VBA_MFX is slowing down #46
Comments
|
Hi Antonius, Which model are you trying to invert with MFX? Best |
|
Hi,
sorry for my late reply. I just came back to this... I'm fitting
discounting functions to choice data, nothing fancy. I could not upload
files so I attached them to the email. You might have to adjust the path in
the beginning of VBA_fit_multi_subject.m
I assume the problem might be related to the diagnostic windows opening...
I have not found an option to turn them off. I run Matlab itself
with -nodisplay in the terminal, but the problem continues.
Let me know if I can help with anything.
Best,
Antonius
…On Thu, Sep 28, 2017 at 3:42 PM, Lionel RIGOUX ***@***.***> wrote:
Hi Antonius,
Which model are you trying to invert with MFX?
It would be nice if you could post a minmal code on
https://gist.github.com/ so we can try to reproduce your problem.
Best
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Hey Antonius
This is a Github thread and answering to this email is logged into github. Because of this (I guess) I could not see the files you attached.
Please send me privately the code, or start a Gist. Please ensure to enclose all dependencies.
I’ll then try to reproduce your bug.
|
|
Hi, sorry not for beeing clear enough. Unzip everything.
"Die-hard-discounting" is the main folder, "main_exp" includes (simulated)
log files, "_output" priors for modeling. The main script to run is
VBA_fit_multi_subject.m. Folder locations in line 21-24 need to be
adjusted, depending on the location of the folders.
hope this helps.
Best,
Antonius
On Tue, Dec 5, 2017 at 3:01 PM, Lionel RIGOUX <[email protected]>
wrote:
… How should I organize all the folders and what should I change to run it?
> On 5. Dec 2017, at 14:58, Antonius Wiehler ***@***.***>
wrote:
>
> done. (sent to your gmail).
>
> On Tue, Dec 5, 2017 at 2:55 PM, Lionel RIGOUX ***@***.***>
> wrote:
>
> > Hey Antonius
> >
> > This is a Github thread and answering to this email is logged into
github.
> > Because of this (I guess) I could not see the files you attached.
> > Please send me privately the code, or start a Gist. Please ensure to
> > enclose all dependencies.
> > I’ll then try to reproduce your bug.
> >
> >
> >
> > —
> > You are receiving this because you authored the thread.
> > Reply to this email directly, view it on GitHub
> > <#46#
issuecomment-349310793>,
> > or mute the thread
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c7qbOoHYPO6INK6WUXvLKQo4P08axks5s9UthgaJpZM4PnOT1>
> > .
> >
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I got the script running with no windows. For me, even the first files take way more than “few seconds” to run, as I am closer to 3min so far. I will let run overnight while logging the duration this if I can reproduce you bug.
Are you sure the lengthening is due to the repetition and not the specific parametrization you’re testing in later loops? Meaning, if you reverse the order of model inversion, do you still see an increase of duration or does it reverse?
… On 5. Dec 2017, at 15:55, Antonius Wiehler ***@***.***> wrote:
Hi, sorry not for beeing clear enough. Unzip everything.
"Die-hard-discounting" is the main folder, "main_exp" includes (simulated)
log files, "_output" priors for modeling. The main script to run is
VBA_fit_multi_subject.m. Folder locations in line 21-24 need to be
adjusted, depending on the location of the folders.
hope this helps.
Best,
Antonius
On Tue, Dec 5, 2017 at 3:01 PM, Lionel RIGOUX ***@***.***>
wrote:
> How should I organize all the folders and what should I change to run it?
>
> > On 5. Dec 2017, at 14:58, Antonius Wiehler ***@***.***>
> wrote:
> >
> > done. (sent to your gmail).
> >
> > On Tue, Dec 5, 2017 at 2:55 PM, Lionel RIGOUX ***@***.***>
> > wrote:
> >
> > > Hey Antonius
> > >
> > > This is a Github thread and answering to this email is logged into
> github.
> > > Because of this (I guess) I could not see the files you attached.
> > > Please send me privately the code, or start a Gist. Please ensure to
> > > enclose all dependencies.
> > > I’ll then try to reproduce your bug.
> > >
> > >
> > >
> > > —
> > > You are receiving this because you authored the thread.
> > > Reply to this email directly, view it on GitHub
> > > <#46#
> issuecomment-349310793>,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-auth/AV_
> c7qbOoHYPO6INK6WUXvLKQo4P08axks5s9UthgaJpZM4PnOT1>
> > > .
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> >
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great, thanks for checking! Let me know what the result is. I will try the
inversion. how did you manage to supress the windows?
Best,
Antonius
On Tue, Dec 5, 2017 at 6:56 PM, Lionel RIGOUX <[email protected]>
wrote:
… I got the script running with no windows. For me, even the first files
take way more than “few seconds” to run, as I am closer to 3min so far. I
will let run overnight while logging the duration this if I can reproduce
you bug.
