[gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial
Justin Lemkul
jalemkul at vt.edu
Tue May 21 13:55:16 CEST 2013
On 5/21/13 5:41 AM, Vishal Kumar Jaiswal wrote:
> Following your advice I compiled gromacs with DGMX_CPU_ACCELERATION=SSE4.1
> and now it is working :) . Thanks a lot
>
I suggested this as a diagnostic measure (not a fix), and it is good that it is
working properly, but is also indicative of a problem with the AVX_256
acceleration. Please file a bug report on redmine.gromacs.org with all the
details provided below, as well as .log files from successful and failed runs,
and a .tpr file that can be used to reproduce the problem. With that
information, we should be able to fix the bug so no one else encounters it again.
-Justin
> 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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--
========================================
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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