Dear developers!
I am now trying to perform some test concerning molecular dynamics.
I have nwchem-6.5+mpi on my computer. But I don't quite understand if I should run dna example in parallel session, as there is an analyze module (in documentation it is said that this module should not be runned in parallel mode):
md
system dna_em
sd 100
end
task md optimize
task shell "cp dna_em.qrs dna_md.rst"
md
system dna_md
equil 0 data 1000
record scoor 10
isotherm 100.0
record rest 100
end
task md dynamics
analyze
system dna_md
reference dna_em.qrs
file dna_md.trj
super dna_super.trj
rmsd
scan dna_scan
end
task analyze
I have the following output after parallel mode:
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 = Tue Jan 26 15:23:57 2016
compiled = ??_???_27_16:57:07_2015
source = /usr/local/Nwchem-6.5
nwchem branch = 6.5
nwchem revision = 26243
ga revision = 10506
input = dna.nw
prefix = dna.
data base = ./dna.db
status = startup
nproc = 2
time left = -1s
Memory information
------------------
heap = 131066 doubles = 1.0 Mbytes
stack = 4718591 doubles = 36.0 Mbytes
global = 1572864 doubles = 12.0 Mbytes (distinct from heap & stack)
total = 6422521 doubles = 49.0 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/local/Nwchem-6.5/src/data/amber_s/
/usr/local/Nwchem-6.5/src/data/amber_q/
/usr/local/Nwchem-6.5/src/data/amber_x/
/usr/local/Nwchem-6.5/src/data/amber_u/
./
Parameter files used to resolve force field parameters
/usr/local/Nwchem-6.5/src/data/amber_s/amber.par
/usr/local/Nwchem-6.5/src/data/amber_q/amber.par
/usr/local/Nwchem-6.5/src/data/amber_x/amber.par
/usr/local/Nwchem-6.5/src/data/amber_u/amber.par
./amber.par
PDB geometry dna.pdb
Created segment ./DT_5.sgm
Created segment ./DG.sgm
Created segment ./DC.sgm
Created segment ./DA_3.sgm
Created sequence ./dna.seq
Parameter file /usr/local/Nwchem-6.5/src/data/amber_s/amber.par
Parameter file /usr/local/Nwchem-6.5/src/data/amber_q/amber.par
Parameter file /usr/local/Nwchem-6.5/src/data/amber_x/amber.par
Parameter file /usr/local/Nwchem-6.5/src/data/amber_u/amber.par
Total charge 0.000000
Created topology dna.top
Topology dna.top
No command file found: Default restart directives
Solute centered in x-dimension
Solute centered in y-dimension
Solute centered in z-dimension
Boxsize determined to 1.968800 2.003300 2.599200
Created restart dna_em.rst
Task times cpu: 0.0s wall: 0.0s
NWChem Input Module
-------------------
Task times cpu: 0.4s wall: 0.4s
NWChem Input Module
-------------------
Task times cpu: 0.0s wall: 0.0s
NWChem Input Module
-------------------
Task times cpu: 3.9s wall: 3.9s
NWChem Input Module
-------------------
Analysis Input Module
---------------------
Analysis Module
---------------
Reference coordinates read from dna_em.qrs
Number of atoms is 388
Topology read from dna.top
Opening trj file dna_md.trj
Closing trj file
Trajectory file header from dna_md.trj
Opening trj file dna_md.trj
Opening copy file dna_super.trj
mpirun noticed that process rank 1 with PID 11248 on node localhost.localdomain exited on signal 11 (Segmentation fault).
make: *** [all] error 139
And following output after sequential mode:
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 = Tue Jan 26 15:45:50 2016
compiled = ??_???_27_16:57:07_2015
source = /usr/local/Nwchem-6.5
nwchem branch = 6.5
nwchem revision = 26243
ga revision = 10506
input = dna.nw
prefix = dna.
data base = ./dna.db
status = startup
nproc = 1
time left = -1s
Memory information
------------------
heap = 131066 doubles = 1.0 Mbytes
stack = 4718591 doubles = 36.0 Mbytes
global = 1572864 doubles = 12.0 Mbytes (distinct from heap & stack)
total = 6422521 doubles = 49.0 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/local/Nwchem-6.5/src/data/amber_s/
/usr/local/Nwchem-6.5/src/data/amber_q/
/usr/local/Nwchem-6.5/src/data/amber_x/
/usr/local/Nwchem-6.5/src/data/amber_u/
./
Parameter files used to resolve force field parameters
/usr/local/Nwchem-6.5/src/data/amber_s/amber.par
/usr/local/Nwchem-6.5/src/data/amber_q/amber.par
/usr/local/Nwchem-6.5/src/data/amber_x/amber.par
/usr/local/Nwchem-6.5/src/data/amber_u/amber.par
./amber.par
Deleted existing topology dna.top
Deleted existing sequence ./dna.seq
PDB geometry dna.pdb
Created sequence ./dna.seq
Parameter file /usr/local/Nwchem-6.5/src/data/amber_s/amber.par
Parameter file /usr/local/Nwchem-6.5/src/data/amber_q/amber.par
Parameter file /usr/local/Nwchem-6.5/src/data/amber_x/amber.par
Parameter file /usr/local/Nwchem-6.5/src/data/amber_u/amber.par
Total charge 0.000000
Created topology dna.top
Deleted existing restart dna_em.rst
Topology dna.top
No command file found: Default restart directives
Solute centered in x-dimension
Solute centered in y-dimension
Solute centered in z-dimension
Boxsize determined to 1.968800 2.003300 2.599200
Created restart dna_em.rst
Task times cpu: 0.0s wall: 0.0s
NWChem Input Module
-------------------
Task times cpu: 0.6s wall: 0.6s
NWChem Input Module
-------------------
Task times cpu: 0.0s wall: 0.0s
NWChem Input Module
-------------------
Task times cpu: 5.6s wall: 5.7s
NWChem Input Module
-------------------
Analysis Input Module
---------------------
Analysis Module
---------------
Reference coordinates read from dna_em.qrs
Number of atoms is 388
Topology read from dna.top
Opening trj file dna_md.trj
Closing trj file
Trajectory file header from dna_md.trj
Opening trj file dna_md.trj
Opening copy file dna_super.trj
make: *** [all] segmentation fault
Besides I have different out-files in these two cases. Can you explain me a reason?
But I need to obtain trajectory file. So what should I do in order to get this information?
And what data would be written in .trj while parallel mode?
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