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@vishal-VPCCW16FG [CMAKE] vishal@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 <jalem...@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@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> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? 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