Manual

©
Materials
Design,
Inc.,
2014
v2.15

MEDEA®

2.15

Table
of
Contents

I.
Installation
and
Basic
Operation
......................................................................................................................................
2

A.
Installation
scenarios
.....................................................................................................................................................
5

B.
Installation
from
DVD
.....................................................................................................................................................
8

C.
Using
the
Materials
Design
Maintenance
Program
..........................................................................................
16

D.
Adding
Resources
to
your
MedeA®
installation
...............................................................................................
18

E.
Updating
an
existing
MedeA®
installation
...........................................................................................................
22

F.
TaskServer
administration
and
configuration
...................................................................................................
26

G.
Sharing
and
Security
.....................................................................................................................................................
36

H.
Performing
computations
with
MedeA®
.............................................................................................................
41

II.
Functionality
and
Use
.......................................................................................................................................................
45

A.
MEDEA®
overview
...........................................................................................................................................................
47

B.
InfoMaticA
.........................................................................................................................................................................
50

C.
Building
and
Structure
Editing
.................................................................................................................................
56

D.
Builders
..............................................................................................................................................................................
69

E.
Flowcharts
......................................................................................................................................................................
101

F.
MedeA®-‐Vasp-‐5.3
.........................................................................................................................................................
113

G.
Analysis
of
Results
......................................................................................................................................................
142

H.
Electronics
(Fermi
Surfaces
and
Electronic
Transport)
............................................................................
155

I.
Automated
Convergence
...........................................................................................................................................
161

J.
MedeA®-‐Phonon
2.0
....................................................................................................................................................
164

K.
Combi
................................................................................................................................................................................
179

L.
PrediBond
.......................................................................................................................................................................
181

M.
MedeA®-‐Gibbs
..............................................................................................................................................................
182

N.
MOPAC
2009/2012
......................................................................................................................................................
194

O.
Transition
State
Search
............................................................................................................................................
198

P.
Forcefields
......................................................................................................................................................................
204

Q.
MedeA®-‐Lammps
........................................................................................................................................................
222

R.
Thermal
Conductivity
................................................................................................................................................
225

S.
Viscosity
...........................................................................................................................................................................
227

T.
Diffusion
..........................................................................................................................................................................
228

III.
Theoretical
Background
...............................................................................................................................................
230

A.
Density
Functional
Theory
......................................................................................................................................
232

B.
Thermodynamics
........................................................................................................................................................
242

C.
Statistical
Thermodynamics
...................................................................................................................................
248

D.
Forcefields
for
materials
simulations
................................................................................................................
254

E.
Monte
Carlo
methods
.................................................................................................................................................
263

F.
Calculating
the
stability
of
surfaces
and
interfaces
......................................................................................
274

G.
Theory
of
Elasticity
.....................................................................................................................................................
277

H.
Vibrations
in
Solids
–
Phonons
.............................................................................................................................
285

I.
Transition
States
...........................................................................................................................................................
298

J.
Electronic
Transport
...................................................................................................................................................
304

K.
MOPAC
................................................................................................................................................................................
308

IV.
Appendix
.............................................................................................................................................................................
312

A.
Frequently
Asked
Questions
..................................................................................................................................
313

B.
Release
notes
.................................................................................................................................................................
323

C.
Standards
and
Reference
Energies
......................................................................................................................
324

D.
Brillouinzones
..............................................................................................................................................................
327

E.
Units
and
Constants
in
MedeA
...............................................................................................................................
349

MedeA®
User's
Guide

Installation
and
Basic
Operation

2
©
Materials
Design
Inc.,2014
v2.15

I. INSTALLATION
AND
BASIC
OPERATION

Overview
...................................................................................................................................................................................
3

Hardware
and
software
requirements
........................................................................................................................
4

A.
Installation
scenarios
.....................................................................................................................................................
5

1.
Single
machine
................................................................................................................................................................
5

2.
Small
cluster
....................................................................................................................................................................
6

3.
Larger
clusters
and
external
queuing
systems
.................................................................................................
7

B.
Installation
from
DVD
.....................................................................................................................................................
8

1.
Installing
MedeA
............................................................................................................................................................
8

2.
MedeA
TaskServer
on
multicore
machines
.....................................................................................................
14

C.
Using
the
Materials
Design
Maintenance
Program
..........................................................................................
16

Starting
the
Maintenance
Program
..........................................................................................................................
16

1.
Install
Patches
...............................................................................................................................................................
16

2.
Manage
Job
server
.......................................................................................................................................................
16

3.
Manage
Services
(Windows)
or
Manage
Daemons
(Linux):
.....................................................................
17

4.
Manage
Databases
(Windows
with
MSQL
server)
........................................................................................
17

5.
Install
in
Start
menu
...................................................................................................................................................
17

6.
Update
from
the
Web
or
Update
Installation
..................................................................................................
17

D.
Adding
Resources
to
your
MedeA®
installation
...............................................................................................
18

1.
Adding
another
front
end
........................................................................................................................................
18

2.
Installing
another
JobServer
...................................................................................................................................
19

3.
Replacing
the
JobServer
...........................................................................................................................................
20

4.
Adding
more
TaskServers
.......................................................................................................................................
21

E.
Updating
an
existing
MedeA®
installation
...........................................................................................................
22

1.
Update
from
DVD
........................................................................................................................................................
22

2.
Update
from
the
Internet
.........................................................................................................................................
22

3.
Registering
additional
TaskServers
with
the
JobServer
............................................................................
23

4.
Adding
additional
Queues
.......................................................................................................................................
23

5.
Attaching
a
TaskServer
to
a
Queue
......................................................................................................................
24

F.
TaskServer
administration
and
configuration
...................................................................................................
26

1.
Configuring
a
TaskServer
to
use
an
external
queue
.....................................................................................
28

2.
Configuring
the
TaskServer
to
work
with
a
ftp
to
a
supercomputer
....................................................
31

3.
Using
the
TaskServer
in
manual
mode
..............................................................................................................
33

4.
Performing
computations
with
MedeA®
...........................................................................................................
34

G.
Sharing
and
Security
.....................................................................................................................................................
36

1.
Secure
JobServer
with
https
and
username/password
authentication
..............................................
36

2.
JobServer:
Users
Administration
to
define
authorized
users
..................................................................
37

3.
TaskServer:
Users
Administration
to
define
authorized
users
...............................................................
38

4.
JobServer:
TaskServers
Administration
to
enable
secure
communication
.......................................
39

5.
TaskServer:
JobServers
to
enable
secure
communication
........................................................................
39

6.
JobServer:
TaskServers
to
change
the
address
from
http
to
https
........................................................
40

H.
Performing
computations
with
MedeA®
.............................................................................................................
41

1.
Starting
the
MEDEA
GUI
.............................................................................................................................................
41

2.
Launching
a
job
in
MEDEA®
.....................................................................................................................................
41

3.
Monitoring
a
running
job
.........................................................................................................................................
42

4.
Hold
/
Resume
a
running
job
.................................................................................................................................
42

5.
Terminate
a
job
............................................................................................................................................................
43

6.
Restarting
a
held/interrupted
job
........................................................................................................................
44

MedeA®
User's
Guide

Installation
and
Basic
Operation

v2.15
©
Materials
Design
Inc.,2014

3

Overview

MEDEA’s
tiered
architecture
consists
of
the
MEDEA®
graphical
user
interface
(main
tier),
the

JobServer
(middle
tier),
and
the
TaskServer
(end
tier).

The
middle
tier
or
JobServer
is
the
central
hub
for
computational
job
control,
job
preprocessing,

and
job
post
processing.
The
JobServer
maintains
a
database
of
job
related
data
and
also
stores

computational
results
on
the
disk.

There
is
no
direct
communication
between
the
MEDEA®
GUI
and
TaskServers,
instead
all
data
flows

through
the
JobServer.

These
tiers
can
be
on
the
same
or
different
machines;
there
is
no
conceptual

difference
between
running
all
three
tiers
on
one
laptop
or
using
three
different
machines
for
GUI,

JobServer,
and
TaskServer.

