Chem Compute Science Gateway for Undergraduates. Mark J. Perri, M.S. Reeves, R.M. Whitnell

Transcription

1 Chem Compute Science Gateway for Undergraduates Mark J. Perri, M.S. Reeves, R.M. Whitnell

2 Chemcompute.org Computational Chemistry GAMESS (Quantum) TINKER (MD)

3 About Sonoma State University One of 23 California State Universities PUI (Primarily Undergraduate University) No Chemistry Graduate Program No resources for computational chemistry

4 Gateway Goals Provide Accessibility to Undergraduates Free Accessible from anywhere Dorm room (Run jobs before lab!) Other countries Personal device in lecture

5 International Usage

6 Road Map 1. Use in Undergraduate Curriculum 2. Barriers to Computational Chemistry 3. Student Comments

7 Computational Chemistry Calculate properties and visualize molecules Essential to Undergraduate Curriculum

8 Use in Curriculum General Chemistry Molecular Orbital Theory Bonding Organic Chemistry Reactivity Selectivity

9 Use in Curriculum Physical Chemistry Wave functions Spectroscopy y 1 if = e sinj 2p a 3/ 2 o r a o e -r 2 a o

10 Use in Curriculum Inorganic Chemistry Group Theory Biochemistry Binding Visualizations

11 Road Map 1. Use in Curriculum 2. Barriers to Computational Chemistry 3. Student Comments

12 Barriers to Access at PUI 1. Hardware 2. Software 3. Curriculum Materials

13 Barriers to Access at PUI 1. Hardware Server hardware is expensive Computer labs not convenient

14 Hardware: Original Configuration Web Hosting: Single core VM donated by SSU Compute nodes: four HP desktops

15 Usage Follows Class Calendar Jobs Sep-16 Dec-16 Mar-17 Jun-17 Sep- 17 Dec-17 Mar-18 Month

16 Hardware: Original Configuration Web Hosting: Single core VM donated by SSU Out of Memory! Compute nodes: four HP desktops 100% Usage, heating up lab! XSEDE to the rescue! (TG-CDA170003)

17 Hardware: XSEDE Configuration Web Hosting: Jetstream Current: Single VM (Django) Future: Load Balancing (openstack)

18 Hardware: XSEDE Configuration Compute Nodes (Short Jobs) Jetstream: Virtual Private Cluster Typical Job: 1 core, 10 minutes Short Queue Time Openstack scaling 1 10 nodes Majority of Jobs run on Jetstream

19 Hardware: XSEDE Configuration Compute Nodes (Long Jobs): Comet Bridges Minority of Jobs run on Comet/Bridges Redundancy: important for scheduled labs

20 Web Framework Django (2.0) / Python 3 Celery (task queue) RabbitMQ (message queue) Web Server runs Slurm Client

21 Barriers to Access at PUI 2. Software Easy to use software is expensive Free software requires computer expertise Generating input file too much for undergraduates

22 Students hate the terminal

23 Students hate the terminal

24 Barriers to Access at PUI 2. Software / Graphical Interface Typical Run: Compute Molecular Orbitals for benzene ( Where are the electrons? )

25 Generate Input File Draw molecule Transfer 2D to 3D Or: Search database for molecule (JSME / DIY molecules / JSmol)

26 Generate Input File Symmetrize and Align Molecule for GAMESS D6h C H

27 Generate Input File (Work in progress) (CH5M3D)

28 TODO: Improve User Experience SGCI Incubator Consulting Paul Parsons Christopher Watkins Stephanie Knab I m not great with CSS

29 Output Undergraduates don t like to wait Resubmit jobs if it takes too long Get intermediate output to user ASAP

30 Intermediate Output Helper script on compute node Extract atom coordinates Transfer coordinates to user Download full output when job is finished

31 Visualization of Output File Students don t like to read output files JSmol Cclib / uvspecgen / mpld3 / d3

32 Suggestions for Common Errors Parsed by Django

33 Visualization of MD Output

34 Barriers to Access 3. Lab Exercises Few web repositories Instructions specific to software package / version

35 Barriers to Access Chem Compute: Built-in Experiments On-screen Instructions Work in Progress

36 Road Map 1. Use in Curriculum 2. Barriers to Computational Chemistry 3. Student Comments

37 Personal Observations from Class Use All students completed experiments Students feel comfortable using a website

38 Personal Observations from Class Use All students completed experiments Students feel comfortable using a website Individual Project Molecules related to research Many required several hours

39 Personal Observations from Class Use All students completed experiments Students feel comfortable using a website Individual Project Molecules related to research Many required several hours Exposes many misconceptions

40 Student Misconceptions I thought a 4d orbital was in 4-D

41 Student Misconceptions I thought a 4d orbital was in 4-D I didn t know what a node was

42 Student Misconceptions I thought a 4d orbital was in 4-D I didn t know what a node was I didn t understand constructive interference

43 Student Comments I didn t think I was good at computers

44 Student Comments I didn t think I was good at computers I love that there s so much math in orbitals!

45 Student Comments I didn t think I was good at computers I love that there s so much math in orbitals! I wish I used this in Organic

46 Student Comments I didn t think I was good at computers I love that there s so much math in orbitals! I wish I used this in Organic I liked the ability to see the orbitals and move the molecules around

47 Student Comments I didn t think I was good at computers I love that there s so much math in orbitals! I wish I used this in Organic I liked the ability to see the orbitals and move the molecules around Can I use this in my research too?

48 Student Comments (P-Chem) PRE POST I feel confident using computers to solve chemical problems I felt that the computer lab assignment was engaging In this course, my instructor enables me to participate actively in learning My instructor stimulates interest in the course

49 Student Comments (Gen Chem) PRE POST I feel confident using computers to solve chemical problems I felt that the computer lab assignment provided deeper insight 4.1 The web interface made computational experiments approachable for me. 3.8 I feel engaged in this course In this course, my instructor enables me to participate actively in learning My instructor stimulates interest in the course

50 Use in Research Undergraduate Honors Thesis Binding of Acetylcholine to a polymer 12,600 CPU Hours

51 Use in Research Students in Indonesia Binding of methanol to bio molecules Few thousand CPU hours

52 Science Gateways Community Institute Extended Developer Support Sudhakar Pamidighantam, Eroma Abeysighe, Marcus Christie, Suresh Marru, Marlon Pierce Incubator Consulting Paul Parsons, Christopher Watkins, Stephanie Knab

53 Acknowledgements Melissa Reeves, Rob Whitnell Jeremy Fischer Sonoma State University (RSCAP, EEE) XSEDE Science Gateway TG-CDA Perri MJ, Weber SH (2014) J. Chem Ed doi: /ed