[Smeagol-discuss] problem running Smeagol in parallel

[Zhiyong Zhang]

Hello Ivan, 

Thank you very much for the suggestions. I am using the examples in the Example directory. I used 1 processor only and it works. If I use two processor then it doesn't work. 

Regards,
Zhiyong

----- Original Message -----
From: "Ivan Rungger" <runggeri at tcd.ie>
To: "Zhiyong Zhang" <zyzhang at stanford.edu>
Cc: smeagol-discuss at lists.tchpc.tcd.ie
Sent: Monday, March 21, 2011 4:14:22 AM
Subject: Re: [Smeagol-discuss] problem running Smeagol in parallel

Hello Zhiyong,
 
  can you send the input file? It might just be that the system is too 
small to run in parallel, you might try to run it on 1 or 2 processors 
in parallel, and see if it runs.

Cheers,

 Ivan

Zhiyong Zhang wrote:
> Dear All, 
>
> I have compiled Smeagol but having problem running it in parallel. 
>
> I can run the compiled program in serial without problem but when I run it in parallel I got the following error: 
>
> InitMesh: MESH =    16 x    16 x    16 =        4096
> InitMesh: Mesh cutoff (required, used) =   150.000   171.794 Ry
>  
> * Maximum dynamic memory allocated =     8 MB
> [nx5:02823] *** Process received signal ***
> [nx5:02823] Signal: Segmentation fault (11)
> [nx5:02823] Signal code: Address not mapped (1)
> [nx5:02823] Failing at address: 0xf3
> [nx5:02821] *** Process received signal ***
> [nx5:02821] Signal: Segmentation fault (11)
> [nx5:02821] Signal code: Address not mapped (1)
> [nx5:02821] Failing at address: 0xf3
> [nx5:02823] [ 0] /lib64/tls/libpthread.so.0 [0x3e1300c5b0]
> [nx5:02823] [ 1] /home/paulzim/openmpi-1.3_10.1/lib/libmpi.so.0(MPI_Comm_size+0x60) [0x2a95e8e9e0]
> [nx5:02823] [ 2] /home/zzhang/Smeagol/smeagol.1.0b/Src/smeagol(Cblacs_pinfo+0x9d) [0x84dc95]
> [nx5:02823] [ 3] /home/zzhang/Smeagol/smeagol.1.0b/Src/smeagol(blacs_get__+0x1e0) [0x84aaa8]
> [nx5:02823] [ 4] /home/zzhang/Smeagol/smeagol.1.0b/Src/smeagol(cdiag_+0x28e) [0x5df07a]
> [nx5:02823] [ 5] /home/zzhang/Smeagol/smeagol.1.0b/Src/smeagol(diagk_+0x7a0) [0x50a40c]
> [nx5:02823] [ 6] /home/zzhang/Smeagol/smeagol.1.0b/Src/smeagol(diagon_+0x1019) [0x4f588d]
> [nx5:02823] [ 7] /home/zzhang/Smeagol/smeagol.1.0b/Src/smeagol(MAIN__+0xe950) [0x5fd5b0]
> [nx5:02823] [ 8] /home/zzhang/Smeagol/smeagol.1.0b/Src/smeagol(main+0x2a) [0x4260e2]
> [nx5:02823] [ 9] /lib64/tls/libc.so.6(__libc_start_main+0xdb) [0x3e1251c40b]
> [nx5:02823] [10] /home/zzhang/Smeagol/smeagol.1.0b/Src/smeagol(ztrsm_+0x6a) [0x42602a]
>
> Here are the object files linked in: 
> /home/paulzim/openmpi-1.3_10.1/bin/mpif90 -o smeagol \
>        -w -mp -O3  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 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 fermispin.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 out
 co
>  or.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 linpack.o  bsd.o libfdf.a \
>        leads_complex.o negf.o identify.o diagonal_alex.o misc.o selfenergy.o gauleg.o transm.o invert.o decimate_leads.o gensvd.o rank.o negfk.o negf2g.o negf2k.o localdos.o gaucheb.o  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 \
>                  -L/opt/intel/mkl/10.0.5.025/lib/em64t/ -lmkl_scalapack_lp64 -lmkl_solver_lp64_sequential -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_lp64 -Wl,--end-group -lpthread
>
> As you see I am using mkl/10.0.5.025/lib/em64t/.
>
> The parallel execution env is as follows,
> PATH=/usr/local/bin/:/home/paulzim/openmpi-1.3_10.1/bin/
> LD_LIBRARY_PATH=/opt/intel/mkl/10.0.5.025/lib/em64t/:/home/paulzim/openmpi-1.3_10.1/lib/:/opt/intel/fce/10.0.023/lib:/usr/lib64/:/lib64/tls
>
> Thank you so much!
> Zhiyong
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