One
installation
image
allows
installing
MEDEA®,
JobServer,
and
TaskServers
(running

computationally
intensive
codes
like
VASP,
LAMMPS,
and
GIBBS)
on
both
Windows
and
Linux

operating
systems.

MEDEA®
uses
either
Microsoft
SQL
or
MySQL
to
manage
experimental
databases,
code
specific
data

and
data
generated
by
the
user.
Technically
the
SQL
server
can
reside
on
any
networked
machine;

typically
it
is
installed
on
the
machine
running
MEDEA®
and/or
the
JobServer.

MEDEA®

DVD
(for
Windows
and
Linux)

OS

GUI

JobServer

TaskServer

Using
multiple
cores

Queuing
System

WINDOWS
XP/VISTA/7/8

Full
user
interface

Embedded
databases

X86
(32bit),
X86_64
(64
bit)

IntelMPI
(on
DVD)

Supports
LSF,HPC

LINUX
REDHAT,
SUSE,
CENTOS

Full
user
interface

embedded
databases

X86
(32bit),
X86_64
(64
bit)

IntelMPI
(on
DVD)

Supports
LSF,
PBS,
GridEngine,
SLURM

Administrative
rights

MEDEA®
requires
administrative
rights
during
installation:
Installing
of
SQL
and
MEDEA,
creation
of

services
cannot
be
done
with
basic
user
permissions.

In
Windows
Vista
and
Windows7
make
sure
that
you
are
not
only
administrator,
but
also
running

MDMaintenance.exe
with
administrative
rights.

The
most
effective
way
is
to
grant
the
final
MEDEA®
user
temporary
administrative
rights,
perform

the
installation
and
rescind
administrative
rights
after
successful
testing.

GUI JobServer TaskServer

MedeA®
User's
Guide

Installation
and
Basic
Operation

4
©
Materials
Design
Inc.,2014
v2.15

Hardware
and
software
requirements

While
there
are
no
hard
limits
in
terms
of
hardware
resources
for
any
of
the
MEDEA®
components,

MEDEA’s
graphical
visualization
and
atomistic
modeling
require
high-‐end
hardware
to
deliver

satisfying
performance.
As
a
rule
of
thumb
a
recent
upper-‐end
dual/quad
core
Windows
PC
will
be

sufficient
to
run
all
three
components:
the
graphical
interface,
the
JobServer,
and
the
TaskServer

with
all
computational
codes
for
small
to
medium
sized
systems.

For
larger
systems
or
more
demanding
calculations
(tasks)
a
cluster
configuration
is
recommended,

typically
a
Windows
or
Linux
blade
server
will
do
a
fine
job
on
running
the
TaskServer
and

computational
codes.
Detailed
hardware/software
requirements
and
component
specific
demands

are
as
follows:

Component
Requirement

Operating
system
Windows
XP/Server2003/Vista/Windows
7

Linux
(Centos,
REDHAT,
DEBIAN,
FEDORA,
SUSE,
UBUNTU,
ORACLE)

Architecture/Processor
Most
32bit
and
64bit
architectures
from
Intel
and
AMD:

OpteronAMD
,
ItaniumIntel
,
Core2,
Core2Duo,
i5,
i7

32
bit:
AthlonAMD
,
Pentium
IV,
XEONIntel

CPU
speed
Strong
floating
point
performance
required

No
lower/upper
hard
limit
on
clock
speed,
the
more
the
better

Memory
requirements

1-‐2
GB
RAM
per
CPU
core;
2
GB/core
is
recommended
for
VASP

Hard
Drive
space
5
GB
minimum
for
a
full
MEDEA®
installation

60-‐180
GB
for
storing
user
generated
data

Video
Card
OpenGL
2.1
and
higher
and
at
least
128
MB
of
memory

Network
Fast
Ethernet,
100
MBit
or
faster

Display
Screen
resolution
of
1024x800
at
minimum

Key
requirements
by
component:

MEDEA

Graphics
memory
and
speed

Display

Main
memory

JOBSERVER

RAID
or
automated
backup

Disk
space

TASKSERVER

CPU:
floating
point
performance

Main
memory

MedeA®
User's
Guide

Installation
and
Basic
Operation

v2.15
©
Materials
Design
Inc.,2014

5

A.
Installation
scenarios

MEDEA’s
tiered
architecture
lets
you
combine
components
in
a
number
of
ways
thus
adapting
to
the

needs
of
your
specific
compute
environment.
Here
are
a
few
scenarios
how
to
install
the
software:

1.
Single
machine

In
a
stand-‐alone
configuration,
MEDEA®
runs
on
a
single
Windows
or
Linux
machine
having
one
or

multiple
processing
units
(e.g.
multicore
CPU's).
All
components,
that
is
the
graphical
user
interface,

the
JobServer,
(and
their
databases)
and
the
TaskServer
are
installed
on
this
machine
and
all

computations
run
locally.

Procedure

1. Download
Installation
DVD

2. Attach
Installation
DVD

3. Perform
Default
installation

4. Start
MedeA

5. Request
license
file

6. Restart
MedeA

MedeA®
User's
Guide

Installation
and
Basic
Operation

6
©
Materials
Design
Inc.,2014
v2.15

2.
Small
cluster

• One
or
more
PCs,
each
running
the
MEDEA®
GUI

• A
single,
central
JobServer
on
one
of
the
above
machines
or
a
dedicated
machine

• TaskServers
on
some/each
of
the
above
machines,
additional
TaskServers
on
other

networked
resources
(Windows/Linux)

• Access
to
the
JobServer’s
web
interface
from
any
smartphone
or
computer

There
is
a
single,
central
JobServer.

Laptops
can
have
a
local
JobServer
to
work
when
operating
as
a
stand-‐alone
single
machine,
but
all

computations
on
the
shared
TaskServers
go
through
the
central
JobServer.

Procedure

1. Download
Installation
DVD

2. Attach
Installation
DVD
to
JobServer

3. Default
installation
of
JobServer

4. Default
Installation
on
GUI

5. TaskServers

a. In
case
TaskServer
does
not
share
MD/
folder:

i. Attach
Installation
DVD
to
JobServer

ii. Custom
Installation
TaskServer
on
any
TaskServer

b. With
shared
MD/
folder

i. Start
Maintenance
Program
on
TaskServer
and
create
TaskServer
daemon

6. Attach
Installation
DVD
to
frontend

7. Perform
Default
installation

8. Start
MedeA
on
frontend

9. Request
license
file
for
GUI

10. Restart
MedeA

MedeA®
User's
Guide

Installation
and
Basic
Operation

v2.15
©
Materials
Design
Inc.,2014

7

3.
Larger
clusters
and
external
queuing
systems

When
several
compute
intensive
applications
share
the
same
resources,
it
is
recommended
to
make

use
of
queuing
systems
like
e.g.
PBS, LSF, SLURM, and GridEngine.
MEDEA'S
TaskServer
supports

external
queuing
systems
under
Linux/Unix
by
providing
templates
for
queue
submission
(batch)

scripts.

Note
that
MEDEA®
does
not
provide
management
tools
for
external
queuing
systems.
You
will
need

to
adapt
the
template
scripts
provided
along
with
the
TaskServer
to
fit
your
local
installation.
The

current
implementation
requires
one
TaskServer
client
per
queue
and
queuing
system
user
to
be

installed
on
the
gateway
machine
that
is
the
login
or
head
node
of
a
supercomputer
or
massively

parallel
machine.
Configurable
scripts
for
the
PBS, LSF, and
GridEngine
queuing
systems
are

provided
for
each
of
the
computationally
intensive
codes
(VASP,
LAMMPS,
MOPAC,
and
GIBBS)
in

relevant
subfolders
of
C:MD2.0TaskServerTools
or
~/MD/2.0/TaskServer/Tools.

