[gmx-users] AIX XLC Gromacs-5.1-rc1. Undefined reference. Underscore issue.
Carlos Aguni
sorlaker at gmail.com
Thu Aug 20 21:04:57 CEST 2015
Hello Mark!
Thank you for your advice!
I'm now using Gromacs-5.1.
I've added -DGMX_BUILD_MDRUN_ONLY=ON on the previous cmake configuration.
Here's my cmake and error log now:
export TPREFIX=/home/ibm/softwares/gromacs/xlc/vsx/omp1/flagO0/
export flags1="-qnoinline -O0 -qsmp=omp"
export blaslapackflags="-L/usr/lib -lessl -L/opt/ibm/xlf/15.1.2/lib/
-lxlf90 -lxlf90_t -L/opt/ibm/xlsmp/4.1.2/lib -lxlomp_ser "
cmake .. -DGMX_MPI=on -DGMX_DOUBLE=off -DCMAKE_INSTALL_PREFIX=$TPREFIX
-DBUILD_SHARED_LIBS=OFF -DGMX_FFT_LIBRARY=essl -DGMX_OPENMP=on
-DCMAKE_VERBOSE_MAKEFILE=on -DGMX_GPU=off -DGMX_EXTERNAL_LAPACK=ON
-DGMX_EXTERNAL_BLAS=ON -DGMX_BLAS_USER="$blaslapackflags"
-DGMX_LAPACK_USER="$blaslapackflags" -DCMAKE_CXX_FLAGS="$flags1"
-DCMAKE_C_FLAGS="$flags1" -DGMX_THREAD_MPI=off -DGMX_SIMD=IBM_VSX
-DCMAKE_C_COMPILER=mpixlc -DCMAKE_CXX_COMPILER=mpixlc++
-DFFT_LINKER_FLAGS="" -DLINEAR_ALGEBRA_LIBRARIES=""
-DCOVERAGE_EXTRA_FLAGS="" -DCMAKE_VERBOSE_MAKEFILE=ON
-DCMAKE_SHARED_LINKER_FLAGS="-qnoextname" -DGMX_BUILD_MDRUN_ONLY=ON
-DGMX_BUILD_SHARED_EXE=OFF
------------------------------------------------------------------------
---------
Error log:
Linking CXX executable ../../bin/mdrun_mpi
cd /home/ibm/crash/2gromacs-5.1-agosto/gromacs-5.1/single/src/programs &&
/usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun.dir/link.txt
--verbose=1
/usr/bin/mpixlc++ -qarch=auto -qaltivec -std=c++0x -qnoinline -O0
-qsmp=omp -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall
-Wno-unused-function -O3 -DNDEBUG
CMakeFiles/mdrun.dir/mdrun_main.cpp.o
CMakeFiles/mdrun_objlib.dir/mdrun/membed.c.o
CMakeFiles/mdrun_objlib.dir/mdrun/resource-division.cpp.o
CMakeFiles/mdrun_objlib.dir/mdrun/runner.cpp.o
CMakeFiles/mdrun_objlib.dir/mdrun/md.cpp.o
CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o
CMakeFiles/mdrun_objlib.dir/mdrun/repl_ex.cpp.o -o ../../bin/mdrun_mpi
-rdynamic ../../lib/libgromacs_mdrun_mpi.a -lrt
/opt/ibmmath/essl/5.3/FFTW3/src/lib64/libfftw3_essl.a -L/usr/lib -lessl
-L/opt/ibm/xlf/15.1.2/lib/ -lxlf90 -lxlf90_t -L/opt/ibm/xlsmp/4.1.2/lib
-lxlomp_ser
../../lib/libgromacs_mdrun_mpi.a(copyrite.cpp.o): In function
`gmx_print_version_info(_IO_FILE*)':
copyrite.cpp:(.text+0x1310): undefined reference to
`gmx_fft_get_version_info'
copyrite.cpp:(.text+0x15f4): undefined reference to
`gmx_fft_get_version_info'
../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function
`gmx_fft_init_many_1d':
fft.cpp:(.text+0x98): undefined reference to `gmx_fft_init_1d'
../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function
`gmx_fft_init_many_1d_real':
fft.cpp:(.text+0x1a8): undefined reference to `gmx_fft_init_1d_real'
../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function
`gmx_many_fft_destroy':
fft.cpp:(.text+0x300): undefined reference to `gmx_fft_destroy'
../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function
`gmx_fft_many_1d_real$AF7_4':
fft.cpp:(.text+0xfd0): undefined reference to `gmx_fft_1d_real'
../../lib/libgromacs_mdrun_mpi.a(fft.cpp.o): In function
`gmx_fft_many_1d$AF8_3':
fft.cpp:(.text+0x10c0): undefined reference to `gmx_fft_1d'
Thanks in advance!
