Dear David,
Thanks for the reply! I was wondering if you have had the same issue with this force field, such that you could only use one domain for all the SWM4-NDP calculations?
Knowing that I could only use one MPI rank, is there a way to get the calculation work on two nodes? One of my systems has 10k water molecules :(
Regards,
Kester
--------- 원본 메일 ---------
보낸사람 : David van der Spoel <sp...@xray.bmc.uu.se>
받는사람 : <gmx-us...@gromacs.org>
받은날짜 : 2014년 9월 19일(금) 02:11:26
제목 : Re: [gmx-users] Problem with: Shell particles are not implemented with domain deOn 2014-09-18 14:26, Justin Lemkul wrote: > > > On 9/18/14 8:01 AM, Kester Wong wrote: >> Dear gromacs users, >> >> >> Has anyone experienced a problem with running polarisable water model >> SWM4-NDP >> with the following warning: Shell particles are not implemented with >> domain >> decomposition? >> > > Out of curiosity, what is the source of your SWM4-NDP topology? http://virtualchemistry.org/pol.php > >> The md.log also stated the following: Number of hardware threads >> detected (12) >> does not match the number reported by OpenMP (1). I don't think this >> is the >> cause, as this message was also found in my other "working" calculations. >> >> >> I have tried using OpenMP and also tried a variety of -ntmpi and >> -ntomp settings. >> > > The only valid option here is -ntmpi 1 and -ntomp equal to whatever > number of cores you're using. Until I finish the DD implementation for > shells/Drudes, only OpenMP is supported here. > > -Justin > >> The same calculation did not work in GROMACS versions 5.0 and 5.0.1, >> in the >> following cluster: >> >> >> Gromacs version: VERSION 5.0.1 >> >> Precision: double >> >> Memory model: 64 bit >> >> MPI library: MPI >> >> OpenMP support: enabled >> >> GPU support: disabled >> >> invsqrt routine: gmx_software_invsqrt(x) >> >> SIMD instructions: NONE >> >> FFT library: fftw-3.3.3 >> >> RDTSCP usage: disabled >> >> C++11 compilation: disabled >> >> TNG support: enabled >> >> Tracing support: disabled >> >> Built on: Thu Sep 18 20:14:41 KST 2014 >> >> Built by: r...@master.hpc [CMAKE] >> >> Build OS/arch: Linux 2.6.18-274.7.1.el5 x86_64 >> >> Build CPU vendor: GenuineIntel >> >> Build CPU brand: Intel(R) Xeon(R) CPU X3220 @ 2.40GHz >> >> Build CPU family: 6 Model: 15 Stepping: 11 >> >> Build CPU features: apic clfsh cmov cx8 cx16 lahf_lm mmx msr pdcm pse >> sse2 sse3 >> ssse3 >> >> C compiler: /usr/bin/cc GNU 4.1.2 >> >> C compiler flags: -Wextra -Wno-missing-field-initializers >> -Wno-sign-compare >> -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter >> -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG >> >> C++ compiler: /usr/bin/c++ GNU 4.1.2 >> >> C++ compiler flags: -Wextra -Wno-missing-field-initializers >> -Wpointer-arith >> -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops >> -O3 -DNDEBUG >> >> Boost version: 1.55.0 (internal) >> >> >> Using 24 MPI processes >> Using 1 OpenMP thread per MPI process >> >> >> However, the same input files worked in another cluster (albeit very >> slowly, >> ~0.3ns/day). >> >> >> Gromacs version: VERSION 5.0 >> >> Precision: single >> >> Memory model: 64 bit >> >> MPI library: MPI >> >> OpenMP support: enabled >> >> GPU support: disabled >> >> invsqrt routine: gmx_software_invsqrt(x) >> >> SIMD instructions: AVX_256 >> >> FFT library: fftpack (built-in) >> >> RDTSCP usage: enabled >> >> C++11 compilation: disabled >> >> TNG support: enabled >> >> Tracing support: disabled >> >> Built on: Thu Aug 28 16:44:08 KST 2014 >> >> Built by: root@kant [CMAKE] >> >> Build OS/arch: Linux 2.6.32-431.23.3.el6.x86_64 x86_64 >> >> Build CPU vendor: GenuineIntel >> >> Build CPU brand: Intel(R) Core(TM) i5-4670 CPU @ 3.40GHz >> >> Build CPU family: 6 Model: 60 Stepping: 3 >> >> Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt >> lahf_lm >> mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp >> sse2 sse3 >> sse4.1 sse4.2 ssse3 tdt x2apic >> >> C compiler: /usr/bin/gcc GNU 4.4.7 >> >> C compiler flags: -mavx -Wno-maybe-uninitialized -Wextra >> -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall >> -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer >> -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG >> >> C++ compiler: /usr/bin/g++ GNU 4.4.7 >> >> C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers >> -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer >> -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG >> >> Boost version: 1.55.0 (internal) >> >> >> >> Using 1 MPI process >> >> Using 16 OpenMP threads >> >> >> Regards, >> Kester >> >> >> >> > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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