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
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