Procedure

1. Download
Installation
DVD

2. Attach
Installation
DVD
to
JobServer

3. Default
installation
of
JobServer

4. Default
Installation
on
GUI

5. TaskServers

a. In
case
TaskServer
does
not
share
MD/
folder:

i. Attach
Installation
DVD
to
JobServer

ii. Custom
Installation
TaskServer
on
any
TaskServer

b. With
shared
MD/
folder

i. Start
Maintenance
Program
on
TaskServer
and
create
TaskServer
daemon

6. Configure
Queuing
system
integration

7. Attach
Installation
DVD
to
frontend

8. Perform
Default
installation

9. Start
MedeA
on
frontend

10. Request
license
file
for
GUI

11. Restart
MedeA

Cluster
Queing
System

MedeA®
User's
Guide

Installation
and
Basic
Operation

8
©
Materials
Design
Inc.,2014
v2.15

B.
Installation
from
DVD

Databases
and
Daemons

MEDEA®
uses
a
variety
of
databases.
Some
are
structure
databases
such
as
ICSD
and
Pauling,
others

contain
user
generated
results
and
internal
data
like
potentials
and
parameters
used
in
VASP

calculations.
MEDEA®
2.15
uses
SQLite
as
the
default
database
manage
system
and
still
supports

MSQL
and
MySQL
from
previous
version.

Administrative
rights
and
services

MEDEA®
requires
the
JobServer
and
TaskServer
to
run
in
the
background.

Windows
provides
a

mechanism,
called
Services,
to
accomplish
that.
On
Linux
these
mechanisms
are
called
daemons.

You
can
ask
for
temporary
administrative
rights
or
have
your
administrator
install
MEDEA®

for
you.

1.
Installing
MedeA

The
MEDEA®
installer
will
guide
you
through
the
installation
process
which
will
take
some
minutes.

You
will
see
progress
updates
and
warnings,
if
you
system
needs
some
changes
to
run
some
of
the

provided
codes.
At
any
time
you
can
scroll
back
and
forth
within
the
installer
message
window
in

order
to
inspect
the
individual
steps
of
the
installation.

Windows:
Start
the
Installer
as
actual
user

Insert
the
MEDEA®
DVD
(or
mount
the
ISO
file)
to
auto
start
the
MEDEA®
Software
manager.
In
case

the
Software
manager
does
not
start
automatically,
click
on
the
Start/Run
button
in
the
Windows

Start
menu
and
use
Browse
to
locate
MDMaintenance.exe
in
the
DVD
's
Windows-x86 directory.

Right-‐click
and
select
"Run
as
administrator".

Linux:
Start
the
Installer
as
actual
user
(with
sudo
rights)

Create
a
user
medea
and
give
this
user
sudo
rights.

Log
on
as
user
medea
and
perform
the
installation:

Run
the
installer
in
the
top
level
of
the
DVD
with
Linux-x86_64/MDMaintenance.x

You
might
need
to
install

libXScrnSaver
or
similar
packages
missing
from
your
distribution1

1
REDHAT,
FEDORA:
yum install libXScrnSaver
DEBIAN,
UBUNTU:

apt-get install libXScrnSaver
SUSE:
yast –i libXScrnSaver

MedeA®
User's
Guide

Installation
and
Basic
Operation

v2.15
©
Materials
Design
Inc.,2014

9

MedeA
on
Windows
and
Linux
look
and
behaves
the
same
way.
So
unlike
many
Linux
programs,
the

entire
MedeA
distribution
is
in
one
folder,
including
databases,
executables
and
generated
results.

The
location
of
temporary
files
can
be
changed
any
time;
the
best
place
is
to
install
in
a
directory

owned
by
the
actual
MedeA
user
or
group.

Welcome to the Materials Design Installer, which will install MedeA along with its associated software and
databases.
When you click on the 'Next' button, I will ask you for information about what you want to install and where
to install it. Nothing will be actually installed until you ask, so you can review and change the
information as you wish.

• Click
Next
to
continue
and
select
the
installation
mode,
standard
installation
or

custom
installation.
Please
note
that
the
actual
size
of
packages
and
databases
changes

with
each
update
and
depending
on
the
specific
databases
present
on
the
DVD.

Installation Selection
Please choose if you want a
þ standard installation, which will install everything
¡ custom installation, where you choose what and where to install
The following packages will be installed:
JobServer 7.23 MB
TaskServer 972.89 MB
MEDEA 149.69 MB
Databases 1.67 GB
Total 2.77 GB
in C: /MD
Please make sure all the information above is correct and then click on the 'Install' button to start the
installation.
Install
i. Standard
Installation

The
standard
installation
provides
default
paths
and
installs
all
components
on
the
present
DVD.

Note
that
Standard
Installation
will
select
C:MD
on
Windows
or
~/MD
on
Linux.

The
drive
or
partition
you
select
for
MEDEA®,
should
have
at
least
20
GB
available
for
storing
results

of
calculations
performed
with
MEDEA.

On
Windows,
you
cannot
install
on
a
user
drive,
which
is
unmounted
after
logging
out.

ii. Custom
Installation

If
you
would
like
to
change
the
MEDEA®
installation
or
select
specific
modules
for
installation,
select

Custom
Installation.
Keep
in
mind
that
for
maintenance
it
is
best
to
have
the
whole
MEDEA®

program
tree,
database
files,
and
Job
data
on
a
single
hard
disk
partition.

Installation Parameters
Please choose if you want a
¡ Standard installation, which will install everything
þ Custom installation, where you choose what and where to install
Choose the packages to install:
þ JobServer 7.23 MB
þ TaskServer 972.89 MB
þ MedeA 149.69 MB
Total 1.10 GB
in C:/MD …
Choose the databases to install:
þ Pearson 509.56 MB
þ MedeA 290.52 MB
þ MaterialsDesign 241.00 kB
þ NCD_Inorganic 82.08 MB
þ NCD_Organic 225.76 MB
þ ICSD 605.39 MB
Total 1.67 GB
at C: /MD …
Please make sure all the information above is correct and then click on the 'Install' button to start the
installation.
Install
Installation
Progress

• Click
Install
to
continue

In
the
next
step,
the
MEDEA®
installer
will
install
all
the
selected
MEDEA®
components:

MedeA®
User's
Guide

Installation
and
Basic
Operation

10
©
Materials
Design
Inc.,2014
v2.15

Installation Progress
JobServer -- done
TaskServer -- done
MedeA -- done
Databases -- done
The postinstall script completed successfully
Make
sure
you
scroll
down
to
the
very
bottom
of
the
installer
window
to
see
the
latest
messages.
If

you
activate
other
windows
while
installing,
the
installer
window
may
turn
blank
for
some
time

before
displaying
an
updated
status.
Once
all
components
are
selected,
the
Installation Progress
in

the
installer
window
displays
the
current
status,
followed
by
done
for
successful
installation
of
each

component.

Creating
links
and
shortcuts

Install to Start Menu
Use the following dialog to put shortcuts in the Start Menu so that you can start MedeA and access JobServer
and TaskServer.
On
Linux
you
might
see
a
request
for
your
sudo
password
unless
you
install
as
administrator:
Your

password
will
not
be
shown
(it
appears
as
******).
Click
on
the
Check
button
and
it
turns
into
an

inactive
OK
button
if
the
password
is
correct
and
you
have
sudo
rights.
Otherwise
you
cannot

install
shortcuts
for
all
users.

Please provide your password to use 'sudo' for creation of shortcuts for all users:
Your password: Check
Shortcuts
þ MedeA þ JobServer þ TaskServer þ Maintenance
Location
¨ Desktop
þ Start Menu Folder: Materials Design 2 for ¢ Current User ¤ All Users
Create
In
this
step
the
installer
will
create
shortcuts
and
Start
menu
entries
for
MEDEA.
Please
make
sure
to

create
the
start
menu
entries
(default),
as
this
will
later
be
used
to
configure
and
update
MEDEA®.

• Click
Create
for
and
you
proceed
to
the
next
section.

Setting
up
JobServer
and
TaskServer
as
services

In
the
next
installation
step
you
will
be
asked
if
you
would
like
to
configure
the
JobServer
and

TaskServer
as
system
services
in
order
to
start
automatically
during
the
boot
phase.

Note
that
in
order
to
run
calculations
or
look
at
results
from
calculation
in
your
browser,
you
need

to
start
these
processes
either
as
a
service
or
through
the
Start menu ≫ All
Programs
≫

Materials
Design
2

≫
debugJobServer
/
debugTaskServer
entries.
We
strongly
recommend

that
you
install
and
run
these
processes
as
system
services.

