[gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial
Vishal Kumar Jaiswal
vishal3990 at gmail.com
Tue May 21 11:41:44 CEST 2013
Following your advice I compiled gromacs with DGMX_CPU_ACCELERATION=SSE4.1
and now it is working :) . Thanks a lot
- Vishal
Undergraduate Student
Department of Chemistry
Indian Institute of Technology Guwahati
On Tue, May 21, 2013 at 7:45 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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://vt.edu/Pages/Personal/justin>
>>> <h**ttp://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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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