[gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial

[Justin Lemkul]

On 5/20/13 2:29 AM, Vishal Kumar Jaiswal wrote:
> I am trying to complete the lysozyme in water tutorial in gromacs 4.6.1 and
> i am getting this error in the energy minimization step
> I was able to complete the entire tutorial on another computer ( my
> personal laptop) . ( I was getting the same error while doing energy
> minimization on another system (polymer in water) which forced me to check
> gromacs correcctness by doing the lysozyme tutorial)
>

How do the configurations of your laptop and the problematic machine differ?

-Justin

>
> The following is the verbose output to my terminal :
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
> Step=    0, Dmax= 1.0e-02 nm, Epot=         -nan Fmax= 1.50489e+13, atom=
> 14918
> -------------------------------------------------------
> Program mdrun, VERSION 4.6.1
> Source code file: /home/vishal/Downloads/gromacs-4.6.1/src/mdlib/pme.c,
> line: 827
>
> Fatal error:
> 3483 particles communicated to PME node 2 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated.
>
> Following is the entry from "em.log" file
>
> Linking all bonded interactions to atoms
> There are 8522 inter charge-group exclusions,
> will use an extra communication step for exclusion forces for PME
>
> The initial number of communication pulses is: X 1
> The initial domain decomposition cell size is: X 1.83 nm
>
> The maximum allowed distance for charge groups involved in interactions is:
>                   non-bonded interactions           1.000 nm
>              two-body bonded interactions  (-rdd)   1.000 nm
>            multi-body bonded interactions  (-rdd)   1.000 nm
>
>
> Making 1D domain decomposition grid 4 x 1 x 1, home cell index 0 0 0
>
> Initiating Steepest Descents
> Charge group distribution at step 0: 3184 3300 3308 3255
> Grid: 5 x 11 x 11 cells
> Started Steepest Descents on node 0 Mon May 20 11:36:21 2013
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
>
>             Step           Time         Lambda
>                0        0.00000        0.00000
>
> DD  step 0 load imb.: force  8.8%
>
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.6.1
> Source code file: /home/vishal/Downloads/gromacs-4.6.1/src/mdlib/pme.c,
> line: 827
>
> Fatal error:
> 3483 particles communicated to PME node 2 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated.
>
>
> The following is the hardware information of the pc on which error is
> showing ttaken from "em.log" file
>
>
> Gromacs version:    VERSION 4.6.1
> Precision:          single
> Memory model:       64 bit
> MPI library:        thread_mpi
> OpenMP support:     enabled
> GPU support:        disabled
> invsqrt routine:    gmx_software_invsqrt(x)
> CPU acceleration:   AVX_256
> FFT library:        fftw-3.3.3-sse2
> Large file support: enabled
> RDTSCP usage:       enabled
> Built on:           Fri May 10 13:45:48 IST 2013
> Built by:           vishal at aditya-HCL-Desktop [CMAKE]
> Build OS/arch:      Linux 3.0.0-19-generic x86_64
> Build CPU vendor:   GenuineIntel
> Build CPU brand:    Intel(R) Core(TM) i5-2400 CPU @ 3.10GHz
> Build CPU family:   6   Model: 42   Stepping: 7
> Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx msr
> nonstop_tsc pcid pclmuldq pdcm popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2
> ssse3 tdt x2apic
> C compiler:         /usr/bin/gcc GNU gcc (Ubuntu/Linaro 4.6.1-9ubuntu3)
> 4.6.1
> C compiler flags:   -mavx   -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value   -fomit-frame-pointer
> -funroll-all-loops -fexcess-precision=fast  -O3 -DNDEBUG
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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