On
Linux
these
two
programs
are
located
in
MD/2.0/JobServer/debugJobServer
and

MD/2.0/TaskServer/debugTaskServer

iii. With
shared
memory
support

The
TaskServer
is
capable
of
running
calculations
on
multiple
cores.
You
have
to
configure
the

number
of
cores
on
its
administration
page: http://localhost:23000/ServerAdmin/manager.tml

MedeA®
User's
Guide

Installation
and
Basic
Operation

v2.15
©
Materials
Design
Inc.,2014

11

Setup JobServer and TaskServer as Services
The JobServer and TaskServer can be run manually, but should be set up as Windows services.
¨ add distributed memory support for cluster
Use the following buttons to set up the services

JobServer and TaskServer (with shared memory support)
Job Server
Task Server (with shared memory support) .
Run TaskServer as user W7medea password ***** Check
iv. With
distributed
memory
support
(WIndows)

If
you
have
a
dedicated
cluster,
you
can
perform
calculations
across
multiple
machines
in

distributed
memory
mode.
Enter
your
password
(obscured
by
*****)
and
press
the
Check
button
to

prepare
your
system
for
doing
so.
You
have
to
finish
the
setup
at

http://localhost:23000/ServerAdmin/manager.tml

Setup JobServer and TaskServer as Services
The JobServer and TaskServer can be run manually, but should be set up as Windows services.
þ add distributed memory support for clusters
For MPI/Windows you need to supply your password to run TaskServer in your name as
user: PCmedea

password: ***** Check
Please enter your password and confirm with the Check button.
Of course you can install and configure MPI yourself, if you don't want to enter your password here.
1. Install smpd:
C://Windows-x86_64/IntelMPI/bin/smpd.exe -install
2. Register mpiexec:
C://Windows-x86_64/IntelMPI/bin/mpiexec.exe -register
3. Change service mdTaskServer to run in your name (and with your password)
Use the following buttons to set up the services

JobServer and TaskServer (distributed memory support)
Job Server
Task Server (distributed memory support)
Run TaskServer as user W7medea password***** Check
Firewall

You
might
see
a
warning
from
your
firewall:
Accept
and
allow
the
Process
manager
service
for

MPI
applications
to
work.
Consult
with
your
IT
administrator
about
implications
for
private
and

public
networks.

The
installer
continues
with
the
proper
installation
of
those
two
services.

• Click
on
Next
a
last
time
to
see

Installation and Setup is Completed
Congratulations! The installation and setup is complete.
Press EXIT to leave the installer.
• Click
on
Exit
to
leave
the
installer.

v. Installing
TaskServers
on
multiple
machines

For
configurations
with
multiple
TaskServers
you
have
to
repeat
the
TaskServer
installation
on

each
machine:

• Perform
a
Custom
Installation
and
select
only
the
TaskServer
component

You
don't
have
to
worry
a
lot
about
keeping
your
MEDEA®
installation
up
to
date
as
you
can
use
the

installed
Maintenance
program
(MDMaintenance)
to
update
from
the
web.
This
will
download
the

current
version
of
modules
and
codes

MedeA®
User's
Guide

Installation
and
Basic
Operation

12
©
Materials
Design
Inc.,2014
v2.15

Configuration
files

Configuration
files
are
not
overwritten
by
any
software
update
–
this
includes
your
license
file

license.txt,
all
.options files,
and
queuing
system
scripts
generated
from
template_X.tcl.

Calculated
results
on
the
JobServer

MEDEA®
stores
results
in
its
MDJobs
database
and
in
the
MD/2.0/Jobs
directory;
backing
up
this

directory
is
sufficient
to
recreate
the
parts
residing
in
the
MDJobs
database
as
well.
Just
perform
a

frequent
backup
of
the
entire
MD
directory
for
peace
of
mind.

Backup

Exclude
the
temporary
MD/2.0/TaskServer/Tasks
directory
from
backups
as
this
directory
contains

often
large
temporary
files.

Hardware
failure

Restoring
a
backup
to
a
new
machine
requires
reimporting
Jobs
for
the
JobServer
(to
recreate
the

MDJobs
database)
and
a
new
license
for
the
GUI.
Please
contact
Materials
Design’s
support
team
for

this
rare
event.

2.

Change
the
TaskServer
to
run
on
multiple
cores

Open
http://localhost:23000/ServerAdmin/manager.tml
on
your
browser
and

• Change
Number
of
Parallel
Cores

• Confirm
with
Apply

TaskServer Home | Tasks | Administration http://medea — v2.15 6/27/14
Users | JobServers | Log
This page allows you to manage the server on this machine. Use the area below to change the
settings of parameters that affect how the server runs.
If you want to stop the server — meaning that no more jobs can be run until it is restarted — use
the button at the bottom of the page.
Parameter Value
Installation Directory C:/MD/2.0
Working Directory C:/MD/2.0/TaskServer
Queue Type
direct One of ‘direct’ or ‘mpi’.You can also use 'PBS', 'LSF' or
'GridEngine' if you set up the appropriate file from the template.
Simultaneous tasks 1 How many tasks to run at once
Port 23000 The port to listen on (default is 23000).
Webmaster sysadmin@local.net
Number of Parallel Cores 4
Workaround fcopy bug þ check to work around a bug that causes file transfers to hang
Save files temporarily
¨ check to keep temporary task directories for debugging. This
is a temporary switch, and will be reset on restarting.
Apply.

Other pages
View and change users
View the log
Reload the Tcl code— needed if the code is changed.
To stop the server, click on the following button. Note that this will terminate all jobs that
are running!

Shutdown the Server.


3.

Verify
automatic
start
of
services
on
Linux

Use
your
Linux
distributions’
administration
tools
to
verify
that
JobServer
or
TaskServer
will
start

automatically
after
reboot.

Check
that
mdjobserver
(if
installed)
starts
automatically

On
REDHAT
systems
the
following
commands
are
important:

chkconfig --list mdjobserver
mdjobserver 0:off 1:off 2:off 3:off 4:off 5:off 6:off
In
this
case
the
mdjobserver
is
not
going
to
start
automatically.
Let's
change
this
for
runlevels
3
and

MedeA®
User's
Guide

Installation
and
Basic
Operation

v2.15
©
Materials
Design
Inc.,2014

13

5:

chkconfig --level 35 mdjobserver on
chkconfig --list mdjobserver
mdjobserver 0:off 1:off 2:off 3:on 4:off 5:on 6:off
Check
that
mdtaskserver
(if
installed)
starts
automatically

chkconfig --list mdtaskserver
mdtaskserver 0:off 1:off 2:off 3:off 4:off 5:off 6:off
In
this
case
the
mdtaskserver
is
not
going
to
start
automatically.
Let's
change
this
for
runlevels
3

and
5:

chkconfig --level 35 mdtaskserver on
chkconfig --list mdtaskserver
mdtaskserver 0:off 1:off 2:off 3:on 4:off 5:on 6:off
On
SUSE
use
the
runlevel
editor
of
YaST.
With
DEBIAN,
UBUNTU,
and
GENTOO
the
installation
of
system

services
is
part
of
installing
mysqld.

4.

Check
firewall
settings
and
allow
connections
for
JobServer
and
TaskServer

If
you
have
a
firewall
in
place,
make
sure
that
the
TaskServer
can
be
reached
from
the
JobServer.

With
iptables
in
place,
the
port
can
be
opened
with
the
following
commands.

iptables -I INPUT -p tcp --dport 23000 -j ACCEPT
You
can
restrict
access
to
the
TaskServer
to
a
single
JobServer
by
specifying
a
network
address:

iptables -I INPUT -p tcp --dport 32000 -j ACCEPT -s <IP of JobServer>
Check
the
current
set
of
rules
in
place
–
and
please
talk
to
your
IT
department:

iptables --list
Chain INPUT (policy ACCEPT)
target prot opt source destination
ACCEPT tcp -- anywhere anywhere tcp dpt:23000
To
keep
the
set
of
rules
working
after
the
next
reboot,
you
need
to
save
them.
This
depends
on

Linux
version
and
specifics
of
your
installation,
for
example
on
REDHAT/Centos/Fedora

/etc/init.d/iptables save
5.

