undefined reference #1120

xuziye0327 · 2017-01-11T08:46:40Z

/usr/local/cmake/bin/cmake .. -DWITH_GPU=ON -DCMAKE_INSTALL_PREFIX=/usr/local/paddle -DOPENBLAS_ROOT=/opt/OpenBLAS/ -DCUDNN_ROOT=/usr/local/cuda-8.0/
make -j && make install

/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7614: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tempnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7561: warning: the use of `tempnam' is dangerous, better use `mkstemp'
../libpaddle_math.a(MathFunctions.cpp.o): In function `int paddle::getrf<float>(CBLAS_ORDER, int, int, float*, int, int*)':
/root/tmp/paddle/paddle/math/MathFunctions.cpp:91: undefined reference to `LAPACKE_sgetrf'
../libpaddle_math.a(MathFunctions.cpp.o): In function `int paddle::getrf<double>(CBLAS_ORDER, int, int, double*, int, int*)':
/root/tmp/paddle/paddle/math/MathFunctions.cpp:105: undefined reference to `LAPACKE_dgetrf'
../libpaddle_math.a(MathFunctions.cpp.o): In function `int paddle::getri<float>(CBLAS_ORDER, int, float*, int, int const*)':
/root/tmp/paddle/paddle/math/MathFunctions.cpp:118: undefined reference to `LAPACKE_sgetri'
../libpaddle_math.a(MathFunctions.cpp.o): In function `int paddle::getri<double>(CBLAS_ORDER, int, double*, int, int const*)':
/root/tmp/paddle/paddle/math/MathFunctions.cpp:131: undefined reference to `LAPACKE_dgetri'
collect2: error: ld returned 1 exit status
make[2]: *** [paddle/math/tests/test_lazyAssign] Error 1
make[1]: *** [paddle/math/tests/CMakeFiles/test_lazyAssign.dir/all] Error 2
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7614: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tempnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7561: warning: the use of `tempnam' is dangerous, better use `mkstemp'
../libpaddle_math.a(MathFunctions.cpp.o): In function `int paddle::getrf<float>(CBLAS_ORDER, int, int, float*, int, int*)':
/root/tmp/paddle/paddle/math/MathFunctions.cpp:91: undefined reference to `LAPACKE_sgetrf'
../libpaddle_math.a(MathFunctions.cpp.o): In function `int paddle::getrf<double>(CBLAS_ORDER, int, int, double*, int, int*)':
/root/tmp/paddle/paddle/math/MathFunctions.cpp:105: undefined reference to `LAPACKE_dgetrf'
../libpaddle_math.a(MathFunctions.cpp.o): In function `int paddle::getri<float>(CBLAS_ORDER, int, float*, int, int const*)':
/root/tmp/paddle/paddle/math/MathFunctions.cpp:118: undefined reference to `LAPACKE_sgetri'
../libpaddle_math.a(MathFunctions.cpp.o): In function `int paddle::getri<double>(CBLAS_ORDER, int, double*, int, int const*)':
/root/tmp/paddle/paddle/math/MathFunctions.cpp:131: undefined reference to `LAPACKE_dgetri'
collect2: error: ld returned 1 exit status
make[2]: *** [paddle/math/tests/test_Tensor] Error 1
make[1]: *** [paddle/math/tests/CMakeFiles/test_Tensor.dir/all] Error 2
make: *** [all] Error 2

The text was updated successfully, but these errors were encountered:

gangliao · 2017-01-11T08:51:50Z

Can you show me your openblas lib dir?

ll /opt/OpenBLAS/lib

@xuziye0327

gangliao · 2017-01-11T08:53:43Z

The problem in your case is caused by gfortran.so, which we did not link to Paddle.
You may need to export LD_LIBRARY_PATH=<gfortran_path>/lib:${LD_LIBRARY_PATH}.

gangliao · 2017-01-11T09:07:28Z

@xuziye0327 Did you build openblas from source by yourself?

gangliao · 2017-01-11T09:12:48Z

@xuziye0327
Can you also post git log info at here? Thanks a lot.

