From owner-nwchem-users@emsl.pnl.gov Thu Jan 19 10:27:45 2006 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 k0JIRipA014232 for ; Thu, 19 Jan 2006 10:27:44 -0800 (PST) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.12.10/8.12.10/Submit) id k0JIRibs014231 for nwchem-users-outgoing-0915; Thu, 19 Jan 2006 10:27:44 -0800 (PST) Date: Thu, 19 Jan 2006 09:57:32 -0800 From: =?ISO-8859-1?Q?Edoardo_Apr=E0?= Subject: Re: [NWCHEM] NWCHEM:geom_rtdb_load: not found In-reply-to: <54861.134.226.112.12.1137684694.squirrel@www.ichec.ie> To: Gemma Kinsella Cc: NWChem Users Message-id: <43CFD30C.6040706@pnl.gov> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1; format=flowed X-Accept-Language: en-us, en User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7.12) Gecko/20050923 Thunderbird/1.0.7 Mnenhy/0.7.3.0 X-pstn-levels: (S:99.90000/99.90000 R:95.9108 P:95.9108 M:97.0232 C:98.7678 ) X-pstn-settings: 3 (1.0000:0.5000) s GT3 gt2 gt1 r p m c X-pstn-addresses: from [db-null] References: <54861.134.226.112.12.1137684694.squirrel@www.ichec.ie> X-OriginalArrivalTime: 19 Jan 2006 17:57:32.0965 (UTC) FILETIME=[D2844D50:01C61D21] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by odyssey.emsl.pnl.gov id k0JIRgpA014219 Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Gemma do you have the mono.pdb file in your $NWCHEM_TOP/examples/md/membrane directory? If the file is there, is it readable for you? Edo Gemma Kinsella wrote: > Dear Ed / NWChem users, > > I have: > > 1) cd $NWCHEM_TOP/examples/md/membrane > 2) add the line "print debug" to the input file, in the part just > before the prepare section: > ... > # Add three biasing potential to force the monomer molecule > # to align in the z-direction > print debug > prepare > system mono_em > ... > 2) rm -f *TMP *out *seq *nam *cmd *qrs *rst .mem* > 3) re-run the calculation > > Three output files are generated nwchem.log (below) and > .membrane_example.cmd & .membrane_example.db which are attached. > > Many thanks, > > PS E-mails from my other account have not been making it to the mailing > list so I'm trying this address. > > > ARMCI configured for 4 cluster nodes. Network protocol is 'TCP/IP > Sockets'. > argument 1 = -p4wd > argument 2 = > /ichec/home/staff/gkinsella/Benchmarking/NWChem/nwchem-4.7/examples/md/membrane/8 > argument 3 = -execer_id > argument 4 = mpiexec > argument 5 = -master_host > argument 6 = h3du27 > argument 7 = -my_hostname > argument 8 = h3du27 > argument 9 = -my_nodenum > argument 10 = 0 > argument 11 = -my_numprocs > argument 12 = 1 > argument 13 = -total_numnodes > argument 14 = 8 > argument 15 = -master_port > argument 16 = 32780 > argument 17 = -remote_info > argument 18 = h3du27 > argument 19 = 1 > argument 20 = h3du25 > argument 21 = 1 > argument 22 = h3du25 > argument 23 = 1 > argument 24 = h3du20 > argument 25 = 1 > argument 26 = h3du20 > argument 27 = 1 > argument 28 = h3du19 > argument 29 = 1 > argument 30 = h3du19 > argument 31 = 1 > > > > > Northwest Computational Chemistry Package (NWChem) 4.7 > ------------------------------------------------------ > > > Environmental Molecular Sciences Laboratory > Pacific Northwest National Laboratory > Richland, WA 99352 > > > > > > COPYRIGHT (C) 1994, 1995, 1996, 1997, 1998, > 1999, 2000, 2001, 2002, 2003, 2004 > Pacific Northwest National Laboratory, > Battelle Memorial Institute. > > >>> All Rights Reserved <<< > > > DISCLAIMER > ---------- > > This material was prepared as an account of work sponsored > by an agency of the United States Government. Neither the > United States Government nor the United States Department > of