[gmx-users] " X particles communicated to PME node Y are more ... " error in lysozyme tutorial
Mark Abraham
mark.j.abraham at gmail.com
Tue May 21 14:35:54 CEST 2013
http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49002 looks like it might be
the issue - fixed between gcc 4.6.1 and 4.6.2. If Vishal would like to
update his gcc to the latest version (which we always recommend, because
such issues are distressingly frequent), then he should be able to take
advantage of the correct and faster AVX_256. Please let us know how it
goes, Vishal. If that fixes the issue then I will add logic to refuse to
build AVX_256 with 4.6.1.
Mark
On Mon, May 20, 2013 at 3:00 PM, Vishal Kumar Jaiswal
<vishal3990 at gmail.com>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.
>
>
> 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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