Yade

HPC error

Asked by mrhappy on 2020-07-27

The people at the Advanced Research Computing center at my University are trying to help me install YADE on the HPC. The following is message that I received from them. Can anyone help them address this issue? Thank you so much!

I configure using the following and that does get me a build environment

cmake -DPYTHON_VERSION=3.7.6 -DENABLE_VTK=off -DUSE_QT5=off -DENABLE_GUI=off -DENABLE_GTS=off -DENABLE_CGAL=off -DENABLE_PFVFLOW=off -DCMAKE_INSTALL_PREFIX=../install ../trunk

But when running make it gets to 92% then fails with a numpy error.

I will continue to work with this. Also if you have any other suggegestions that would be great.

[ 92%] Building CXX object py/CMakeFiles/_utils.dir/_utils.cpp.o
In file included from /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0,
from /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /scratch/st-apeirce-1/myYade/trunk/py/_utils.cpp:8:
/arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with " \
^
In file included from /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/boost-1.73.0-uc6u5oumzasbqciah7s3kcrdyvomakyk/include/boost/python/exception_translator.hpp:10:0,
from /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/boost-1.73.0-uc6u5oumzasbqciah7s3kcrdyvomakyk/include/boost/python.hpp:28,
from /scratch/st-apeirce-1/myYade/trunk/lib/base/Math.hpp:25,
from /scratch/st-apeirce-1/myYade/trunk/lib/computational-geometry/Hull2d.hpp:3,
from /scratch/st-apeirce-1/myYade/trunk/py/_utils.hpp:4,
from /scratch/st-apeirce-1/myYade/trunk/py/_utils.cpp:1:
/arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/boost-1.73.0-uc6u5oumzasbqciah7s3kcrdyvomakyk/include/boost/bind.hpp:41:273: note: #pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.
In file included from /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:21:0,
from /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from /scratch/st-apeirce-1/myYade/trunk/py/_utils.cpp:8:
/arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: error: 'int _import_array()' defined but not used [-Werror=unused-function]
_import_array(void)
^
cc1plus: all warnings being treated as errors
make[2]: *** [py/CMakeFiles/_utils.dir/_utils.cpp.o] Error 1
make[1]: *** [py/CMakeFiles/_utils.dir/all] Error 2
make: *** [all] Error 2
[anajmul@login03 build]$

Thank you!

Question information

Language:
English Edit question
Status:
Answered
For:
Yade Edit question
Assignee:
No assignee Edit question
Last query:
2020-07-27
Last reply:
2020-07-27
Robert Caulk (rcaulk) said : #1

Try adding the flag -DENABLE_USEFUL_WARNINGS=off

Le mar. 28 juil. 2020 à 00:35, mrhappy <email address hidden>
a écrit :

> New question #692095 on Yade:
> https://answers.launchpad.net/yade/+question/692095
>
> The people at the Advanced Research Computing center at my University are
> trying to help me install YADE on the HPC. The following is message that I
> received from them. Can anyone help them address this issue? Thank you so
> much!
>
>
>
> I configure using the following and that does get me a build environment
>
> cmake -DPYTHON_VERSION=3.7.6 -DENABLE_VTK=off -DUSE_QT5=off
> -DENABLE_GUI=off -DENABLE_GTS=off -DENABLE_CGAL=off -DENABLE_PFVFLOW=off
> -DCMAKE_INSTALL_PREFIX=../install ../trunk
>
> But when running make it gets to 92% then fails with a numpy error.
>
> I will continue to work with this. Also if you have any other
> suggegestions that would be great.
>
>
> [ 92%] Building CXX object py/CMakeFiles/_utils.dir/_utils.cpp.o
> In file included from
> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0,
> from
> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
> from
> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
> from /scratch/st-apeirce-1/myYade/trunk/py/_utils.cpp:8:
> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2:
> warning: #warning "Using deprecated NumPy API, disable it with " "#define
> NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
> #warning "Using deprecated NumPy API, disable it with " \
> ^
> In file included from
> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/boost-1.73.0-uc6u5oumzasbqciah7s3kcrdyvomakyk/include/boost/python/exception_translator.hpp:10:0,
> from
> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/boost-1.73.0-uc6u5oumzasbqciah7s3kcrdyvomakyk/include/boost/python.hpp:28,
> from /scratch/st-apeirce-1/myYade/trunk/lib/base/Math.hpp:25,
> from
> /scratch/st-apeirce-1/myYade/trunk/lib/computational-geometry/Hull2d.hpp:3,
> from /scratch/st-apeirce-1/myYade/trunk/py/_utils.hpp:4,
> from /scratch/st-apeirce-1/myYade/trunk/py/_utils.cpp:1:
> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/boost-1.73.0-uc6u5oumzasbqciah7s3kcrdyvomakyk/include/boost/bind.hpp:41:273:
> note: #pragma message: The practice of declaring the Bind placeholders (_1,
> _2, ...) in the global namespace is deprecated. Please use
> <boost/bind/bind.hpp> + using namespace boost::placeholders, or define
> BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.
> In file included from
> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:21:0,
> from
> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
> from /scratch/st-apeirce-1/myYade/trunk/py/_utils.cpp:8:
> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1:
> error: 'int _import_array()' defined but not used [-Werror=unused-function]
> _import_array(void)
> ^
> cc1plus: all warnings being treated as errors
> make[2]: *** [py/CMakeFiles/_utils.dir/_utils.cpp.o] Error 1
> make[1]: *** [py/CMakeFiles/_utils.dir/all] Error 2
> make: *** [all] Error 2
> [anajmul@login03 build]$
>
>
> Thank you!
>
>
>
>
> --
> You received this question notification because your team yade-users is
> an answer contact for Yade.
>
> _______________________________________________
> Mailing list: https://launchpad.net/~yade-users
> Post to : <email address hidden>
> Unsubscribe : https://launchpad.net/~yade-users
> More help : https://help.launchpad.net/ListHelp
>

