[gpaw-users] libmpifort.so: undefined reference compiler issue

Wed Feb 8 17:06:50 CET 2017

Hello gpaw-users,

I’m working to install GPAW onto my home cluster and when compiling gpaw-python I’ve run into this issue:

mpiicc -o build/bin.linux-x86_64-2.7//gpaw-python build/temp.linux-x86_64-2.7/c/_gpaw.o build/temp.linux-x86_64-2.7/c/bc.o build/temp.linux-x86_64-2.7/c/blacs.o build/temp.linux-x86_64-2.7/c/blas.o build/temp.linux-x86_64-2.7/c/bmgs/bmgs.o build/temp.linux-x86_64-2.7/c/cerf.o build/temp.linux-x86_64-2.7/c/fftw.o build/temp.linux-x86_64-2.7/c/hdf5.o build/temp.linux-x86_64-2.7/c/lapack.o build/temp.linux-x86_64-2.7/c/lcao.o build/temp.linux-x86_64-2.7/c/lfc.o build/temp.linux-x86_64-2.7/c/lfc2.o build/temp.linux-x86_64-2.7/c/localized_functions.o build/temp.linux-x86_64-2.7/c/mlsqr.o build/temp.linux-x86_64-2.7/c/mpi.o build/temp.linux-x86_64-2.7/c/operators.o build/temp.linux-x86_64-2.7/c/plane_wave.o build/temp.linux-x86_64-2.7/c/plt.o build/temp.linux-x86_64-2.7/c/point_charges.o build/temp.linux-x86_64-2.7/c/spline.o build/temp.linux-x86_64-2.7/c/symmetry.o build/temp.linux-x86_64-2.7/c/transformers.o build/temp.linux-x86_64-2.7/c/utilities.o build/temp.linux-x86_64-2.7/c/wigner_seitz.o build/temp.linux-x86_64-2.7/c/woperators.o build/temp.linux-x86_64-2.7/c/xc/ensemble_gga.o build/temp.linux-x86_64-2.7/c/xc/libvdwxc.o build/temp.linux-x86_64-2.7/c/xc/libxc.o build/temp.linux-x86_64-2.7/c/xc/m06l.o build/temp.linux-x86_64-2.7/c/xc/pbe.o build/temp.linux-x86_64-2.7/c/xc/pw91.o build/temp.linux-x86_64-2.7/c/xc/revtpss.o build/temp.linux-x86_64-2.7/c/xc/revtpss_c_pbe.o build/temp.linux-x86_64-2.7/c/xc/rpbe.o build/temp.linux-x86_64-2.7/c/xc/tpss.o build/temp.linux-x86_64-2.7/c/xc/vdw.o build/temp.linux-x86_64-2.7/c/xc/xc.o build/temp.linux-x86_64-2.7/c/xc/xc_mgga.o  -L/share/apps/openmpi/1.10.5/lib -L/share/apps/intel/composer_xe_2015.0.090/mkl/lib/intel64 -L/home/mgroves/DFT/libxc-3.0.0/install/lib -L/home/mgroves/DFT/python/2.7/anaconda2/lib/python2.7/config -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_lapack95_lp64 -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 -lmkl_blas95_lp64 -lpthread -lmkl_rt -lm -lxc -lpython2.7 -lpthread -ldl  -lutil -lm  -L/home/mgroves/DFT/python/2.7/anaconda2/lib -Wl,-rpath=/home/mgroves/DFT/python/2.7/anaconda2/lib,--no-as-needed -Xlinker -export-dynamic
/home/mgroves/DFT/python/2.7/anaconda2/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_tmpnam':
/home/ilan/minonda/conda-bld/work/Python-2.7.12/./Modules/posixmodule.c:7631: warning: the use of `tmpnam_r' is dangerous, better use `mkstemp'
/home/mgroves/DFT/python/2.7/anaconda2/lib/python2.7/config/libpython2.7.a(posixmodule.o): In function `posix_tempnam':
/home/ilan/minonda/conda-bld/work/Python-2.7.12/./Modules/posixmodule.c:7578: warning: the use of `tempnam' is dangerous, better use `mkstemp'
build/temp.linux-x86_64-2.7/c/_gpaw.o: In function `main':
c/_gpaw.c:(.text+0x3d): undefined reference to `__kmpc_begin'
c/_gpaw.c:(.text+0x97): undefined reference to `__kmpc_end'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `PMPIX_Comm_group_failed'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPID_Datatype_builtin'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPID_Type_contiguous'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_Type_free_impl'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_Grequest_set_lang_f77'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPID_Wtime_todouble'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_CommGetAttr_fort'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_WinGetAttr'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIU_Handle_get_ptr_indirect'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_Keyval_set_proxy'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPID_Type_commit'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPID_Wtick'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPI_WEIGHTS_EMPTY'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_TypeSetAttr'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_Err_create_code'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_Err_preOrPostInit'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_TypeGetAttr'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPID_Datatype_direct'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_WinSetAttr'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPID_b_use_gettimeofday'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_CommSetAttr'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPID_Datatype_mem'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_Process'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPI_UNWEIGHTED'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `PMPIX_Comm_reenable_anysource'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPID_Datatype_set_contents'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_Add_finalize'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `PMPIX_Comm_remote_group_failed'
/share/apps/intel//impi/5.0.1.035/intel64/lib/libmpifort.so: undefined reference to `MPIR_Err_return_comm'
running build_scripts
error: can't copy 'build/bin.linux-x86_64-2.7/gpaw-python': doesn't exist or not a regular file

