[CP2K:3043] Re: Segfault with psmp

Alin Marin Elena alinm... at gmail.com
Tue Jan 11 16:00:54 CET 2011


Hi Ondrej,

A long shot but I think the problem lies in here 

   nthread = 1
  !$  nthread = omp_get_max_threads()
that will give you the maximum number of threads available on the system
use this instead omp_get_num_threads()

regards,

Alin

On Tuesday 11 January 2011 14:49:37 Ondrej Marsalek wrote:
> Additional confusion: the problem occurs within an 'IF (nthread > 1)',
> even if I set OMP_NUM_THREADS=1. When I print nthread in that place, I
> always get '8'. Is cp2k supposed to honor the value of the env
> variable? If not, what is the proper way to set the number of threads?
> 
> Thanks,
> Ondrej
> 
> PS:
> The threads can also be seen in gdb:
> 
> Starting program:
> /home/andy/build/cp2k/cp2k/exe/Linux-x86-64-intel/cp2k.ssmp W3-H3O.inp
> [Thread debugging using libthread_db enabled]
> [New Thread 0x7ffff7fd3700 (LWP 32192)]
> 
>   **** **** ******  **  PROGRAM STARTED AT               2011-01-11
> 14:38:08.422 ***** ** ***  *** **   PROGRAM STARTED ON                     
>        cassandra **    ****   ******    PROGRAM STARTED BY                 
>                 andy ***** **    ** ** **   PROGRAM PROCESS ID             
>                    32189 **** **  *******  **  PROGRAM STARTED IN         
> /home/andy/W3-H3O-min-global
> 
>  CP2K| version string:                 CP2K version 2.2.94 (Development
> Version) CP2K| is freely available from                         
> http://cp2k.berlios.de/ CP2K| Program compiled at                         
> Tue Jan 11 14:00:00 CET 2011 CP2K| Program compiled on                     
>                        cassandra CP2K| Program compiled for                
>                   Linux-x86-64-intel CP2K| Last CVS entry
>  CP2K| Input file name                                               
> W3-H3O.inp [New Thread 0x7ffff4fe4700 (LWP 32193)]
> [New Thread 0x7ffff4be3700 (LWP 32194)]
> [New Thread 0x7ffff47e2700 (LWP 32195)]
> [New Thread 0x7fffeffff700 (LWP 32196)]
> [New Thread 0x7fffefbfe700 (LWP 32197)]
> [New Thread 0x7fffef7fd700 (LWP 32198)]
> [New Thread 0x7fffef3fc700 (LWP 32199)]
> 
> 
> On Tue, Jan 11, 2011 at 14:25, Ondrej Marsalek
> 
> <ondrej.... at gmail.com> wrote:
> > I have simplified the problem further by doing a ssmp build. The arch
> > file can be found here:
> > 
> > http://marge.uochb.cas.cz/~marsalek/tmp/Linux-x86-64-intel.psmp
> > 
> > And the problem persists as described, regardless of the number of
> > OpenMP threads.
> > 
> > Any ideas how to get this working?
> > 
> > Thanks,
> > Ondrej
> > 
> > On Thu, Jan 6, 2011 at 14:04, Ondrej Marsalek <ondrej.... at gmail.com> 
wrote:
> >> Dear all,
> >> 
> >> I get a segfault with a psmp build of cp2k trunk. The corresponding
> >> popt works. The problem occurs even when run as a single process and
> >> with OMP_NUM_THREADS=1. This is what it looks like to gdb:
> >> 
> >> ==========
> >> ...
> >>  Spin 1
> >> 
> >>  Number of electrons:                                                
> >>         17 Number of occupied orbitals:                              
> >>                   17 Number of molecular orbitals:                  
> >>                              17
> >> 
> >>  Spin 2
> >> 
> >>  Number of electrons:                                                
> >>         16 Number of occupied orbitals:                              
> >>                   16 Number of molecular orbitals:                  
> >>                              16
> >> 
> >>  Number of orbital functions:                                        
> >>        169 Number of independent orbital functions:                  
> >>                  169
> >> 
> >>  Extrapolation method: initial_guess
> >> 
> >> Program received signal SIGSEGV, Segmentation fault.
> >> [Switching to Thread 0x7fffef887700 (LWP 23493)]
> >> __libc_free (mem=0x2020202000000001) at malloc.c:3709
> >> 3709    malloc.c: No such file or directory.
> >>        in malloc.c
> >> (gdb) backtrace
> >> #0  __libc_free (mem=0x2020202000000001) at malloc.c:3709
> >> #1  0x000000000257a6ec in for_deallocate ()
> >> #2  0x00000000016d413b in
> >> QS_COLLOCATE_DENSITY::L_qs_collocate_density_mp_calculate_rho_elec__91
> >> 7__par_region0_2_110 ()
> >>    at
> >> /home/andy/build/cp2k/cp2k/makefiles/../src/qs_collocate_density.F:11
> >> 63 #3  0x0000000002634763 in L_kmp_invoke_pass_parms ()
> >> #4  0x00007fffffff53fc in ?? ()
> >> #5  0x00007fffffff53c4 in ?? ()
> >> #6  0x00007fffffff5380 in ?? ()
> >> ...
> >> ==========
> >> 
> >> The CPU is a Core i7. The arch file and the input that triggers the
> >> segfault (almost immediately after start) are here:
> >> 
> >> http://marge.uochb.cas.cz/~marsalek/tmp/W3-H3O-min-global.tar.gz
> >> http://marge.uochb.cas.cz/~marsalek/tmp/Linux-x86-64-intel.psmp
> >> 
> >> The versions used for the build are:
> >> cp2k trunk checked out today
> >> OpenMPI 1.5
> >> Intel Compiler 11.1.073 and corresponding MKL
> >> 
> >> I understand that this might be difficult or impossible to reproduce,
> >> but would be grateful for any suggestions as for how to try to resolve
> >> this.
> >> 
> >> Thanks,
> >> Ondrej
-- 
I force myself to contradict myself in order to avoid conforming to my own 
taste. -- Marcel Duchamp
Without Questions there are no Answers!
_____________________________________________________________________
Alin Marin ELENA
Advanced Molecular Simulation Research Laboratory  
School of Physics, University College Dublin
----  
Ardionsamblú Móilíneach Saotharlann Taighde
Scoil na Fisice, An Coláiste Ollscoile, Baile Átha Cliath
-----------------------------------------------------------------------------------
Address:
Room 318, UCD Engineering and Material Science Centre
University College Dublin
Belfield, Dublin 4, Ireland
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alin.... at ucdconnect.ie, alinm... at gmail.com
______________________________________________________________________



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