xuziye0327 · 2017-01-11T10:34:51Z

ll /opt/OpenBLAS/lib/
total 11796
drwxr-xr-x 3 root root    4096 Jan 10 22:29 cmake
lrwxrwxrwx 1 root root      30 Jan 10 22:29 libopenblas.a -> libopenblas_haswellp-r0.2.19.a
-rw-r--r-- 1 root root 7837314 Jan 10 22:29 libopenblas_haswellp-r0.2.19.a
-rwxr-xr-x 1 root root 4232264 Jan 10 22:29 libopenblas_haswellp-r0.2.19.so
lrwxrwxrwx 1 root root      31 Jan 10 22:29 libopenblas.so -> libopenblas_haswellp-r0.2.19.so
lrwxrwxrwx 1 root root      31 Jan 10 22:29 libopenblas.so.0 -> libopenblas_haswellp-r0.2.19.so

xuziye0327 · 2017-01-11T10:35:48Z

git log
commit 30931f547749b6c85772927c66640fa6386c09db
Merge: 727edb8 bce067b
Author: gangliao <[email protected]>
Date:   Tue Jan 10 16:28:06 2017 +0800

    Merge pull request #1110 from reyoung/feature/add_third_party_for_gflags

    Make gflags third_party path configurable

commit 727edb873328f8163b40ef0f2339c60a79eb162e
Merge: 709c839 1e6c917
Author: hedaoyuan <[email protected]>
Date:   Tue Jan 10 16:06:51 2017 +0800

    Merge pull request #1109 from hedaoyuan/fix_issue_676

    fix unit test of paramRelu

commit bce067b002eb1660ea25d60bb1251376b3f157f6
Author: Yu Yang <[email protected]>
Date:   Tue Jan 10 15:41:22 2017 +0800

    Make gflags third_party path configurable

commit 1e6c917ecc76905fa0f33090d757f2b6376e437f
Author: hedaoyuan <[email protected]>
Date:   Tue Jan 10 15:30:24 2017 +0800

    fix unit test of paramRelu

commit 709c839af9584571d7bafe9490390deaca569fdf
Merge: 7df67ba af02d7c
Author: gangliao <[email protected]>
Date:   Tue Jan 10 14:25:58 2017 +0800

    Merge pull request #1103 from reyoung/feature/TravisCICacheThirdParty

    Feature/travis ci cache third party

xuziye0327 · 2017-01-11T10:38:49Z

yes i build openblas by myself

xuziye0327 · 2017-01-11T10:41:11Z

I can not find gfortran.so in my system.

gangliao · 2017-01-11T11:27:22Z

@xuziye0327

You have two methods to fix the problem:

Method 1: You can directly download the release libraries of OpenBLAS or MKL. DO NOT BUILD IT BY YOURSELF.

Method 2: If you still want to build it from source, please make sure you have gfortran compiler in your system, which is located in gcc48/bin/gfortran. If you have it, then

cd openblas_dir
make CC=gcc48/bin/gcc FC=gcc48/bin/gfortran

xuziye0327 · 2017-01-11T12:28:12Z

Thanks!
But i get this error now.

[root@hpc1 build]# make -j `nproc` && make install
...
/usr/local/bin/ld: /usr/local/python2.7.13/lib/libpython2.7.a(getcopyright.o): relocation R_X86_64_32 against `.data' can not be used when making a shared object; recompile with -fPIC
/usr/local/bin/ld: /usr/local/python2.7.13/lib/libpython2.7.a(getplatform.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/local/bin/ld: /usr/local/python2.7.13/lib/libpython2.7.a(getversion.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/local/bin/ld: /usr/local/python2.7.13/lib/libpython2.7.a(structmember.o): relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
/usr/local/bin/ld: /usr/local/python2.7.13/lib/libpython2.7.a(parser.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/local/bin/ld: /usr/local/python2.7.13/lib/libpython2.7.a(bytes_methods.o): relocation R_X86_64_32S against symbol `_Py_ctype_table' can not be used when making a shared object; recompile with -fPIC
/usr/local/bin/ld: /usr/local/python2.7.13/lib/libpython2.7.a(getcompiler.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
/usr/local/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
error: command 'g++' failed with exit status 1
make[2]: *** [../paddle/dist/.timestamp] Error 1
make[1]: *** [paddle/api/CMakeFiles/python_api_wheel.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
Scanning dependencies of target test_Tensor
[ 99%] Linking CXX executable test_Tensor
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7614: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tempnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7561: warning: the use of `tempnam' is dangerous, better use `mkstemp'
[ 99%] Built target test_Tensor
make: *** [all] Error 2

When i used sudo, i got this.

