From chemistry-request@ccl.net Sat May 22 03:47:09 2004 Received: from leitl.org (leitl.org [217.172.178.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4M8l7o8024049 for ; Sat, 22 May 2004 03:47:07 -0500 Received: by leitl.org (Postfix, from userid 500) id F287F3A84B5; Sat, 22 May 2004 10:49:57 +0200 (CEST) Date: Sat, 22 May 2004 10:49:57 +0200 From: Eugen Leitl To: chemistry^at^ccl.net Subject: Re: [Beowulf] CCL:running GAMESS using Beowulf cluster (fwd from orbital_jc^at^yahoo.co.uk) (fwd from jmdavis^at^mail2.vcu.edu) Message-ID: <20040522084957.GZ16732^at^leitl.org> Mime-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="iRHoVKTfP8ON3BWx" Content-Disposition: inline User-Agent: Mutt/1.4i X-Spam-Status: No, hits=2.6 required=7.5 tests=FVGT_m_MULTI_ODD2, FVGT_s_OBFU_J,HTML_MESSAGE,IMPRONONCABLE_2,MK_BAD_HTML_04 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --iRHoVKTfP8ON3BWx Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable ----- Forwarded message from Mike Davis ----- From: Mike Davis Date: Fri, 21 May 2004 20:37:39 -0400 To: Eugen Leitl , beowulf^at^beowulf.org Subject: Re: [Beowulf] CCL:running GAMESS using Beowulf cluster (fwd from orbital_jc^at^yahoo.co.uk) User-Agent: Mozilla/5.0 (Macintosh; U; PPC Mac OS X Mach-O; en-US; rv:1.4) = Gecko/20030624 I had one of the gamess linux MPI port people (Charles Castevens)=20 working for me and we still had problems with the mpi version of gamess.=20 We wound up using the sockets version along with a script to submit the=20 jobs to pbs. For this to work you should have gamess (preferably=20 installed in a common location on each node), PBS up and running (a far=20 bigger task usually), modified comp files and rungms, and a script to=20 handle pbs submission. I'm sorry but we never had nearly the time=20 required to do a step by step guide. I will attach a copy of the script and note the modifications: ****************** script: #!/bin/tcsh -f # $cwd -- current working directory # $0 -- program name and path to its location # $1 -- gamess version # $2 -- input file name -- w/o inp # $3 -- nodes (optional) # $4 -- queue (optional) # set wd =3D $cwd set version =3D $1 set name =3D $2 if (null$version =3D=3D null ) goto usage if (null$name =3D=3D null ) goto usage set nodes =3D $3 if (null$nodes =3D=3D null) set nodes=3D1 set queue =3D $4 if (null$queue =3D=3D null ) set queue=3Dp2p cat <${name}.job #!/bin/csh -f #PBS -q $queue #PBS -l nodes=3D$nodes #alias gms "/usr/local/gamess/seqgms" echo "Starting GAMESS with file $name at \`date\` on \`hostname\`" cd $wd #printenv /usr/u2/gamess16feb02r1/new_rungms $name $version $nodes >& $name.log mail $USER < ${name}.err mv /scr/$USER/$name.dat ~/scr/$name.dat mv /scr/$USER/$name.irc ~/scr/$name.irc echo "GAMESS Done with status \$status at \`date\` on \`hostname\`" END chmod u+x ${name}.job # submit the new script qsub ${name}.job #nohup ./${name}.job >& ${name}.err & unalias rm #rm $name.job echo "Success!" exit ************************** rungms mods: if ( `hostname` =3D=3D "nameofyourcluster" ) then echo "creating hostlist using PBS environment PBS_NODEFILE:" echo $PBS_NODEFILE cat $PBS_NODEFILE set HOSTLIST=3D'hostname' # # get the actual value of hostname via rsh for gamess # foreach i (`cat $PBS_NODEFILE`) if ( $i !=3D "hydra1.vcu.edu" ) set HOSTLIST=3D($HOSTLIST `rsh $i hostname`) end # # if we are not on node001 and we are using more than 1 node # build a hostlist and use rsh to get the actual value returned # by hostname # else if ( -e $PBS_NODEFILE ) then echo "creating hostlist using PBS environment PBS_NODEFILE:" cat $PBS_NODEFILE # zero out HOSTLIST set HOSTLIST=3D'' # get the actual value of hostname via rsh for gamess foreach i (`cat $PBS_NODEFILE`) set HOSTLIST=3D($HOSTLIST `rsh $i hostname`) end endif Eugen Leitl wrote: >----- Forwarded message from Jeff C ----- > >From: Jeff C >Date: Fri, 21 May 2004 16:12:20 +0100 (BST) >To: CHEMISTRY^at^ccl.net >Subject: CCL:running GAMESS using Beowulf cluster=20 > >Dear Comp Chem Experts, > >I am new to this field so I will apologize in advance >if the following question is too trivial to the >skilled researchers.