From owner-nwchem-users@emsl.pnl.gov Wed Apr 4 23:55:52 2007 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.8/8.13.8) with ESMTP id l356tpYx028054 for ; Wed, 4 Apr 2007 23:55:52 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.8/8.13.8/Submit) id l356tpB7028053 for nwchem-users-outgoing-0915; Wed, 4 Apr 2007 23:55:51 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Ironport-SG: Throttle X-Ironport-SBRS: 0.1 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: Aq4HACA6FEZCxGT5ZWdsb2JhbACQAgsIBwYIGw X-IronPort-AV: i="4.14,373,1170662400"; d="scan'208"; a="26831800:sNHT21638589" DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=X-YMail-OSG:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-ID; b=X5zYH/iMueSym4ebfc8mqdJ6ovK2kNSreT6boSMF98mWsVL3YESyGq3K9mCSoCZnpwjlfxqDqnFvyoFuHBK3iUnC3MA4K/dJxSnCeAZyfm4JviO3KaHocd3HDpRYdOEODlMK0rGALrio5aLGDjhHsDcrnWe6JhY0aT3AuARaOa8=; X-YMail-OSG: KkB7qNoVM1lIsfhik0etzw03_cchaRv9jv.9zaw.QjuJW51_5zXIBvyA67wvTqUYf6wT3gg7hFFLwVcb5pyiZxmoqPbnzIu_BubF Date: Wed, 4 Apr 2007 23:55:47 -0700 (PDT) From: Francesco Pietra Subject: [NWCHEM] Fwd: rhf/eps MD out of memory To: users nwchem MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="0-1423860317-1175756147=:18377" Content-Transfer-Encoding: 8bit Message-ID: <110606.18377.qm@web58914.mail.re1.yahoo.com> Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk --0-1423860317-1175756147=:18377 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Content-Id: Content-Disposition: inline Perhaps not clear on shortening: 1) Out-of-memory systematically occurs at the stage of examining the orbitals, after that scf energy was already calculated. I relevant, I increased the grid from the default 0.035nm to 0.1nm, getting same out-of-memory at exactly the same stage, 2) With small molecules (I tried molecules with 4 C atoms) the Partial Charges are calculated in a few seconds. 3) With the same big molecule (98 atoms, not made into fragments) as in (1) rhf/6-31G*/geom_optimization was carried out successfully in 38 steps to convergence at default conditions. Thanks francesco pietra --- Francesco Pietra wrote: > Date: Tue, 3 Apr 2007 12:14:25 -0700 (PDT) > From: Francesco Pietra > Subject: Fwd: rhf/eps MD out of memory > To: users nwchem > > Text message and attachments that were said too long > shortened here. I doubt, however, that the issue can > now be appreciated. > > I tried to run a rhf/6-31G*/esp procedure to get > Partial Charges in view of Amber ff MD simulation. > Molecule 98 atoms cut into two residues and > recombined. > > It halted out of memory. End of file out attached > > System 4 nodes (two dual opterons), 16 GB ram. Swap > HOME 96GB available. Set 468mw in ecce to have > 3750mb > per node in nwchem. > > Thanks > francesco pietra > > > > > ____________________________________________________________________________________ > Don't pick lemons. > See all the new 2007 cars at Yahoo! Autos. > http://autos.yahoo.com/new_cars.html ____________________________________________________________________________________ Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL --0-1423860317-1175756147=:18377 