Hi again,
I just filed a bug report here:
http://bugzilla.scilab.org/show_bug.cgi?id=15809
Would it be possible to bring back the old mem-dump approach in scilab 6? I
mean, could I write a gateway that just takes a pointer to the first byte in
memory, figures out the size, and dumps to disk? Or maybe it doesn’t work like
that. Writing a JSON exporter for storing filter coefficients in a math
software package seems a bit ridicules, but hey, if it works it might be worth
it in our case.
Cheers,
Arvid
From: users <users-boun...@lists.scilab.org> on behalf of Clément DAVID
<clement.da...@scilab-enterprises.com>
Reply-To: Users mailing list for Scilab <users@lists.scilab.org>
Date: Monday, 15 October 2018 at 15:48
To: Users mailing list for Scilab <users@lists.scilab.org>
Cc: Clément David <clement.da...@esi-group.com>
Subject: Re: [Scilab-users] HDF5 save is super slow
Hello all,
Correct, I experienced such a slowness while working with Xcos diagrams for
Scilab 5. At first we considered HDF5 for this deep nested list / mlist
data-structure storage however after some tests ; XML might be used for
tree-like storage and HDF5 (or Java types serialization) for big matrices.
AFAIK currently there is no easy way to load/save specifying a format other
than HDF5 ; maybe adding xmlSave/xmlLoad sci_gateway to let the user select an
xml file format for any Scilab structure might provide better performance on
your use-case. JSON might also be another candidate to look at for decent
serialization support.
PS: Scilab 5.5.1 load/save are direct memory dump so this is really the fastest
you can get from Scilab ; HDF5 binary format is good enough for matrices
--
Clément
From: users <users-boun...@lists.scilab.org> On Behalf Of Stéphane Mottelet
Sent: Monday, October 15, 2018 2:36 PM
To: users@lists.scilab.org
Subject: Re: [Scilab-users] HDF5 save is super slow
Hello,
I looked a little bit in the sources: the evident bottleneck is the nested
creation of an hdf5 group each time that a container variable is met.
For the given example, this is particularly evident. If you replace the syslin
structure by the corresponding [A,B;C,D] matrix, then save is ten times faster:
N = 4;
n = 1000;
filters = list();
for i=1:n
G=syslin('c', rand(N,N), rand(N,1), rand(1,N), rand(1,1));
filters($+1) = G;
end
tic();
save('filters.dat', 'filters');
disp(toc());
--> disp(toc());
0.724754
N = 4;
n = 1000;
filters = list()
for i=1:n
G=syslin('c', rand(N,N), rand(N,1), rand(1,N), rand(1,1));
filters($+1) = [G.a G.b;G.c G.d];
end
tic();
save('filters.dat', 'filters');
disp(toc());
--> disp(toc());
0.082302
Serializing container objects seems to be the solution, but it goes towards an
orthogonal direction w.r.t. the hdf5 portability spirit.
S.
Le 15/10/2018 à 12:22, Antoine Monmayrant a écrit :
Le 15/10/2018 à 11:55, Arvid Rosén a écrit :
Hi,
Thanks for getting back to me!
Unfortunately, we used Scilab’s pretty cool way of doing object orientation, so
we have big nested tlist structures with multiple instances of various lists of
filters and other structures, as in my example. Saving those structures in some
explicit manual way would be extremely complicated. Or is there some way of
writing explicit HDF5 saving/loading schemes using overloading? That would be
great! I am sure we could find the main culprits and do something explicit for
them, but as they can be located wherever in a big nested structure, it would
be painful to do anything on the top level.
Another, related I guess, problem here is that the new file format uses about
15 times as much disk space as the old format (for a typical ill-behaved nested
structure). That adds to the save/load time too I guess, but is probably not
the main source here.
Argh, yes, I tested it and in your example, I have a file x8.5 bigger.
I think that both increases in time and size are real issues and should be
reported as bugs.