Check
system
limits

Depending
on
model
size
and
type
of
calculation,
VASP
and
LAMMPS
calculations
can
demand

considerable
amounts
of
memory,
especially
when
running
in
parallel
on
shared
memory
machines.

Please
check
whether
the
following
properties
are
large
enough,
you
can
use
ulimit –a in
bash:

• fsize:
maximum
file
size:
should
be
unlimited

• memlock:
maximum
locked-‐in
memory:
80-‐90%
of
total
main
memory

• rss:
maximum
memory
size:
should
be
unlimited

• nofile:
number
of
open
files:
at
least
20
per
core

• stack:
(memory)
stack
size:
80-‐90%
of
total
main
memory

• cpu:
cpu
time
that
can
be
used:
should
be
unlimited

• nproc:
max.
processed
per
user:
set
to
at
least
1000

• as:
virtual
memory:
should
be
unlimited

• locks:
file
locks:
should
be
unlimited

Modify
/etc/security/limits.conf
to
raise
the
impinging
limits
,
here
are
examples:

# End of file
* soft memlock unlimited
* hard memlock unlimited
* soft nofile 10240
* hard nofile 10240
* soft nproc 3153919
* hard nproc 3153919
You
can
replace
*
with
medea
to
limit
those
changes
to
the
TaskServer
running
as
user
medea
.

Remember
to
restart
the
TaskServer
to
use
the
changed
limits.

MedeA®
User's
Guide

Installation
and
Basic
Operation

14
©
Materials
Design
Inc.,2014
v2.15

2.
MedeA
TaskServer
on
multicore
machines

To
run
calculations
with
the
VASP
versions
4.6
and
5,
LAMMPS,
and
GIBBS
in
parallel
Intel
MPI
is

necessary.
This
note
describes
how
to
install
and
configure
Intel
MPI
and
TaskServers
on
Windows

and
Linux
for
32-‐bit
and
64-‐bit
computer
architectures.
MEDEA®
comes
with
Intel
MPI
as
part
of
the

distribution
and
is
normally
installed
by
the
Installer
program.

A
specific
TaskServer
machine
has
to
be
set
up
as
an
"MPI
filter".
This
way
the
TaskServer
serves
as

a
master
node
running
programs
in
parallel
either
in
shared
memory
mode
or
distributed
memory

mode.
In
shared
memory
mode
programs
run
on
multiple
cores
on
one
or
more
multi
processor

machines
(nodes).
With
distributed
memory
additional
machines
(nodes)
are
used
as
"MPI
slaves".

1.

Configure
Intel
MPI
on
Linux

Under
Linux
you
need
to
make
sure
that
the
user
running
the
TaskServer
can
execute
secure
shell

(ssh)
commands
to
execute
commands
on
the
machines
used
in
parallel.
If
you
already
have
ssh
in

place
and
configured,
you
can
skip
this
section.

i. Configuring
Secure
Shell

• Execute
ssh-keygen -t rsa to
generate
your
ssh
key.
You
will
be
asked
a
few
questions.

Use
defaults
for
each
questions
and
do
not
use
a
passphrase!

• Change
into
the
.ssh
directory
and
add
the
public
key
to
the
list
of
authorized
keys

cd ~/.ssh; cat id_rsa.pub » authorized_keys

• The
public
key
must
be
known
at
all
machines
running
mpi:

If
you
use
automount
or
NFS

and
have
a
shared
home
directory,
you
are
done.
Otherwise,
you
need
to
make
ssh
keys
on

each
machine
and
add
them
to
the
authorized_keys
file
and
share
this
file.
Or
just
copy

the
.ssh
directory
to
each
home
directory.

• Make
sure
your
ssh
files
and
directories
have
the
right
permissions:

~/.ssh
should
have
permissions
700 (rwx------), ~/.ssh/authorized_keys
should
have

permissions
600 (rw-------).
You
can
use
the
chmod
command
to
make
sure
the
permissions

are
correct:
chmod 700 ~/.ssh

ii. Install
necessary
Python
packages

Intel
MPI
works
with
scripts
written
in
the
programming
language
Python.
Make
sure
that
on
each

node
used
for
parallel
calculations
the
Python
software
package
and
relevant
extensions
are

installed.

• The
command
to
open
the
Python
interpreter
must
be
in
the
environment
variable
PATH:

ssh <nodename> python
should
return
the
exact
path
where
the
python
command
is
installed

on
the
computer
<nodename>.
Usually
the
command
yields
/usr/bin/python.
If
the
command

returns
python:
Command not found,
then
Python
is
not
installed.
Install
Python
version
2.2
or

higher
on
<nodename>.

• Verify
that
the
version
of
Python
on
each
computational
node
is
version
2.2
or
higher:

ssh <nodename> python -V

• Use
the
package
manager
of
the
Linux
distribution
installed
on
the
computational
nodes
to

check
for
the
presence
of
a
Python
XML
module
such
as
python-xml
or
libxml2-python.
Install

the
missing
module
if
none
of
the
two
packages
are
present.

iii. Check
default
shell:
/bin/dash
versus
/bin/bash

On
some
systems
(like
UBUNTU)
the
default
shell
/bin/sh
is
/bin/dash
–
and
this
breaks
many
scripts

like
mpirun,
part
of
IntelMPI,
which
work
with
/bin/bash
as
default
shell.

2.

Change
the
TaskServer
to
run
on
multiple
cores

• Change
the
Queue
Type
from
“direct”
to
“mpi”.

• Confirm
with
Apply

• Then
fill
in
the
Number
of
Parallel
Cores

MedeA®
User's
Guide

Installation
and
Basic
Operation

v2.15
©
Materials
Design
Inc.,2014

15

JobServer Home | Summary | Jobs | Administration | Documentation http://medea — v2.15 6/27/14
If you want to stop the server — meaning that no more jobs can be run until it is restarted — use
the button at the bottom of the page.
Parameter Value
Log Level notice
Queue Type
mpi One of ‘direct’ or ‘mpi’.You can also use ‘PBS’, ‘LSF’ or
‘GridEngine’ if you set up the appropriate file from the template.
Use https rather than the
less secure http
¨
Number of Parallel cores 8 The maximum number of cores to use in parallel
Workaround fcopy bug ü check to work around a bug that causes file transfers to hang
¨ check to keep temporary task directories for debugging. This is
a temporary switch, and will be reset on restarting.
Apply. •
Other pages
View the log
are running!

MedeA®
User's
Guide

Installation
and
Basic
Operation

16
©
Materials
Design
Inc.,2014
v2.15

C.
Using
the
Materials
Design
Maintenance
Program

The
Materials
Design
Maintenance
program
is
the
single
tool
to
install,
update,
modify
and
repair

your
MedeA
installation.
Depending
on
its
location,
some
options
are
not
available:
Installation

appears
only
on
an
installation
medium,
whereas
updating
requires
MedeA
(or
parts)
to
be
already

installed.

Starting
the
Maintenance
Program

To
start
the
Materials
Design
Software
manager
on
Windows,
select
All
Programs
»

Materials
Design
2
»
Maintenance
from
the
Windows
Start
menu.
On
Linux
the
Materials
Design

Software
Manager
is
the
program
MDMaintenance.x
in
either
MD/Linux-x86_64
or
MD/Linux-x86.

1.
Install
Patches

Patches
allow
you
to
update
databases
or
modify
other
parts
of
MedeA.
Patches
are
normally

downloaded
automatically
during
an
Update
from
the
Web,
so
it
is
not
very
likely
that
you
have
to

install
patches
by
hand.

2.
Manage
Job
server

Provides
an
interface
to
import
entire
job
directories

from
disk.

Use
Import
for
job
directories
from
a
different

JobServer,
job
numbers
will
change.