[root@hpc1 build]# sudo make -j `nproc` && make install
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7614: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tempnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7561: warning: the use of `tempnam' is dangerous, better use `mkstemp'
/usr/bin/ld: BFD version 2.20.51.0.2-5.44.el6 20100205 internal error, aborting at reloc.c line 443 in bfd_get_reloc_size

/usr/bin/ld: Please report this bug.

collect2: error: ld returned 1 exit status
make[2]: *** [paddle/gserver/tests/test_ConvUnify] Error 1
make[2]: *** Deleting file `paddle/gserver/tests/test_ConvUnify'
make[1]: *** [paddle/gserver/tests/CMakeFiles/test_ConvUnify.dir/all] Error 2
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7614: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tempnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7561: warning: the use of `tempnam' is dangerous, better use `mkstemp'
/usr/bin/ld: BFD version 2.20.51.0.2-5.44.el6 20100205 internal error, aborting at reloc.c line 443 in bfd_get_reloc_size

/usr/bin/ld: Please report this bug.

collect2: error: ld returned 1 exit status
make[2]: *** [paddle/gserver/tests/test_PriorBox] Error 1
make[2]: *** Deleting file `paddle/gserver/tests/test_PriorBox'
make[1]: *** [paddle/gserver/tests/CMakeFiles/test_PriorBox.dir/all] Error 2
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7614: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tempnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7561: warning: the use of `tempnam' is dangerous, better use `mkstemp'
/usr/bin/ld: BFD version 2.20.51.0.2-5.44.el6 20100205 internal error, aborting at reloc.c line 443 in bfd_get_reloc_size

/usr/bin/ld: Please report this bug.

collect2: error: ld returned 1 exit status
make[2]: *** [paddle/gserver/tests/test_LayerGrad] Error 1
make[2]: *** Deleting file `paddle/gserver/tests/test_LayerGrad'
make[1]: *** [paddle/gserver/tests/CMakeFiles/test_LayerGrad.dir/all] Error 2
...
...
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7614: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tempnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7561: warning: the use of `tempnam' is dangerous, better use `mkstemp'
/usr/bin/ld: BFD version 2.20.51.0.2-5.44.el6 20100205 internal error, aborting at reloc.c line 443 in bfd_get_reloc_size

/usr/bin/ld: Please report this bug.

collect2: error: ld returned 1 exit status
make[2]: *** [paddle/math/tests/test_lazyAssign] Error 1
make[2]: *** Deleting file `paddle/math/tests/test_lazyAssign'
make[1]: *** [paddle/math/tests/CMakeFiles/test_lazyAssign.dir/all] Error 2
Scanning dependencies of target test_Tensor
[ 99%] Linking CXX executable test_Tensor
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7614: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'
/usr/local/python2.7.13/lib/libpython2.7.a(posixmodule.o): In function `posix_tempnam':
/root/tmp/Python-2.7.13/./Modules/posixmodule.c:7561: warning: the use of `tempnam' is dangerous, better use `mkstemp'
/usr/bin/ld: BFD version 2.20.51.0.2-5.44.el6 20100205 internal error, aborting at reloc.c line 443 in bfd_get_reloc_size

/usr/bin/ld: Please report this bug.

collect2: error: ld returned 1 exit status
make[2]: *** [paddle/math/tests/test_Tensor] Error 1
make[2]: *** Deleting file `paddle/math/tests/test_Tensor'
make[1]: *** [paddle/math/tests/CMakeFiles/test_Tensor.dir/all] Error 2
make: *** [all] Error 2

This is my g++ version:

[root@hpc1 build]# g++ --version
g++ (GCC) 4.8.5
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

gangliao · 2017-01-11T12:29:59Z

Are you also build python from source ???

gangliao · 2017-01-11T12:31:21Z

You can follow the install docs: https://github.com/PaddlePaddle/Paddle/blob/develop/doc/getstarted/build_and_install/build_from_source_en.md#install-dependencies

gangliao self-assigned this Jan 11, 2017

gangliao closed this as completed Jan 13, 2017

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undefined reference #1120

undefined reference #1120

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undefined reference #1120

undefined reference #1120

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