From owner-nwchem-users@emsl.pnl.gov Wed Mar 19 16:55:52 2008 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.14.1/8.14.1) with ESMTP id m2JNtp0j010509 for ; Wed, 19 Mar 2008 16:55:52 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.14.1/8.14.1/Submit) id m2JNtpch010508 for nwchem-users-outgoing-0915; Wed, 19 Mar 2008 16:55:51 -0700 (PDT) X-Authentication-Warning: odyssey.emsl.pnl.gov: majordom set sender to owner-nwchem-users@emsl.pnl.gov using -f X-Ironport-SG: OK_Domains X-Ironport-SBRS: 6.3 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: Aq8AAHhE4UeB27sVo2dsb2JhbACRAgEBAQEBAQcFCQcWmUEB X-IronPort-AV: E=Sophos;i="4.25,527,1199692800"; d="scan'208";a="70887036" From: Shahriar Anwar To: "DeJong, Wibe A" In-Reply-To: <1692FA5FE0EBFD40B2B4097DAFEA887C035C48EF@EMAIL02.pnl.gov> Subject: Re: [NWCHEM] Newbie help References: <47E189C7.1010508@pnl.gov> <1692FA5FE0EBFD40B2B4097DAFEA887C035C48EF@EMAIL02.pnl.gov> Message-Id: Content-Type: text/plain; charset=US-ASCII; format=flowed Content-Transfer-Encoding: 7bit Mime-Version: 1.0 (Apple Message framework v919.2) Date: Wed, 19 Mar 2008 16:55:45 -0700 Cc: Dunyou Wang , nwchem-users@emsl.pnl.gov X-Mailer: Apple Mail (2.919.2) X-Virus-Scanned: by amavisd-new Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk Bert, I tried that but am still getting the same error. Thanks. Shahriar On Mar 19, 2008, at 3:07 PM, DeJong, Wibe A wrote: Shahriar, You might want to try using mpirun instead of mpiexec. Bert de Jong, Ph.D. Chief Scientist Capability Steward High Performance Software Development Environmental Molecular Science Laboratory Pacific Northwest National Laboratory P.O. Box 999, Mail Stop K8-91 Richland, WA 99352 Phone: (509) 371-6476 Email: bert.dejong@pnl.gov Fax: (509) 371-6445 Room: EMSL 1371 Web: http://mscf.emsl.pnl.gov -----Original Message----- From: owner-nwchem-developers@emsl.pnl.gov [mailto:owner-nwchem-developers@emsl.pnl.gov] On Behalf Of Wang, Dunyou Sent: Wednesday, March 19, 2008 2:47 PM To: Shahriar Anwar Cc: nwchem-users@emsl.pnl.gov Subject: Re: [NWCHEM] Newbie help Hi Shahriar, As stated in your error message, there is something wrong running jobs with your MPI on your machine. As a matter of fact, you probably can't run any MPI jobs (not only NWChem jobs) on your machine if you have that problem. So please consult your sys-admin on that issue. Best regards Dunyou Wang Shahriar Anwar wrote: > Dear Members, > > I am trying to run NWCHEM for the first time and have run into a > problem that I do not know how to resolve. We are using the intel > openmpi compiler. Your help is much appreciated. > > I am trying to run the first example n2.nw in the manual and getting > the following error: > > [sanwar@saguaro1 test]$ more NWChem.e153316 > Can't read MPIRUN_HOST > Can't read MPIRUN_HOST > Can't read MPIRUN_HOST > Can't read MPIRUN_HOST > > FYI, my input file (per the manual) is called n2.nw and its contents are: > > title "Nitrogen cc-pvdz SCF geometry optimization" > geometry > n 0 0 0 > n 0 0 1.08 > end > basis > n library cc-pvdz > end > task scf optimize > > Our machine requires that jobs be submitted with the qsub command and > a shell script. The shell script that I used is called nwrunscript7.sh > and its contents are: > #!/bin/bash > #PBS -N NWChem > #PBS -l nodes=4 > #PBS -l walltime=00:10:00 > #PBS -q devel > #PBS -o nwchem-output7 > > use intel-openmpi-1.2.3 > cd $PBS_O_WORKDIR > mpiexec /home/sanwar/nwchem-5.0/bin/nwchem n2.nw > > The specifics of the machine that I am running this job is: > Saguaro is the centerpiece of Arizona State University's High > Performance Computing Initiative. This machine has 2200 processing > cores available for parallel computing. Saguaro is composed of 220 > dual quadcore Intel Xeon EM64T nodes each with 16 gigabytes of ram, > and manufactured by Dell. Each node communicates via Cisco Infiniband > high speed interconnects and gigabit copper. The cluster also has a > partition for running large numbers of serial jobs comprised of 185 > nodes with dual Xeon MP 64bit processors. > > Also, my .bash_profile reads (with the line use intel-openmpi-1.2.3 added): > > # .bash_profile > > # Get the aliases and functions > if [ -f ~/.bashrc ]; then > . ~/.bashrc > fi > > # User specific environment and startup programs > > PATH=$PATH:$HOME/bin > > export PATH > unset USERNAME > > # Following lines added by sanwar on 20080317 > use intel-openmpi-1.2.3 > PATH=$PATH:/home/sanwar/nwchem-5.0/bin > PATH=$PATH:/home/sanwar/nwchem-5.0 > # Above lines added by sanwar on 20080317 > > Thanks, > > Shahriar > > > >