[gmx-users] Segmentation fault (11)

[Ricardo O. S. Soares]

Hi everyone,

could anyone help me with this? I already searched the mailing archives, with no luck.

I just installed gromacs 4.0.7 in a new computer here, same as always (with mpi support), but now I get this error whem I run MDRUN with or without mpirun (openmpi):


starting mdrun 'Protein in water'
250000 steps, 500.0 ps.
step 0
[host02:21827] *** Process received signal ***
[host02:21827] Signal: Segmentation fault (11)
[host02:21827] Signal code: Address not mapped (1)
[host02:21827] Failing at address: (nil)
[host02:21827] [ 0] [0xddf410]
[host02:21827] *** End of error message ***
Segmentation fault



Any ideas?

Thank you.




---
Ricardo O. S. Soares , MsC.
Group of Biological Physics - Department of Physics & Chemistry
Faculty of Pharmaceutical Sciences at Ribeir?o Preto - University of S?o Paulo.
Av.do Caf?, S/N - ZIP:14040-903 - Ribeir?o Preto, S?o Paulo, Brazil.
Phone: [phone].

ross_usp at yahoo.com.br,rsoares at fcfrp.usp.br


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[Justin A. Lemkul]

Post by Ricardo O. S. Soares
Hi everyone,
could anyone help me with this? I already searched the mailing archives, with no luck.
I just installed gromacs 4.0.7 in a new computer here, same as always
(with mpi support), but now I get this error whem I run MDRUN with or
starting mdrun 'Protein in water'
250000 steps, 500.0 ps.
step 0
[host02:21827] *** Process received signal ***
[host02:21827] Signal: Segmentation fault (11)
[host02:21827] Signal code: Address not mapped (1)
[host02:21827] Failing at address: (nil)
[host02:21827] [ 0] [0xddf410]
[host02:21827] *** End of error message ***
Segmentation fault
Any ideas?

Does the same system run on other machines? An instant seg fault usually just
means that your system is physically unrealistic (insufficient minimization,
inappropriate .mdp parameters for a given force field, etc):

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

Post by Ricardo O. S. Soares
Thank you.
////
---
Ricardo O. S. Soares , MsC.
Group of Biological Physics - Department of Physics & Chemistry
Faculty of Pharmaceutical Sciences at Ribeir?o Preto - University of S?o Paulo.
Av.do Caf?, S/N - ZIP:14040-903 - Ribeir?o Preto, S?o Paulo, Brazil.
Phone: [phone].
ross_usp at yahoo.com.br,rsoares at fcfrp.usp.br
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================