By the way, I rewrote your script to run it under both 6.0 and 5.5:
/////////////////////////////////
N = 4;
n = 10000;
filters = list();
for i=1:n
G=syslin('c', rand(N,N), rand(N,1), rand(1,N), rand(1,1));
filters($+1) = G;
end
ver=getversion('scilab');
if ver(1)<6 then
tic();
save('filters_old.dat', filters);
ts1 = toc();
else
tic();
save('filters_new.dat', 'filters');
ts1 = toc();
end
printf("Time for save %.2fs\n", ts1);
/////////////////////////////////
Hope it helps,
Antoine
I think I might have reported this earlier using Bugzilla, but I’m not sure.
I’ll check and report it if not.
Cheers,
Arvid
From: users
<users-boun...@lists.scilab.org><mailto:users-boun...@lists.scilab.org> on
behalf of "amonm...@laas.fr"<mailto:amonm...@laas.fr>
<amonm...@laas.fr><mailto:amonm...@laas.fr>
Reply-To: "antoine.monmayr...@laas.fr"<mailto:antoine.monmayr...@laas.fr>
<antoine.monmayr...@laas.fr><mailto:antoine.monmayr...@laas.fr>, Users mailing
list for Scilab <users@lists.scilab.org><mailto:users@lists.scilab.org>
Date: Monday, 15 October 2018 at 11:08
To: "users@lists.scilab.org"<mailto:users@lists.scilab.org>
<users@lists.scilab.org><mailto:users@lists.scilab.org>
Subject: Re: [Scilab-users] HDF5 save is super slow
Hello,
I tried your code in 5.5.1 and the last nightly-build of 6.0: I see a slowdown
of around 175 between old save in 5.5.1 and new (and only) save in 6.0.
It's really related to the data structure, because we use hdf5 read/write a lot
here and did not experience significant slowdowns using 6.0.
I think the overhead might come to the translation of your fairly complex
variable (a long array of tlist) in the corresponding hdf5 structure.
In the old save, this translation was not necessary.
Maybe you could try to save your data in a different way.
For example:
3) you could save each element of "filters" in a separate file.
2) you could bypass save and directly write your data in a hdf5 file by using
h5open(), h5write() directly. It means you need to write your own load() for
your custom file format. But this way, you can try to find the best way to
layout your data in hdf5 format.
3) in addition to 2) you could try to save each entry of your "filters" array
as one dataset in a given hdf5 file.
Did you search on bugzilla whether this bug was already submitted?
Could you try to report it?
Antoine
Le 15/10/2018 à 10:11, Arvid Rosén a écrit :
/////////////////////////////////
N = 4;
n = 10000;
filters = list();
for i=1:n
G=syslin('c', rand(N,N), rand(N,1), rand(1,N), rand(1,1));
filters($+1) = G;
end
tic();
save('filters.dat', filters);
ts1 = toc();
tic();
save('filters.dat', 'filters');
ts2 = toc();
printf("old save %.2fs\n", ts1);
printf("new save %.2fs\n", ts2);
printf("slowdown %.1f\n", ts2/ts1);
/////////////////////////////////
--
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
Antoine Monmayrant LAAS - CNRS
7 avenue du Colonel Roche
BP 54200
31031 TOULOUSE Cedex 4
FRANCE
Tel:+33 5 61 33 64 59
email : antoine.monmayr...@laas.fr<mailto:antoine.monmayr...@laas.fr>
permanent email :
antoine.monmayr...@polytechnique.org<mailto:antoine.monmayr...@polytechnique.org>
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
--
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
Antoine Monmayrant LAAS - CNRS
7 avenue du Colonel Roche
BP 54200
31031 TOULOUSE Cedex 4
FRANCE
Tel:+33 5 61 33 64 59
email : antoine.monmayr...@laas.fr<mailto:antoine.monmayr...@laas.fr>
permanent email :
antoine.monmayr...@polytechnique.org<mailto:antoine.monmayr...@polytechnique.org>
+++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
users mailing list
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--
Stéphane Mottelet
Ingénieur de recherche
EA 4297 Transformations Intégrées de la Matière Renouvelable
Département Génie des Procédés Industriels
Sorbonne Universités - Université de Technologie de Compiègne
CS 60319, 60203 Compiègne cedex
Tel : +33(0)344234688
http://www.utc.fr/~mottelet<http://www.utc.fr/%7Emottelet>
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