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