[Smeagol-discuss] Help with installing Smeagol
Amaury melo souza
meloamaury at gmail.com
Wed Apr 16 13:26:57 IST 2008
Hello,
I have been trying to install the Smeagol code. I have been using a
> intel fortran compiler and I have chosen the intel-mkl.make file in
> Sys directory for to be my arch.make file. The compilation begins ok
> but stops with the following error.
>
> Could you give me some advise about this?
>
>
>
>
>
> [root at cigana Src]# make
>
> Compilation architecture to be used: intel-mkl
> If this is not what you want, create the right
> arch.make file using the models in Sys
>
> Hit ^C to abort...
>
> ==> Information about compiler and flags
> sed "s/SIESTA_ARCH/intel-mkl/g" version.F90 > temp0.F90
> sed "s/FFLAGS/ /g" temp0.F90 > temp.F90
> ifort -c -w -mp -tpp5 -O3 temp.F90
>
> (cd fdf ; make module)
> make[1]: Entering directory `/usr/local/smeagol.1.0b/Src/fdf'
> ifort -c -w -mp -tpp5 -O3 fdf.f
> ifort -c -w -mp -tpp5 -O3 parse.f
> ifort -c -w -mp -tpp5 -O3 fdf_mod.f
> ar qv libfdf.a fdf.o fdf_mod.o parse.o
> a - fdf.o
> a - fdf_mod.o
> a - parse.o
> echo libfdf.a
> libfdf.a
> cp libfdf.a ..
> make[1]: Leaving directory `/usr/local/smeagol.1.0b/Src/fdf'
> ifort -c -w -mp -tpp5 -O3 precision.F
> ifort -c -w -mp -tpp5 -O3 sys.F
> ifort -c -w -mp -tpp5 -O3 pseudopotential.f
> ifort -c -w -mp -tpp5 -O3 atmparams.f
> ifort -c -w -mp -tpp5 -O3 basis_types.f
> ifort -c -w -mp -tpp5 -O3 ionew.F
> ifort -c -w -mp -tpp5 -O3 spher_harm.f
> ifort -c -w -mp -tpp5 -O3 old_atmfuncs.f
> ifort -c -w -mp -tpp5 -O3 parallel.f
> ifort -c -w -mp -tpp5 -O3 radfft.f
> ifort -c -w -mp -tpp5 -O3 periodic_table.f
> ifort -c -w -mp -tpp5 -O3 atom.f
> ifort -c -w -mp -tpp5 -O3 xml.f
> ifort -c -w -mp -tpp5 -O3 radial.f
> ifort -c -w -mp -tpp5 -O3 atm_types.f
> ifort -c -w -mp -tpp5 -O3 atmfuncs.f
> ifort -c -w -mp -tpp5 -O3 listsc.f
> ifort -c -w -mp -tpp5 -O3 memoryinfo.F
> ifort -c -w -mp -tpp5 -O3 numbvect.f
> ifort -c -w -mp -tpp5 -O3 sorting.f
> ifort -c -w -mp -tpp5 -O3 alloc.F90
> ifort -c -w -mp -tpp5 -O3 atomlist.f
> ifort -c -w -mp -tpp5 -O3 parsing.f
> ifort -c -w -mp -tpp5 -O3 phonon.F
> ifort -c -w -mp -tpp5 -O3 chemical.f
> ifort -c -w -mp -tpp5 -O3 basis_specs.f
> ifort -c -w -mp -tpp5 -O3 basis_io.F
> ifort -c -w -mp -tpp5 -O3 writewave.F
> ifort -c -w -mp -tpp5 -O3 arw.f
> ifort -c -w -mp -tpp5 -O3 atomlwf.F
> ifort -c -w -mp -tpp5 -O3 bands.F
> ifort -c -w -mp -tpp5 -O3 bessph.f
> ifort -c -w -mp -tpp5 -O3 cgwf.F
> ifort -c -w -mp -tpp5 -O3 chkdim.f
> ifort -c -w -mp -tpp5 -O3 chkgmx.F
> ifort -c -w -mp -tpp5 -O3 chempot.F
> ifort -c -w -mp -tpp5 -O3 coceri.f
