"Subclassing and Composition – A Pythonic Tour of Trade-Offs", Hynek Schlawack
User-friendly Metaworkflows in Quantum Chemistry
1. User-‐friendly
metaworkflows
in
quantum
chemistry
Alexander
Hoffmann,
Sonja
Herres-‐Pawlis,
Sandra
Gesing,
Luis
de
la
Garza,
Jens
Krüger,
and
Richard
Grunzke
sandra.gesing@nd.edu
Science
Gateway
InsKtute
Workshop
September
27,
2013,
Indianapolis,
Indiana
2. MoKvaKon
• Excellent
simulaKon
codes
available
• Huge
amount
of
computaKonal
resources
• Time
consuming
access
even
for
experienced
users
• Impassable
obstacle
for
beginners
Sandra
Gesing
User-‐friendly
metaworkflows
in
quantum
chemistry
2
3. Aims
of
MoSGrid
Molecular
SimulaKon
Grid
• Enabling
easier
access
to
DCIs
• Allowing
inexperienced
scienKsts
to
run
molecular
simulaKons
on
DCIs
• Offering
an
intuiKve
user
interface
(gateway)
• Enabling
easy
access
to
workflows
and
data
repositories
Sandra
Gesing
User-‐friendly
metaworkflows
in
quantum
chemistry
3
4. MoSGrid
in
a
Nutshell
Portal
WS-‐PGRADE
Liferay
Structure
Recipe
Workflow
Result
User-Input
Coordinates
(xyz/pdb)
Portal
Grid
Ressource
Multiplicity/
Charge
Job Type
#CPU/
Memory
High-‐level
middleware
service
level
gUSE
Job Creation
input.gjf
g09
gaussian.log
Distributed
File
System
XtreemFS
Result
Sandra
Gesing
User-‐friendly
metaworkflows
in
quantum
chemistry
DCIs
UNICORE
6
4
5. Data
Repository
•
Repository
consists
of
data
and
metadata
storage
•
MSML
(Molecular
SimulaKon
Mark-‐up
Language)
•
Subset
and
extension
of
CML
(Chemical
Mark-‐up
Language)
•
Unified
data
representaKon
for
molecules,
macromolecules
and
recipes
•
Parsers
and
adapters
used
for
conversions
to
and
from
MSML
Repository
convert
from
MSML
Sandra
Gesing
convert
to
MSML
and
index
User-‐friendly
metaworkflows
in
quantum
chemistry
5
6. Use
of
Workflows
in
Domains
• Quantum
Chemical
CalculaKons
• Based
on
approximated
soluKons
of
the
Schrödinger
equaKon
• Average
scalability
• Gaussian,
NWChem,
…
• Molecular
Dynamics
• based
on
forcefields
describing
molecular
interacKons
• Good
scalability
• Gromacs,
NWChem,
MD-‐eSBM-‐Tools…
• Docking
• Based
on
simplified
forcefields
• Excellent
scalability
• CADDSuite,
FlexX,
Autodock
Vina…
Sandra
Gesing
User-‐friendly
metaworkflows
in
quantum
chemistry
6
8. The
QC
Portlet
@
Mosgrid.de
• Specialised
interface
for
quantum
chemistry
sojware
• Basic
workflows
• Easy
GeneraKon
or
Uploading
of
Input
Files
• Parsing
of
result
files
Sandra
Gesing
User-‐friendly
metaworkflows
in
quantum
chemistry
8
9. The
QC
Portlet
@
Mosgrid.de
Sandra
Gesing
User-‐friendly
metaworkflows
in
quantum
chemistry
9
10. The
QC
Portlet
@
Mosgrid.de
Sandra
Gesing
User-‐friendly
metaworkflows
in
quantum
chemistry
10
11. Example:
Parameter
Sweep
PES
file
• Parameter
Sweep
– Scan
of
a
potenKal
energy
surface
(PES)
– Change
of
one
parameters
crucial
for
theoreKcal
analysis
– ReacKon
path
analysis
– Pre-‐defined
steps
Sandra
Gesing
Parameter
range
Converter
X-‐ray
X-‐ray
(ins
X-‐ray
File)
(ins
X-‐ray
FF
(ins
ile)
file
Input
(ins
ile)
File)
• Input
– Molecular
structure
– Parameter
– Parameter
range
• First
step
– AutomaKc
generaKon
of
input
files
QC
code
X-‐ray
X-‐ray
(ins
X-‐ray
File)
(ins
X-‐ray
FF
(ins
ile)
file
(ins
ile)
File)
Output
• Second
step
– Submission
into
the
grid
• Third
step
Postprocessor
X-‐ray
X-‐ray
(ins
X-‐ray
FF
ile)
(ins
X-‐ray
(ins
ile)
plot
FFile)
Result
(ins
ile)
User-‐friendly
metaworkflows
in
quantum
chemistry
– Plomng
of
obtained
energies
against
the
chosen
parameter
11
12. Example:
High-‐Throughput
X-ray
X-ray
X-ray
(ins X-ray
File)
– NaKve
X-‐ray
format
needs
to
be
converted
into
a
computaKonal
readable
mol
file.
– Time-‐consuming
process
of
manual
conversion
can
be
transferred
into
the
portlet.
