[gpaw-users] Library-linking issue while compiling gpaw using mkl library

Michael F. Peintinger mpei at thch.uni-bonn.de
Tue Jul 13 22:44:48 CEST 2010 

Yes, I use it with the mkl and intel compilers.

My customize.py is attached and should be self explanatory

regards

michael
(mpei)


On Tue, 2010-07-13 at 16:19 -0400, ksaha at physics.udel.edu wrote: 
> Dear gpaw-users,
> 
> Did anybody get success in compliling the gpaw using intel mkl library? I
> am getting some linking issue as follows:
> 
> mpicc -o build/bin.linux-x86_64-2.4//gpaw-python
> build/temp.linux-x86_64-2.4/c/xc.o build/temp.linux-x86_64-2.4/c/blas.o
> build/temp.linux-x86_64-2.4/c/rpbe.o build/temp.linux-x86_64-2.4/c/lfc2.o
> build/temp.linux-x86_64-2.4/c/compiled_WITH_SL.o
> build/temp.linux-x86_64-2.4/c/mgga.o build/temp.linux-x86_64-2.4/c/pw91.o
> build/temp.linux-x86_64-2.4/c/vasiliev02prb.o
> build/temp.linux-x86_64-2.4/c/lapack.o
> build/temp.linux-x86_64-2.4/c/plane_wave.o
> build/temp.linux-x86_64-2.4/c/libxc.o
> build/temp.linux-x86_64-2.4/c/spline.o
> build/temp.linux-x86_64-2.4/c/utilities.o
> build/temp.linux-x86_64-2.4/c/tpss_ec.o
> build/temp.linux-x86_64-2.4/c/mpi.o build/temp.linux-x86_64-2.4/c/vdw.o
> build/temp.linux-x86_64-2.4/c/wigner_seitz.o
> build/temp.linux-x86_64-2.4/c/_gpaw.o
> build/temp.linux-x86_64-2.4/c/mlsqr.o build/temp.linux-x86_64-2.4/c/hdf5.o
> build/temp.linux-x86_64-2.4/c/ensemble_gga.o
> build/temp.linux-x86_64-2.4/c/transformers.o
> build/temp.linux-x86_64-2.4/c/localized_functions.o
> build/temp.linux-x86_64-2.4/c/lcao.o build/temp.linux-x86_64-2.4/c/lb94.o
> build/temp.linux-x86_64-2.4/c/pbe.o build/temp.linux-x86_64-2.4/c/blacs.o
> build/temp.linux-x86_64-2.4/c/symmetry.o
> build/temp.linux-x86_64-2.4/c/tpss.o
> build/temp.linux-x86_64-2.4/c/point_charges.o
> build/temp.linux-x86_64-2.4/c/tpss_ex.o
> build/temp.linux-x86_64-2.4/c/d2Excdn2.o
> build/temp.linux-x86_64-2.4/c/cerf.o build/temp.linux-x86_64-2.4/c/bc.o
> build/temp.linux-x86_64-2.4/c/lfc.o build/temp.linux-x86_64-2.4/c/plt.o
> build/temp.linux-x86_64-2.4/c/operators.o
> build/temp.linux-x86_64-2.4/c/io_wrappers.o
> build/temp.linux-x86_64-2.4/c/bmgs/bmgs.o
> build/temp.linux-x86_64-2.4/c/libxc/src/util.o
> build/temp.linux-x86_64-2.4/c/libxc/src/special_functions.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_am05.o
> build/temp.linux-x86_64-2.4/c/libxc/src/mgga.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_perdew.o
> build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_pz.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_xc_hcth.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_c_am05.o
> build/temp.linux-x86_64-2.4/c/libxc/src/functionals.o
> build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_b3lyp.o
> build/temp.linux-x86_64-2.4/c/libxc/src/mgga_c_tpss.o
> build/temp.linux-x86_64-2.4/c/libxc/src/mgga_x_m06l.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_xalpha.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_pbe.o
> build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_b3p86.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_b86.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_b88.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_dk87.o
> build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_b3pw91.o