Reconnect
takes
the
existing
Job
directory
and
(with
an

empty
Job
database)
will
recreate
the
Job
database

keeping
job
numbers.
This
is
used
for
migrating
from
an

older
JobServer.

MedeA®
User's
Guide

Installation
and
Basic
Operation

v2.15
©
Materials
Design
Inc.,2014

17

3.
Manage
Services
(Windows)
or
Manage
Daemons
(Linux):

Allows
you,
with
sufficient
system
privilges,
to
create/remove
and
start/stop
the
automatic
start
of

JobServer
and
TaskServer.
The
lower
right
part
of
the
window
shows
the
current
status
of
the

services
or
daemons.

Welcome to the Materials Design Service Manager, which enables the JobServer and TaskServer to start
automatically
Use the buttons below to control the services.
JobServer: Remove Service Stop Service
TaskServer: Remove Service Stop Service
¨ configure with distributed memory support
If you are running the TaskServer with distributed memory support and your password changes, you have to
‘Reauthenticate MPI services’ to make the mpi daemon and TaskServer aware of your new password.
TaskServerManual: Remove Service Stop Service
Add additional TaskServer with its own queue:
Queuename: Add TaskServer & Queue
CExit
JobServer: running TaskServer: running TaskServerManual: running
Configure
with
distributed
memory
support

is
only
required
in
rare
circumstance
under

Windows,
where
you
have
a
dedicated
network
between
nodes
and
want
to
deploy
MPI
across

nodes.

Additional
TaskServers,
such
as
TaskServerManual,
are
created
with
Add
TaskServer
&
Queue
and

require
a
successful
installation
with
both
JobServer
and
TaskServer
running.
You
can
create
a

secondary
TaskServer,
inheriting
the
options
from
the
initial
TaskServer.

More
details
are
in
I.E.
3.

Registering
additional
TaskServers
with
the
JobServer

4.
Manage
Databases
(Windows
with
MSQL
server)

Check
connection
of
databases
to
the
MSQL
server.
You
can
attach/detach
databases
from
the
MSQL

server
if
they
are
not
currently
used
by
a
program.
If
the
MSQL
server
is
not
running
this

functionality
is
unavailable.

Before
moving
any
database
file
in
C:MDDatabases
you
have
to
detach
them
from
the
SQL
server!

5.
Install
in
Start
menu

creates
shortcuts
for
MEDEA®,
,
JOBSERVER,
TASKSERVER
(if
installed)
in
Start
menu
and
desktop

Desktop
shortcuts
and
menu
entries
on
Linux
require
xdg-utils

6.
Update
from
the
Web
or
Update
Installation

Update
the
installed
MEDEA®
software
from
the
Materials
Design
update
server
or,
if
started
from

the
DVD,
the
current
DVD.
Note
that
your
local
firewall
may
block
the
web
feature
and
you
have
to

open
a
web
proxy.
Detailed
instructions
are
in
I.E.
Updating
an
existing
MedeA®
installation

MedeA®
User's
Guide

Installation
and
Basic
Operation

18
©
Materials
Design
Inc.,2014
v2.15

D.
Adding
Resources
to
your
MedeA®

installation

The
first
Installation
from
the
DVD
guides
you
to
create
a
working
system
on
your
PC:
the
MEDEA®

front
end,
the
JobServer,
and
TaskServer
are
all
installed
and
working
together.
That
is
perfect
for

learning
to
use
the
interface
and
run
the
first
calculations.

Adding
resources
to
your
MEDEA®
installations
can
be
accomplished
in
many
different
ways
and

there
are
a
plenty
of
solutions.
Now
the
separation
into
three
tiers
becomes
obvious
and
in
the

following
section
covers
most
cases:
Adding
another
front
end,
migrating
to
a
bigger
repository
for

Jobs,
and
adding
more
computing
power.

The
clear
separation
into
three
tiers
allows
for
adding
or
changing
components
much
impact
on

ongoing
calculations,
as
a
quick
guideline,
only
the
tier
and
its
neighbor
are
affected.

1.
Adding
another
front
end

Let’s
start
with
a
simple
and
common
procedure,
to
add
second
front
end
on
a
laptop
to
access
the

already
finished
calculations
on
the
existing
MEDEA®
installation.
There
is
no
need
for
a
complete

installation,
as
the
laptop
is
frequently
turned
on
and
off.

Install
from
DVD:

MEDEA®

+
SQL
+
databases

Get
new
license:

C:/MD/2.0/license.txt

Connect
to
JobServer:

Edit
MedeA Preferences
Name IP-address

Copy
environment
settings

~/MedeA2.settings

~/MedeA

Perform
a
custom
installation
without
installing
the
JobServer
and
TaskServer.
You
will
need
to
get

a
license
for
the
new
machine.

Edit
the
servers.dat
file
and
enter
the
fully
qualified
name
or
IP-‐address
of
the
existing
JobServer.

If
you
have
some
custom
additions
to
MedeA,
you
should
copy
the
environment
settings
from
your

home
directory,
abbreviated
as
“~”,
to
the
home
directory
on
the
new
machine.
On
Windows
just

open
a
command
shell
(prompt)
and type %HOMEDRIVE%%HOMEPATH%
to
find
this
directory,
which
is

normally
C:Documents and Settings<Username>.
On
Linux
the
command
cd
or
cd ~
take
you
into
your

home
directory.

MedeA®
User's
Guide

Installation
and
Basic
Operation

v2.15
©
Materials
Design
Inc.,2014

19

2.
Installing
another
JobServer

Adding
another
JobServer
involves
all
three
tiers
as
the
JobServer
is
the
central
piece
of
the
MEDEA®

installation
and
talks
to
the
graphical
front
end
and
the
TaskServers.
The
installation
process
is
split

in
two
parts,
first
to
add
and
test
another
JobServer
without
interrupting
the
running
JobServer.

The
next
section
will
deal
with
replacing
an
existing
JobServer.

Warning:
Do
not
connect
two
or
several
JobServers
to
one
and
the
same
TaskServer.
This
should
be

a
temporary
solution
only
as
the
“faster”
JobServer
uses
available
TaskServer
resources
and
the

queuing
concept
is
ignored.
Even
more
severe
is
that
files
of
running
calculation
might
be

overwritten
and,
hence,
corrupted.

Install
from
DVD:
JobServer

Add
new
JobServer
to

Preferences
Name/IP-Address

Create
Queues

Attach
TaskServer
Name/IP-Address

During
the
custom
installation
select
only
JobServer
and
perform
configuration
as
a
service.

Create
queues
and
attach
TaskServers
as
described
in
section
I.E.
4.
Adding
additional
Queues

Add
the
new
JobServer
(with
File»Preferences»Job
Servers)
to
the
servers.dat
file.

MedeA®
User's
Guide

Installation
and
Basic
Operation

20
©
Materials
Design
Inc.,2014
v2.15

3.
Replacing
the
JobServer

When
planning
to
replace
an
existing
JobServer,
the
previous
procedure
creates
a
new
JobServer,

but
it
leaves
the
need
to
transfer
the
already
computed
results
to
the
new
JobServer
to
have
all

computed
results
in
one
central
place.

Install
from
DVD:
JobServer
Install
from
DVD

Add
new
JobServer
to

Preferences
Name/IP-Address

Create
Queues

Attach
TaskServers
Name/IP-Address

Import
Jobs:
Maintenance

Delete
old
JobServer
in
Preferences
Name/IP-Address

During
the
custom
installation
skip
everything
but
SQL,
JobServer,
and
the
configuration
as
a

service.

Duplicate
your
existing
JobServer
by
creating
the
same
Queues
and
attach
the
existing
TaskServers.

Of
course
you
can
rename
and
change
settings
based
on
the
experience
gained
in
the
meantime.

You
can
use
the
maintenance
tool
to
import
the
Jobs
to
the
new
JobServer,
provided
the
Job

directory
is
accessible
to
both
machines,
for
example
by
sharing
the
directory
on
the
local
network.

The
imported
Jobs
have
to
be
attached
to
a
queue
-‐
this
is
done
with
the
web
interface
of
the

JobServer.

After
testing
and
transferring
you
can
remove
the
entry
of
the
old
JobServer
in
the
file
servers.dat.

