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

Michael R. C. Williams michael.williams at yale.edu
Tue Jul 13 22:37:13 CEST 2010 

Dear Kamal,

This customize.py works for me:

scalapack = True

compiler = 'mpicc -O3 -xHOST -ipo -static -no-prec-div -std=c99 -fPIC'

mpicompiler = 'mpicc -O3 -xHOST -ipo -static -no-prec-div -std=c99 -fPIC'

library_dirs += ['/home2/mrw47/intel/mkl/10.2.3.029/lib/em64t/']

libraries = ['mkl_scalapack_lp64',
             'mkl_blacs_openmpi_lp64',
             'mkl_lapack',
             'mkl_intel_lp64',
             'mkl_sequential',
             'mkl_core',
             'iomp5',
             'pthread']

define_macros += [('GPAW_NO_UNDERSCORE_CBLACS', '1')]
define_macros += [('GPAW_NO_UNDERSCORE_CSCALAPACK', '1')]

You can just replace 'mkl_blacs_openmpi_lp64' with 'mkl_blacs_intelmpi_lp64' if you are set up to use Intel's MPI instead of OpenMPI. Perhaps it is worth checking that the first 'mpicc' that is found is actually linked to the Intel MPI libraries and not OpenMPI ones. I'm not an MPI expert, but my impression is that OpenMPI is much more standard. Hope that helps,

Mike

On Jul 13, 2010, at 4:19 PM, 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
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