WIP: documentation for the pp pipeline

garlic/doc/Makefile

@@ -1,8 +1,8 @@
-all: execution.pdf execution.txt
+all: execution.pdf execution.txt pp.pdf pp.txt
 
 %.pdf: %.ms
-	groff -ms -t -Tpdf $^ > $@
+	groff -ms -t -p -Tpdf $^ > $@
-	#killall -HUP mupdf
+	-killall -HUP mupdf
 
 %.txt: %.ms
-	groff -ms -t -Tutf8 $^ > $@
+	groff -ms -t -p -Tutf8 $^ > $@

garlic/doc/pp.ms

@@ -0,0 +1,75 @@
+.TL
+Garlic: experiment results
+.AU
+Rodrigo Arias Mallo
+.AI
+Barcelona Supercomputing Center
+.\"#####################################################################
+.nr GROWPS 3
+.nr PSINCR 1.5p
+.\".nr PD 0.5m
+.nr PI 2m
+\".2C
+.\"#####################################################################
+.LP
+Consider a program of interest for which an experiment has been designed to
+measure some properties. When the experiment is executed, it will generate some
+results which are generally non-deterministic. The experimenter may want to
+present some information in a visual plot or graph based on these results.
+.PP
+In this escenario, the experiment depends on the program\[em]any
+changes in the program will cause nix to build the experiment again using the
+updated program. The results will also depend on the experiment, and
+the graph on the results. This chain of dependencies can be shown in
+the following dependency tree:
+.PS
+right
+circlerad=0.22; arrowhead=7;
+circle "Prog"
+arrow
+circle "Exp"
+arrow
+circle "Result"
+arrow
+circle "Graph"
+.PE
+Ideally, the dependencies should be handled by nix, so it can detect any
+change and rebuild the necessary parts automatically. Unfortunately, nix
+is not able to build R as a derivation directly as it requires access
+to the
+.I "target cluster"
+with several user accounts. In addition, the results are often
+non-deterministic so the graph G cannot depend on the content of the
+results.
+.PP
+In order to let several users use the results from a cache, we use the
+.I "nix store"
+to make them available for read only. To generate the results from the
+experiment, we add some extra steps that must be executed manually.
+.PS
+right
+circlerad=0.22; arrowhead=7;
+circle "Prog"
+arrow
+E: circle "Exp"
+RUN: circle "Run" at E + (0.8,-0.5)
+FETCH: circle "Fetch" at E + (1.6,-0.5)
+R: circle "Result" at E + (2.4,0)
+arrow
+G: circle "Graph"
+arrow dashed from E to RUN chop
+arrow dashed from RUN to FETCH chop
+arrow dashed from FETCH to R chop
+arrow from E to R chop
+.PE
+The run and fetch steps are provided by the helper tool
+.I garlic ,
+which launches the experiment using the user credential at the
+.I "target cluster"
+and then fetches the results, placing them in a directory known by nix.
+Is the directory is not found, nix will issue a message to suggest the
+user to launch the experiment and it will fail to build the result
+derivation. When the result is successfully built by any user, the
+derivation won't need to be rebuilt again until the experiment changes,
+as the hash only depends on the experiment and not on the contents of
+the results.