subject:"\[gmx\-users\] segmentation fault from power6 kernel"

Re: [gmx-users] segmentation fault from power6 kernel

2011-11-03 Thread Fabio AFFINITO

Hi Mark,
today I tested the 4.5.5 version. It seems here there's not that problem. 
Anyway, I will take some days to make more tests.

Thank you,

Fabio

- Messaggio originale -
Da: "Mark Abraham" 
A: "Discussion list for GROMACS users" 
Inviato: Giovedì, 3 novembre 2011 14:40:39
Oggetto: Re: [gmx-users] segmentation fault from power6 kernel


On 3/11/2011 7:59 PM, Fabio Affinito wrote:

Thank you, Mark.
Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6.
I also tried to run on a linux cluster and it went ok.

Sounds like a bug. Please file a report here http://redmine.gromacs.org 
including your observations and a .tpr that will reproduce them.

Thanks,

Mark





Fabio




The most likely issue is some normal "blowing up" scenario leading to a
table-lookup-overrun segfault in the 3xx series kernels. I don't know
why the usual error messages in such scenarios did not arise on this
platform. Try setting the environment variable GMX_NOOPTIMIZEDKERNELS to
1 to see if this is a power6-specific kernel issue. Try running the .tpr
on another platform.

Mark



--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] segmentation fault from power6 kernel

2011-11-03 Thread Mark Abraham


On 3/11/2011 7:59 PM, Fabio Affinito wrote:

Thank you, Mark.
Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6.
I also tried to run on a linux cluster and it went ok.


Sounds like a bug. Please file a report here http://redmine.gromacs.org 
 including your observations and a .tpr 
that will reproduce them.


Thanks,

Mark




Fabio



The most likely issue is some normal "blowing up" scenario leading to a
table-lookup-overrun segfault in the 3xx series kernels. I don't know
why the usual error messages in such scenarios did not arise on this
platform. Try setting the environment variable GMX_NOOPTIMIZEDKERNELS to
1 to see if this is a power6-specific kernel issue. Try running the .tpr
on another platform.

Mark




-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] segmentation fault from power6 kernel

2011-11-03 Thread Fabio Affinito


Thank you, Mark.
Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6.
I also tried to run on a linux cluster and it went ok.


Fabio



The most likely issue is some normal "blowing up" scenario leading to a
table-lookup-overrun segfault in the 3xx series kernels. I don't know
why the usual error messages in such scenarios did not arise on this
platform. Try setting the environment variable GMX_NOOPTIMIZEDKERNELS to
1 to see if this is a power6-specific kernel issue. Try running the .tpr
on another platform.

Mark


--
Fabio Affinito, PhD
SuperComputing Applications and Innovation Department
CINECA - via Magnanelli, 6/3, 40033 Casalecchio di Reno (Bologna) - ITALY
Tel: +39 051 6171794  Fax: +39 051 6132198
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] segmentation fault from power6 kernel

2011-11-02 Thread Mark Abraham


On 3/11/2011 6:42 AM, Fabio AFFINITO wrote:

Dear all,
I've trying to run a simulation on a IBM Power6 cluster. At the
beginning of the simulation I've got a segmentation fault. I investigated with 
TotalView and I've found that this segmentation violation originates in the 
pwr6kernel310.F
Up to now, I still didn't find what is behind this seg violation. I would like 
to ask if anybody is aware of a bug behind this function.
The simulation is obtained by using Gromacs 4.5.3 compiled in double precision.
The options that I specified in the configure are:
--disable-threads --enable-power6 --enable-mpi

The log file doesn't provide much informations:

Log file opened on Wed Nov  2 20:11:02 2011
Host: sp0202  pid: 11796682  nodeid: 0  nnodes:  1
The Gromacs distribution was built Thu Dec 16 14:44:40 GMT+01:00 2010 by
propro01@sp0201 (AIX 1 00C3E6444C00)


  :-)  G  R  O  M  A  C  S  (-:

Gromacs Runs One Microsecond At Cannonball Speeds

 :-)  VERSION 4.5.3  (-:

 Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
   Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
 Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
 Michael Shirts, Alfons Sijbers, Peter Tieleman,

Berk Hess, David van der Spoel, and Erik Lindahl.

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 Copyright (c) 2001-2010, The GROMACS development team at
 Uppsala University&  The Royal Institute of Technology, Sweden.
 check out http://www.gromacs.org for more information.

  This program is free software; you can redistribute it and/or
   modify it under the terms of the GNU General Public License
  as published by the Free Software Foundation; either version 2
  of the License, or (at your option) any later version.