> ifort -c -w -mp -tpp5 -O3 conjgr.f
> ifort -c -w -mp -tpp5 -O3 constr.f
> ifort -c -w -mp -tpp5 -O3 coxmol.f
> ifort -c -w -mp -tpp5 -O3 cross.f
> ifort -c -w -mp -tpp5 -O3 denmat.F
> ifort -c -w -mp -tpp5 -O3 detover.F
> ifort -c -w -mp -tpp5 -O3 meshsubs.F
> ifort -c -w -mp -tpp5 -O3 meshmatrix.F
> ifort -c -w -mp -tpp5 -O3 dfscf.f
> ifort -c -w -mp -tpp5 -O3 dhscf.F
> ifort -c -w -mp -tpp5 -O3 diagon.F
> ifort -c -w -mp -tpp5 -O3 digcel.f
> ifort -c -w -mp -tpp5 -O3 fft3d.F
> ifort -c -w -mp -tpp5 -O3 diagg.F
> ifort -c -w -mp -tpp5 -O3 diagk.F
> ifort -c -w -mp -tpp5 -O3 diagkp.F
> ifort -c -w -mp -tpp5 -O3 diag2g.F
> ifort -c -w -mp -tpp5 -O3 diag2k.F
> ifort -c -w -mp -tpp5 -O3 diagpol.f
> ifort -c -w -mp -tpp5 -O3 diagsprl.F
> ifort -c -w -mp -tpp5 -O3 dipole.F
> ifort -c -w -mp -tpp5 -O3 dismin.f
> ifort -c -w -mp -tpp5 -O3 dnaefs.f
> ifort -c -w -mp -tpp5 -O3 dot.f
> ifort -c -w -mp -tpp5 -O3 dynamics.F
> ifort -c -w -mp -tpp5 -O3 efield.F
> ifort -c -w -mp -tpp5 -O3 egandd.F
> ifort -c -w -mp -tpp5 -O3 ener3.F
> ifort -c -w -mp -tpp5 -O3 extrapol.F
> ifort -c -w -mp -tpp5 -O3 extrapolon.F
> ifort -c -w -mp -tpp5 -O3 fermid.F
> ifort -c -w -mp -tpp5 -O3 fixed.F
> ifort -c -w -mp -tpp5 -O3 forhar.f
> ifort -c -w -mp -tpp5 -O3 gradient.F
> ifort -c -w -mp -tpp5 -O3 grdsam.F
> ifort -c -w -mp -tpp5 -O3 hsparse.f
> ifort -c -w -mp -tpp5 -O3 idiag.f
> ifort -c -w -mp -tpp5 -O3 initatom.f
> ifort -c -w -mp -tpp5 -O3 initdm.F
> ifort -c -w -mp -tpp5 -O3 inver.f
> ifort -c -w -mp -tpp5 -O3 iodm.F
> ifort -c -w -mp -tpp5 -O3 iohs.F
> ifort -c -w -mp -tpp5 -O3 iolwf.F
> ifort -c -w -mp -tpp5 -O3 iorho.F
> ifort -c -w -mp -tpp5 -O3 ioxv.F
> ifort -c -w -mp -tpp5 -O3 ipack.f
> ifort -c -w -mp -tpp5 -O3 kgrid.F
> ifort -c -w -mp -tpp5 -O3 kgridinit.F
> ifort -c -w -mp -tpp5 -O3 kinefsm.f
> ifort -c -w -mp -tpp5 -O3 ksv.F
> ifort -c -w -mp -tpp5 -O3 ksvinit.f
> ifort -c -w -mp -tpp5 -O3 madelung.F
> ifort -c -w -mp -tpp5 -O3 matel.f
> ifort -c -w -mp -tpp5 -O3 memory.F
> ifort -c -w -mp -tpp5 -O3 minvec.f
> ifort -c -w -mp -tpp5 -O3 mulliken.F
> ifort -c -w -mp -tpp5 -O3 naefs.f
> ifort -c -w -mp -tpp5 -O3 neighb.f
> ifort -c -w -mp -tpp5 -O3 nlefsm.f
> ifort -c -w -mp -tpp5 -O3 on_subs.F
> ifort -c -w -mp -tpp5 -O3 ordern.F
> ifort -c -w -mp -tpp5 -O3 outcell.f
> ifort -c -w -mp -tpp5 -O3 outcoor.f
> ifort -c -w -mp -tpp5 -O3 overfsm.f
> ifort -c -w -mp -tpp5 -O3 paste.f
> ifort -c -w -mp -tpp5 -O3 pdos.F
> ifort -c -w -mp -tpp5 -O3 pdosg.F
> ifort -c -w -mp -tpp5 -O3 pdosk.F
> ifort -c -w -mp -tpp5 -O3 phirphi.f
> ifort -c -w -mp -tpp5 -O3 pixmol.f
> ifort -c -w -mp -tpp5 -O3 plcharge.F
