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mozi-diary.lyx
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#LyX 2.3 created this file. For more info see http://www.lyx.org/
\lyxformat 544
\begin_document
\begin_header
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\usepackage{url}
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\end_header
\begin_body
\begin_layout Title
MOZI.AI Diary
\end_layout
\begin_layout Subsection*
26 Dec 2019 - Initial setup; SQL game start
\end_layout
\begin_layout Standard
Downloads: `
\family typewriter
wget -r --no-parent https://mozi.ai/datasets/
\family default
` grabs 998796 KBytes of uncompressed scm files.
A tar.gz of the same is 45.5MBytes and a tar.bz2 is only 26.2 MBytes.
\end_layout
\begin_layout Standard
The file
\family typewriter
/home/ubuntu/datasets/smpdb_chebi_wname.scm
\family default
loaded in 127 secs elapsed; 210 secs system time, with 900MB virt 610MB
resident.
Total of 972747 atoms, like so:
\family typewriter
(cog-report-counts) $4 = ((ConceptNode .
98388) (PredicateNode .
1) (ListLink .
49808) (MemberLink .
773191) (EvaluationLink .
49808) (MoleculeNode .
1551))
\end_layout
\begin_layout Standard
So zero seconds to run
\family typewriter
(gene-go-annotation '("IGF1") "biological_process molecular_function cellular_co
mponent")
\family default
and results ..
pfft.
\end_layout
\begin_layout Standard
How about SQL?
\end_layout
\begin_layout Standard
\family typewriter
(sql-create "postgres:///biosci")
\end_layout
\begin_layout Standard
\family typewriter
(sql-open "postgres:///biosci")
\end_layout
\begin_layout Standard
\family typewriter
(store-atomspace)
\end_layout
\begin_layout Standard
The store took 233 seconds (ouch) at about 4.3K atoms/sec.
Close and re-open.
Load takes 121 seconds elapsed (8.1K atoms/sec) so this is hardly any improvemen
t at all, compared to the file-load.
Why? Where's the bottleneck? Apparently its postgres, which runs at 70%
cpu while guile runs at 22%
\end_layout
\begin_layout Standard
Effing A.
OC_OMP is busted, issue
\family typewriter
opencog/cogutil#218
\family default
and
\family typewriter
opencog/atomspace#2460
\family default
Fixing this causes guile to run at 780% CPU ...
apparently thrashing ...
wtf ...
but now it works great, loaded 72860 atoms in total in 43 seconds (22624
per second).
So ...
3x faster than file input.
\end_layout
\begin_layout Subsection*
31 Dec 2019 - SQL Game failure
\end_layout
\begin_layout Standard
See
\family typewriter
~/work/load-files.scm
\family default
to load all the files..
total of 6.4M atoms – 5.2GB virt, 3.9G RSS Loaded in 760 seconds for 8.4K/sec,
but there are many duplicate atoms in the datasets ...
\end_layout
\begin_layout Standard
SQL fails ...
Error: do_store_single_atom: Maxiumum Link size is 330.
Atom was:
\family typewriter
(ListLink (ConceptNode "https://www.ncbi.nlm.nih.gov/pubmed/?term=14596917")
\family default
...
etc.
Oh well.
\end_layout
\begin_layout Standard
Up to then, store rate was 3.1K/second ..
disappointing, as usual ...
\end_layout
\begin_layout Standard
Annotation took 335 seconds, RAM usage grew to 4.06GB and created an 8.4MB
file...
\end_layout
\begin_layout Standard
Try again:
\family typewriter
HUGETLB_MORECORE=yes LD_PRELOAD=/usr/lib/libhugetlbfs.so.0
\family default
takes 730 seconds (so 8.8K atoms/sec) which is just a hair faster than before,
and annotation takes 330 seconds (effectively no difference.)
\end_layout
\begin_layout Standard
Loading parallel takes 628 seconds to load (16% faster), so this is ...
losing, given how much cpu time it burned.
Ouch Parallelism in guile still sucks.
Try again, two files (two threads) at a time: 657 seconds., i.e.
11% faster.
Three threads: 669 seconds.
Oof.
Four threads: 691 seconds.
\end_layout
\begin_layout Standard
Using
\family typewriter
(n-par-map 12)
\family default
in gene-go.scm shortens execution time to 130 seconds from 330 seconds,
but at 12x larger CPU usage, so this is a big waste.
