I've opened http://redmine.gromacs.org/issues/1259 to discuss this issue. All users are warned that such issues are possible, and if you don't run the regression test suite, you can be at the mercy of a buggy compiler!
Mark On Tue, May 21, 2013 at 2:35 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > 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 < > vishal3...@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@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? Read http://www.gromacs.org/**Support/Mailing_Lists< >> http://www.gromacs.org/Support/Mailing_Lists> >> > >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> 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 >> > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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