> build/temp.linux-x86_64-2.4/c/libxc/src/mgga_c_m06l.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_lg93.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lda_xc_teter93.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_optx.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_pbea.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_pw86.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_rpa.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lda_x.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lca.o
> build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_b1wc.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_b86_mgc.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_wigner.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_c_pw91.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_wc.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_pw.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_c_lyp.o
> build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_x3lyp.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_xc_lb.o
> build/temp.linux-x86_64-2.4/c/libxc/src/mgga_x_tpss.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_g96.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_ft97.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_pw91.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_mpbe.o
> build/temp.linux-x86_64-2.4/c/libxc/src/mgga_c_revtpss.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_vwn.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_xc_edf1.o
> build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_o3lyp.o
> build/temp.linux-x86_64-2.4/c/libxc/src/mgga_x_revtpss.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_xc_xlyp.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lda.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_amgb.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_c_pbe.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lca_omc.o
> build/temp.linux-x86_64-2.4/c/libxc/src/hyb_gga_xc_pbeh.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_x_rpbe.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lda_c_hl.o
> build/temp.linux-x86_64-2.4/c/libxc/src/gga_c_p86.o
> build/temp.linux-x86_64-2.4/c/libxc/src/lca_lch.o 
> -L/usr/lib64/python2.4/config -lblas -llapack -lpython2.4 -lpthread -ldl 
> -lutil -lm  -L/share/apps/intel/mkl/10.2.0.013/lib/em64t
> /share/apps/intel/mkl/10.2.0.013/lib/em64t/libmkl_scalapack_lp64.a
> /share/apps/intel/mkl/10.2.0.013/lib/em64t/libmkl_solver_lp64_sequential.a
> -Wl,--start-group
> /share/apps/intel/mkl/10.2.0.013/lib/em64t/libmkl_intel_lp64.a
> /share/apps/intel/mkl/10.2.0.013/lib/em64t/libmkl_sequential.a
> /share/apps/intel/mkl/10.2.0.013/lib/em64t/libmkl_core.a
> /share/apps/intel/mkl/10.2.0.013/lib/em64t/libmkl_blacs_intelmpi_lp64.a
> -Wl,--end-group -lpthread -L/usr/kerberos/lib64 -Xlinker -export-dynamic
> /usr/lib64/python2.4/config/libpython2.4.a(posixmodule.o): In function
> `posix_tmpnam':
> (.text+0x665): warning: the use of `tmpnam_r' is dangerous, better use
> `mkstemp'
> /usr/lib64/python2.4/config/libpython2.4.a(posixmodule.o): In function
> `posix_tempnam':
> (.text+0x748): warning: the use of `tempnam' is dangerous, better use
> `mkstemp'
> build/temp.linux-x86_64-2.4/c/lapack.o: warning: memset used with constant
> zero length parameter; this could be due to transposed parameters
> build/temp.linux-x86_64-2.4/c/mpi.o: In function `diagonalize':
> c/mpi.c:(.text+0x33bb): undefined reference to `Cblacs_gridinit_'
> c/mpi.c:(.text+0x33fa): undefined reference to `Cblacs_gridinfo_'
