Dear developers!
I have now some problems with running NWChem tests. Here is some additional information about system:
Architecture: x86-64
System: Red Hat Linux 7.0
compilators: gfortran, gcc
openmpi and openmpi-devel have been installed
path to compilators:/usr/bin
path to openmpi libraries: /usr/lib64/openmpi/bin/
NWChem test location: /home/apalov/NWchem_tests/benzene
NWChem files location: /usr/local/Nwchem-6.5/src
export PATH=$PATH:/usr/bin:/usr/sbin:/usr/local/:/usr/lib64/openmpi/bin/
export NWCHEM_TOP=/usr/local/Nwchem-6.5
export NWCHEM_TARGET=LINUX64
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/usr/lib64/openmpi
export MPI_LIB=$MPI_LOC/lib
export MPI_INCLUDE=/usr/include/openmpi-x86_64
export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib
export FG=gfortran
export CC=gcc
Nwchem 6.5 is installed on personal computer with 8 cores.
$HOME directory is /root/ for admin; here is a .nwchemrc file that is a symbolic link to /usr/local/Nwchem-6.5/src/data/default.nwchemrc ( I use following command: ln -s /usr/local/Nwchem-6.5/src/data/default.nwchemrc .nwchemrc)
default.nwchemrc content:
export nwchem_basis_library /usr/local/Nwchem-6.5/src/basis/libraries/
export nwchem_nwpw_library /usr/local/Nwchem-6.5/src/nwpw/libraryps/
ffield amber
export amber_1 /usr/local/Nwchem-6.5/src/data/amber_s/
export amber_2 /usr/local/Nwchem-6.5/src/data/amber_q/
export amber_3 /usr/local/Nwchem-6.5/src/data/amber_x/
export amber_4 /usr/local/Nwchem-6.5/src/data/amber_u/
export spce /usr/local/Nwchem-6.5/src/data/solvents/spce.rst
export charmm_s /usr/local/Nwchem-6.5/src/data/charmm_s/
export charmm_x /usr/local/Nwchem-6.5/src/data/charmm_x/
after running nwchem command I have following output:
[root@localhost benzene]# make -f makefile.h
nwchem benzene.nw
argument 1 = benzene.nw
Northwest Computational Chemistry Package (NWChem) 6.5
------------------------------------------------------
Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
Richland, WA 99352
Copyright (c) 1994-2014
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 = localhost.localdomain
program = nwchem
date = Mon Dec 21 19:46:24 2015
compiled = ??_???_27_16:57:07_2015
source = /usr/local/Nwchem-6.5
nwchem branch = 6.5
nwchem revision = 26243
ga revision = 10506
input = benzene.nw
prefix = benzene.
data base = /home/apalov/NWchem_tests/benzene//benzene.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 = /home/apalov/NWchem_tests/benzene/
0 scratch = /home/apalov/NWchem_tests/benzene/
NWChem Input Module
-------------------
Prepare Module
--------------
Force field amber
Directories used for fragment and segment files
./
Parameter files used to resolve force field parameters
./amber.par
Deleted existing sequence ./benzene.seq
PDB geometry benzene.pdb
Created sequence ./benzene.seq
A SEGMENT FILE COULD NOT BE FOUND FOR spce
**********
* 0: pre_dimens failed 9999
**********
0::Received an Error in Communication
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 3 DUP FROM 0
with errorcode 9999.
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.
make: *** [all] error 15
As I understand nwchem cannot define the size of my system as it cannot find fragment and segment files located in /home/apalov/NWchem_tests/benzene but I don't know where and how I should define a path to them.
Please, help.
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