topic Re: Installing smeagol Problem in Intel® oneAPI Math Kernel Library

Installing smeagol Problem

fengya0785 — Wed, 18 Mar 2009 08:13:50 GMT

Hello all
I try to install smeagol ,but I meet some problem.
software version
mkl 10.1.1.019
ifort 10.1
intel mpi 3.0
siesta 2.0.2
smeagol 1.3

[shell]mpiifort -o 
-Vaxlib -ip precision.o atom.o atmparams.o atmfuncs.o listsc.o memoryinfo.o numbvect.o parallel.o sorting.o atomlist.o ionew.o atm_types.o old_atmfuncs.o radial.o parsing.o alloc.o phonon.o spher_harm.o periodic_table.o version.o basis_types.o pseudopotential.o basis_specs.o sys.o basis_io.o chemical.o xml.o writewave.o negfmod.o arw.o atomlwf.o bands.o bessph.o cgwf.o chkdim.o chkgmx.o chempot.o coceri.o conjgr.o constr.o coxmol.o cross.o denmat.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 dynamics.o efield.o egandd.o ener3.o extrapol.o extrapolon.o fermid.o fixed.o forhar.o gradient.o grdsam.o hsparse.o idiag.o initatom.o initdm.o inver.o iodm.o iohs.o iolwf.o iorho.o ioxv.o ipack.o kgrid.o kgridinit.o kinefsm.o ksv.o ksvinit.o madelung.o matel.o meshmatrix.o memory.o meshsubs.o minvec.o mulliken.o naefs.o neighb.o nlefsm.o on_subs.o ordern.o outcell.o outcoor.o overfsm.o paste.o pdos.o pdosg.o pdosk.o phirphi.o pixmol.o plcharge.o timestamp.o propor.o pulayx.o ranger.o ran3.o recipes.o reclat.o redata.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 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 transfer.o broadcast_basis.o sig.o eggbox.o get_wmix.o read_kgrid.o read_kgridinit.o nag.o libfdf.a 
leads_complex.o negf.o identify.o diagonal_alex.o misc.o sigma.o sigmawrap.o noise_svd.o writematrix.o eigenvalues.o selfenergy.o selfenergy2.o gauleg.o transm.o invert.o decimate_leads.o gensvd.o rank.o negfk.o negf2g.o negf2k.o localdos.o gaucheb.o linpack.smeagol.a dmbk.o emt2g.o emt2k.o emtg.o emtk.o emtrans.o bulktrans.o vmattr.o vvbias.o hsleads.o hsl.o hslk.o reademtr.o pasbias.o shifth.o absdiff.o 
libmpi_f90.a 
-lpthread -L/opt/intel/mkl/10.1.1.019/lib/em64t -lmkl_scalapack_ilp64 /opt/intel/mkl/10.1.1.019/lib/em64t/libmkl_scalapack.a -L/opt/intel/mkl/10.1.1.019/lib/em64t -lmkl_blacs_intelmpi_ilp64 /opt/intel/mkl/10.1.1.019/lib/em64t/libmkl_blacs_ilp64.a /opt/intel/mkl/10.1.1.019/lib/em64t/libmkl_lapack.a /opt/intel/mkl/10.1.1.019/lib/em64t/libmkl_core.a /opt/intel/mkl/10.1.1.019/lib/em64t/libguide.a 
detover.o: In function `detover':
/root/smeagol/Src/detover.F:221: undefined reference to `zgefa_'
/root/smeagol/Src/detover.F:222: undefined reference to `zgedi_'
make: *** [siesta] Error 1
[/shell]

I use nm command to find "zgefa_"and "zgedi_" in MKL library ,but feedback nothing.does MKL not contain these matrix library (zgefa and zgedi)

[shell][root@mu01 em64t]# pwd
/opt/intel/mkl/10.1.1.019/lib/em64t
[root@mu01 em64t]# nm -A lib* |grep zgedi_
nm: libmkl_cdft.a: File format not recognized
nm: libmkl_em64t.a: File format not recognized
nm: libmkl_lapack.a: File format not recognized
nm: libmkl_scalapack.a: File format not recognized
nm: libmkl.so: File format not recognized
nm: libmkl_solver.a: File format not recognized

[/shell]

could any one hlep? thanks very much

Re: Installing smeagol Problem

ArturGuzik — Wed, 18 Mar 2009 11:01:30 GMT

Quoting - fengya0785

I use nm command to find "zgefa_"and "zgedi_" in MKL library ,but feedback nothing.does MKL not contain these matrix library (zgefa and zgedi)

Hi,

I think that they (zgefa, zgedi) come from LINPACK. try to find/get them at Netlib. Or equivalent in MKL? Are they for factorization of complex matrices?

A.

Re: Installing smeagol Problem

fengya0785 — Thu, 19 Mar 2009 07:54:35 GMT

Quoting - ArturGuzik

Hi,

I think that they (zgefa, zgedi) come from LINPACK. try to find/get them at Netlib. Or equivalent in MKL? Are they for factorization of complex matrices?

A.

hi A.
thanks for youranswer , I have fixed it. they (zgefa,zgedi) come from LINPACK, I can find them in the Smeagol's src. then I found the slution in the maillist ~

:)

Slution: (quote from the maillist: http://lists.tchpc.tcd.ie/pipermail/smeagol-discuss/2008-October/000510.html)
" the reason for the problem I think is that the linpack routines can
not be compiled, which is becase the "-c" option is missing after ifort.
To use the linpack routines provided with smeagol you have to add the
following lines to your arch.make:

TRANSPORTFLAGS= -c $(FFLAGS)
SOURCE_DIR= ../ "

Re: Installing smeagol Problem

ArturGuzik — Thu, 19 Mar 2009 08:46:58 GMT

Quoting - fengya0785

TRANSPORTFLAGS= -c $(FFLAGS)
SOURCE_DIR= ../ "

Hi,

-c option tells ifort to just compile (prevents linking), so it doesn't sound like problem with compiling itself, rather linking and/or order of compilation (although I don't think the LINPACK routines has modules/dependencies).

Anyway, glad to hear you resolved it.

A.