\end_layout
\begin_layout Subsection*
2 Jan 2020
\end_layout
\begin_layout Standard
A haha.
OK, parents is a variable.
So is the type of annotation.
In the table
\begin_inset Quotes eld
\end_inset
idle
\begin_inset Quotes erd
\end_inset
is elapsed seconds on an idle system,
\begin_inset Quotes eld
\end_inset
busy
\begin_inset Quotes erd
\end_inset
is elapsed seconds on busy system.
All measurements with
\family typewriter
HUGETLB_MORECORE=yes LD_PRELOAD=/usr/lib/libhugetlbfs.so.0
\family default
set.
The gene list is the basic list of 681 genes.
\end_layout
\begin_layout Standard
\begin_inset Tabular
<lyxtabular version="3" rows="9" columns="6">
<features tabularvalignment="middle">
<column alignment="center" valignment="top">
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type
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#parents
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\begin_inset Text
\begin_layout Plain Layout
idle (secs)
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busy (secs)
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RSS (GBytes)
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load, 1 thread
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-
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730
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3.9
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-
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657
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847-957
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0
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4.06
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\begin_inset Text
\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
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24059
\end_layout
\end_inset
</cell>
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\begin_layout Plain Layout
\end_layout
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\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
pathway
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
0
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
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\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
crash
\end_layout
\end_inset
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\begin_layout Plain Layout
\end_layout
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\end_layout
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</cell>
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<row>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
biogrid
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
0
\end_layout
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\begin_inset Text
\begin_layout Plain Layout
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\begin_inset Text
\begin_layout Plain Layout
crash
\end_layout
\end_inset
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\begin_layout Plain Layout
\end_layout
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\begin_inset Text
\begin_layout Plain Layout
\end_layout
\end_inset
</cell>
</row>
</lyxtabular>
\end_inset
\end_layout
\begin_layout Standard
The crashes are becoming increasingly mysterious: they crash, but hand-running
the code by cut-n-paste does NOT crash.
That's weird.
A haha.
The crash is avoided by saying
\family typewriter
(use-modules (annotation util))
\family default
and the crash was because of
\family typewriter
(GroundedSchemaNode
\begin_inset Quotes eld
\end_inset
scm:stuff
\begin_inset Quotes erd
\end_inset
)
\family default
with
\begin_inset Quotes eld
\end_inset
stuff
\begin_inset Quotes erd
\end_inset
being in util.
Aieee!!!!
\end_layout
\begin_layout Subsection*
4 Jan 2020
\end_layout
\begin_layout Standard
Apparently only half the files need to be loaded.
Only the
\begin_inset Quotes eld
\end_inset
current
\begin_inset Quotes erd
\end_inset
ones, not the base ones.
There's also a new list of 1482 genes to supplant the list of 681.
\end_layout
\begin_layout Standard
Audit:
\end_layout
\begin_layout Itemize
\family typewriter
find-pathway-name
\family default
would be faster if written out, instead of using GetLink.
\end_layout
\begin_layout Itemize
\family typewriter
is-cellular-component?
\family default
is buggy – the last setter wins.
See issue #89
\end_layout
\begin_layout Itemize
Crash, when
\family typewriter
gene-pathway-annotation
\family default
with
\family typewriter
#:namespace
\family default
set...
\family typewriter
In procedure cog-new-link: Wrong type argument in position 2 (expecting
opencog atom):
\backslash
"ECSIT
\backslash
"
\family default
.
Stack:
\family typewriter
In annotation/functions.scm:
\backslash
n 301:22 13 (find-pathway-genes _ _)
\family default
See issue #91
\end_layout
\begin_layout Standard
So again, with the new current files, and the old 681-gene list.
#atoms is the total number of atoms in the atomspace.
The par=2 column is with (n-par-map 2) for gene-go.scm on idle system (seconds)
\begin_inset Tabular
<lyxtabular version="3" rows="26" columns="7">
<features tabularvalignment="middle">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<column alignment="center" valignment="top">
<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
type
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
#parents
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
idle (secs)
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
par=2
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
busy (secs)
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
RSS/Virt GB
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
#atoms
\end_layout
\end_inset
</cell>
</row>
<row>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
load, 1 threads
\end_layout
\end_inset
</cell>
<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
\begin_inset Text
\begin_layout Plain Layout
-