From owner-nwchem-users@emsl.pnl.gov Wed Jul 21 01:15:52 2004 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 i6L8FpHQ008880 for ; Wed, 21 Jul 2004 01:15:51 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.12.10/8.12.10/Submit) id i6L8FpsT008879 for nwchem-users-outgoing; Wed, 21 Jul 2004 01:15:51 -0700 (PDT) Message-ID: <40FE2626.1070809@pnl.gov> Date: Wed, 21 Jul 2004 01:15:34 -0700 From: Edoardo Apra` Organization: PNNL User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7a) Gecko/20040205 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Jesus Centeno Garrido CC: nwchem-users@emsl.pnl.gov Subject: Re: binaries installation problems References: <1089384538.12101.32.camel@kaliman.iimatercu.unam.mx> <40EEB448.4000706@pnl.gov> <1090350099.31047.22.camel@jesus.ciencias.uchile.cl> In-Reply-To: <1090350099.31047.22.camel@jesus.ciencias.uchile.cl> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Jesus 1) please do not use mpirun to spawn nwchem since the nwchem binaries available for download use TCGMSG and not MPI. More details at http://www.emsl.pnl.gov/docs/nwchem/doc/user/node44.html 2) What Linux distribution are you using and what nwchem tar file have you downloaded 3) Could you please send your input file? Thanks, Edo Jesus Centeno Garrido wrote: >hi everybody, recently i downloaded the nwchem-4.6 binaries, i'd tried to >install it but i couldn't do it. here is a list of output it generates when i try to >run a calculation (at the end, there is the variables initialization file i wrote): > >nwchem: Symbol `emacs_meta_keymap' has different size in shared object, consider re-linking >nwchem: Symbol `emacs_meta_keymap' has different size in shared object, consider re-linking >nwchem: Symbol `emacs_meta_keymap' has different size in shared object, consider re-linking >nwchem: Symbol `emacs_meta_keymap' has different size in shared object, consider re-linking >nwchem: Symbol `emacs_meta_keymap' has different size in shared object, consider re-linking >nwchem: Symbol `emacs_meta_keymap' has different size in shared object, consider re-linking >nwchem: Symbol `emacs_meta_keymap' has different size in shared object, consider re-linking >nwchem: Symbol `emacs_meta_keymap' has different size in shared object, consider re-linking >rtdb_seq_get: type mismatch "geometry:ngeom" in ./li6-d4h-b3lyp.db: arg=1010, db=1000 >rtdb_seq_get: type mismatch "geometry:ngeom" in ./li6-d4h-b3lyp.db: arg=1010, db=1000 >0:0:geom_rtdb_delete:failed deleting known entry:: 0 >Last System Error Message from Task 0:: No such file or directory > 0: ARMCI aborting 0 (0). >system error message: No such file or directory >----------------------------------------------------------------------------- >It seems that [at least] one of the processes that was started with >mpirun did not invoke MPI_INIT before quitting (it is possible that >more than one process did not invoke MPI_INIT -- mpirun was only >notified of the first one, which was on node n0). > >mpirun can *only* be used with MPI programs (i.e., programs that >invoke MPI_INIT and MPI_FINALIZE). You can use the "lamexec" program >to run non-MPI programs over the lambooted nodes. >----------------------------------------------------------------------------- >0:Terminate signal was sent, status=: 15 >Last System Error Message from Task 0:: Permission denied >Killed >Killed >0:Terminate signal was sent, status=: 15 >Last System Error Message from Task 0:: Permission denied >Killed >0:Terminate signal was sent, status=: 15 >Last System Error Message from Task 0:: Permission denied >Killed >0:Terminate signal was sent, status=: 15 >Last System Error Message from Task 0:: Permission denied >Killed >0:Terminate signal was sent, status=: 15 >Last System Error Message from Task 0:: Permission denied >Killed >0:Terminate signal was sent, status=: 15 >Last System Error Message from Task 0:: Permission denied >Killed > > >@@@@@@@@@@@@@@@@@@@@@@@@@@@ >nwchem_init: > > > > >>#!/bin/bash >>NWCHEM_TOP=/usr/local/nwchem-4.6/ >>NWCHEM_TARGET=LINUX >>SCRATCH_DEF_DIR=/tmp >>MPI_COMM=VIA >>NWCHEM_BASIS_LIBRARY=/usr/local/nwchem-4.6/usr.local.lib.nwchem/libraries/ >>FFIELD=amber >>AMBER_1=/usr/local/nwchem-4.6/usr.local.lib.nwchem/amber_s/ >>AMBER_2=/usr/local/nwchem-4.6/usr.local.lib.nwchem/amber_q/ >>AMBER_3=/usr/local/nwchem-4.6/usr.local.lib.nwchem/amber_x/ >>AMBER_4=/usr/local/nwchem-4.6/usr.local.lib.nwchem/amber_u/ >>SPCE=/usr/local/nwchem-4.6/usr.local.lib.nwchem/solvents/spce.rst >>CHARMM_S=/usr/local/nwchem-4.6/usr.local.lib.nwchem/charmm_s/ >>CHARMM_X=/usr/local/nwchem-4.6/usr.local.lib.nwchem/charmm_x/ >> >> >>MPI_LIB=/opt/lam-7.0/lib >>LIBMPI="-lmpi -llam -lpthread" >>#MPI_INCLUDE=/usr/include/ >> >> >>export SCRATCH_DEF_DIR NWCHEM_TOP NWCHEM_TARGET MPI_COMM NWCHEM_BASIS_LIBRARY FFIELD >>export AMBER_1 AMBER_2 AMBER_3 AMBER_4 SPCE CHARMM_S CHARMM_X MPI_LIB LIBMPI >>export PATH="$PATH":/usr/local/nwchem-4.6/bin >> >> > > > > -- Edoardo Aprà - PNNL - Battelle Blvd - Richland, WA 99352, MS K8-91 Tel +1-509-376-1280 Fax +1-509-376-0420