=20 > >Currently I am trying to learn how to use gamess. The >procedure is simple when comes to running gamess with >single CPU. However, I am clueless when trying to run >gamess on our newly built 16 nodes Beowulf cluster >using MPI. I hope someone out there can give me the >step-by-step guide. > >Much appreciated. > >Jeff Chen =20 > > > >=09 >=09 > =09 >____________________________________________________________ >Yahoo! Messenger - Communicate instantly..."Ping"=20 >your friends today! Download Messenger Now=20 >http://uk.messenger.yahoo.com/download/index.html > > >-=3D This is automatically added to each message by the mailing script =3D- >To send e-mail to subscribers of CCL put the string CCL: on your Subject:= =20 >line >and send your message to: CHEMISTRY^at^ccl.net > >Send your subscription/unsubscription requests to:=20 >CHEMISTRY-REQUEST^at^ccl.net HOME Page: http://www.ccl.net | Jobs Page:=20 >http://www.ccl.net/jobs=20 >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow^at^nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > >----- End forwarded message ----- >=20 > >------------------------------------------------------------------------ > >_______________________________________________ >Beowulf mailing list, Beowulf^at^beowulf.org >To change your subscription (digest mode or unsubscribe) visit=20 >http://www.beowulf.org/mailman/listinfo/beowulf >=20 > ----- End forwarded message ----- --=20 Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net --iRHoVKTfP8ON3BWx Content-Type: application/pgp-signature Content-Disposition: inline -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.2-rc1-SuSE (GNU/Linux) iD8DBQFArxQ1dbAkQ4sp9r4RAs1LAKCvQUanT+NggVeQy1MGXjrCeYixNACcC9ib uL4IVmiML+LWaGxxdUIdvSo= =hQgi -----END PGP SIGNATURE----- --iRHoVKTfP8ON3BWx-- From chemistry-request@ccl.net Sat May 22 21:13:13 2004 Received: from pernis.its.uu.se (pernis.its.uu.se [130.238.4.153]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4N2DCGx004782 for ; Sat, 22 May 2004 21:13:12 -0500 Received: by pernis.its.uu.se (Postfix, from userid 205) id 21EAF3BA; Sun, 23 May 2004 04:16:04 +0200 (MSZ) Received: from pernis.its.uu.se(127.0.0.1) by pernis.its.uu.se via virus-scan id s1106; Sun, 23 May 04 04:16:03 +0200 Received: from xray.bmc.uu.se (xray.bmc.uu.se [130.238.41.195]) by pernis.its.uu.se (Postfix) with ESMTP id 7A3281F7; Sun, 23 May 2004 04:16:00 +0200 (MSZ) Received: from mail.telepac.pt (regulus3.student.UU.SE [130.238.5.5]) by xray.bmc.uu.se (8.11.6/8.8.7) with ESMTP id i4N2Den12714; Sun, 23 May 2004 04:13:40 +0200 Date: Sun, 23 May 2004 04:23:25 +0100 From: "Filipe Maia" To: "Alex Sutcliffe" , chemistry..at..ccl.net Subject: Re: CCL:using DOCK without sybil References: <20040202235310.20e965e2.a_sutcliffe..at..iprimus.com.au> Message-ID: Content-Type: text/plain; format=flowed; charset=iso-8859-1 MIME-Version: 1.0 In-Reply-To: <20040202235310.20e965e2.a_sutcliffe..at..iprimus.com.au> User-Agent: Opera M2/7.50 (Linux, build 673) X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i4N2DDGx004786 On Mon, 2 Feb 2004 23:53:10 +1100, Alex Sutcliffe wrote: > Hi CCLers, > > I would like to use DOCK but don't have access to sybil. In order to > convert my molecules to mol2 format I had hoped to use openbabel to do a > simple conversion, however GRID gave me this: > > Improper ATOM record substructure id for ***** in ./mymolecule.mol2 http://home.pchome.com.tw/team/gentamicin/mol/mol.htm I don't know if pmol2q is of any help. > > I do have an example of a molecule in mol2 format that is acceptable > which I intend to compare with mymolecule with but I just thought that > someone else had probably been down this road already. > > Any much appreciated! > > Alex Sutcliffe > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY..at..ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST..at..ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow..at..nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > -- Don't go around saying the world owes you a living. The world owes you nothing. It was here first. -- Mark Twain