From owner-nwchem-users@emsl.pnl.gov Wed Jul 26 07:59:54 2006 Received: from odyssey.emsl.pnl.gov (localhost [127.0.0.1]) by odyssey.emsl.pnl.gov (8.13.6/8.13.6) with ESMTP id k6QExrjL016912 for ; Wed, 26 Jul 2006 07:59:53 -0700 (PDT) Received: (from majordom@localhost) by odyssey.emsl.pnl.gov (8.13.6/8.13.6/Submit) id k6QExrRT016911 for nwchem-users-outgoing-0915; Wed, 26 Jul 2006 07:59:53 -0700 (PDT) X-Ironport-SG: OK_Domains X-Ironport-SBRS: 4.4 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AQAAAPsex0SCeYYVFBSBEQEBAgcCDAUIHQ X-IronPort-AV: i="4.07,185,1151910000"; d="scan'208,217"; a="2558826:sNHT23755942" Message-ID: X-Originating-IP: [202.185.71.27] X-Originating-Email: [nasr974@hotmail.com] X-Sender: nasr974@hotmail.com In-Reply-To: <44C68A16.7060300@pnl.gov> From: "Nasr Y.M.J.O." To: dunyou.wang@pnl.gov Cc: nwchem-users@emsl.pnl.gov Subject: Re: [NWCHEM] QA-Tests Date: Wed, 26 Jul 2006 14:59:02 +0000 Mime-Version: 1.0 Content-Type: text/html; format=flowed X-OriginalArrivalTime: 26 Jul 2006 14:59:03.0221 (UTC) FILETIME=[08AC0E50:01C6B0C4] Sender: owner-nwchem-users@emsl.pnl.gov Precedence: bulk

Dear Dunyou,

I am still getting the same error. As per your first suggestion, I dont have these files in the src directory. However, I tried to make all directories within the /share/apps/nwchem-4.7 writable but the error persists. As per the second suggestion, the same error as well. Also, /share/apps directory has big capacity (60 GB).

I tried to create my own scratch and permanent directories and edit the script runtests.mpi.unix (I am not too sure wether I did edit it the right way) but it seemed that the calculation hanged.

I also tried to run one of the examples under the examples directory directly from /tmp and /share/apps directories by invoking the mpirun command but it seemed that the calaculation hanged as well stopping at these two lines:

permanent directory = .

scratch directory = . 

(I waited for around 20 minutes before aborting the calculation myself since in the included "ok" output file it should take about 3 minutes by using one processor while am using 7 processors!).

PS: I run the hpl program on my cluster to test the mpi and its running fine.

Sorry for the long email. Any new thoughts are appreciated.

