segmentation fault in GROMACS 4.5.5

[tev...@gmail.com]

Greetings,

I tried to run Bias Exchange Metadynamics on my laptop (quad core with 8 threads) with PLUMED 1.3 and GROMACS 4.5.5. GROMACS was compiled with threads disabled. The tests ran fine, yet when I tried my system using just 3 replicas I got this:

step 1: Water molecule starting at atom 8356 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step1b.pdb to ./#step1b.pdb.4#

Back Off! I just backed up step1c.pdb to ./#step1c.pdb.4#
Wrote pdb files with previous and current coordinates
[thomasASUS:13490] *** Process received signal ***
[thomasASUS:13490] Signal: Segmentation fault (11)
[thomasASUS:13490] Signal code: Address not mapped (1)
[thomasASUS:13490] Failing at address: 0x5a46ba0
[thomasASUS:13490] [ 0] /lib64/libpthread.so.0() [0x349c00f500]
[thomasASUS:13490] [ 1] /home/thomas/Programs/gromacs-4.5.5_gnu_openmpi/dp_build_dir/lib/libgmx_mpi_d.so.6(+0x217d2e) [0x2b45ded86d2e]
[thomasASUS:13490] *** End of error message ***
Wrote pdb files with previous and current coordinates


I tried to run unbiased MD on the same starting configurations with the same .mdp file and didn't get any warnings about atom clashes. Also when I tried to run BEMD using all the 8 replicas I didn't get errors about waters moving too fast, but a different stacktrace:

starting mdrun 'Protein in water'
50000 steps,    100.0 ps.
50000 steps,    100.0 ps.
[thomasASUS:11863] *** Process received signal ***
[thomasASUS:11863] Signal: Segmentation fault (11)
[thomasASUS:11863] Signal code: Address not mapped (1)
[thomasASUS:11863] Failing at address: 0x10551
..........
[thomasASUS:11863] [ 0] /lib64/libpthread.so.0() [0x349c00f500]
[thomasASUS:11863] [ 1] mdrun_d4.5.5_gnu_openmpi_plumed(meta_force_calculation+0x7aa) [0x4260fa]
[thomasASUS:11863] [ 2] mdrun_d4.5.5_gnu_openmpi_plumed(do_md+0x66cb) [0x4d8e9b]
[thomasASUS:11863] [ 3] mdrun_d4.5.5_gnu_openmpi_plumed(mdrunner+0xa61) [0x4d1db1]
[thomasASUS:11863] [ 4] mdrun_d4.5.5_gnu_openmpi_plumed(main+0x1388) [0x4dd5d8]
[thomasASUS:11863] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd) [0x349b41ecdd]
[thomasASUS:11863] [ 6] mdrun_d4.5.5_gnu_openmpi_plumed() [0x409cf9]
[thomasASUS:11863] *** End of error message ***
..........
mpirun noticed that process rank 5 with PID 13727 on node thomasASUS exited on signal 11 (Segmentation fault).


I suspect the latter error might be due to insufficient memory, but I don't have any possible explanation why the 3 replicas failed. Do you have any ideas what may be wrong? I can sent you a tarball with the input files on a personal communication if that may be necessary.

thanks in advance,
Thomas

[tev...@gmail.com]

Just another minor detail: I use the TIP4P-Ew water model which is prone to these type of errors ("Water molecule cannot be settled") but as I said I properly minimized the system and run unbiased MD successfully from these starting configurations.

Thomas

[Carlo Camilloni]

Dear Thomas,

it looks like your are adding very large forces to your system, but it will be more helpful

if you post your plumed input file.

Best,

Carlo

On 26 Mar 2013, at 19:44, tev...@gmail.com wrote:

Just another minor detail: I use the TIP4P-Ew water model which is prone to these type of errors ("Water molecule cannot be settled") but as I said I properly minimized the system and run unbiased MD successfully from these starting configurations.

