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 <jalem...@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@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. >> >> > 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 <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://vt.edu/Pages/Personal/justin> >>> <h**ttp://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> >>> <htt**p://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<h**ttp://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? Read >>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**========== > > 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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