many thanks

nasr

From:  Dunyou Wang <dunyou.wang@pnl.gov>
To:  "Nasr Y.M.J.O." <nasr974@hotmail.com>
CC:  nwchem-users@emsl.pnl.gov
Subject:  Re: [NWCHEM] QA-Tests
Date:  Tue, 25 Jul 2006 14:16:06 -0700
>Dear Nasr,
>
>Please try the two procedures to fix the errors you are facing:
>
>1.  check in your $NWCHEM_TOP/src directory
>     remove any file names containing 'dir_check_p' or 'dir_check_s'
>     then restart your QA tests again
>
>If the above step doesn't work for you then:
>
>2.  your disk space of the /share/apps directory at might be full,
>so
>     move your QA tests directory  to /tmp   or /scratch
>     and do your tests there
>
>Hope this will help
>Dunyou
>
>
>Nasr Y.M.J.O. wrote:
>>Dear All,
>>  I am trying to run the QA tests for nwchem 4.7 using the
>>doqmtests.mpi and runtests.mpi.unix in a linux cluster (Rocks 4.1,
>>MPICH 1.2.7) but facing some errors. Below is a typical output. I
>>tried to change the scratch and permanent directories but the error
>>still persists.
>>  PS: the directory /share/apps is visible to all compute nodes. Im
>>running the tests as a root. SSH doesnot require any password. Also
>>when I SSH to any of the compute nodes I could see the scratch and
>>testoutputs directories and open them!  Any advice is appreciated.
>>Many thanks
>>  Nasr
>>
>>
>>ARMCI configured for 7 cluster nodes. Network protocol is 'TCP/IP
>>Sockets'.
>>
>>argument 1 = auh2o.nw
>>
>>argument 2 = -p4pg
>>
>>argument 3 = /share/apps/nwchem-4.7/QA/scratchdir/PIfgqCbF1427
>>
>>argument 4 = -p4wd
>>
>>argument 5 = /share/apps/nwchem-4.7/QA/scratchdir
>>
>>
>>
>>
>>
>>============================== echo of input deck
>>==============================
>>
>># This input exposed bug in freeze core atomic for centers with
>>ECPs
>>
>>echo
>>
>>start Au+(H2O)2
>>
>>title "Au+(H2O)2, H2O aVTZ using optimal MP2/aVDZ geometry"
>>
>>charge 1 # Overall +1 charge
>>
>>geometry
>>
>>symmetry group C2
>>
>>Au 0.0 0.0 0.009361
>>
>>O 0.0 2.036904 0.009358
>>
>>H 0.125560 2.461223 -0.856506
>>
>>H -0.776831 2.461225 0.411874
>>
>>end
>>
>>basis spherical
>>
>>Au library LANL2DZ_ECP
>>
>>H library 6-31g
>>
>>O library 6-31g
>>
>>end
>>
>>ecp spherical
>>
>>Au library LANL2DZ_ECP
>>
>>end
>>
>>mp2
>>
>>freeze core atomic
>>
>>end
>>
>>task mp2 # Perform a single point MP2
>>
>>================================================================================
>>
>>
>>
>>
>>
>>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 = www.um.edu.my
>>
>>program = /share/apps/nwchem-4.7/bin/LINUX/nwchem
>>
>>date = Wed Jul 26 00:00:06 2006
>>
>>compiled = Fri Jul 21 02:17:51 MYT 2006
>>
>>source = /usr/local/nwchem-4.7
>>
>>nwchem branch = 4.7
>>
>>input = auh2o.nw
>>
>>prefix = Au+(H2O)2.
>>
>>data base = ./Au+(H2O)2.db
>>
>>status = startup
>>
>>nproc = 7
>>
>>time left = -1s
>>
>>
>>
>>
>>
>>Memory information
>>
>>------------------
>>
>>heap = 98692353 doubles = 753.0 Mbytes
>>
>>stack = 98692353 doubles = 753.0 Mbytes
>>
>>global = 197384704 doubles = 1505.9 Mbytes (distinct from heap &
>>stack)
>>
>>total = 394769410 doubles = 3011.9 Mbytes
>>
>>verify = yes
>>
>>hardfail = no
>>
>>
>>
>>Directory information
>>
>>---------------------
>>
>>0 permanent = .
>>
>>0 scratch = .
>>
>>could not open a file in permanent directory:
>>
>>could not open a file in scratch directory:
>>
>>Both permanent and scratch directory not accessible
>>
>>******** Fatal Error ******** 911
>>
>>------------------------------------------------------------------------
>>
>>------------------------------------------------------------------------
>>
>>current input line :
>>
>>0:
>>
>>------------------------------------------------------------------------
>>
>>------------------------------------------------------------------------
>>
>>There is an error in the input file
>>
>>------------------------------------------------------------------------
>>
>>For more information see the NWChem manual at
>>
>>http://www.emsl.pnl.gov/docs/nwchem/nwchem.html
>>
>>
>>
>>For further details see manual section:
>>
>>2:2:******** Fatal Error ********:: 911
>>
>>2:2:******** Fatal Error ********:: 911
>>
>>Last System Error Message from Task 2:: Permission denied
>>
>>[2] MPI Abort by user Aborting program !
>>
>>[2] Aborting program!
>>
>>could not open a file in permanent directory:
>>
>>could not open a file in scratch directory:
>>
>>Both permanent and scratch directory not accessible
>>
>>******** Fatal Error ******** 911
>>
>>------------------------------------------------------------------------
>>
>>------------------------------------------------------------------------
>>
>>current input line :
>>
>>0:
>>
>>------------------------------------------------------------------------
>>
>>------------------------------------------------------------------------
>>
>>There is an error in the input file
>>
>>------------------------------------------------------------------------
>>
>>For more information see the NWChem manual at
>>
>>http://www.emsl.pnl.gov/docs/nwchem/nwchem.html
>>
>>
>>
>>For further details see manual section:
>>
>>4:4:******** Fatal Error ********:: 911
>>
>>4:4:******** Fatal Error ********:: 911
>>
>>Last System Error Message from Task 4:: Permission denied
>>
>>---------------
>>
>>hostname = www.um.edu.my
>>
>>program = /share/apps/nwchem-4.7/bin/LINUX/nwchem
>>
>>date = Wed Jul 26 00:00:06 2006
>>
>>compiled = Fri Jul 21 02:17:51 MYT 2006
>>
>>source = /usr/local/nwchem-4.7
>>
>>nwchem branch = 4.7
>>
>>input = auh2o.nw
>>
>>prefix = Au+(H2O)2.
>>
>>data base = ./Au+(H2O)2.db
>>
>>status = startup
>>
>>nproc = 7
>>
>>time left = -1s
>>
>>
>>
>>
>>
>>Memory information
>>
>>------------------
>>
>>heap = 98692353 doubles = 753.0 Mbytes
>>
>>stack = 98692353 doubles = 753.0 Mbytes
>>
>>global = 197384704 doubles = 1505.9 Mbytes (distinct from heap &
>>stack)
>>
>>total = 394769410 doubles = 3011.9 Mbytes
>>
>>verify = yes
>>
>>hardfail = no
>>
>>
>>
>>Directory information
>>
>>---------------------
>>
>>0 permanent = .
>>
>>0 scratch = .
>>
>>0:Child process terminated prematurely, status=: 0
>>
>>0:Child process terminated prematurely, status=: 0
>>
>>Last System Error Message from Task 0:: No such file or directory
>>
>>p2_5274: p4_error: : 911
>>
>>p2_5274: (19.894844) net_send: could not write to fd=5, errno = 32
>>
>>Interrupt
>>
>>ARMCI master: wait for child process (server) failed:: No such file
>>or directory
>>
>>[0] MPI Abort by user Aborting program !
>>
>>[0] Aborting program!
>>
>>p0_1517: p4_error: : 0
>>
>>Killed by signal 2.
>>
>>Killed by signal 2.
>>
>>Killed by signal 2.
>>
>>Killed by signal 2.
>>
>>Killed by signal 2.
>>
>>p0_1517: (33.298651) net_send: could not write to fd=4, errno = 32
>>
>>
>>
>>------------------------------------------------------------------------
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