> c/mpi.c:(.text+0x345b): undefined reference to `Cblacs_pnum_'
> c/mpi.c:(.text+0x4060): undefined reference to `Cpdgemr2d_'
> c/mpi.c:(.text+0x40d3): undefined reference to `Cblacs_gridexit_'
> build/temp.linux-x86_64-2.4/c/mpi.o: In function `inverse_cholesky':
> c/mpi.c:(.text+0x4379): undefined reference to `Cblacs_gridinit_'
> c/mpi.c:(.text+0x43b8): undefined reference to `Cblacs_gridinfo_'
> c/mpi.c:(.text+0x4419): undefined reference to `Cblacs_pnum_'
> c/mpi.c:(.text+0x488c): undefined reference to `Cpdgemr2d_'
> c/mpi.c:(.text+0x4943): undefined reference to `Cblacs_gridexit_'
> build/temp.linux-x86_64-2.4/c/blacs.o: In function `new_blacs_context':
> c/blacs.c:(.text+0x819): undefined reference to `Cblacs_pinfo_'
> c/blacs.c:(.text+0x84b): undefined reference to `Cblacs_gridinit_'
> build/temp.linux-x86_64-2.4/c/blacs.o: In function `get_blacs_gridinfo':
> c/blacs.c:(.text+0x8b5): undefined reference to `Cblacs_gridinfo_'
> build/temp.linux-x86_64-2.4/c/blacs.o: In function `get_blacs_local_shape':
> c/blacs.c:(.text+0x94a): undefined reference to `Cblacs_gridinfo_'
> build/temp.linux-x86_64-2.4/c/blacs.o: In function `blacs_destroy':
> c/blacs.c:(.text+0x9c0): undefined reference to `Cblacs_gridexit_'
> build/temp.linux-x86_64-2.4/c/blacs.o: In function `scalapack_redist':
> c/blacs.c:(.text+0xbbb): undefined reference to `Cpdtrmr2d_'
> c/blacs.c:(.text+0xc25): undefined reference to `Cpztrmr2d_'
> c/blacs.c:(.text+0xc9a): undefined reference to `Cpdgemr2d_'
> c/blacs.c:(.text+0xcf3): undefined reference to `Cpzgemr2d_'
> build/temp.linux-x86_64-2.4/c/blacs.o: In function
> `scalapack_diagonalize_ex':
> c/blacs.c:(.text+0x128d): undefined reference to `Cblacs_gridinfo_'
> build/temp.linux-x86_64-2.4/c/blacs.o: In function
> `scalapack_general_diagonalize_ex':
> c/blacs.c:(.text+0x2495): undefined reference to `Cblacs_gridinfo_'
> 
> * Using standard lapack
> * Compiling gpaw with mpiicc
> * Compiling with ScaLapack
> * Architecture: linux-x86_64
> * Building a custom interpreter
> * linking FAILED!  Only serial version of code will work.
> 
> Here is the mkl library I put in customize.py:
> 
> extra_link_args = ['-L/share/apps/intel/mkl/10.2.0.013/lib/em64t
> /share/apps/intel/mkl/10.2.0.013/lib/em64t/libmkl_scalapack_lp64.a
> /share/apps/intel/mkl/10.2.0.013/lib/em64t/libmkl_solver_lp64_sequential.a
> -Wl,--start-group
> /share/apps/intel/mkl/10.2.0.013/lib/em64t/libmkl_intel_lp64.a
> /share/apps/intel/mkl/10.2.0.013/lib/em64t/libmkl_sequential.a
> /share/apps/intel/mkl/10.2.0.013/lib/em64t/libmkl_core.a
> /share/apps/intel/mkl/10.2.0.013/lib/em64t/libmkl_blacs_intelmpi_lp64.a
> -Wl,--end-group -lpthread']
> 
> Thanks in advance for your suggestion!
> 
> Regards.
> Kamal
> 
> ==========================================================
>  Kamal K. Saha
>  Department of Physics and Astronomy
>  University of Delaware
>  Newark, DE 19716-2570
>  Phone: (302) 831-8519, Fax: (302) 831-1637
> 
>  http://web.physics.udel.edu/about/directory/postdoc/kamal-k-saha
> ==========================================================
> 
> _______________________________________________
> gpaw-users mailing list
> gpaw-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users

-- 
Dipl. Chem. Michael F. Peintinger

Institute of Physical
and Theoretical Chemistry

Wegelerstr.12
D-53115 Bonn

Phone: 0228/73-2998
E-Mail: mpei at thch.uni-bonn.de
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