I’m compiling this with openmpi and intel compilers and I’m at a bit of a loss as to how to get this to work.  Here is my customize.py file:

compiler = 'icc'
mpicompiler = 'mpiicc'
mpilinker = 'mpiicc'

scalapack = True

library_dirs += ['/share/apps/openmpi/1.10.5/lib','/share/apps/intel/composer_xe_2015.0.090/mkl/lib/intel64']
libraries = ['mkl_intel_lp64' ,'mkl_sequential' ,'mkl_core',
             'mkl_lapack95_lp64',
             'mkl_scalapack_lp64', 'mkl_blacs_openmpi_lp64',
             'mkl_blas95_lp64',
             'pthread',
    'mkl_rt','m'
             ]

libraries += ['xc']
# change this to your installation directory
LIBXCDIR='/home/mgroves/DFT/libxc-3.0.0/install/'
library_dirs += [LIBXCDIR + 'lib']
include_dirs += [LIBXCDIR + 'include']

extra_compile_args = ['-O3','-fPIC','-std=c99']

extra_compile_args += ['-qopenmp']

define_macros += [('GPAW_NO_UNDERSCORE_CBLACS', '1')]
define_macros += [('GPAW_NO_UNDERSCORE_CSCALAPACK', '1')]
define_macros += [('PARALLEL', '1')]
define_macros += [("GPAW_ASYNC",1)]
define_macros += [("GPAW_MPI2",1)]

Here is my PATH variable

[mgroves at kepler gpaw-1.1.0]$ echo $PATH
/share/apps/intel//impi/5.0.1.035/intel64/bin:/share/apps/intel//impi/5.0.1.035/intel64/bin:/share/apps/intel/composer_xe_2015.0.090/bin/intel64:/share/apps/intel/composer_xe_2015.0.090/mpirt/bin/intel64:/share/apps/intel/composer_xe_2015.0.090/debugger/gdb/intel64_mic/bin:/share/apps/intel/bin:/share/apps/intel/advisor_xe_2015.1.0.367266/bin64:/share/apps/intel/vtune_amplifier_xe_2015.1.0.367959/bin64:/share/apps/intel/inspector_xe_2015.1.0.366509/bin64:/share/apps/intel//impi/5.0.1.035/intel64/bin:/share/apps/intel//itac/9.0.1.033/intel64/bin:/share/apps/intel/composer_xe_2015.0.090/bin/intel64:/share/apps/intel/composer_xe_2015.0.090/mpirt/bin/intel64:/share/apps/intel/composer_xe_2015.0.090/debugger/gdb/intel64_mic/bin:/home/mgroves/DFT/ase/tools:/home/mgroves/DFT/python/2.7/anaconda2/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/ibutils/bin:/usr/java/latest/bin:/opt/maven/bin:/opt/maui/bin:/opt/torque/bin:/opt/torque/sbin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/home/mgroves/bin

And here is my LD_LIBRARY_PATH

[mgroves at kepler gpaw-1.1.0]$ echo $LD_LIBRARY_PATH
/share/apps/openmpi/1.10.5/lib:/home/mgroves/DFT/libxc-3.0.0/install/lib:/share/apps/intel//impi/5.0.1.035/intel64/lib:/share/apps/intel//impi/5.0.1.035/intel64/lib:/share/apps/intel/composer_xe_2015.0.090/compiler/lib/intel64:/share/apps/intel/composer_xe_2015.0.090/mpirt/lib/intel64:/share/apps/intel/composer_xe_2015.0.090/ipp/../compiler/lib/intel64:/share/apps/intel/composer_xe_2015.0.090/ipp/lib/intel64:/share/apps/intel/composer_xe_2015.0.090/compiler/lib/intel64:/share/apps/intel/composer_xe_2015.0.090/mkl/lib/intel64:/share/apps/intel/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4:/share/apps/intel//impi/5.0.1.035/intel64/lib:/share/apps/intel//itac/9.0.1.033/mic/slib:/share/apps/intel//itac/9.0.1.033/intel64/slib:/share/apps/intel/composer_xe_2015.0.090/compiler/lib/intel64:/share/apps/intel/composer_xe_2015.0.090/mpirt/lib/intel64:/share/apps/intel/composer_xe_2015.0.090/ipp/../compiler/lib/intel64:/share/apps/intel/composer_xe_2015.0.090/ipp/lib/intel64:/share/apps/intel/composer_xe_2015.0.090/compiler/lib/intel64:/share/apps/intel/composer_xe_2015.0.090/mkl/lib/intel64:/share/apps/intel/composer_xe_2015.0.090/tbb/lib/intel64/gcc4.4::/opt/python/lib

Does anyone know as to what I’m missing so that gpaw-python finds these undefined references?

Thanks!

Michael

Michael Groves, PhD
Assistant Professor
Department of Chemistry and Biochemistry
California State University, Fullerton
mgroves at fullerton.edu<mailto:mgroves at fullerton.edu>
(657)278-7018

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