOAD=${EXTRAE_HOME}/lib/libompitracef.so # For Fortran apps
## Run the desired program
$*
And, I launched it using mpirun -np 2 ./trace.sh ./pi
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vineetsoni
commented on August 11, 2024
Is it normal that ldd ${EXTRAE_HOME}/lib/libompitrace.so shows that libgomp.so isn't there in the dependency?
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gllort
commented on August 11, 2024
Hi Vineet, yes, this is normal. The tracing library does not call the symbols in libgomp directly, so it's not required as a dependency. Can you try disabling the following option in the extrae.xml file?
<counters enabled="no" ...
If the issue is now fixed, the problem seems to come from the default installation of PAPI (library to read hardware counters), that includes many modules, but particularly also the mx module for Myrinet statistics. This seems to get stuck during initialization. Our recommendation would be to install PAPI from sources only with the components you may need (typically the default is fine and no extra modules are needed). PAPI can be obtained from https://icl.utk.edu/papi and installed in your user's space with the default options: ./configure --prefix=<install-path> && make && make install
Then you can reconfigure Extrae to use this version of PAPI adding the flag --with-papi=<install-path> to the configure line. Also, rebuild is needed after changing the configure options: make clean && make && make install
Hope this helps!
-- G.
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vineetsoni
commented on August 11, 2024
Indeed, disabling the counters works!
I will install Extrae with PAPI built from the source.
Thanks!
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gllort
commented on August 11, 2024
Cheers! :)
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