Energy, nor Battelle, nor any of their employees, MAKES > ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL > LIABILITY OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, > OR USEFULNESS OF ANY INFORMATION, APPARATUS, PRODUCT, > SOFTWARE, OR PROCESS DISCLOSED, OR REPRESENTS THAT ITS USE > WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS. > > > LIMITED USE > ----------- > > This software (including any documentation) is being made > available to you for your internal use only, solely for use > in performance of work directly for the U.S. Federal > Government or work under contracts with the U.S. Department > of Energy or other U.S. Federal Government agencies. This > software is a version which has not yet been evaluated and > cleared for commercialization. Adherence to this notice > may be necessary for the author, Battelle Memorial > Institute, to successfully assert copyright in and > commercialize this software. This software is not intended > for duplication or distribution to third parties without > the permission of the Manager of Software Products at > Pacific Northwest National Laboratory, Richland, > Washington, 99352. > > > ACKNOWLEDGMENT > -------------- > > This software and its documentation were produced with > Government support under Contract Number DE-AC06-76RLO-1830 > awarded by the United States Department of Energy. The > Government retains a paid-up non-exclusive, irrevocable > worldwide license to reproduce, prepare derivative works, > perform publicly and display publicly by or for the > Government, including the right to distribute to other > Government contractors. > > > Job information > --------------- > > hostname = h3du27 > program = /opt/packages/nwchem-4.7/bin/nwchem > date = Tue Jan 17 18:11:45 2006 > > compiled = Thu Oct 20 11:30:29 BST 2005 > source = /home/staff/pfarrell/rpm/BUILD/nwchem-4.7 > nwchem branch = 4.7 > input = nwchem.nw > prefix = .membrane_example. > data base = ./.membrane_example.db > status = startup > nproc = 8 > time left = -1s > > > > Memory information > ------------------ > > heap = 13107201 doubles = 100.0 Mbytes > stack = 13107201 doubles = 100.0 Mbytes > global = 26214400 doubles = 200.0 Mbytes (distinct from heap & > stack) > total = 52428802 doubles = 400.0 Mbytes > verify = yes > hardfail = no > > > Directory information > --------------------- > > 0 permanent = . > 0 scratch = . > > > > > NWChem Input Module > ------------------- > > > Prepare Module > -------------- > > Force field amber > > > Directories used for fragment and segment files > > > /opt/packages/nwchem-4.7/data/amber_s/ > > /opt/packages/nwchem-4.7/data/amber_q/ > > /opt/packages/nwchem-4.7/data/amber_x/ > > /opt/packages/nwchem-4.7/data/amber_u/ > ./ > > Parameter files used to resolve force field parameters > > > /opt/packages/nwchem-4.7/data/amber_s/amber.par > > /opt/packages/nwchem-4.7/data/amber_q/amber.par > > /opt/packages/nwchem-4.7/data/amber_x/amber.par > > /opt/packages/nwchem-4.7/data/amber_u/amber.par > ./amber.par > SEQUENCE GENERATION > > geom_rtdb_load: not found or rtdb corrupt: geometry -> geometry > geom_rtdb_load: open geometies: 1 > 1 geom_rtdb_load: "geometry" -> "geometry" > > ********** > * 0: pre_mkseq: geom_rtdb_load failed 0 > ********** > 0:0::: 0 > p0_20465: p4_error: : 0 > p0_20465: (3.046875) net_send: could not write to fd=4, errno = 32 > 4:Child process terminated prematurely, status=: 0 > 6:Child process terminated prematurely, status=: 0 > 2:Child process terminated prematurely, status=: 0 > > -- Edoardo Aprà - PNNL - P.O. Box 999, MS K8-91 - Richland, WA 99352 Fax +1-509-376-0420