From owner-chemistry@ccl.net Wed Nov 12 04:58:00 2008 From: "mr shabbir shabbir__nenu.edu.cn" To: CCL Subject: CCL: NMR shielding or deshielding Message-Id: <-38085-081112045645-17186-s0kGHJ+EP7T8BWxHKdgXlQ*_*server.ccl.net> X-Original-From: "mr shabbir" Date: Wed, 12 Nov 2008 04:56:39 -0500 Sent to CCL by: "mr shabbir" [shabbir!^!nenu.edu.cn] Hello CCL users I am in bit confusion and need some comments to clarify it. I have calculated the NMR spectra of complex system consist of an alkali metal atom with a complexant. During the formation of complex alkali metal transfer its s electron to the electron deficient complexant and all the atoms of complexant shows a downfield shift (lower chemical shift value) while two atoms and their Hydrogens in that complexant shows upfield (higher chemical shift value). When I looked at the HOMO Orbital of that alkali MetalComplex, there is no electron density on these two atoms and their Hydrogen. So Can I present this HOMO diagram to support the higher chemical shift value of these only atoms and say that these became deshielded during the formation of MetalComplex? And one thing more Can my downfield shieldings (lower chemical shift value) of all other atoms rationalize the formation of charge metalcomplex..? Thanks Mr shabbir From owner-chemistry@ccl.net Wed Nov 12 07:55:01 2008 From: "John McKelvey jmmckel:+:gmail.com" To: CCL Subject: CCL: MPI Message-Id: <-38086-081112071454-3423-HkNPfj+JV76uW+gZNip/ew:_:server.ccl.net> X-Original-From: "John McKelvey" Content-Type: multipart/alternative; boundary="----=_Part_9047_33353351.1226492082224" Date: Wed, 12 Nov 2008 07:14:42 -0500 MIME-Version: 1.0 Sent to CCL by: "John McKelvey" [jmmckel++gmail.com] ------=_Part_9047_33353351.1226492082224 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Folks, I am a newbie as to running parallel under linux, and need to install MPI under RHEL4/AMD-64bit. Simple question: Where to start? All suggestions gratefully appreciated! Best regards! John McKelvey ------=_Part_9047_33353351.1226492082224 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Folks,

I am a newbie as to running parallel under linux, and need to install MPI under RHEL4/AMD-64bit.

Simple question: Where to start?

All suggestions gratefully appreciated!

Best regards!