The
Job
directory
still
contains
all
the
calculated
results
–
delete
only
after
verifying
that
the
import

worked
exactly
as
planned.

MedeA®
User's
Guide

Installation
and
Basic
Operation

v2.15
©
Materials
Design
Inc.,2014

21

4.
Adding
more
TaskServers

The
most
pleasant
task
is
to
add
more
computing
resources
to
MedeA.

Install
from
DVD:

TaskServer

Add
TaskServer
Name IP-address

Attach
to
Queue

Adapt
Queue_Template.tcl

Install
the
TaskServer
from
DVD
and
create
the
service.

If
feeding
into
a
batch
system,
adapt
the
respective
queue
(batch)
script.

Finally
add
the
TaskServer
to
the
list
of
TaskServers
known
to
the
JobServer
and
attach
to
selected

Queues.

MedeA®
User's
Guide

Installation
and
Basic
Operation

22
©
Materials
Design
Inc.,2014
v2.15

E.
Updating
an
existing
MedeA®

installation

You
can
update
your
version
of
MEDEA®
using
an
installation
medium
(DVD)
or
via
the
Internet.

Updating
MEDEA®
will
not
affect
any
of
your
saved
settings,
results,
and
other
user
data.

1.
Update
from
DVD

To
update
from
DVD,
insert
the
DVD
to
bring
up
the
Software
Manager
and
select

Update
existing

MEDEA2.
The
instructions
that
follow
are
very
similar
to
what
is
described
below
for
the
Internet

update.

2.
Update
from
the
Internet

To
update
via
the
Internet
you
will
need
password
access
to
the
Materials
Design
Update
server.
If

you
haven’t
received
a
password
yet,
send
an
email
to
support@materialsdesign.com
to
receive
the

update
credentials
(username
and
password).

•
Bring
up
the
MEDEA®
Software
Manager
by
clicking
on
(Windows)
Start
Menu
≫
All

Programs
≫
Materials
Design
2
≫
Maintenance

•
In
the
MEDEA®
Software
manager
click
Update
from
the
web

Materials Design Updater
Welcome to the Materials Design Updater, which will update MEDEA 2 along with its associated software and
databases.
Select the server below (or type in the name if it is not in the list) and click the "Update" button to
update your installation to the latest version
Update server: http://update.materialsdesign.com Update
•
Click
on
Update
to
continue

In
the
pop
up
dialogue
enter
as
Username
your

user-‐ID
or
email
address
and
provide
your

password,
then
click
OK.

If
you
haven’t
received
a
password
yet,
send
us

mail
to
support@materialsdesign.com
to
receive

appropriate
update
credentials
for
the
customers

sections
of
our
website
and
update
server.

You
can
always
retrieve
or
change
your

password
on

www.materialsdesign.com/user/password.

The
Updater
will
compare
your
current
installation
with
the
MEDEA®
disk
image
on
the
Materials

Design
update
server.
This
process
may
take
a
couple
of
minutes.

Examining the installation. This will take a minute or two...
If
there
is
a
more
recent
version
of
the
updater,
the
following
message
appears
in
a
pop-‐up
window:

There is a new version of the installer.
Do you wish to update it first (recommended)?:
Yes No
Confirm
with
Yes
to
get
the
Maintenance
program
up
to
date
first.

Click continue to actually update the installer.
Continue Exit
Getting the following files:
./Windows-x86/MDMaintenance.exe Setup.exe -- 211 changes applied.
Updating the packing list...done.
Checking maintenance shortcuts...
The… update is complete.
Finish
You
need
to
close
and
re-‐open
the
maintenance
program
if
the
Updater
itself
was
updated.

Repeat
steps
1-‐3
above
to
continue
the
update.

The
Updater
displays
the
latest
version
number
(here
2.15)
followed
by
the
release
notes
and
a

listing
of
changed
files,
new
files,
and
extra
files.
Click
each
button
to
display
or
hide
the

corresponding
listing.
Note
that
the
number
and
type
of
files
displayed
depends
on
your
current

version
of
MEDEA®
and
may
therefore
differ
from
the
listing
displayed
below.

Click
Continue
to
proceed
with
the
update

MedeA®
User's
Guide

Installation
and
Basic
Operation

v2.15
©
Materials
Design
Inc.,2014

23

The newest version is 2.15
There are 1 changed files, 18 new files and 0 extra files.
Show changed files
Show new files
Show extra files
Click continue to actually update your installation. Don't worry! I will not delete any files without your
permission.
Continue Exit
Getting the following files:
./2.0/Manual.pdf…:
…
Updating the packing list...done.
Checking maintenance shortcuts...
The update is complete.
Finish
Follow
the
progress
of
your
update
in
the
installer
window.
If
the
Installer
announces
the
download

of
patches
e.g.
for
the
databases,
follow
the
instructions
to
install
the
patches.
In
most
cases
the

installer
will
simply
update
a
number
of
files

Click
Exit
to
terminate
the
Updater
once
the
update
is
complete

Working
with
multiple
Queues

3.
Registering
additional
TaskServers
with
the
JobServer

In
order
to
have
the
JobServer
send
computational
tasks
to
TaskServers
other
than
your
default

machine
you
need
to
register
these
machines
with
the
JobServer.
In
the
following
we
assume
you

have
successfully
installed
the
TaskServer
on
a
machine,
i.e.
the
page
http://<taskserver>:23000
is

accessible
by
a
standard
web
browser,
with
<taskserver>
a
placeholder
for
your
actual
IP
address

or
machine
name.

On
the
JobServer
administration
page
click
the
TaskServer
link
in
the
blue
navigation
bar.
On
the

following
page
(see
below)
type
in
a
name
for
the
TaskServer
and
the
network
address
of
the

machine
running
it:

In
the
below
example
we
have
registered
two
machines,
“local”
and
“workstation”.

•
Use
the
Check
button
to
check
if
the
TaskServer
machine
is
reachable
from
the
JobServer

•
Click
Change
to
modify
any
of
the
settings
for
a
TaskServer
or
to
make
it
Active/Inactive

Manage TaskServers | Queues | TaskServers | Users | Log
This page allows you to manage the Task Servers this Job Server uses.
Add Task Server
Use this section to add a new task server. The name is a convenient description that is used
just for display. The url should have the form http://<machine or ip address>:port. By default,
task servers listen on port 23000.
Name:
URL: http://<machine>:23000 Add
Name URL Active Status
Local http://localhost:23000 ✓ up Check Change
Workstation http://workstation:23000 ✓ up Check Change
Note
that
Linux
machines
may
have
difficulties
recognizing
Windows
machines
in
a
heterogeneous

network.
This
is
a
network
configuration
issue
and
is
not
influenced
by
the
way
MEDEA®
handles

TaskServers.
A
simple
test
to
make
sure
your
network
is
set
up
correctly
is
to
use
the
ping

command
to
check
if
the
two
machines
can
“see”
each
other.

4.
Adding
additional
Queues

When
submitting
a
job
through
the
MEDEA®
interface
you
are
asked
to
choose
a
queue.

A
queue
is

simply
a
group
of
TaskServers.
The
JobServer
uses
queues
to
let
you
control
where
and
how
to
run

your
jobs.

The
JobServer
interface
lets
you
define
queues
and
attach
TaskServers
to
it.
To
define
and
edit

MedeA®
User's
Guide

Installation
and
Basic
Operation

24
©
Materials
Design
Inc.,2014
v2.15

queues
click
on
the
Administration
link
in
the
JobServer
Home
page.
Next
select
Queues
from
the

blue
navigation
bar
to
bring
up
the
servers
queue
admin
page
(see
example
below).

To
define
a
new
queue,
fill
out
the
text
fields
at
the
bottom
and
click
Add
Queue

In
the
below
example
we
have
defined
4
queues
with
varying
attributes.
Besides
the
default
local

queue,
we
have
set
up
a
queue
for
a
parallel
system
with
8
processors
(parallel)
,
a
slow
queue

(Slow)
and
a
fast
queue
(Fast).
In
the
following
we
will
attach
TaskServers
to
these
queues.