(ins X-ray
(insFile)
(insFile)
(insFile)
File)
Converter
X-‐ray
X-‐ray
(ins
X-‐ray
File)
(ins
X-‐ray
FF
(ins
ile)
le
Mol
fi
(ins
ile)
File)
• Input
– X-‐ray
data
• First
step
– Conversion
into
mol
file
• Second
step
Converter
X-‐ray
X-‐ray
(ins
X-‐ray
File)
(ins
X-‐ray
FF
(ins
ile)
file
Input
(ins
ile)
File)
– Conversion
into
job
file
with
pre-‐defined
job
parameters
(funcKonal,
basis
set)
• Third
step
QC
code
– Submission
into
the
grid
X-‐ray
X-‐ray
(ins
X-‐ray
File)
(ins
X-‐ray
FF
(ins
ile)
file
Output
(ins
ile)
File)
Sandra
Gesing
User-‐friendly
metaworkflows
in
quantum
chemistry
12
13. Example:
TransiKon
State
Analysis
• Zinc
complex
reacKng
with
lacKde
135
111
0
Sandra
Gesing
User-‐friendly
metaworkflows
in
quantum
chemistry
13
14. Example:
TransiKon
State
Analysis
• Input
TS
Input
file
– TransiKon
state
job
file
(e.g.
QST3
file)
QC
code
• First
step
– CalculaKon
of
TS
geometry
TS
geometry
• Second
step
Converter
Frequency
Input
file
QC
code
QC
code
Frequency
Output
Sandra
Gesing
IRC
Input
file
IRC
Output
– Conversion
into
job
files
for
frequency
and
IRC
calculaKons
• Third
step
– CalculaKon
of
frequency
and
reacKon
path
User-‐friendly
metaworkflows
in
quantum
chemistry
14
15. Example:
Spectroscopic
Analysis
Structure
Time-‐dependent
Density
FuncKonal
Theory
λ / nm
1200900
4
8.0x10
600
300
BP86
PW91
TPSSh
B3LYP
PBE0
CAM-B3LYP
wB97xd
BHLYP
4
4.0x10
0.0
2
4
6
E / eV
Orbital
analysis
Sandra
Gesing
User-‐friendly
metaworkflows
in
quantum
chemistry
15
17. Example:
Spectroscopic
Analysis
Metaworkflow
Freq
WF
Sandra
Gesing
Opt
W
F
F
Opt
W
TD
WF
Pop
WF
User-‐friendly
metaworkflows
in
quantum
chemistry
Solv
WF
17
19. Coarse-‐grained
WF
Interoperability
Workflow
system
A
Workflow
editor
A
WF
A
DCI
A
Workflow
system
B
Workflow
editor
B
WF
B
Sandra
Gesing
DCI
B
User-‐friendly
metaworkflows
in
quantum
chemistry
19
20. Coarse-‐grained
WF
Interoperability
Workflow
system
A
Workflow
editor
A
WF
A
Meta
WF
WF
B
DCI
A
Meta
WF
WF
B
Workflow
system
B
Workflow
editor
B
WF
B
Sandra
Gesing
DCI
B
User-‐friendly
metaworkflows
in
quantum
chemistry
20
21. Fine-‐grained
WF
Interoperability
Workflow
system
A
Workflow
editor
A
WF
A
DCI
A
Workflow
system
B
Workflow
editor
B
WF
B
Sandra
Gesing
DCI
B
User-‐friendly
metaworkflows
in
quantum
chemistry
21
22. Fine-‐grained
WF
Interoperability
Workflow
system
A
Workflow
editor
A
WF
A
DCI
A
Convert
to
type
A
Workflow
system
B
Workflow
editor
B
WF
B
Sandra
Gesing
DCI
B
User-‐friendly
metaworkflows
in
quantum
chemistry
22
23. Workflows
in
Quantum
Chemistry
• Applica'on
at
the
QC
codes
implemented
in
MoSGrid:
ü Gaussian
ü NWChem
• Great
help
for
users
(via
standard
recipes
in
the
repository)
• Possibility
to
generate
own
complex
workflows
• FacilitaKon
of
data
extracKon
and
postprocessing
• Meta-‐workflows
allow
re-‐use
of
basic
workflows!
Sandra
Gesing
User-‐friendly
metaworkflows
in
quantum
chemistry
23
24. Sustainability
MoSGrid
(ended
31.12.2012)
but
partners
parKcipate
in
SCI-‐BUS
(SCIenKfic
gateway
Based
User
Support)
•
EU
project
01.10.2011
–
30.09.2014
•
Extension
of
the
MoSGrid
portal
with
an
interacKve
molecule
editor
based
on
WebGL
and
a
semanKc
search
ER-‐flow
(Building
an
European
Research
Community
through
Interoperable
Workflows
and
Data)
•
EU
project
01.10.2012
–
30.09.2014
•
IntegraKon
of
applicaKons
in
SHIWA
simulaKon
plaqorm
•
Study
of
data
exchange
between
workflow
systems
•
Community
management
Sandra
Gesing
User-‐friendly
metaworkflows
in
quantum
chemistry
24
25. Acknowledgements
München,
LMU
• Sonja
Herres-‐Pawlis
• Alexander
Hoffmann
Tübingen,
BioinformaIcs
• Oliver
Kohlbacher
• Jens
Krüger
• Luis
de
la
Garza
Berlin,
Zuse
InsItut
• Thomas
Steinke
• Patrick
Schäfer
Dresden,
ZIH
• Ralf
Müller-‐Pfefferkorn
• Richard
Grunzke
Köln,
RRZK
• Lars
Packschies
• MarKn
Kruse
Sandra
Gesing
MTA
SZTAKI,
Computer
and
AutomaKon
Research
InsKtute,
Budapest
Centre
for
Parallel
CompuKng,
University
of
Westminster,
London
User-‐friendly
metaworkflows
in
quantum
chemistry
25