   :-)  mdrun_d (double precision)  (-:


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
  --- Thank You ---  

Input Parameters:
integrator   = md
nsteps   = 250
init_step= 0
ns_type  = Grid
nstlist  = 10
ndelta   = 2
nstcomm  = 10
comm_mode= Linear
nstlog   = 2500
nstxout  = 2500
nstvout  = 2500
nstfout  = 0
nstcalcenergy= 10
nstenergy= 2500
nstxtcout= 2500
init_t   = 0
delta_t  = 0.002
xtcprec  = 1000
nkx  = 50
nky  = 50
nkz  = 50
pme_order= 4
ewald_rtol   = 1e-05
ewald_geometry   = 0
epsilon_surface  = 0
optimize_fft = TRUE
ePBC = xyz
bPeriodicMols= FALSE
bContinuation= FALSE
bShakeSOR= FALSE
etc  = Nose-Hoover
nsttcouple   = 10
epc  = No
epctype  = Isotropic
nstpcouple   = -1
tau_p= 1
ref_p (3x3):
   ref_p[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
   ref_p[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
   ref_p[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
compress (3x3):
   compress[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
   compress[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
   compress[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
refcoord_scaling = No
posres_com (3):
   posres_com[0]= 0.0e+00
   posres_com[1]= 0.0e+00
   posres_com[2]= 0.0e+00
posres_comB (3):
   posres_comB[0]= 0.0e+00
   po

[gmx-users] segmentation fault from power6 kernel

2011-11-02 Thread Fabio AFFINITO

Dear all,
I've trying to run a simulation on a IBM Power6 cluster. At the
beginning of the simulation I've got a segmentation fault. I investigated with 
TotalView and I've found that this segmentation violation originates in the 
pwr6kernel310.F
Up to now, I still didn't find what is behind this seg violation. I would like 
to ask if anybody is aware of a bug behind this function.
The simulation is obtained by using Gromacs 4.5.3 compiled in double precision.
The options that I specified in the configure are:
--disable-threads --enable-power6 --enable-mpi

The log file doesn't provide much informations:

Log file opened on Wed Nov  2 20:11:02 2011
Host: sp0202  pid: 11796682  nodeid: 0  nnodes:  1
The Gromacs distribution was built Thu Dec 16 14:44:40 GMT+01:00 2010 by
propro01@sp0201 (AIX 1 00C3E6444C00)


 :-)  G  R  O  M  A  C  S  (-:

   Gromacs Runs One Microsecond At Cannonball Speeds

:-)  VERSION 4.5.3  (-:

Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
  Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
   Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,

   Berk Hess, David van der Spoel, and Erik Lindahl.

   Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

 This program is free software; you can redistribute it and/or
  modify it under the terms of the GNU General Public License
 as published by the Free Software Foundation; either version 2
 of the License, or (at your option) any later version.

  :-)  mdrun_d (double precision)  (-:


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
  --- Thank You ---  


 PLEASE READ AND CITE THE FOLLOWING REFERENCE 
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
  --- Thank You ---  

Input Parameters:
   integrator   = md
   nsteps   = 250
   init_step= 0
   ns_type  = Grid
   nstlist  = 10
   ndelta   = 2
   nstcomm  = 10
   comm_mode= Linear
   nstlog   = 2500
   nstxout  = 2500
   nstvout  = 2500
   nstfout  = 0
   nstcalcenergy= 10
   nstenergy= 2500
   nstxtcout= 2500
   init_t   = 0
   delta_t  = 0.002
   xtcprec  = 1000
   nkx  = 50
   nky  = 50
   nkz  = 50
   pme_order= 4
   ewald_rtol   = 1e-05
   ewald_geometry   = 0
   epsilon_surface  = 0
   optimize_fft = TRUE
   ePBC = xyz
   bPeriodicMols= FALSE
   bContinuation= FALSE
   bShakeSOR= FALSE
   etc  = Nose-Hoover
   nsttcouple   = 10
   epc  = No
   epctype  = Isotropic
   nstpcouple   = -1
   tau_p= 1
   ref_p (3x3):
  ref_p[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  ref_p[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   compress (3x3):
  compress[0]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[1]={ 0.0e+00,  0.0e+00,  0.0e+00}
  compress[2]={ 0.0e+00,  0.0e+00,  0.0e+00}
   refcoord_scaling = No
   posres_com (3):
  posres_com[0]= 0.0e+00
  posres_com[1]= 0.0e+00
  posres_com[2]= 0.0e+00
   posres_comB (3):
  posres_comB[0]= 0.0e+00
  posres_comB[1]= 0.0e+00
  posres_comB[2]= 0.0e+00
   andersen_seed= 815131
   rlist

Re: [gmx-users] segmentation fault from power6 kernel

Re: [gmx-users] segmentation fault from power6 kernel

Re: [gmx-users] segmentation fault from power6 kernel

Re: [gmx-users] segmentation fault from power6 kernel

[gmx-users] segmentation fault from power6 kernel

5 matches

Site Navigation

Mail list logo

Footer information