Are you sure the lengthening is due to the repetition and not the specific
parametrization you’re testing in later loops? Meaning, if you reverse the
order of model inversion, do you still see an increase of duration or does
it reverse?
> On 5. Dec 2017, at 15:55, Antonius Wiehler ***@***.***>
wrote:
>
> Hi, sorry not for beeing clear enough. Unzip everything.
> "Die-hard-discounting" is the main folder, "main_exp" includes
(simulated)
> log files, "_output" priors for modeling. The main script to run is
> VBA_fit_multi_subject.m. Folder locations in line 21-24 need to be
> adjusted, depending on the location of the folders.
>
> hope this helps.
>
> Best,
> Antonius
>
> On Tue, Dec 5, 2017 at 3:01 PM, Lionel RIGOUX ***@***.***>
> wrote:
>
> > How should I organize all the folders and what should I change to run
it?
> >
> > > On 5. Dec 2017, at 14:58, Antonius Wiehler ***@***.***
>
> > wrote:
> > >
> > > done. (sent to your gmail).
> > >
> > > On Tue, Dec 5, 2017 at 2:55 PM, Lionel RIGOUX <
***@***.***>
> > > wrote:
> > >
> > > > Hey Antonius
> > > >
> > > > This is a Github thread and answering to this email is logged into
> > github.
> > > > Because of this (I guess) I could not see the files you attached.
> > > > Please send me privately the code, or start a Gist. Please ensure
to
> > > > enclose all dependencies.
> > > > I’ll then try to reproduce your bug.
> > > >
> > > >
> > > >
> > > > —
> > > > You are receiving this because you authored the thread.
> > > > Reply to this email directly, view it on GitHub
> > > > <#46#
> > issuecomment-349310793>,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-auth/AV_
> > c7qbOoHYPO6INK6WUXvLKQo4P08axks5s9UthgaJpZM4PnOT1>
> > > > .
> > > >
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> > #46#
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> >
> > >
> >
> > —
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aL26qoHhJtdeXOnmLv0btk5ks5s9Uy2gaJpZM4PnOT1>
> > .
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So far I’m just doin a close all /clc after each iteration to avoid crowding the memory. You should see with Jean (and whoever wrote the MFX function) about implementing a proper verbose/display switch.
BTW, could you ask/help Jean to switch his copy of the toolbox to the development branch, he’s started pushing frenetically directly to the master and that’s not good...
… On 5. Dec 2017, at 19:00, Antonius Wiehler ***@***.***> wrote:
great, thanks for checking! Let me know what the result is. I will try the
inversion. how did you manage to supress the windows?
Best,
Antonius
On Tue, Dec 5, 2017 at 6:56 PM, Lionel RIGOUX ***@***.***>
wrote:
> I got the script running with no windows. For me, even the first files
> take way more than “few seconds” to run, as I am closer to 3min so far. I
> will let run overnight while logging the duration this if I can reproduce
> you bug.
> Are you sure the lengthening is due to the repetition and not the specific
> parametrization you’re testing in later loops? Meaning, if you reverse the
> order of model inversion, do you still see an increase of duration or does
> it reverse?
>
>
>
> > On 5. Dec 2017, at 15:55, Antonius Wiehler ***@***.***>
> wrote:
> >
> > Hi, sorry not for beeing clear enough. Unzip everything.
> > "Die-hard-discounting" is the main folder, "main_exp" includes
> (simulated)
> > log files, "_output" priors for modeling. The main script to run is
> > VBA_fit_multi_subject.m. Folder locations in line 21-24 need to be
> > adjusted, depending on the location of the folders.
> >
> > hope this helps.
> >
> > Best,
> > Antonius
> >
> > On Tue, Dec 5, 2017 at 3:01 PM, Lionel RIGOUX ***@***.***>
> > wrote:
> >
> > > How should I organize all the folders and what should I change to run
> it?
> > >
> > > > On 5. Dec 2017, at 14:58, Antonius Wiehler ***@***.***
> >
> > > wrote:
> > > >
> > > > done. (sent to your gmail).
> > > >
> > > > On Tue, Dec 5, 2017 at 2:55 PM, Lionel RIGOUX <
> ***@***.***>
> > > > wrote:
> > > >
> > > > > Hey Antonius
> > > > >
> > > > > This is a Github thread and answering to this email is logged into
> > > github.
> > > > > Because of this (I guess) I could not see the files you attached.
> > > > > Please send me privately the code, or start a Gist. Please ensure
> to
> > > > > enclose all dependencies.
> > > > > I’ll then try to reproduce your bug.
> > > > >
> > > > >
> > > > >
> > > > > —
> > > > > You are receiving this because you authored the thread.
