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jpsreport, warning during build process on JURECA #805

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gjaeger opened this issue Jun 25, 2020 · 6 comments
Closed

jpsreport, warning during build process on JURECA #805

gjaeger opened this issue Jun 25, 2020 · 6 comments

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@gjaeger
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gjaeger commented Jun 25, 2020 •
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When compiling on JURECA (cmake 3.14.0, Boost 1.69.0, Python 3.6.8) I get the following hints for jpsreport:

relating to OpenMP:

./jpscore/jpsreport/Analysis.cpp:319: Warnung: »#pragma omp parallel« wird ignoriert [-Wunknown-pragmas]
 #pragma omp parallel for

./jpscore/jpsreport/Analysis.cpp:344: Warnung: »#pragma omp parallel« wird ignoriert [-Wunknown-pragmas]
 #pragma omp parallel for

./jpscore/jpsreport/Analysis.cpp:367: Warnung: »#pragma omp parallel« wird ignoriert [-Wunknown-pragmas]
 #pragma omp parallel for

./jpscore/jpsreport/Analysis.cpp:391: Warnung: »#pragma omp parallel« wird ignoriert [-Wunknown-pragmas]
 #pragma omp parallel for

./jpscore/jpsreport/Analysis.cpp:420: Warnung: »#pragma omp parallel« wird ignoriert [-Wunknown-pragmas]
 #pragma omp parallel for

./jpscore/jpsreport/Analysis.cpp:449: Warnung: »#pragma omp parallel« wird ignoriert [-Wunknown-pragmas]
 #pragma omp parallel for

relating to Boost and Python:

In file included from /usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/io.hpp:19,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/PedData.h:37,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/Analysis.h:39,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/Analysis.cpp:31:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp: In Elementfunktion »void boost::numeric::ublas::matrix_binary<E1, E2, F>::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)«:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: Warnung: diese »if«-Klausel beschützt nicht … [-Wmisleading-indentation]
                 if (it2_ != it2_end_)
                 ^~
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: Anmerkung: … diese Anweisung, aber letztere ist verwirrend eingerückt, als wäre sie abhängig von »if«
                     if (it2_ != it2_end_) {
                     ^~
In file included from /usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/io.hpp:19,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/general/../methods/PedData.h:37,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/general/../Analysis.h:39,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/general/ArgumentParser.cpp:31:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp: In Elementfunktion »void boost::numeric::ublas::matrix_binary<E1, E2, F>::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)«:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: Warnung: diese »if«-Klausel beschützt nicht … [-Wmisleading-indentation]
                 if (it2_ != it2_end_)
                 ^~
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: Anmerkung: … diese Anweisung, aber letztere ist verwirrend eingerückt, als wäre sie abhängig von »if«
                     if (it2_ != it2_end_) {
                     ^~
In file included from /usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/io.hpp:19,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/PedData.h:37,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/PedData.cpp:29:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp: In Elementfunktion »void boost::numeric::ublas::matrix_binary<E1, E2, F>::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)«:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: Warnung: diese »if«-Klausel beschützt nicht … [-Wmisleading-indentation]
                 if (it2_ != it2_end_)
                 ^~
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: Anmerkung: … diese Anweisung, aber letztere ist verwirrend eingerückt, als wäre sie abhängig von »if«
                     if (it2_ != it2_end_) {
                     ^~
In file included from /usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/io.hpp:19,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/PedData.h:37,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/Method_A.h:34,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/Method_A.cpp:29:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp: In Elementfunktion »void boost::numeric::ublas::matrix_binary<E1, E2, F>::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)«:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: Warnung: diese »if«-Klausel beschützt nicht … [-Wmisleading-indentation]
                 if (it2_ != it2_end_)
                 ^~
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: Anmerkung: … diese Anweisung, aber letztere ist verwirrend eingerückt, als wäre sie abhängig von »if«
                     if (it2_ != it2_end_) {
                     ^~
In file included from /usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/io.hpp:19,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/../methods/PedData.h:37,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/../Analysis.h:39,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/Method_C.h:31,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/Method_B.h:32,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/Method_B.cpp:29:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp: In Elementfunktion »void boost::numeric::ublas::matrix_binary<E1, E2, F>::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)«:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: Warnung: diese »if«-Klausel beschützt nicht … [-Wmisleading-indentation]
                 if (it2_ != it2_end_)
                 ^~
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: Anmerkung: … diese Anweisung, aber letztere ist verwirrend eingerückt, als wäre sie abhängig von »if«
                     if (it2_ != it2_end_) {
                     ^~
In file included from /usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/io.hpp:19,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/../methods/PedData.h:37,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/../Analysis.h:39,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/Method_C.h:31,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/Method_C.cpp:29:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp: In Elementfunktion »void boost::numeric::ublas::matrix_binary<E1, E2, F>::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)«:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: Warnung: diese »if«-Klausel beschützt nicht … [-Wmisleading-indentation]
                 if (it2_ != it2_end_)
                 ^~
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: Anmerkung: … diese Anweisung, aber letztere ist verwirrend eingerückt, als wäre sie abhängig von »if«
                     if (it2_ != it2_end_) {
                     ^~
In file included from /usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/io.hpp:19,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/../methods/PedData.h:37,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/../Analysis.h:39,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/Method_D.h:31,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/Method_D.cpp:29:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp: In Elementfunktion »void boost::numeric::ublas::matrix_binary<E1, E2, F>::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)«:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: Warnung: diese »if«-Klausel beschützt nicht … [-Wmisleading-indentation]
                 if (it2_ != it2_end_)
                 ^~
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: Anmerkung: … diese Anweisung, aber letztere ist verwirrend eingerückt, als wäre sie abhängig von »if«
                     if (it2_ != it2_end_) {
                     ^~
In file included from /usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/io.hpp:19,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/../methods/PedData.h:37,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/../Analysis.h:39,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/Method_I.h:31,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/Method_I.cpp:29:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp: In Elementfunktion »void boost::numeric::ublas::matrix_binary<E1, E2, F>::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)«:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: Warnung: diese »if«-Klausel beschützt nicht … [-Wmisleading-indentation]
                 if (it2_ != it2_end_)
                 ^~
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: Anmerkung: … diese Anweisung, aber letztere ist verwirrend eingerückt, als wäre sie abhängig von »if«
                     if (it2_ != it2_end_) {
                     ^~
In file included from /usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/io.hpp:19,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/../methods/PedData.h:37,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/../Analysis.h:39,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/Method_J.h:31,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/Method_J.cpp:29:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp: In Elementfunktion »void boost::numeric::ublas::matrix_binary<E1, E2, F>::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)«:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: Warnung: diese »if«-Klausel beschützt nicht … [-Wmisleading-indentation]
                 if (it2_ != it2_end_)
                 ^~
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: Anmerkung: … diese Anweisung, aber letztere ist verwirrend eingerückt, als wäre sie abhängig von »if«
                     if (it2_ != it2_end_) {
                     ^~
In file included from /usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/io.hpp:19,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/methods/PedData.h:37,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/Analysis.h:39,
                 from /p/home/jusers/jaeger1/jureca/jpscore/jpsreport/main.cpp:32:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp: In Elementfunktion »void boost::numeric::ublas::matrix_binary<E1, E2, F>::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)«:
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: Warnung: diese »if«-Klausel beschützt nicht … [-Wmisleading-indentation]
                 if (it2_ != it2_end_)
                 ^~
/usr/local/software/jureca/Stages/2019a/software/Boost/1.69.0-gpsmpi-2019a.1-Python-3.6.8/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: Anmerkung: … diese Anweisung, aber letztere ist verwirrend eingerückt, als wäre sie abhängig von »if«
                     if (it2_ != it2_end_) {
                     ^~

