[Pw_forum] new user problem running Si
beaudet at uiuc.edu
beaudet at uiuc.edu
Mon Jun 16 21:58:36 CEST 2008
Nick,
Sorry it has taken a while to get back to you. After I posted I had a meeting, and several other things. I tried recompiling several different ways and while I get through the compile SEEMINGLY OK the code crashes at various points - usually at the very beginning.
I've got:
Quantum Espresso 4.0
Intel compilers version 10.1.011 and mkl version 10.0.1.014
BLAS and LAPACK are up to date on my Umbuntu distribution
I suspect it has to do with the parallel environment more than the particular compiler - but I could be wrong.
The simplest thing I've tried is using intel compilers. I used the following configure command:
./configure CXX=icpc CC=icc F90=ifort F77=ifort MPIF90=ifort
see attachment configintel
When I run an example I get:
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libc.so.6 00007F49D8CD6980 Unknown Unknown Unknown
libc.so.6 00007F49D8CD7481 Unknown Unknown Unknown
libmpich.so.1.0 00007F49D94C75BF Unknown Unknown Unknown
libmpich.so.1.0 00007F49D94D40E2 Unknown Unknown Unknown
libmpich.so.1.0 00007F49D94D4259 Unknown Unknown Unknown
libmpich.so.1.0 00007F49D94A3DC8 Unknown Unknown Unknown
libmpich.so.1.0 00007F49D9494A43 Unknown Unknown Unknown
libmpich.so.1.0 00007F49D94B86C9 Unknown Unknown Unknown
libmpich.so.1.0 00007F49D94B7FE4 Unknown Unknown Unknown
pw.x 000000000048F539 Unknown Unknown Unknown
pw.x 00000000005D02FD Unknown Unknown Unknown
pw.x 000000000040BE64 Unknown Unknown Unknown
pw.x 000000000040BDE2 Unknown Unknown Unknown
libc.so.6 00007F49D8C7A1C4 Unknown Unknown Unknown
pw.x 000000000040BD29 Unknown Unknown Unknown
It doesn't matter if I just execute ./pw.x or "mpirun -n 4 ./pw.x". It crashes immediately with or without redirected input.
In the post to the forum pw.x ran for a little bit and then crashed (this is the best so far). In that case the following configure was used:
./configure CXX=mpic++ CC=mpicc F90=mpif90 F77=mpif77 MPIF90=mpif90
see attachment configmpi
It crashes serial or parallel (i.e. with or without "mpirun -n 4").
Also, I tried gfortran but it basically went like intel where the crash was immediate.
Thanks for any help,
Todd Beaudet
PS. Are you married now? My wife and I are expecting our second son around Aug. 15! I hope all is well.
---- Original message ----
>Date: Fri, 13 Jun 2008 15:53:37 -0400
>From: "Nichols A. Romero" <naromero at gmail.com>
>Subject: Re: [Pw_forum] new user problem running Si
>To: "PWSCF Forum" <pw_forum at pwscf.org>
>
> Todd,
>
> You should tells us the following information.
> 1. compiler
> 2. math library
> 3. serial or parallel run
> 4. PWscf version
>
> On Fri, Jun 13, 2008 at 3:35 PM, <beaudet at uiuc.edu>
> wrote:
>
> experienced PWscf users,
>
> I have compiled the code. When I run the Si
> example the code crashes after the second
> iteration...
>
> iteration # 2 ecut= 18.00 Ry beta=0.70
> CG style diagonalization
> ethr = 7.69E-04, avg # of iterations = 3.0
> p0_3521: p4_error: interrupt SIGSEGV: 11
>
> when I backtrace using a debugger I get the
> following:
>
> (gdb) backtrace
> #0 0x000000000050ed55 in __scf__mix_type_axpy ()
> #1 0x00000000004e2770 in mix_rho_ ()
> #2 0x00000000004cae58 in electrons_ ()
> #3 0x000000000040f39c in MAIN__ ()
>
> I suspect a problem with the environment when I
> compiled the code. I'm using Intel Core2 Quad CPU
> Q6600 and Ubuntu 8.04 - the Hardy Heron. Below is
> the input file I was using. Does anyone have a
> idea on how I might proceed? I can provide more
> information if necessary.
>
> &control
> calculation = 'scf'
> restart_mode='from_scratch',
> prefix='silicon',
> tstress = .true.
> tprnfor = .true.
> pseudo_dir =
> '/home/beaudet/espresso/espresso-4.0/pseudo/',
> outdir='/tmp/'
> /
> &system
> ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1,
> ecutwfc =18.0,
> /
> &electrons
> diagonalization='cg'
> mixing_mode = 'plain'
> mixing_beta = 0.7
> conv_thr = 1.0d-8
> /
> ATOMIC_SPECIES
> Si 28.086 Si.vbc.UPF
> ATOMIC_POSITIONS
> Si 0.00 0.00 0.00
> Si 0.25 0.25 0.25
> K_POINTS
> 10
> 0.1250000 0.1250000 0.1250000 1.00
> 0.1250000 0.1250000 0.3750000 3.00
> 0.1250000 0.1250000 0.6250000 3.00
> 0.1250000 0.1250000 0.8750000 3.00
> 0.1250000 0.3750000 0.3750000 3.00
> 0.1250000 0.3750000 0.6250000 6.00
> 0.1250000 0.3750000 0.8750000 6.00
> 0.1250000 0.6250000 0.6250000 3.00
> 0.3750000 0.3750000 0.3750000 1.00
> 0.3750000 0.3750000 0.6250000 3.00
>
> Thanks,
>
> Todd Beaudet
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
> --
> Nichols A. Romero, Ph.D.
> DoD User Productivity Enhancement and Technology
> Transfer (PET) Group
> High Performance Technologies, Inc.
> Reston, VA
> 443-567-8328 (C)
> 410-278-2692 (O)
>________________
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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