Thomas

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[Thomas Evangelidis]

Dear Carlo,

Here's the plumed input file for CV1. If that doesn't make sense I can send you all input files and command line to reproduce it.

thanks,
Thomas

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

HILLS HEIGHT 0.20 W_STRIDE 1000

PRINT W_STRIDE 1000
BIASXMD

HILLS_LABEL A

################################################################
########################## The Groups ##########################
################################################################

cg-> 10 32 46 72 89 106 123 cg<-
ca-> 5 27 41 53 67 84 101 118 ca<-

ncacocbcg-> 1 5 7 10 23 24 25 27 29 32 37 38 39 41 43 46 49 50 51 53 55 63 64 65 67 69 72 80 81 82 84 86 89 97 98 99 101 103 106 114 115 116 118 120 123 126 127 128 130 132 145 ncacocbcg<-


#############################################################
########################## The CVs ##########################
#############################################################

# CV1 Coordination number CA
COORD LIST <ca> <ca> NN 8 MM 10 R_0 0.65 D_0 0.0 SIGMA 0.7

# CV2 Coordination number CG
COORD LIST <cg> <cg> NN 8 MM 10 R_0 0.50 D_0 0.0 SIGMA 0.5

ALIGN_ATOMS LIST <ncacocbcg>

## set the bias force equal to zero beyond a boundary
INVERT CV 1 LIMIT1 57.0 LIMIT2 96.0
#INVERT CV 2 LIMIT1 36.0 LIMIT2 63.0

LWALL CV 1 LIMIT 57.0 KAPPA 100.0
UWALL CV 1 LIMIT 96.00 KAPPA 100.0
LWALL CV 2 LIMIT 36.0 KAPPA 100.0
UWALL CV 2 LIMIT 63.0 KAPPA 100.0


## Store an array containing the current value of the bias potential (and of the derivatives with respect to the CVs) on a grid. In
## this way the computational cost of metadynamics becomes constant all over the simulation and corresponds to the cost of evaluating a single Gaussian
## function on the whole grid with a frequency given by the stride between subsequent hills.
GRID CV 1 MIN -100.00 MAX 220.00 NBIN 2000
#GRID CV 2 MIN -65.00 MAX 90.00 NBIN 2000
WRITE_GRID FILENAME bias.dat W_STRIDE 10000

## monitor a CV during a metadynamics run without applying a bias on it (only for bias-exchange metadynamics)
#NOHILLS CV 1
NOHILLS CV 2


ENDMETA

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

Thomas Evangelidis

PhD student

University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tev...@pharm.uoa.gr

          tev...@gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/

[Carlo Camilloni]

have you already checked if one of the collective variables is on the walls or very near to them at time 0?

This is probably the simplest explanation, otherwise try to switch off both the HILLS, GRID, WALLS, INVERT

keywords and start just analysing the CVs, and then add the keywords back one by one.

Carlo

[Thomas Evangelidis]

Yes, the problem was the wall limits.

many thanks!

Thomas

[faridesa...@gmail.com]

hi, could you explain more how should solve this issue?

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

Thomas Evangelidis

PhD student

University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tev...@pharm.uoa.gr

          tev...@gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/

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[Thomas Evangelidis]

On Mon, 10 Aug 2020 at 22:24, <faridesa...@gmail.com> wrote:

hi, could you explain more how should solve this issue?

Hi and sorry for the late reply. It's been many years since I posted this question and I don't quite remember, but I think that I just expanded the wall limits. Unfortunately, I have the input files in some other hard drive and I can't check them right now. Just be careful cause the syntax has changed a lot since the time of this post. 

~Thomas

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

Dr. Thomas Evangelidis

Research Scientist

IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic

  & 

CEITEC - Central European Institute of Technology, Brno, Czech Republic 

email: tev...@gmail.com, Twitter: tevangelidis, LinkedIn: Thomas Evangelidis

website: https://sites.google.com/site/thomasevangelidishomepage/

[Faride Sadeghkhani]

thanks for the reply.

I expanded the wall limits, too. but unfortunately, the problem has not been solved. 😞

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