Error in prepare task.

From NWChem

Viewed 343 times, With a total of 0 Posts
Jump to: navigation, search

Just Got Here
Threads 1
Posts 1
I get the following log when running this minimal example on this pdb: http://files.rcsb.org/download/2NIP.pdb. I might do sth. stupid, but cannot figure out what. Since the pdb is taken directly from the database, I don't assume sth.'s wrong with the file. But you never know...

Any help would be appreciated.

Thanks, C.

File 2nip.nw:
start 2nip

prepare
 system 2nip_em
 new_top new_seq
 amber
end

task prepare


Command:
$> nwchem 2nip.nw


Output:
argument  1 = 2nip.nw
                                         
                                         


              Northwest Computational Chemistry Package (NWChem) 6.6
              ------------------------------------------------------


                    Environmental Molecular Sciences Laboratory
                       Pacific Northwest National Laboratory
                                Richland, WA 99352

                              Copyright (c) 1994-2015
                       Pacific Northwest National Laboratory
                            Battelle Memorial Institute

             NWChem is an open-source computational chemistry package
                        distributed under the terms of the
                      Educational Community License (ECL) 2.0
             A copy of the license is included with this distribution
                              in the LICENSE.TXT file

                                  ACKNOWLEDGMENT
                                  --------------

            This software and its documentation were developed at the
            EMSL at Pacific Northwest National Laboratory, a multiprogram
            national laboratory, operated for the U.S. Department of Energy
            by Battelle under Contract Number DE-AC05-76RL01830. Support
            for this work was provided by the Department of Energy Office
            of Biological and Environmental Research, Office of Basic
            Energy Sciences, and the Office of Advanced Scientific Computing.


           Job information
           ---------------

    hostname        = XXX
    program         = nwchem
    date            = Thu Jun 23 10:36:11 2016

    compiled        = Mon_Feb_15_08:24:17_2016
    source          = /build/nwchem-MF0R1k/nwchem-6.6+r27746
    nwchem branch   = 6.6
    nwchem revision = 27746
    ga revision     = 10594
    input           = 2nip.nw
    prefix          = 2nip.
    data base       = ./2nip.db
    status          = startup
    nproc           =        1
    time left       =     -1s



           Memory information
           ------------------

    heap     =   13107194 doubles =    100.0 Mbytes
    stack    =   13107199 doubles =    100.0 Mbytes
    global   =   26214400 doubles =    200.0 Mbytes (distinct from heap & stack)
    total    =   52428793 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

                                       /usr/share/nwchem/amber_s/
                                       /usr/share/nwchem/amber_q/
                                       /usr/share/nwchem/amber_x/
                                       /usr/share/nwchem/amber_u/
                                       ./

 Parameter files used to resolve force field parameters

                                       /usr/share/nwchem/amber_s/amber.par
                                       /usr/share/nwchem/amber_q/amber.par
                                       /usr/share/nwchem/amber_x/amber.par
                                       /usr/share/nwchem/amber_u/amber.par
                                       ./amber.par
 PDB geometry                          2nip.pdb


 **********
 *   0: Illegal link    1
 **********
0:0::: 1
(rank:0 hostname:XXX pid:15940):ARMCI DASSERT fail. ../../ga-5-4/armci/src/common/armci.c:ARMCI_Error():208 cond:0
Last System Error Message from Task 0:: No such file or directory
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 4 DUP FROM 0 
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------


Platform: Ubuntu16.04 amd64, nwchem version 6.6+r277746-2 installed via apt repository


Forum >> NWChem's corner >> Running NWChem



Who's here now Members 0 Guests 0 Bots/Crawler 1


AWC's: 2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC