From owner-nwchem-users@emsl.pnl.gov Mon Apr 24 07:10:02 2006 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.6/8.13.6) with ESMTP id k3OEA2w1024587 for ; Mon, 24 Apr 2006 07:10:02 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.6/8.13.6/Submit) id k3OEA1sn024586 for nwchem-users-outgoing-0915; Mon, 24 Apr 2006 07:10:01 -0700 (PDT) Date: Mon, 24 Apr 2006 10:07:08 -0300 From: JunJun Liu Subject: Re: [NWCHEM] Asking help for doing my tests In-reply-to: To: "Straatsma, T P" , nwchem-users@emsl.pnl.gov Message-id: MIME-version: 1.0 Content-type: text/plain; format=flowed; delsp=yes; charset=utf-8 Content-transfer-encoding: 8bit DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:date:to:subject:from:content-type:mime-version:references:content-transfer-encoding:message-id:in-reply-to:user-agent; b=ZO77IGVCCjA+TcLFIonN0CRbJl5QYtF03KtsFfp69D/U3B9vYXru1aIHiY+MzHFb7PeKk++a4B7pkSq3Zc2u7icaQAjX5rHfpTLvlhoA7sV9js0o6PpN9H3o+Ks5233kcH6TvjkwyQ6kJrUGJsaCxnUph0P3KOIchY09YGRbpvM= User-Agent: Opera Mail/9.00 (Linux) References: Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Dear Dr.Straatsma, So you didn't see the "msa too small" or "nga_put" error? This case is actuallly a simple test, and I don't want to use it to do any research. My problem is that whatever I tried to calculated, the program aborted with "msa too small" or "nga_put" error. The program acutally aborted just right after any NWCHem module starts. If this case runs fine with your NWChem, I think there's a problem with our NWChem compilation. Can you give me some suggestions? I guess if it's a problem with the program compilation, the problem would be related to GA library. But how can I make a test to ensure this? Thanks a lot! Best Regards! Liu On Mon, 24 Apr 2006 10:55:14 -0300, Straatsma, T P wrote: > With the attached files your job should run fine on both a single > processor or on two. > From your input I assume you wish to do an energy minimization. You > should use 'task md optimize' rather than 'task md dynamics'. Also the > 'system' keyword is used to determine all file names. If you rename the > DAEL.pdb to ts4r.pdb you should not be needing to use the 'source' > keyword at all. > > > T.P.Straatsma, Associate Division Director > Computational Biology and Bioinformatics > Computational Sciences and Mathematics Division > Pacific Northwest National Laboratory > P.O.Box 999, MSIN K7-90 > Richland, WA 99352 > Tel. (509) 375-2802, (509) 372-4625 > Fax (509) 374-4720 > > > > -----Original Message----- > From: owner-nwchem-users@emsl.pnl.gov > [mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of JunJun Liu > Sent: Sunday, April 23, 2006 2:46 PM > To: nwchem-users@emsl.pnl.gov > Subject: [NWCHEM] Asking help for doing my tests > > Hello everybody, > > The "nga_put" error is very hard to get rid of. That make me feeling so > upset:( However, job should continue. Now I want to ensure if this > "nga_put" problem is caused by the program compilation. I hope anyone of > you who is kind and has time can do me a favor by doing the following > simple tests. Please look into the attachment for the small molecular > structure and the input file. Please note that it's better to remove all > the calculated files including top and rst files before a new test being > submitted so that any unwanted mistakes could be avoid, thanks! > > 1). Please submit the job with 2 CPUs. In our cluster, it quited with > "msa too small". > 2). If you also get this error, please comment out the "msa" keyword in > the MD input deck and re-submit it again. In our cluster, it quited with > "nga_put:cannot locate region: [83:102 ,83:102 ]:: -997" > 3). If you get the nga_put error too, then please delete the last > residue(residue number is 4) and re-submit the job with 2 CPUs. In our > culster, it terminated normally. > > Please let me know what you get with your NWChem program. Thank you very > much! > > All the best! > > Liu > -- JunJun Liu College of Chemistry Central China Normal University WuHan 430079 P.R. China