Robert Caulk (rcaulk) said : #2

*ENABLE_USEFUL_ERRORS=off

Le mar. 28 juil. 2020 à 00:40, Robert Caulk <email address hidden> a écrit :

> Try adding the flag -DENABLE_USEFUL_WARNINGS=off
>
> Le mar. 28 juil. 2020 à 00:35, mrhappy <
> <email address hidden>> a écrit :
>
>> New question #692095 on Yade:
>> https://answers.launchpad.net/yade/+question/692095
>>
>> The people at the Advanced Research Computing center at my University are
>> trying to help me install YADE on the HPC. The following is message that I
>> received from them. Can anyone help them address this issue? Thank you so
>> much!
>>
>>
>>
>> I configure using the following and that does get me a build environment
>>
>> cmake -DPYTHON_VERSION=3.7.6 -DENABLE_VTK=off -DUSE_QT5=off
>> -DENABLE_GUI=off -DENABLE_GTS=off -DENABLE_CGAL=off -DENABLE_PFVFLOW=off
>> -DCMAKE_INSTALL_PREFIX=../install ../trunk
>>
>> But when running make it gets to 92% then fails with a numpy error.
>>
>> I will continue to work with this. Also if you have any other
>> suggegestions that would be great.
>>
>>
>> [ 92%] Building CXX object py/CMakeFiles/_utils.dir/_utils.cpp.o
>> In file included from
>> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0,
>> from
>> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
>> from
>> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
>> from /scratch/st-apeirce-1/myYade/trunk/py/_utils.cpp:8:
>> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2:
>> warning: #warning "Using deprecated NumPy API, disable it with " "#define
>> NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
>> #warning "Using deprecated NumPy API, disable it with " \
>> ^
>> In file included from
>> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/boost-1.73.0-uc6u5oumzasbqciah7s3kcrdyvomakyk/include/boost/python/exception_translator.hpp:10:0,
>> from
>> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/boost-1.73.0-uc6u5oumzasbqciah7s3kcrdyvomakyk/include/boost/python.hpp:28,
>> from /scratch/st-apeirce-1/myYade/trunk/lib/base/Math.hpp:25,
>> from
>> /scratch/st-apeirce-1/myYade/trunk/lib/computational-geometry/Hull2d.hpp:3,
>> from /scratch/st-apeirce-1/myYade/trunk/py/_utils.hpp:4,
>> from /scratch/st-apeirce-1/myYade/trunk/py/_utils.cpp:1:
>> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/boost-1.73.0-uc6u5oumzasbqciah7s3kcrdyvomakyk/include/boost/bind.hpp:41:273:
>> note: #pragma message: The practice of declaring the Bind placeholders (_1,
>> _2, ...) in the global namespace is deprecated. Please use
>> <boost/bind/bind.hpp> + using namespace boost::placeholders, or define
>> BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.
>> In file included from
>> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:21:0,
>> from
>> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
>> from /scratch/st-apeirce-1/myYade/trunk/py/_utils.cpp:8:
>> /arc/software/spack-0.14.0-110/opt/spack/linux-centos7-broadwell/gcc-5.4.0/py-numpy-1.18.1-s25izmnxfevo37f4smdmmybifn7e4poo/lib/python3.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1:
>> error: 'int _import_array()' defined but not used [-Werror=unused-function]
>> _import_array(void)
>> ^
>> cc1plus: all warnings being treated as errors
>> make[2]: *** [py/CMakeFiles/_utils.dir/_utils.cpp.o] Error 1
>> make[1]: *** [py/CMakeFiles/_utils.dir/all] Error 2
>> make: *** [all] Error 2
>> [anajmul@login03 build]$
>>
>>
>> Thank you!
>>
>>
>>
>>
>> --
>> You received this question notification because your team yade-users is
>> an answer contact for Yade.
>>
>> _______________________________________________
>> Mailing list: https://launchpad.net/~yade-users
>> Post to : <email address hidden>
>> Unsubscribe : https://launchpad.net/~yade-users
>> More help : https://help.launchpad.net/ListHelp
>>
>

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