Content-Type: application/octet-stream; name=end_out Content-Transfer-Encoding: base64 Content-Description: pat364901797 Content-Disposition: attachment; filename=end_out aWQ9LTEgc2l6ZT0zODczMTc3NgoqKioqKioqKioqKioqKioqKioqIEFSTUNJ IElORk8gKioqKioqKioqKioqKioqKioqKioqKioqClRoZSBhcHBsaWNhdGlv biBhdHRlbXB0ZWQgdG8gYWxsb2NhdGUgYSBzaGFyZWQgbWVtb3J5IHNlZ21l bnQgb2YgMzg3MzE3NzYgYnl0ZXMgaW4gc2l6ZS4gVGhpcyBtaWdodCBiZSBp biBhZGRpdGlvbiB0byBzZWdtZW50cyB0aGF0IHdlcmUgYWxsb2NhdGVkIHN1 Y2Nlc2Z1bGx5IHByZXZpb3VzbHkuIFRoZSBjdXJyZW50IHN5c3RlbSBjb25m aWd1cmF0aW9uIGRvZXMgbm90IGFsbG93IGVub3VnaCBzaGFyZWQgbWVtb3J5 IHRvIGJlIGFsbG9jYXRlZCB0byB0aGUgYXBwbGljYXRpb24uClRoaXMgaXMg bW9zdCBvZnRlbiBjYXVzZWQgYnk6CjEpIHN5c3RlbSBwYXJhbWV0ZXIgU0hN TUFYIChsYXJnZXN0IHNoYXJlZCBtZW1vcnkgc2VnbWVudCkgYmVpbmcgdG9v IHNtYWxsIG9yCjIpIGluc3VmZmljaWVudCBzd2FwIHNwYWNlLgpQbGVhc2Ug YXNrIHlvdXIgc3lzdGVtIGFkbWluaXN0cmF0b3IgdG8gdmVyaWZ5IGlmIFNI TU1BWCBtYXRjaGVzIHRoZSBhbW91bnQgb2YgbWVtb3J5IG5lZWRlZCBieSB5 b3VyIGFwcGxpY2F0aW9uIGFuZCB0aGUgc3lzdGVtIGhhcyBzdWZmaWNpZW50 IGFtb3VudCBvZiBzd2FwIHNwYWNlLiBNb3N0IFVOSVggc3lzdGVtcyBjYW4g YmUgZWFzaWx5IHJlY29uZmlndXJlZCB0byBhbGxvdyBsYXJnZXIgc2hhcmVk IG1lbW9yeSBzZWdtZW50cywKc2VlIGh0dHA6Ly93d3cuZW1zbC5wbmwuZ292 L2RvY3MvZ2xvYmFsL3N1cHBvcnQuaHRtbApJbiBzb21lIGNhc2VzLCB0aGUg cHJvYmxlbSBtaWdodCBiZSBjYXVzZWQgYnkgaW5zdWZmaWNpZW50IHN3YXAg c3BhY2UuCioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioqKioq KioqKioqKioqKioqKioqKioKMDphbGxvY2F0ZTogZmFpbGVkIHRvIGNyZWF0 ZSBzaGFyZWQgcmVnaW9uIDogLTEKMDphbGxvY2F0ZTogZmFpbGVkIHRvIGNy ZWF0ZSBzaGFyZWQgcmVnaW9uIDogLTEKTGFzdCBTeXN0ZW0gRXJyb3IgTWVz c2FnZSBmcm9tIFRhc2sgMDo6IEludmFsaWQgYXJndW1lbnQKICAwOiBBUk1D SSBhYm9ydGluZyAtMSAoMHhmZmZmZmZmZmZmZmZmZmZmKS4KICAwOiBBUk1D SSBhYm9ydGluZyAtMSAoMHhmZmZmZmZmZmZmZmZmZmZmKS4Kc3lzdGVtIGVy cm9yIG1lc3NhZ2U6IEludmFsaWQgYXJndW1lbnQKMzpTaWdJbnRIYW5kbGVy OiBpbnRlcnJ1cHQgc2lnbmFsIHdhcyBjYXVnaHQ6IDIKMzpTaWdJbnRIYW5k bGVyOiBpbnRlcnJ1cHQgc2lnbmFsIHdhcyBjYXVnaHQ6IDIKTGFzdCBTeXN0 ZW0gRXJyb3IgTWVzc2FnZSBmcm9tIFRhc2sgMzo6IE5vIHN1Y2ggZmlsZSBv ciBkaXJlY3RvcnkKICAzOiBBUk1DSSBhYm9ydGluZyAyICgweDIpLgogIDM6 IEFSTUNJIGFib3J0aW5nIDIgKDB4MikuCnN5c3RlbSBlcnJvciBtZXNzYWdl OiBObyBzdWNoIGZpbGUgb3IgZGlyZWN0b3J5CjE6U2lnSW50SGFuZGxlcjog aW50ZXJydXB0IHNpZ25hbCB3YXMgY2F1Z2h0OiAyCjE6U2lnSW50SGFuZGxl cjogaW50ZXJydXB0IHNpZ25hbCB3YXMgY2F1Z2h0OiAyCkxhc3QgU3lzdGVt IEVycm9yIE1lc3NhZ2UgZnJvbSBUYXNrIDE6OiBObyBzdWNoIGZpbGUgb3Ig ZGlyZWN0b3J5CiAgMTogQVJNQ0kgYWJvcnRpbmcgMiAoMHgyKS4KICAxOiBB Uk1DSSBhYm9ydGluZyAyICgweDIpLgpzeXN0ZW0gZXJyb3IgbWVzc2FnZTog Tm8gc3VjaCBmaWxlIG9yIGRpcmVjdG9yeQoyOlNpZ0ludEhhbmRsZXI6IGlu dGVycnVwdCBzaWduYWwgd2FzIGNhdWdodDogMgoyOlNpZ0ludEhhbmRsZXI6 IGludGVycnVwdCBzaWduYWwgd2FzIGNhdWdodDogMgpMYXN0IFN5c3RlbSBF cnJvciBNZXNzYWdlIGZyb20gVGFzayAyOjogTm8gc3VjaCBmaWxlIG9yIGRp cmVjdG9yeQogIDI6IEFSTUNJIGFib3J0aW5nIDIgKDB4MikuCiAgMjogQVJN Q0kgYWJvcnRpbmcgMiAoMHgyKS4Kc3lzdGVtIGVycm9yIG1lc3NhZ2U6IE5v IHN1Y2ggZmlsZSBvciBkaXJlY3RvcnkKIENyZWF0aW5nOiBob3N0PWRlYjY0 LCB1c2VyPWZyYW5jZXNjbywKICAgICAgICAgICBmaWxlPS9ob21lL2ZyYW5j ZXNjby9ud2NoZW01MC9iaW4vbndjaGVtLCBwb3J0PTU3NDI5CiAgNDogaW50 ZXJydXB0KDEpCldhaXRBbGw6IE5vIGNoaWxkcmVuIG9yIGVycm9yIGluIHdh aXQ/Cg== --0-1423860317-1175756147=:18377--