topic Link error: Lapack + blas + blacs + scalapack in Intel® oneAPI Math Kernel Library

Link error: Lapack + blas + blacs + scalapack

Sangamesh_B_ — Mon, 31 Aug 2009 13:35:12 GMT

Hello all,

I'm trying to compile parallel version of siesta-2.0.2 on Cent OS 5.2 with Intel compiler(ifort-10.1.008) and MKL(10.0.5.025) using MVAPICH2-1.04p1.

For linking MKL, I've followed:

http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/

But still its giving error.

/opt/mpi/mvapich2/1.4rc1/intel/bin/mpif90 -I/opt/libs/netcdf/4.0.1/intel/include/ -openmp -o siesta \
automatic_cell.o arw.o atomlwf.o bands.o bessph.o cgwf.o chkdim.o chkgmx.o chempot.o coceri.o constr.o coxmol.o cross.o denmat.o denmatlomem.o detover.o dfscf.o dhscf.o diagon.o digcel.o fft3d.o diagg.o diagk.o diagkp.o diag2g.o diag2k.o diagpol.o diagsprl.o dipole.o dismin.o dnaefs.o dot.o efield.o egandd.o ener3.o ener3lomem.o extrapol.o extrapolon.o fixed.o fsiesta.o gradient.o gradientlomem.o grdsam.o hsparse.o idiag.o initatom.o initdm.o inver.o iodm.o iohs.o iolwf.o iozm.o ipack.o iopipes.o kgrid.o kgridinit.o kinefsm.o ksv.o ksvinit.o kpoint_grid.o find_kgrid.o linpack.o madelung.o matel.o meshmatrix.o memory.o meshsubs.o m_check_supercell.o mulliken.o minvec.o naefs.o neighb.o m_non_collinear.o ordern.o outcell.o outcoor.o paste.o pdos.o pdosg.o pdosk.o pdoskp.o phirphi.o pixmol.o plcharge.o propor.o pulayx.o ranger.o ran3.o reclat.o redcel.o reinit.o reord.o rhoofd.o rhoofdsp.o rhooda.o savepsi.o shaper.o timer.o vmb.o vmat.o vmatsp.o volcel.o xc.o xijorb.o cellxc.o cdiag.o rdiag.o cgvc.o cgvc_zmatrix.o iocg.o ioeig.o iofa.o iokp.o iomd.o repol.o typecell.o ofc.o poison.o readsp.o radfft.o siesta.o io.o spin_init.o coor.o atm_transfer.o broadcast_basis.o eggbox.o dsyevds.o zheevds.o optical.o phirphi_opt.o reoptical.o transition_rate.o initparallel.o show_distribution.o setspatial.o setatomnodes.o uncell.o cart2frac.o obc.o precision.o sys.o m_cell.o recipes.o files.o spatial.o parallel.o parallelsubs.o parsing.o chemical.o xcmod.o atom.o atmparams.o m_mpi_utils.o m_fdf_global.o m_history.o m_iorho.o atmfuncs.o listsc.o memoryinfo.o m_memory.o numbvect.o sorting.o atomlist.o atm_types.o old_atmfuncs.o radial.o m_smearing.o alloc.o phonon.o spher_harm.o periodic_table.o version.o timestamp.o basis_types.o xml.o pseudopotential.o basis_specs.o basis_io.o onmod.o densematrix.o writewave.o on_subs.o fermid.o m_broyddj.o electrostatic.o mneighb.o globalise.o siesta_cmlsubs.o siesta_cml.o units.o zmatrix.o m_broyden_mixing.o forhar.o m_walltime.o m_wallclock.o m_iostruct.o nlefsm.o overfsm.o conjgr.o conjgr_old.o redata.o m_broyddj_nocomm.o broyden_optim.o ioxv.o dynamics.o md_out.o nag.o pxf.o libfdf.a libwxml.a libxmlparser.a libmpi_f90.a\
/opt/libs/netcdf/4.0.1/intel/lib/libnetcdf.a -L/opt/intel/mkl/10.0.5.025/lib/em64t /opt/intel/mkl/10.0.5.025/lib/em64t/libmkl_solver_lp64.a -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -Wl,--end-group -lpthread
cdiag.o: In function `cdiag':

/siesta_new/siesta-2.0.2/Src/cdiag.F:253: undefined reference to `descinit_'
/siesta_new/siesta-2.0.2/Src/cdiag.F:262: undefined reference to `numroc_'
/siesta_new/siesta-2.0.2/Src/cdiag.F:263: undefined reference to `numroc_'
....
.....

I tried all the ways (using blacs/scalapack or static/dynamic). But no luck.

What's wrong thing am doing here?

Re: Link error: Lapack + blas + blacs + scalapack

ArturGuzik — Tue, 01 Sep 2009 00:43:45 GMT

Quoting - sangamesh

Hello all,

I'm trying to compile parallel version of siesta-2.0.2 on Cent OS 5.2 with Intel compiler(ifort-10.1.008) and MKL(10.0.5.025) using MVAPICH2-1.04p1.

-L/opt/intel/mkl/10.0.5.025/lib/em64t /opt/intel/mkl/10.0.5.025/lib/em64t/libmkl_solver_lp64.a -Wl,--start-group -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_lp64 -Wl,--end-group -lpthread
cdiag.o: In function `cdiag':

/siesta_new/siesta-2.0.2/Src/cdiag.F:253: undefined reference to `descinit_'
/siesta_new/siesta-2.0.2/Src/cdiag.F:262: undefined reference to `numroc_'
/siesta_new/siesta-2.0.2/Src/cdiag.F:263: undefined reference to `numroc_'

Hi,

the undefined references come from ScalaPack. it seems you're missing it.

$MKLPATH/libmkl_scalapack_ilp64.a $MKLPATH/libmkl_solver_ilp64.a -Wl,--start-group $MKLPATH/libmkl_intel_ilp64.a $MKLPATH/libmkl_intel_thread.a $MKLPATH/libmkl_core.a $MKLPATH/libmkl_blacs_intelmpi_ilp64.a -Wl,--end-group -openmp -lpthread

A.

Re: Link error: Lapack + blas + blacs + scalapack

Sangamesh_B_ — Mon, 07 Sep 2009 06:08:54 GMT

Quoting - ArturGuzik

Thanks ArturGuzik. Your suggestion solved the problem.
But the Intel advisor for linking MKL, doesn't allow to select both blacs and scalapack. Why so?

http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor/

Re: Link error: Lapack + blas + blacs + scalapack

ArturGuzik — Mon, 07 Sep 2009 07:54:14 GMT

Quoting - sangamesh

Hi,

BLACS is used as the communication layer of ScaLAPACK so if you pick the latter then that you also pick BLACS. Anyway, Gennady can provide more reliable answer.

A.