John McKelvey

------=_Part_9047_33353351.1226492082224-- From owner-chemistry@ccl.net Wed Nov 12 09:05:00 2008 From: "Andrew R Turner andrew.turner{}ed.ac.uk" To: CCL Subject: CCL: MPI Message-Id: <-38087-081112085950-2143-MpVT5GWsqZ1k0NgZCcSLdQ]~[server.ccl.net> X-Original-From: Andrew R Turner Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 12 Nov 2008 13:59:21 +0000 MIME-Version: 1.0 Sent to CCL by: Andrew R Turner [andrew.turner**ed.ac.uk] Hi John, I would say the best place to start is with MPICH: http://www-unix.mcs.anl.gov/mpi/mpich1/ You can get MPI1 and MPI2 from them and most codes can make use of the MPICH libraries. There is also OpenMPI: http://www.open-mpi.org/ but I am not as familiar with that. Cheers Andy Quoting "John McKelvey jmmckel:+:gmail.com" : > Folks, > > I am a newbie as to running parallel under linux, and need to install MPI > under RHEL4/AMD-64bit. > > Simple question: Where to start? > > All suggestions gratefully appreciated! > > Best regards! > > John McKelvey > ======================================== Dr Andrew R. Turner e: andrew.turner.:.ed.ac.uk t: +44 (0)131 651 3578 p: Edinburgh Parallel Computing Centre University of Edinburgh EH9 3JZ ======================================== -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From owner-chemistry@ccl.net Wed Nov 12 09:40:00 2008 From: "Antonio M. =?ISO-8859-1?Q?M=E1rquez?= Cruz marquez . us.es" To: CCL Subject: CCL: MPI Message-Id: <-38088-081112092413-13562-5tHrVfTFXE04V4vaWBcYyQ#server.ccl.net> X-Original-From: "Antonio M." =?ISO-8859-1?Q?M=E1rquez?= Cruz Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Wed, 12 Nov 2008 14:23:47 +0100 Mime-Version: 1.0 Sent to CCL by: "Antonio M." =?ISO-8859-1?Q?M=E1rquez?= Cruz [marquez_._us.es] Hi John, You can start by downloading some MPI distribution (for example OpenMPI can be found at: http://www.open-mpi.org/ ). It is relatively simple to configure and compile the package to have an operating MPI distribution at your site. One important point is that when you configure your MPI distribution you need to specify wich compiler (Fortran and or C) you are going to use. If you use different compilers for different applications you need to build different MPI libraries/interfeces for each one of them. Currently I'm in charge of a cluster that includes some AMD servers and workstations with Opteron processors. We are using OpenMPI combined with the PathScale suite of compilers and have very good performances in our parallel applications. Hope this helps. Regards, On Wed, 2008-11-12 at 07:14 -0500, John McKelvey jmmckel:+:gmail.com wrote: > > Folks, > > I am a newbie as to running parallel under linux, and need to install > MPI under RHEL4/AMD-64bit. > > Simple question: Where to start? > > All suggestions gratefully appreciated! > > Best regards! > > John McKelvey > > -- Antonio M. Márquez Cruz Universidad de Sevilla From owner-chemistry@ccl.net Wed Nov 12 10:56:00 2008 From: "Justin Finnerty justin.finnerty_._uni-oldenburg.de" To: CCL Subject: CCL: MPI Message-Id: <-38089-081112105429-29440-qFAeJuu0oV0CroGtBJXKvQ!=!server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Wed, 12 Nov 2008 16:17:08 +0100 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty\a/uni-oldenburg.de] On Wed, 2008-11-12 at 07:14 -0500, John McKelvey jmmckel:+:gmail.com wrote: > > Folks, > > I am a newbie as to running parallel under linux, and need to install > MPI under RHEL4/AMD-64bit. > > Simple question: Where to start? I would add that it depends on what you want to do. If you are only writing your own MPI code then look at OpenMPI as it comes with an RPM specfile for building a set of RPMs. This makes it much easier to manage in the long-term. However, while MPI implementations are supposed to be source compatible they are not object compatible. What this means is that you will have to install the matching MPI library for each software you use. For example we have had to install LAM MPI, OpenMPI, MPICH and MPICH2 on our cluster to support the computational chemistry software we use (eg NWChem, ORCA etc). (I also strongly recommend the OSC mpiexec program for MPICH and MPICH2) Four MPI installations provides a major problem with configuring your user environment as you can only have _one_ MPI implementation configured at a time. We solved this using the Modules program, which allows us to load and unload settings for each MPI and disallows loading of two simultaneously. You can also use it to configure your chemistry software, which can then load the required MPI module. (The Modules program should be part of RHEL4 installation.) http://www.lam-mpi.org/ http://www.open-mpi.org/ http://www-unix.mcs.anl.gov/mpi/mpich1/ http://www.mcs.anl.gov/research/projects/mpich2/ Cheers Justin > -- Dr Justin Finnerty Rm W3-1-165 Ph 49 (441) 798 3726 Carl von Ossietzky Universität Oldenburg From owner-chemistry@ccl.net Wed Nov 12 11:30:01 2008 From: "Oleksandr nablaoblada[#]yahoo.com" To: CCL Subject: CCL: DALTON Message-Id: <-38090-081112105609-29672-uHjd5/Nn9dRkWcbCu1BemQ]|[server.ccl.net> X-Original-From: Oleksandr Content-Type: text/plain; charset=us-ascii Date: Wed, 12 Nov 2008 06:55:58 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Oleksandr [nablaoblada * yahoo.com] Dear colleagues, Does anybody know -how to set up in Dalton different DFT potential/kernel combinations like B3LYP/LDA or B3LYP/BLYP? -how to restart cubic response calculation. For Quadratic Resp. there is .QRREST keyword but for *Cubic no keyword is given. Thank you in advance Oleksandr Loboda, PhD. From owner-chemistry@ccl.net Wed Nov 12 16:34:00 2008 From: "Ol Ga eurisco1]~[pochta.ru" To: CCL Subject: CCL:G: Quad Q8200 vs. Quad6600 ? Message-Id: <-38091-081112163304-8493-4s151BQXxUrvrjgJG9iAzw~~server.ccl.net> X-Original-From: "Ol Ga" Date: Wed, 12 Nov 2008 16:33:00 -0500 Sent to CCL by: "Ol Ga" [eurisco1:pochta.ru] Hello! Would you allow me to address for necessary advice? We want to buy Intel Core 2 Quad Q8200 (2.33 GHz 4M 1333MHz, S775) _OR_ Intel Core 2 Quad6600 (2400MHz, LGA775, 8192Kb, 1066MHz). We want to build SMP-box system with DDR2 pc2-6400 800 MHz 4x2048 MB and use it for calculations on Gaussian03 (Opensuse 10.3 is an OS). But we dont have opportunity to test Quad Q8200-based machine on our real calculations by using Gaussian03 (EM64T). And thus we are something worried what to buy. Possible you have already tested or worked on both Quad Q8200 and Quad6600. Your concrete answer is extremely necessary. Thank you very much in advance. Sincerely, Ol Ga