From owner-nwchem-users@emsl.pnl.gov Mon Oct 17 19:09:16 2005 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.12.10/8.12.10) with ESMTP id j9I29GSN011973 for ; Mon, 17 Oct 2005 19:09:16 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.12.10/8.12.10/Submit) id j9I29G3x011972 for nwchem-users-outgoing-0915; Mon, 17 Oct 2005 19:09:16 -0700 (PDT) Date: Mon, 17 Oct 2005 22:09:08 -0400 (EDT) From: kawatkar@chem.uga.edu Subject: [NWCHEM] memory problem in DFT optimization To: nwchem-users@emsl.pnl.gov Cc: mscf-consulting@emsl.pnl.gov Message-id: <33234.128.192.9.210.1129601348.squirrel@webmail.chem.uga.edu> MIME-version: 1.0 X-Mailer: SquirrelMail/1.4.3a-12.EL4 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 8bit Importance: Normal X-Priority: 3 (Normal) User-Agent: SquirrelMail/1.4.3a-12.EL4 X-UGAChemistry-MailScanner-Information: Please contact the ISP for more information X-UGAChemistry-MailScanner: Found to be clean X-MailScanner-From: kawatkar@chem.uga.edu Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Hello, I am running a dft optimization of a system containing 275 atoms. I tried test jobs on interactive queue using 4 and 8 processors. The jobs crashed with following memory related error: ----------- Superposition of Atomic Density Guess ------------------------------------- Sum of atomic energies: -7864.35961411 ------------------------------------------------------------------------ ao_replicated: insufficient memory 14677362 ------------------------------------------------------------------------ ------------------------------------------------------------------------ current input line : 299: task dft optimize ------------------------------------------------------------------------ ------------------------------------------------------------------------ You need to assign at least 14677362 bytes more local memory ------------------------------------------------------------------------ ---- The input deck I used is as follows: ------- start test echo permanent_dir /home/kawatkar/GMII/modelB title "modelB containing 275 atoms of the binding site" geometry units angstroms print xyz autosym noautoz Zn 0.00000 0.00000 0.00000 C 6.43300 0.00000 0.00000 H 5.95000 0.95600 0.00000 H 7.26300 0.05800 0.67300 H 6.78100 -0.16500 -0.99900 C 5.50200 -1.14700 0.43900 H 5.98100 -2.11300 0.22700 H 5.33900 -1.12400 1.52000 C 4.16300 -1.05600 -0.20300 N 3.93900 -1.14800 -1.56700 H 4.62500 -1.38100 -2.26900 C 2.62300 -0.89200 -1.79700 H 2.17500 -0.92200 -2.77800 N 1.99900 -0.63900 -0.66400 C 2.94500 -0.74100 0.33300 H 2.67100 -0.59900 1.36700 C 1.95000 4.63500 -0.40200 H 1.50200 4.47100 -1.35900 H 2.25800 5.65600 -0.31900 H 2.80500 3.99900 -0.29300 C 0.98200 4.30400 0.75600 H 1.32600 4.77300 1.68300 H -0.02200 4.69300 0.54600 C 0.88000 2.80200 1.01900 O 0.61000 2.05400 0.01900 O 1.09200 2.39900 2.19800 C -1.15600 8.75700 0.50100 H -0.84500 9.40900 1.29100 H -1.84800 9.26900 -0.13200 H -0.30300 8.45800 -0.07100 C -1.83300 7.50800 1.10300 O -2.01900 6.48700 0.42000 N -2.18800 7.57700 2.37300 H -1.93600 8.39200 2.91300 C -2.92900 6.50000 3.04100 H -3.82400 6.26900 2.46000 C -2.14500 5.15500 3.10500 H -1.99300 4.81600 2.07800 H -1.14100 5.31800 3.51700 C -2.86000 4.08900 3.90000 C -4.17300 3.68600 3.79800 H -4.96700 4.03100 3.15200 N -4.43600 2.65700 4.68300 H -5.23700 2.04000 4.61000 C -3.27400 2.33800 5.34900 C -3.01100 1.33400 6.28800 H -3.78000 0.62500 6.57900 C -1.71900 1.24700 6.79500 H -1.47800 0.46800 7.51400 C -0.70800 