From owner-nwchem-users@emsl.pnl.gov Mon May 19 11:41:02 2008 Received: from odyssey.emsl.pnl.gov (localhost.pnl.gov [127.0.0.1]) by odyssey.emsl.pnl.gov (8.14.1/8.14.1) with ESMTP id m4JIf151021685 for ; Mon, 19 May 2008 11:41:02 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.14.1/8.14.1/Submit) id m4JIf1mQ021684 for nwchem-users-outgoing-0915; Mon, 19 May 2008 11:41:01 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Ironport-SG: OK_Domains X-Ironport-SBRS: 6.3 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AmQAANZmMUiBGwLKo2dsb2JhbACBVpBaAQEBAQEBBwUIBxGWSYRLAQ X-IronPort-AV: E=Sophos;i="4.27,511,1204531200"; d="scan'208";a="76333487" X-DKIM: Sendmail DKIM Filter v2.4.2 mailrelay1.tugraz.at m4JIeVUB008738 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=tugraz.at; s=mailrelay; t=1211222443; bh=rfWep8hiPErXFGnqjr/Z/Qja0s+AhZcq4aue5 pQ9/Uk=; h=From:To:Subject:Date:User-Agent:References:In-Reply-To: MIME-Version:Content-Disposition:Message-Id:Organization: Content-Type:Content-Transfer-Encoding; b=Sh619wuYfPx/ygznbJr3O7hJ Uh8TvZ9Vczs0E+InuuGA0pLou58jLqezTGfH1Z1oPoaPE2GCZebGWVjkOFJuM0hqwPr RkJfNiWOM4GWUnDFYCgZt1JONiZleFi/NMz75D5sraATPPnOSsT/gRHZCRz2oAi6lS2 y7Vf48t/F9zj4= From: =?iso-8859-1?q?J=F6rg_Sa=DFmannshausen?= To: users nwchem Subject: Re: [NWCHEM] MKL libraries Date: Mon, 19 May 2008 20:40:29 +0200 User-Agent: KMail/1.9.5 References: <131791.17788.qm@web57609.mail.re1.yahoo.com> In-Reply-To: <131791.17788.qm@web57609.mail.re1.yahoo.com> MIME-Version: 1.0 Content-Disposition: inline Message-Id: <200805192040.30230.sassmannshausen@tugraz.at> Organization: TU-Graz, ICTM Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Spam-Scanner: SpamAssassin 3.002004 X-Spam-Score-relay: -2.6 X-Scanned-By: MIMEDefang 2.64 on 129.27.10.18 Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Hi Francesco, as Jeff pointed out, it is always good to use an highly optimised BLAS library for your program. I noticed a few days ago that the difference between mkl-10.0.1.014 and ATLAS3.7.11 is only marginal (for a different program though). So that might be an alternative to mkl. Also, some people are saying that GotoBLAS works well with their system. You can test out that fairly quickly by building NWChem and then link it manually to the libraries you want to test. As I am using Debian as well (currently etch) I am a bit curious about your experiences with lenny. Also, what I would like to know is: you need libnuma for the OpenMPI, or? Currently I am using MPICH2 but I am hearing people saying that OpenMPI is better, what are your experiences? I think it would be benificial if you could share you experiences with different BLAS versions here so other people could gain from that as well. Let me know how you getting on with the compilation of NWChem, as I have done it recently I might be able to help if you are stuck. Best wishes from a rainy Graz! Jörg Am Montag 19 Mai 2008 18:44 schrieb Francesco Pietra: > nwchem 5.1 was installed from binary > nwchem-5.1-LINUX64-RHELWS4-ifort-AMD64.tar.bz2 on a NUMA-type machine with > two dual-opteron, runtime provided by intel version 9. OS debian Linux > amd64 etch. > > The two raid1 HHDDs have been moved to a new 4-socket dual-opteron > NUMA-type machine; nwchem worked fine. > > Now, on the latter machine, I upgraded the OS to "lenny", intel compilers > to vers 10.0.1.014 with MKL libraries 10.0.1.014 added, openmpi to vers > 10.1 with libnuma vers 1.0.2-1. > > As I have noticed a tremendous speed up by the mkl libraries of the QMMM > part of a molecular dynamics package, I wonder whether using mkl libraries > for nwchem in my type of system might be beneficial. If so, should I build > nwchem from source with intel compilers on openmpi? Is it a list of flags > to that scope, or the binary you provide is anyway expected to be faster? > > Thanks > francesco pietra -- ************************************************************* Jörg Saßmannshausen Institut für Chemische Technologie von Materialien TU-Graz Stremayrgasse 16 8010 Graz Austria phone: +43 (0)316 873 8954 fax: +43 (0)316 873 4959 homepage: http://sassy.formativ.net/ Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html