From owner-chemistry@ccl.net Sat Mar 20 12:26:00 2010 From: "Egon Willighagen egon.willighagen[a]gmail.com" To: CCL Subject: CCL: 2nd Call for Papers: Semantic Chemistry with the Resource Description Framework (CINF Symposium, ACS Autumn 2010) 240th ACS National Meeting & Exposition Message-Id: <-41498-100320110128-26305-gsdV3XHebrPatZRHza6LGw..server.ccl.net> X-Original-From: Egon Willighagen Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Date: Sat, 20 Mar 2010 16:00:55 +0100 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [egon.willighagen * gmail.com] 2nd Call for Papers: Semantic Chemistry with the Resource Description Framework (CINF Symposium, ACS Autumn 2010) 240th ACS National Meeting & Exposition We now invite papers for our symposium on the use of the Resource Description Framework (RDF) technologies in semantic knowledge representation and data exchange in chemistry at the 240th National Meeting & Exposition of the American Chemical Society (ACS) in Boston this fall. Semantic Chemistry has been around for a while, but is seeing a revival wit= h the adoption of the Resource Description Framework (RDF) and matching technologies in chemistry. RDF triples provide a simple structure that allo= w data and knowledge alike to be presented in a single framework. Derived technologies include the capturing of ontologies with the Web Ontology Language (OWL) and performing queries with SPARQL. A wide variety of free and open source product make it easy to set up servers with large amounts o= f RDF data, while integration with HTML is available too with RDFa. The RDF symposium at the 240th ACS national meeting in Boston invites submissions of talks about the use of RDF in chemistry and cheminformatics. Topics could include the use of OWL ontologies, OWL axioms, reasoning and interference, RDF in user interfaces, such as RDFa in web front ends, visualization, querying systems, and applications thereof, such as linking data sets, compound classification, cloud computing, web services, data aggregation, semantic publishing, and literature mining. Abstracts may be submitted via http://abstracts.acs.org/ now. You=92ll find the RDF session as part of the CINF division symposiums. The submission deadline is March 28, 2010. In case of questions, please email Egon Willighagen at egon.willighagen[A]farmbio.uu.se or Martin Braendle at braendle[A]chem.ethz.ch. --=20 Post-doc %a% Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers From owner-chemistry@ccl.net Sat Mar 20 23:04:01 2010 From: "Adam Tenderholt atenderholt%gmail.com" To: CCL Subject: CCL:G: Gaussun 03 multiple nodes Message-Id: <-41499-100317205700-21560-qohBWnZLWN1gX2CvNlL6Yw|-|server.ccl.net> X-Original-From: Adam Tenderholt Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 17 Mar 2010 14:58:12 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt:gmail.com] This may be a silly question, but have you made sure that you can ssh between nodes without a password? Adam On Wed, Mar 17, 2010 at 12:45 PM, Jamin Krinsky jamink!A!berkeley.edu wrote: > Dear Jason, Peter, > LINDA is the engine for running Gaussian in network parallel, we used to = use > it in our facility. G03 (linux at least) will run shared-memory (one node= ) > parallel without LINDA (that's what we are currently doing). Gaussian > doesn't come with LINDA, you have to buy it for extra $. Peter either > doesn't have LINDA or the cluster/queue/parallel environment is not set u= p > correctly (LINDA has it's own interfacing system so the mpi implementatio= n > shouldn't be the problem). Keep in mind that in G03 many job types are no= t > network (e.g. LINDA) parallelizable. > Regards, > Jamin > > > On Wed, Mar 17, 2010 at 8:21 AM, Jason Swails jason.swails---gmail.com > wrote: >> >> Sent to CCL by: Jason Swails [jason.swails!A!gmail.com] >> On Wed, Mar 17, 2010 at 3:15 AM, Peter Khlyabich khlyabic]^[usc.edu >> wrote: >> > >> > Sent to CCL by: "Peter =A0Khlyabich" [khlyabic%%usc.edu] >> > Dear colleagues, >> > >> > I'm trying to run Gaussian 03 E01. on multiple nodes. Unfortunately I >> > faced problems. When I run 1 node and 8 processors the calculations ar= e done >> > without problems. As soon as the number of nodes is increased to 2 and= more >> > I have problem with communication between the nodes as I suppose. >> >> Gaussian parallel engine is LINDA, which is strictly shared memory >> parallelization. =A0Thus, it should only run on a single node (multiple >> nodes would be operating in a distributed memory parallel environment >> as opposed to shared memory). =A0I believe that NWChem and (maybe?) >> QChem operate using MPI and distributed memory. >> >> Good luck! >> Jason >> >> -- >> --------------------------------------- >> Jason M. Swails >> Quantum Theory Project, >> University of Florida >> Ph.D. Graduate Student >> 352-392-4032 >> >> >> >> - This is automatically added to each message by the mailing script - >> E-mail to subscribers: CHEMISTRY-$-ccl.net or use: >> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message >> >> E-mail to administrators: CHEMISTRY-REQUEST-$-ccl.net or use >> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message>> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml>> =A0 =A0 =A0http://www.ccl.net/spammers.txt>> >> > > > > -- > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink-$-berkeley.edu, 510-643-0616 > http://glab.cchem.berkeley.edu > > From owner-chemistry@ccl.net Sat Mar 20 23:49:01 2010 From: "Rajagopala Reddy Seelam rajagopalaseelam^^^gmail.com" To: CCL Subject: CCL: negative eigen value for virtual orbital reg Message-Id: <-41500-100320233910-31993-MJHR9TE2ze2CdY2EbeVBug{:}server.ccl.net> X-Original-From: "Rajagopala Reddy Seelam" Date: Sat, 20 Mar 2010 23:39:06 -0400 Sent to CCL by: "Rajagopala Reddy Seelam" [rajagopalaseelam(~)gmail.com] Dear CCL members, Can a virtual(unoccupied) orbital have negative eigen value.Generally occupied orbitals have negative eigen value and unoccupied orbitals have positive eigen values.If we get any negative eigen values for unoccupied orbitals was that mean optimization not done correctly.Can any one of you please clarify my doubt. Thank you so much Regards, Rajagopala Reddy