[gmx-users] Problem with: Shell particles are not implemented with domain decomposition

[Justin Lemkul]

On 9/18/14 1:11 PM, David van der Spoel wrote:
> On 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

Does that topology reproduce all of the properties in the Lamoureux paper?  The 
massless Drude and standard oxygen mass are not, strictly speaking, right for 
the SWM4-NDP model.  Also, though it is not shown in the paper, epsilon for the 
O atom has more significant figures in the CHARMM force field files, so epsilon 
is actually 0.88259, not 0.882573, though I imagine any difference would be very 
small.

-Justin

>
>>
>>> 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:           root at 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 at 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
>>>
>>>
>>>
>>>
>>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================