Rename python module and write first logbook

Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>

log/logbook_RR.md

+<!-----------------------------------------------------------------------------
+This document should be written based on the Github flavored markdown specs:
+https://github.github.com/gfm/
+It can be converted to html or pdf with pandoc:
+pandoc -s -o logbook.html  -f gfm -t html logbook.md
+pandoc test.txt -o test.pdf
+or with the kramdown converter:
+kramdown --template document  -i GFM  -o html logbook.md
+
+If checked in as part of a github project html is automatically generated if
+using the github web interface.
+
+Optional: Document how much time was spent. A simple python command line tool
+for time tracking is [Watson](http://tailordev.github.io/Watson/).
+------------------------------------------------------------------------------>
+
+<!-----------------------------------------------------------------------------
+The Agenda section is a scratchpad area for planning and Todo list
+------------------------------------------------------------------------------>
+# Agenda
+
+* Fix prioritaze_vector_ops transformation
+* Reuse same expressions
+* Create variables to accumulate forces (reduction)
+* Provide a way to express simulation specific kernels (cell lists, PBC, neighbor lists) in a more clean way with new syntax
+* Runtime functions (VTK printing, read and write to files)
+* GPU support
+* LLVM support
+* OpenMP support
+* MPI support
+* waLBerla as backend
+* LAMMPS as backend (?)
+* Provide test cases (LJ, EAM, DEM, Configurational Forces + Energy Minimization, ...)
+* Separate performance strategies from code (parallelism, gathering), allow to experiment different strategies
+* Coupling interfaces
+* Many-body potentials code generation?
+* Long-range forces?
+
+<!-- ![Plot title](figures/example.png "ALT Text") -->
+
+<!-----------------------------------------------------------------------------
+START BLOCK PREAMBLE -  Global information required in all steps: Add all
+information required to build and benchmark the application. Should be extended
+and maintained during the project.
+------------------------------------------------------------------------------>
+# Project Description
+
+* Start date: DD/MM/YYYY
+* Ticket ID:
+* Home HPC center:
+* Contact HPC center:
+   * Name: Rafael Ravedutti Lucio Machado
+   * Fon: +49 9131 85 67296
+   * E-Mail: rafael.r.ravedutti@fau.de
+
+<!-----------------------------------------------------------------------------
+Formulate a clear and specific performance target
+------------------------------------------------------------------------------>
+## Target
+
+Performance analysis of the MD-Bench, a molecular dynamics mini-app based on miniMD. The main goal is to provide a performance model for molecular dynamics and evaluate the performance for different strategies on different targets.
+
+<!-----------------------------------------------------------------------------
+## Customer Info
+
+* Name: <CUSTOMERNAME>
+* E-Mail: john.doe@foo.bar
+* Fon: <PHONENUMBER>
+* Web: <URL>
+------------------------------------------------------------------------------>
+
+## Application Info
+
+* Name: PAIRS
+* Domain: Particle Simulations
+* Version: 0.0.1
+
+<!-----------------------------------------------------------------------------
+All steps required to build the software including dependencies
+------------------------------------------------------------------------------>
+## How to build software
+
+<!-----------------------------------------------------------------------------
+Describe in detail how to configure and setup the testcases(es)
+------------------------------------------------------------------------------>
+## Testcase description
+
+<!-----------------------------------------------------------------------------
+All steps required to run the testcase and control affinity for application
+------------------------------------------------------------------------------>
+## How to run software
+
+
+<!-----------------------------------------------------------------------------
+END BLOCK PREAMBLE
+------------------------------------------------------------------------------>
+
+<!-----------------------------------------------------------------------------
+START BLOCK ANALYST - This block is required for any new analyst taking over
+the project
+# Transfer to Analyst: <NAME-TAG>
+
+* Start date: DD/MM/YYYY
+* Contact HPC center:
+   * Name:
+   * Fon:
+   * E-Mail:
+------------------------------------------------------------------------------>
+
+<!-----------------------------------------------------------------------------
+###############################################################################
+START BLOCK BENCHMARKING - Run helper script machine-state.sh and store results
+in directory session-<ID> named <hostname>.txt. Document everything that you
+consider to be relevant for performance.
+###############################################################################
+------------------------------------------------------------------------------>
+## Benchmarking <NAME-TAG>
+
+### Testsystem