Carlos.
On Thu, Aug 20, 2015 at 7:42 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> GROMACS 5.1 is out, please don't install 5.1-rc1 any more. There's a little
> bit of advice about using custom linear algebra libraries at
>
> http://manual.gromacs.org/documentation/5.1/install-guide/index.html#linear-algebra-libraries
> but
> you don't need to bother with such libraries unless you know mdrun will be
> used to do normal-mode analysis or something. You might still run into
> problems - if so, we'll want to know how you ran cmake in the first place.
>
> Mark
>
> On Thu, Aug 20, 2015 at 1:20 AM Carlos Aguni <sorlaker at gmail.com> wrote:
>
> > Helo guys!
> >
> > I'm trying to compile Gromacs-5.1-rc1 with XLC 13.1.2 & ESSL 5.3 and I'm
> > facing
> > an undefined reference error.
> > Here's what I got:
> >
> > $ cd
> /home/ibm/crash/gromacs-agosto/2/gromacs-5.1-rc1/single/share/template
> > && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt
> > --verbose=1
> >
> > $ /usr/bin/mpixlc++ -qarch=auto -qaltivec -std=c++0x -qnoinline -O0
> > -qsmp=omp -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall
> > -Wno-unused-function -O3 -DNDEBUG -qextname
> > CMakeFiles/template.dir/template.cpp.o -o ../../bin/template -rdynamic
> > ../../lib/libgromacs_mpi.so.1.0.0 -ldl -lrt -lessl -L/usr/lib -lessl
> > -L/opt/ibm/xlf/15.1.2/lib/ -lxlf90 -lxlf90_t -Wl,-rpath,"\$ORIGIN/../lib"
> >
> > /opt/ibm/xlC/13.1.2/bin/.orig/xlc++: warning: 1501-218 file
> > ../../lib/libgromacs_mpi.so.1.0.0 contains an incorrect file suffix
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlaev2_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dorm2r_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to
> > `gmx_fft_init_1d_real'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlascl_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slaev2_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slarnv_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slartg_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlasr_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to
> > `gmx_fft_init_2d_real'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `ssyevr_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to
> `gmx_fft_1d_real'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slasr_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `sorm2r_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlaset_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slacpy_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlapy2_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlarnv_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to
> > `gmx_fft_get_version_info'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `gmx_fft_1d'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slanst_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dgeqr2_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `sgeqr2_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to
> `gmx_fft_cleanup'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `ssteqr_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dsteqr_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlacpy_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slapy2_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlartg_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to
> `gmx_fft_destroy'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slascl_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `slaset_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to `dlanst_'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to
> `gmx_fft_2d_real'
> >
> > ../../lib/libgromacs_mpi.so.1.0.0: undefined reference to
> `gmx_fft_init_1d'
> >
> > I think that's an underscore problem. Because ESSL has those functions
> but
> > the
> >
> > flags responsible to solve that (-qextname -qnoextname) isn't working:
> >
> > $ objdump -x /usr/lib/libessl.so | grep dlaev2
> >
> > 0000000000000000 l df *ABS* 0000000000000000
> > /home/essl/src/work/dlaev2.f
> >
> > 0000000000aa67a0 l F .text 000000000000023c 0x60 dlaev2
> >
> > $ objdump -x /usr/lib/libessl.so | grep dlacpy
> >
> > 0000000000000000 l df *ABS* 0000000000000000
> > /home/essl/src/work/dlacpyd.f
> >
> > 0000000000000000 l df *ABS* 0000000000000000
> > /home/essl/src/work/dlacpy.f
> >
> > 0000000000a99ca0 l F .text 0000000000000440 0x60 dlacpyd
> >
> > 0000000000a9a0e0 l F .text 00000000000003b0 0x60 dlacpy
> >
> >
> > Can anyone help?
> >
> >
> > Thanks in advance!
> >
> > Carlos.
> > --
> > Gromacs Users mailing list
> >
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