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

Justin Lemkul jalemkul at vt.edu
Tue May 21 04:15:52 CEST 2013



On 5/20/13 9:00 AM, Vishal Kumar Jaiswal wrote:
>                            LAPTOP- WORKING
>                            PC -NOT WORKING
>
> Gromacs version:    VERSION 4.6.1
>                                           VERSION 4.6.1
> Precision:          single
>                                                                same
> Memory model:       32 bit
>                                                            64 bit
> MPI library:        thread_mpi
>                                                            same
> OpenMP support:     enabled
>                                                       same
> GPU support:        enabled
>                                                        disabled
> invsqrt routine:    gmx_software_invsqrt(x)
>                                                     same
> CPU acceleration:   SSE4.1
>                                                      AVX_256
> FFT library:        fftw-3.2.2
>                                                             fftw-3.3.3-sse2
> Large file support: enabled
>                                                            same
> RDTSCP usage:       disabled
>                                                          enabled
> Built on:           Fri Mar 15 14:30:08 IST 2013
>                                       Fri May 10 13:45:48 IST 2013
> Built by:           vishal at vishal-VPCCW16FG [CMAKE]
>                            vishal at aditya-HCL-Desktop [CMAKE]
> Build OS/arch:      Linux 3.0.0-12-generic i686
>                                  Linux 3.0.0-19-generic x86_64
> Build CPU vendor:   GenuineIntel
>                                                         GenuineIntel
>
>
>
> Build CPU brand:    Intel(R) Core(TM)2 Duo CPU P8700  @ 2.53GHz
>       Intel(R) Core(TM) i5-2400 CPU @ 3.10GHz
> Build CPU family:   6   Model: 23   Stepping: 10
>                                              6   Model: 42   Stepping: 7
>
> Build CPU features: apic clfsh cmov cx8 cx16 lahf_lm mmx msr pdcm pse sse2
> sse3 sse4.1 ssse3
>                              : PC - 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
>                           PC -  /usr/bin/gcc GNU gcc (Ubuntu/Linaro
> 4.6.1-9ubuntu3) 4.6.1
>
> C compiler flags:   -msse4.1   -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value   -fomit-frame-pointer
> -funroll-all-loops -fexcess-precision=fast  -O3 -DNDEBUG
>                               PC -    -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
>
>
> C++ compiler:       /usr/bin/c++ GNU c++ (Ubuntu/Linaro 4.6.1-9ubuntu3)
> 4.6.1
>                             PC - none
>
> C++ compiler flags: -msse4.1   -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value   -fomit-frame-pointer
> -funroll-all-loops -fexcess-precision=fast  -O3 -DNDEBUG
>                                PC -none
>
> CUDA compiler:      nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c)
> 2005-2012 NVIDIA Corporation;Built on Fri_Sep_21_17:24:42_PDT_2012;Cuda
> compilation tools, release 5.0, V0.2.1221
>                                  PC (none)
>
> CUDA driver:        5.0                             none
> CUDA runtime:       5.0                          none
>
>
> These are taken from gromacs log files. ( Though i have CUDA installed on
> laptop i dont use it for GROMACS as the NVIDIA compte capability is 1.2)
> I am able to run the tutorial on PC now using GROMACS 4.5.7
>
> Please tell me if you want more details.
>

It would be useful to get to the root of the error, because this smells of a 
bug.  One idea that comes to mind is to manually set SSE4.1 as the CPU 
acceleration on the non-working PC to see if AVX_256 is the problem.

-Justin

>
> On Mon, May 20, 2013 at 5:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>> --
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>>

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

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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