> ifort -c -w -mp -tpp5 -O3 timestamp.f
> ifort -c -w -mp -tpp5 -O3 propor.f
> ifort -c -w -mp -tpp5 -O3 pulayx.F
> ifort -c -w -mp -tpp5 -O3 ranger.f
> ifort -c -w -mp -tpp5 -O3 ran3.f
> ifort -c -w -mp -tpp5 -O3 recipes.f
> ifort -c -w -mp -tpp5 -O3 reclat.f
> ifort -c -w -mp -tpp5 -O3 redata.F
> ifort -c -w -mp -tpp5 -O3 redcel.F
> ifort -c -w -mp -tpp5 -O3 reinit.F
> ifort -c -w -mp -tpp5 -O3 reord.f
> ifort -c -w -mp -tpp5 -O3 rhoofd.f
> ifort -c -w -mp -tpp5 -O3 rhoofdsp.f
> ifort -c -w -mp -tpp5 -O3 rhooda.f
> ifort -c -w -mp -tpp5 -O3 savepsi.F
> ifort -c -w -mp -tpp5 -O3 shaper.f
> ifort -c -w -mp -tpp5 -O3 timer.F
> ifort -c -w -mp -tpp5 -O3 vmb.F
> ifort -c -w -mp -tpp5 -O3 vmat.f
> ifort -c -w -mp -tpp5 -O3 vmatsp.f
> ifort -c -w -mp -tpp5 -O3 volcel.f
> ifort -c -w -mp -tpp5 -O3 xc.f
> ifort -c -w -mp -tpp5 -O3 xijorb.f
> ifort -c -w -mp -tpp5 -O3 cellxc.F
> ifort -c -w -mp -tpp5 -O3 cdiag.F
> ifort -c -w -mp -tpp5 -O3 rdiag.F
> ifort -c -w -mp -tpp5 -O3 cgvc.F
> ifort -c -w -mp -tpp5 -O3 iocg.f
> ifort -c -w -mp -tpp5 -O3 ioeig.f
> ifort -c -w -mp -tpp5 -O3 iofa.f
> ifort -c -w -mp -tpp5 -O3 iokp.f
> ifort -c -w -mp -tpp5 -O3 iomd.f
> ifort -c -w -mp -tpp5 -O3 repol.F
> ifort -c -w -mp -tpp5 -O3 typecell.f
> ifort -c -w -mp -tpp5 -O3 ofc.f
> ifort -c -w -mp -tpp5 -O3 poison.F
> ifort -c -w -mp -tpp5 -O3 readsp.F
> ifort -c -w -mp -tpp5 -O3 siesta.F
> ifort -c -w -mp -tpp5 -O3 io.f
> ifort -c -w -mp -tpp5 -O3 spin_init.f
> ifort -c -w -mp -tpp5 -O3 coor.f
> ifort -c -w -mp -tpp5 -O3 transfer.f
> ifort -c -w -mp -tpp5 -O3 broadcast_basis.F
> ifort -c -w -mp -tpp5 -O3 sig.f
> ifort -c -w -mp -tpp5 -O3 eggbox.F
> ifort -c -w -mp -tpp5 -O3 bsd.f
> ifort -c -w -mp -tpp5 -O3 ../NETransport/leads_complex.F
> ifort -c -w -mp -tpp5 -O3 ../NETransport/negf.F
> ifort -c -w -mp -tpp5 -O3 ../NETransport/identify.f
> ifort -c -w -mp -tpp5 -O3 ../NETransport/diagonal_alex.f
> ifort -c -w -mp -tpp5 -O3 ../NETransport/misc.f
> ifort -c -w -mp -tpp5 -O3 ../NETransport/selfenergy.F
> ifort -c -w -mp -tpp5 -O3 gauleg.f
> ifort -c -w -mp -tpp5 -O3 ../NETransport/transm.F
> ifort -c -w -mp -tpp5 -O3 ../NETransport/invert.f
> ifort -c -w -mp -tpp5 -O3 ../NETransport/decimate_leads.f
> ifort -c -w -mp -tpp5 -O3 ../NETransport/gensvd.f
> ifort -c -w -mp -tpp5 -O3 ../NETransport/rank.F
> ifort -c -w -mp -tpp5 -O3 ../NETransport/negfk.F
> ifort -c -w -mp -tpp5 -O3 ../NETransport/negf2g.f
> ifort -c -w -mp -tpp5 -O3 ../NETransport/negf2k.F
> fortcom: Error: ../NETransport/negf2k.F, line 1176: This name does not
> have a type, and must have an explicit type. [ISPIN]
> rhoG(II,JJ)=rho0L(II,JJ,ISPIN)