2.13300 6.37300 H 0.29200 2.03700 6.79300 C -0.96400 3.11400 5.42200 H -0.16200 3.75500 5.06500 C -2.26300 3.23400 4.89500 C -3.32500 7.03200 4.44100 O -4.44000 7.54600 4.64600 N -2.40900 6.87000 5.40000 H -1.54500 6.39500 5.18000 C -2.58900 7.40900 6.78800 H -3.62200 7.34100 7.05600 H -2.29300 8.43800 6.80200 C -1.70900 6.63400 7.79300 H -0.75800 6.40200 7.28600 C -1.36400 7.53600 8.99000 H -2.26400 7.91600 9.48500 H -0.78300 6.98600 9.73900 H -0.77100 8.40300 8.67700 C -2.33200 5.28900 8.22600 H -2.57100 4.70500 7.33200 H -1.56900 4.71200 8.76500 C -3.58100 5.40200 9.11000 H -4.39600 5.93200 8.60200 H -3.93600 4.40300 9.37300 H -3.37600 5.93500 10.04500 C -0.42800 -4.44600 -2.41100 H -1.42800 -4.68500 -2.12100 H -0.39300 -4.26200 -3.46500 H 0.22000 -5.26400 -2.17200 C -0.00100 -3.18800 -1.64900 H 1.09100 -3.12500 -1.57900 H -0.33000 -2.28400 -2.16700 C -0.54000 -3.12200 -0.21800 O -0.61500 -2.00400 0.35300 O -0.87900 -4.22200 0.32400 C -6.45000 -5.84800 -2.83700 H -5.86700 -6.50900 -2.22900 H -6.98700 -6.41600 -3.56700 H -5.80300 -5.15500 -3.33100 C -7.53100 -5.11400 -2.01100 H -8.27300 -4.69100 -2.69800 H -8.06700 -5.84900 -1.39400 C -6.96000 -4.01400 -1.15900 C -6.19800 -4.31400 -0.02500 H -6.08700 -5.35100 0.28900 C -5.58100 -3.29900 0.70000 H -4.97600 -3.55200 1.56300 C -5.72400 -1.96400 0.31600 H -5.25900 -1.17200 0.89400 C -6.48800 -1.65300 -0.81000 H -6.57700 -0.62100 -1.13400 C -7.09800 -2.67500 -1.53900 H -7.68600 -2.43000 -2.42100 C -2.83000 -10.28500 -2.65700 H -2.92100 -10.97500 -1.84500 H -3.36500 -10.65800 -3.50400 H -1.79700 -10.16600 -2.91200 C -3.41400 -8.93100 -2.18100 H -3.39600 -8.20200 -3.00200 H -4.47500 -9.07300 -1.92700 C -2.67500 -8.33300 -0.96300 H -2.57300 -9.08700 -0.17100 H -1.65300 -8.05400 -1.25400 C -3.38300 -7.08900 -0.38900 H -3.61300 -6.38700 -1.20100 H -4.35000 -7.37500 0.03900 N -2.58700 -6.36900 0.61200 H -1.84100 -5.76400 0.23900 C -2.99700 -5.95200 1.82900 N -4.02000 -6.55800 2.48000 H -4.50100 -7.34800 2.08600 H -4.39800 -6.12500 3.30900 N -2.35400 -4.95200 2.41100 H -1.69600 -4.40000 1.81900 H -2.57600 -4.61500 3.34200 C 4.88800 -9.16600 1.52300 H 4.69500 -10.10700 1.05300 H 4.15300 -8.98600 2.27800 H 5.86000 -9.18400 1.96900 C 4.82500 -8.06200 0.42300 H 5.83900 -7.85800 0.05500 H 4.26400 -8.44500 -0.43800 C 4.16400 -6.78800 0.89400 C 4.83300 -5.85500 1.69400 H 5.88500 -6.00600 1.93000 C 4.17600 -4.73900 2.21000 H 4.70400 -4.02600 2.83700 C 2.81800 -4.53300 1.92700 O 2.11700 -3.47800 2.41400 H 2.70700 -2.85500 2.88600 C 2.13600 -5.44500 1.11300 H 1.09300 -5.25600 0.87700 C 2.81100 -6.55200 0.61300 H 2.27200 -7.26200 -0.01400 C 6.08500 -0.29100 4.40200 H 6.12100 0.21900 3.46200 H 6.89000 0.04700 5.02000 H 6.17800 -1.34400 4.23800 C 4.73800 -0.03000 5.08000 H 4.75500 -0.34700 6.13200 H 4.47400 1.03500 5.08200 C 3.64300 -0.82700 4.39900 O 3.88800 -1.77100 3.66200 O 2.37800 -0.50900 4.64700 H 2.28000 0.28800 5.18800 C -3.25500 4.58100 -6.04900 H -2.45100 4.01500 -6.47200 C -2.59300 5.55500 -5.02200 H -2.11200 6.36800 -5.58100 H -3.36400 6.02100 -4.39900 C -1.57900 4.82200 -4.18600 N -1.66800 4.59900 -2.82000 H -2.22700 5.10400 -2.14200 C -0.67800 3.72100 -2.47100 H -0.54600 3.34400 -1.46400 N 0.04300 3.37200 -3.52000 C -0.50900 4.05200 -4.58200 H -0.10700 3.95200 -5.58400 C -4.24700 3.62600 -5.35100 O -5.45400 3.93900 -5.23500 N -3.73200 2.52500 -4.78000 H -2.76900 2.27900 -4.96300 C -4.58500 1.54300 -4.06600 H -5.53400 1.42500 -4.58900 C -3.95000 0.14300 -4.02200 H -4.63400 -0.48300 -3.44300 H -3.91100 -0.26300 -5.04200 C -2.60800 0.11700 -3.38200 N -1.41600 0.36600 -4.05500 H -1.29500 0.46600 -5.05200 C -0.41400 0.41300 -3.14000 H 0.60200 0.67700 -3.38300 N -0.89500 0.19200 -1.93300 C -2.25500 0.01100 -2.06600 H -2.88400 -0.14900 -1.20300 C -5.15300 1.99400 -2.66900 O -5.79300 1.19100 -1.96000 N -4.89800 3.26500 -2.28000 H -4.19100 3.82400 -2.73500 C -5.61400 3.84300 -1.14300 H -6.36800 3.15500 -0.82600 H -6.08600 4.75000 -1.45900 C -4.68800 4.11100 0.05600 H -3.94600 4.88800 -0.15400 H -5.32600 4.45700 0.87800 C -3.96900 2.82900 0.50000 O -4.68900 1.85600 0.87400 O -2.70400 2.82100 0.44500 C -9.29000 3.26900 2.09600 H -10.33100 3.11400 2.29100 H -9.17800 3.89900 1.23900 H -8.83300 3.73400 2.94400 C -8.42700 2.04200 1.79500 H -8.48800 1.32200 2.62800 C -8.83400 1.32500 0.50800 H -8.79000 2.00800 -0.34900 H -8.17100 0.47900 0.29700 H -9.85700 0.93800 0.58700 O -7.12000 2.60600 1.72600 H -6.43200 2.02700 1.33800 C -11.83400 -2.54400 3.25200 H -11.79300 -2.43700 2.18900 H -12.65300 -3.18100 3.51500 H -11.96800 -1.58500 3.70500 C -10.52600 -3.18400 3.81300 H -10.79100 -3.80600 4.67800 H -10.09900 -3.86700 3.06900 C -9.47000 -2.18900 4.25700 C -9.55100 -1.59600 5.52400 H -10.37100 -1.86300 6.18900 C -8.60500 -0.66600 5.95800 H -8.70400 -0.20100 6.93900 C -7.54600 -0.31600 5.11700 O -6.58000 0.59500 5.48100 H -6.61500 0.76600 6.43000 C -7.44000 -0.89100 3.84900 H -6.59700 -0.61400 3.22000 C -8.39600 -1.81700 3.43500 H -8.29200 -2.26400 2.44900 C -6.17700 -3.35300 8.40300 H -5.79100 -4.12700 9.03600 H -7.14100 -3.05100 8.75600 H -6.26200 -3.71900 7.40100 C -5.22400 -2.15100 8.42900 O -4.46400 -1.92400 7.49800 N -5.25800 -1.37500 9.51500 H -5.90700 -1.53000 10.27100 C -4.33100 -0.26500 9.62300 H -3.91900 -0.32900 10.62900 H -3.54700 -0.47100 8.89500 C -4.86300 1.15400 9.39300 O -4.15500 2.12700 9.76200 N -6.08900 1.29700 8.87500 H -6.64800 0.48800 8.64100 C -6.63000 2.62900 8.57500 H -5.83300 3.28100 8.28500 H -7.11400 3.02200 9.44400 H -7.33800 2.55600 7.77700 O -0.16800 -1.64200 4.92400 C 0.08900 -2.91500 5.49600 H 0.49100 -2.74000 6.49900 H -0.82900 -3.51100 5.57700 H 0.82600 -3.47700 4.90400 C -0.58300 -1.71700 3.56800 H 0.11700 -2.31000 2.97500 C -0.61100 -0.25500 3.04600 H -0.45600 0.36900 3.93200 O 0.49800 -0.05800 2.17200 H 0.78400 0.92500 2.25500 C -1.95900 0.24300 2.39700 H -2.20800 1.18700 2.89400 O -1.81100 0.51600 1.00500 H -2.16400 1.46200 0.79800 C -3.15700 -0.69900 2.61500 H -3.17700 -1.38100 1.75000 O -4.37600 0.01200 2.73700 H -4.40800 0.70300 2.02100 C -2.93500 -1.58800 3.84100 H -2.69900 -0.99700 4.73700 O -1.81500 -2.40800 3.49600 C -4.13100 -2.48800 4.13400 H -4.42200 -2.99300 3.21100 H -4.97100 -1.86400 4.45100 O -3.86400 -3.52500 5.08200 H -3.88500 -3.10600 5.96000 H -3.76000 5.11800 -6.82400 end basis * library 6-31G** end dft iterations 500 xc b3lyp decomp end set geometry:actlist integer 6:16 21:26 37:54 62:74 79:84 89:102 107:124 129:143 148:154 157:167 174:184 192:197 202:209 214:228 248:274 task dft optimize ------- I saw some messages on the nwchem archives about these types of error but could not find any solution in them. Does anyone have an idea what could be the problem ? I also tried allocating more memory with memory setting but it did give similar error. Thanks for your help, ################################################### Sameer P. Kawatkar Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602. Phone: 706-542-0263 URL: http://glycam.ccrc.uga.edu/users/sameer/index.html