+
+* Host/Clustername:
+* Cluster Info URL:
+* CPU type:
+* Memory capacity:
+* Number of cores per node:
+* Interconnect:
+
+### Software Environment
+
+**Compiler**:
+* Vendor:
+* Version:
+
+**Libraries**:
+* <LIBRARYNAME>:
+   * Version:
+
+**OS**:
+* Distribution:
+* Version:
+* Kernel version:
+
+<!-----------------------------------------------------------------------------
+Create a runtime profile. Which tool was used? How was the profile created.
+Describe and discuss the runtime profile.
+------------------------------------------------------------------------------>
+## Runtime Profile <NAME-TAG>-<ID>
+
+<!-----------------------------------------------------------------------------
+Perform a static code review.
+------------------------------------------------------------------------------>
+## Code review <NAME-TAG>-<ID>
+
+<!-----------------------------------------------------------------------------
+Application benchmarking runs. What experiment was done? Add results or
+reference plots in directory session-<NAME-TAG>-<ID>. Number all sections
+consecutivley such that every section has a unique ID.
+------------------------------------------------------------------------------>
+## Result <NAME-TAG>-<ID>
+
+### Problem: <DESCRIPTION>
+
+
+### Measurement <NAME-TAG>-<ID>.1
+
+Example for table:
+
+| NP | runtime |
+|----|---------|
+| 1  | 2558.89 |
+| 2  | 1425.20 |
+| 4  | 741.97  |
+| 8  | 449.23  |
+| 10 | 371.39  |
+| 20 | 233.90  |
+
+```
+Verbatim Text
+```
+
+<!-----------------------------------------------------------------------------
+Document the initial performance which serves as baseline for further progress
+and is used to compute the achieved speedup. Document exactly how the baseline
+was created.
+------------------------------------------------------------------------------>
+## Baseline
+
+* Time to solution:
+* Performance:
+
+
+<!-----------------------------------------------------------------------------
+Explain which tool was used and how the measurements were done. Store and
+reference the results. If applicable discuss and explain profiles.
+------------------------------------------------------------------------------>
+## Performance Profile <NAME-TAG>-<ID>.2
+
+<!-----------------------------------------------------------------------------
+Analysis and insights extracted from benchmarking results. Planning of more
+benchmarks.
+------------------------------------------------------------------------------>
+## Analysis <NAME-TAG>-<ID>.3
+
+
+<!-----------------------------------------------------------------------------
+Document all changes with  filepath:linenumber and explanation what was changed
+and why. Create patch if applicable and store patch in referenced file.
+------------------------------------------------------------------------------>
+## Optimisation <NAME-TAG>-<ID>.4: <DESCRIPTION>
+
+
+<!-----------------------------------------------------------------------------
+###############################################################################
+END BLOCK BENCHMARKING
+###############################################################################
+------------------------------------------------------------------------------>
+
+<!-----------------------------------------------------------------------------
+Wrap up the final result and discuss the speedup.
+Optional: Document how much time was spent. A simple python command line tool
+for time tracking is [Watson](http://tailordev.github.io/Watson/).
+------------------------------------------------------------------------------>
+## Summary
+
+* Time to solution:
+* Performance:
+* Speedup:
+
+## Effort
+
+* Time spent:
+
+<!-----------------------------------------------------------------------------
+END BLOCK ANALYST
+------------------------------------------------------------------------------>
+
+<!-----------------------------------------------------------------------------
+START BLOCK SUMMARY - This block is only required if multiple analysts worked
+on the project.
+------------------------------------------------------------------------------>
+# Overall Summary
+
+* End date: DD/MM/YYYY
+
+## Total Effort
+
+* Total time spent:
+* Estimated core hours saved:
+
+<!-----------------------------------------------------------------------------
+END BLOCK SUMMARY
+------------------------------------------------------------------------------>

new_syntax.py

-import part_prot as pt
+import pairs
 from ir.assign import Assign
 from ir.bin_op import BinOp
 import ast
@@ -177,7 +177,7 @@ sigma = 1.0
 epsilon = 1.0
 sigma6 = sigma ** 6
 
-psim = pt.simulation("lj_ns")
+psim = pairs.simulation("lj_ns")
 psim.add_real_property('mass', 1.0)
 psim.add_vector_property('position')
 psim.add_vector_property('velocity')

particle.py

-import part_prot as pt
+import pairs
 from ir.layouts import Layout_SoA
 
 dt = 0.005
@@ -8,7 +8,7 @@ sigma = 1.0
 epsilon = 1.0
 sigma6 = sigma ** 6
 
-psim = pt.simulation("lj")
+psim = pairs.simulation("lj")
 mass = psim.add_real_property('mass', 1.0)
 position = psim.add_vector_property('position')
 velocity = psim.add_vector_property('velocity')