> --------------------------------------^
> fortcom: Error: ../NETransport/negf2k.F, line 1176: The number of
> subscripts is incorrect. [RHO0L]
> rhoG(II,JJ)=rho0L(II,JJ,ISPIN)
> --------------------------^
> compilation aborted for ../NETransport/negf2k.F (code 1)
> make: *** [negf2k.o] Error 1
> [root at cigana Src]#
>
>
>
>
>
>
> thank`s very much Sir.
>
> Amaury Melo
>
>
>
>
>
>
>
>
>
>
>
> 2008/4/10, sanvitos at tcd.ie <sanvitos at tcd.ie>:
> >
> >
> > Welcome to Smeagol!
> >
> > We have now received your project and the Smeagol License and we are in
> > the position to give you Smeagol 1.0.
> >
> > Smeagol will be available for download at following link, where you will
> > be asked to type both your username and password.
> >
> > url: http://smeagol.tchpc.tcd.ie/downloads
> >
> > login: Alvesjla
> > password: 8kHHwb98
> >
> > Please keep this e-mail since updates and patches will be distributed
> > in the same way.
> >
> > We don\'t know if you have any experience with SIESTA, but our suggestion
> > is to compile it first. Usually most of the problems (like libraries and
> > compatibility issues with mpi) arise at this stage and have nothing
> > to do with Smeagol. Another suggestion is to subscribe to the SIESTA
> > mailing list.
> >
> > There is a README file in the Smeagol main directory containing the main
> > instructions for compiling Smeagol (it has been compiled succesfully
> > with siesta1.3p but it hasn\'t been compiled with siesta1.3f1p - I can\'t
> > guarantee it will work). There are some small changes that you need
> > to do to the code in order to patch everything up. As of yet it is not
> > compliant with siesta.2.0. There is also a doc directory containing a
> > manual for Smeagol.
> >
> > We can help you in a few ways:
> >
> > 1) There is a Smeagol mailing list where to post query and look for
> > previous questions. Keeping the list vital is important for both users
> > and developers, so do not hesitate in using it. Please subscribe at:
> >
> > http://lists.tchpc.tcd.ie/listinfo/smeagol-discuss
> >
> > 2) There is also a wiki page where you can find some additional
> > information. You can edit part of the pages if you find it useful. The
> > link is:
> >
> > http://smeagol.tchpc.tcd.ie/wiki/
> >
> > 3) You can of course write privately to your Smeagol collaborators.
> > Unless the questions are reserved we appreciate if you can also copy to
> > smeagol at tcd.ie . This is where we keep a record of the questions, which
> > are used to make the wiki.
> >
> >
> >
> > Enjoy !
> >
> > The Smeagol Team
> >
> >
> >
>
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