The compilation of jpscore and jpsreport is completed without errors (cmake log - make log).
@chraibi
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chraibi commented Jun 25, 2020

@bsteinb any idea?

@zeroset
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zeroset commented Jun 25, 2020

For the first warnings the reason is that no OpenMP Module is loaded. We could think about suppressing this warning. But for the computation you should load a OpenMP module and recompile everything.

The Boost related warnings should be disabled... I have to check why boost is not marked as system includes...

@bsteinb
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bsteinb commented Jun 25, 2020

There is no OpenMP module (as in $ module load OpenMP), because OpenMP is included in the compiler. I think the issue here is that the OpenMP::OpenMP_CXX target is not mentioned in the target_link_libraries(report ...) statement in jpsreport/CMakeList.txt (similar to target_link_libraries(core ...) in libcore/CMakeList.txt).

@gjaeger
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gjaeger commented Jun 25, 2020

In addition, this was my workflow for building from source:

module load CMake
module load GCC
module load ParaStationMPI
module load Boost

mkdir build && cd build

../scripts/setup-deps.sh

cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$(pwd)/deps ..

make

@bsteinb
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bsteinb commented Jun 25, 2020 •
edited
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The Boost warning is due to a bug (not really a bug, more like a rough edge) in EasyBuild which we use to install the modules: easybuilders/easybuild-framework#3331

To work around this, you can do this before building:

$ export CPLUS_INCLUDE_PATH="$CPATH"
$ unset CPATH

Although that does seem like overkill for getting rid of a few warnings.

@zeroset zeroset mentioned this issue Jun 25, 2020
Merged
@bsteinb
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bsteinb commented Jun 25, 2020

BTW, the make log can be made much more useful by running make VERBOSE=1.

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@bsteinb @zeroset @chraibi @gjaeger