<p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">Dear David, Justin, Mark and all, </p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;"><br></p><p style="font-family: Gulim; font-size: 10pt; border: 0px; padding: 0px; margin: 0px; cursor: text;">Many thanks for your feedback, that really helped clarify a lot of the questions I had. </p><div style="font-family: 돋움, arial; font-size: 12px; margin-top: 30px; margin-left: 0.8em; color: rgb(0, 102, 204); font-weight: bold;">--------- 원본 메일 ---------</div><p style="font-family: Gulim; font-size: 10pt; line-height: 1.5; margin-bottom: 0px; margin-top: 0px;"><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><b>보낸사람</b> : Justin Lemkul <jalemkul@vt.edu><br><b>받는사람</b> : <gmx-users@gromacs.org><br><b>받은날짜</b> : 2014년 9월 18일(목) 21:26:41<br><b>제목</b> : Re: [gmx-users] Problem with: Shell particles are not implemented with domain de<br><!-- original content --><div style="margin-top:5px;"><pre>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?
</pre></div></div></blockquote></p><p style="font-family: Gulim; font-size: 10pt; line-height: 1.5; margin-bottom: 0px; margin-top: 0px;"><br></p><p style="font-family: Gulim; font-size: 10pt; line-height: 1.5; margin-bottom: 0px; margin-top: 0px;">I obtained the SWM4-NDP code from virtualchemistry.org.</p><p style="font-family: Gulim; font-size: 10pt; line-height: 1.5; margin-bottom: 0px; margin-top: 0px;"><font face="monospace"><span style="font-size: 12px; line-height: 18px; white-space: pre;"><br></span></font><blockquote style="font-family: Gulim; font-size: 12px; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><div style="margin-top:5px;"><pre>> 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.
>
</pre><pre>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.</pre><pre>-Justin
</pre></div></div></blockquote><font face="monospace"><span style="font-size: 12px; line-height: 18px; white-space: pre;"></span></font></p><p style="font-family: Gulim; font-size: 10pt; line-height: 1.5; margin-bottom: 0px; margin-top: 0px;"><br></p><p style="font-family: Gulim; font-size: 10pt; line-height: 1.5; margin-bottom: 0px; margin-top: 0px;"><font face="monospace"><span style="font-size: 12px; line-height: 18px; white-space: pre;">Say for example, if I allocate 24 CPUs over 2 nodes (knowing that the calculation would only run on one domain), then theoretically speaking the valid setting should be -ntmpi 24 and -ntomp 1?</span><br><span style="font-size: 12px; line-height: 18px; white-space: pre;">In the cases of (-ntmpi 24 -ntomp 1) and (-ntmpi 1 -ntomp 1), the resulting Fatal error says: Setting the number of thread-MPI threads is only supported with thread-MPI and Gromacs was compiled without thread-MPI</span></font></p><p style="font-family: Gulim; font-size: 10pt; line-height: 1.5; margin-bottom: 0px; margin-top: 0px;"><span style="font-family: monospace; font-size: 12px; line-height: 18px; white-space: pre;">Do you have a ballpark estimate on when will the support for DD will be made available? I am more than happy to be the first one using/testing it.</span></p><p style="font-family: Gulim; font-size: 10pt; line-height: 1.5; margin-bottom: 0px; margin-top: 0px;"><br></p><p style="margin-bottom: 0px; margin-top: 0px;"><font face="arial, 돋움"><span style="font-size: 12px; line-height: 18px;"><br></span></font><blockquote style="font-family: Gulim; font-size: 12px; line-height: 1.5; border-left-style: solid; border-left-width: 2px; margin: 0pt 0pt 0pt 0.8em; padding-left: 1em;"><div style="font-family:arial,돋움;line-height:1.5"><div style="margin-top:5px;"><pre><br></pre><pre>> 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@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
jalemkul@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
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https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request@gromacs.org.</pre><pre><br></pre><pre><br></pre></div></div></blockquote><font face="monospace"><span style="font-size: 12px; line-height: 18px; white-space: pre;">Regards,</span></font></p><p style="margin-bottom: 0px; margin-top: 0px;">Kester</p><p style="font-family: Gulim; font-size: 10pt;"></p></p>
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