Note
that
queues
are
just
named
groups
of
TaskServers!
To
have
a
queue
behave
in
a
certain
way,

you
need
to
configure
a
TaskServer
correspondingly
and
attach
it
to
the
queue!

Click
on
the
Change
button
on
the
right
of
a
given
queue’s
row
to
configure
the
queue
and
to
attach

TaskServers
to
the
selected
queue.

http://localhost:32000/ServerAdmin/queues.tml

The
default
installation
creates
a
local
queue,
Jobs
are
processed
in
the
sequence
they
are
submitted

to
the
JobServer.
By
creating
different
queues
(such
as
Fast
and
Slow),
jobs
in
the
Fast
queue
have
a

higher
priority
over
jobs
in
the
slow
queue.

JobServer Home | Summary | Jobs | Administration | Documentation
http://medea — v2.15
6/27/14
Queue Description
Default
Priority
Number of
Cores
Number of
Jobs
Is
Active
local ONumber of Jobserver 5 1 1 ✓ Change
parallel mpi queue 5 8 1 ✓ Change
Fast Short Jobs 15 1 2 ✓ Change
Slow Big Jobs 2 1 4 ✓ Change
5 1 1 ✓ Add Queue
JobServer Home | Summary | Jobs | Administration | Documentation
http://medea — v2.15
6/27/14
5.
Attaching
a
TaskServer
to
a
Queue

In
the
following
we
assume
you
have
installed
one
or
more
TaskServers,
you
have
registered
them

with
the
JobServer
and
you
have
defined
one
or
several
Queues.

Now
all
that
is
left
is
to
tell
the

JobServer
which
Queue
you
want
feed

the
TaskServer.

In
the
present
example
we
have
registered
a
TaskServer
machine
called
workstation.
Before
we
can

use
it
though,
we
need
to
attach
it
to
a
queue.

To
reach
the
Queue
admin
page
(see
above),
click
Job
Control
≫
View
and
Control
Jobs
in
MEDEA,

then
click
Administration
and
on
the
next
screen
Queues
(blue
navigation
bar).
On
the
Queue

admin
page
click
the
Change
button
next
to
the
Queue
you
would
like
to
edit
and
you
will
get
to

below
page

•
In
the
upper
section
of
this
page
you
can
review
and
change
the
attributes
of
the
queue.
In

the
lower
half,
you
need
to
define
which
TaskServer
to
attach
to
the
queue.

In
the
table
labeled
TaskServer
(marked
in
green)
select
workstation
and
click
Add.

Note
that
the

status
of
the
button
changes
from
Add
to
Remove
once
you
have
added
a
TaskServer.

Note
that
present
in
the
list
are
only
those
TaskServers
which
were
previously
registered
with
the

JobServer.
In
other
words
the
JobServer
does
not
know
about
a
TaskServer
machine
until
you

register
it.

MedeA®
User's
Guide

Installation
and
Basic
Operation

v2.15
©
Materials
Design
Inc.,2014

25

Manage TaskServers | Queues | TaskServer | Users | Log
Edit the 'parallel' queue
Item Value
Queue parallel
Description MPI queue
Default Priority 5
Number of cores 8
Number of Jobs 1
Is Active ✓
Reset Update
Task servers used by the queue
The following table shows the task servers connected to this queue. You may remove any task
server by pressing the Remove button. If there are other task servers available, you can select
one or more to add in the last row of the table and then press the Add button.
TaskServer
local Remove
workstation Add
Manage TaskServers | Queues | TaskServer | Users | Log

MedeA®
User's
Guide

Installation
and
Basic
Operation

26
©
Materials
Design
Inc.,2014
v2.15

F.
TaskServer
administration
and
configuration

The
MEDEA®
TaskServer
gives
you
a
number
of
options
how
to
run
your
computational
tasks,
e.g.

you
can
choose
to
run
serial,
parallel
or
through
a
queuing
system
or
you
can
limit
the
number
of

CPUs
used
on
a
specific
TaskServer
machine.
This
section
describes
what
options
are
available
to

configure
how
task
are
run.

In
the
following
we
assume
that
a
TaskServer
was
installed
and
can
be
contacted
through
the
links

JobServer
Home
»
Administration
»
Task
Servers
or
directly
through
the
link

where
you
need
to
use
the
name
of
your
machine
instead
of

<task_server>.

Both
links
should
open
the
following
page:

Materials
Design
Task
Controller
on
MEDEA

This is the home page for the task controller running on medea, port 23000. This page, and all
of the other pages in this site, has the same navigation bars at the top and bottom of the
window. You can use these to quickly move from one part of the task controller to another.
The links take you to other parts of the task controller as follows:
TaskServer Home
Brings you back to this page. You can always come back here if
you get lost.
Tasks
Provides information on the tasks currently running. You can
look at their files, etc. Please remember that a task is deleted
when it completes, so if you get an error about "file not found"
it probably means that the task completed.
Administration
Allows you to administer this site. You can change the port,
shut the task controller down, etc.
There is 1 task running of 1 allowed.

Click
on
the
Administration
link
in
the
green
navigation
bar
to
proceed
to
the
page
with
TaskServer

configuration
options:

MedeA®
User's
Guide

Installation
and
Basic
Operation

v2.15
©
Materials
Design
Inc.,2014

27

Users | Log
If you want to stop the server — meaning that no more jobs can be run until it is restarted —
use the button at the bottom of the page.
Parameter Value
Queue Type
mpi One of ‘direct’ or ‘mpi’.You can also use
‘PBS’, ‘LSF’ or ‘GridEngine’ if you set up the appropriate file from
the template.
Log level notice
Number of parallel cores 1
Workaround fcopy bug ü check to work around a bug that causes file transfers to hang
¨ check to keep temporary task directories for debugging. This is a
temporary switch, and will be reset on restarting.
Apply.
Other pages
View the log
are running!
Users | Log

The
Working
Directory
is
where
the
TaskServer
writes
temporary
files.
This
is
just
a
scratch
area
as

all
relevant
data
are
exported
back
to
the
JobServer
upon
completion
of
tasks.

The
Queue
Type
determines
the
way
the
executables
of
VASP.
LAMMPS,
and
GIBBS
will
run
by
the

TaskServer.
The
following
options
exist:

• direct
–
uses
MEDEA’s
queues
and
serial
executables,
on
Windows
also
shared
memory

• mpi
–
uses
Intel
mpi
included
in
MEDEA®
to
run
parallel
jobs
in
shared
memory
mode.
Works

with
LAMMPS,
GIBBS,
VASP.

• PBS,
LSF,
GridEngine,
etc.
–
expects
a
file
<template>.tcl
in
the
directory

<md_install_dir>2.0TaskServerTools<code>.
Currently,
templates
for
t
VASP4.6.X,

VASP5.X,
LAMMPS,
and
GIBBS
exist
for:

• PBS
(Linux):
works
with
PBS,
OpenPBS,
or
Torque

• LSF
(Windows/Unix/Linux)

• GridEngine

• Windows-‐HPC:
supports
Windows
HPC
–
requires
a
different
set
of
executables

• manual:
supports
running
on
remote
systems
with
manual
transfer

Attention:
MEDEA®
does
not
include
any
of
the
above
queuing
systems.
You
need
to
install,

configure,
and
manage
external
queuing
systems
like
PBS
or
LSF

–
and
we
rely
on
you
to
properly

administer
them.

In
order
to
run
e.g.
with
PBS,
copy
the
file
template_PBS.tcl
to
PBS.tcl
and
set
the
queue
type
to
PBS

in
the
TaskServer
Administration
page.
The
file
PBS.tcl
provides
a
number
of
parameters
that
can

be
set
to
adapt
the
script
to
your
local
environment.
The
script
has
to
be
created
for
each
of
the

used
computing
codes,
allowing
using
different
queues
and
other
settings
for
a
specific
code.

Choose
the
number
of
Simultaneous
task
such
that
there
is
no
more
than
one
tasks
per
processors.

If
the
TaskServer
machine
is
also
in
interactive
use,
consider
leaving
at
least
one
CPU
available.

Manual

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