> > > > > Reply to this email directly, view it on GitHub
> > > > > <#46#
> > > issuecomment-349310793>,
> > > > > or mute the thread
> > > > > <https://github.com/notifications/unsubscribe-auth/AV_
> > > c7qbOoHYPO6INK6WUXvLKQo4P08axks5s9UthgaJpZM4PnOT1>
> > > > > .
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> > > > —
> > > > You are receiving this because you commented.
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> > > #46#
> issuecomment-349311531>,
> > > or mute the thread <https://github.com/notifications/unsubscribe-
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> > >
> > > >
> > >
> > > —
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> > > <#46#
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> >
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Ouch, I could have done that. *facepalm* Great immediate fix!
I will speak to Jean tomorrow, he left already.
Best,
Antonius
On Tue, Dec 5, 2017 at 7:04 PM, Lionel RIGOUX <[email protected]>
wrote:
… So far I’m just doin a close all /clc after each iteration to avoid
crowding the memory. You should see with Jean (and whoever wrote the MFX
function) about implementing a proper verbose/display switch.
BTW, could you ask/help Jean to switch his copy of the toolbox to the
development branch, he’s started pushing frenetically directly to the
master and that’s not good...
> On 5. Dec 2017, at 19:00, Antonius Wiehler ***@***.***>
wrote:
>
> great, thanks for checking! Let me know what the result is. I will try
the
> inversion. how did you manage to supress the windows?
>
> Best,
> Antonius
>
> On Tue, Dec 5, 2017 at 6:56 PM, Lionel RIGOUX ***@***.***>
> wrote:
>
> > I got the script running with no windows. For me, even the first files
> > take way more than “few seconds” to run, as I am closer to 3min so
far. I
> > will let run overnight while logging the duration this if I can
reproduce
> > you bug.
> > Are you sure the lengthening is due to the repetition and not the
specific
> > parametrization you’re testing in later loops? Meaning, if you reverse
the
> > order of model inversion, do you still see an increase of duration or
does
> > it reverse?
> >
> >
> >
> > > On 5. Dec 2017, at 15:55, Antonius Wiehler ***@***.***
>
> > wrote:
> > >
> > > Hi, sorry not for beeing clear enough. Unzip everything.
> > > "Die-hard-discounting" is the main folder, "main_exp" includes
> > (simulated)
> > > log files, "_output" priors for modeling. The main script to run is
> > > VBA_fit_multi_subject.m. Folder locations in line 21-24 need to be
> > > adjusted, depending on the location of the folders.
> > >
> > > hope this helps.
> > >
> > > Best,
> > > Antonius
> > >
> > > On Tue, Dec 5, 2017 at 3:01 PM, Lionel RIGOUX <
***@***.***>
> > > wrote:
> > >
> > > > How should I organize all the folders and what should I change to
run
> > it?
> > > >
> > > > > On 5. Dec 2017, at 14:58, Antonius Wiehler <
***@***.***
> > >
> > > > wrote:
> > > > >
> > > > > done. (sent to your gmail).
> > > > >
> > > > > On Tue, Dec 5, 2017 at 2:55 PM, Lionel RIGOUX <
> > ***@***.***>
> > > > > wrote:
> > > > >
> > > > > > Hey Antonius
> > > > > >
> > > > > > This is a Github thread and answering to this email is logged
into
> > > > github.
> > > > > > Because of this (I guess) I could not see the files you
attached.
> > > > > > Please send me privately the code, or start a Gist. Please
ensure
> > to
> > > > > > enclose all dependencies.
> > > > > > I’ll then try to reproduce your bug.
> > > > > >
> > > > > >
> > > > > >
> > > > > > —
> > > > > > You are receiving this because you authored the thread.
> > > > > > Reply to this email directly, view it on GitHub
> > > > > > <#46#
> > > > issuecomment-349310793>,
> > > > > > or mute the thread
> > > > > > <https://github.com/notifications/unsubscribe-auth/AV_
> > > > c7qbOoHYPO6INK6WUXvLKQo4P08axks5s9UthgaJpZM4PnOT1>
> > > > > > .
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> > > > > —
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> > > > #46#
> > issuecomment-349311531>,
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> > > >
> > > > >
> > > >
> > > > —
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> > issuecomment-349312450>,
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Hey Antonius,
Your script ran overnight and is till running. So far I’ve seen no consistent slowing of the inversion across the ~250 blocs than were inverted, one bloc taking between 150 and 350s. I guess the accumulation of windows was indeed the issue (it can be quite memory greedy).
I suggest that:
- you insert a clc and a close all between each block of MFX inversion
- ask Jean for a more elegant solution using a noDisplay and a verbose flag in the MFX (and please on the development branch)
- see if you still have the problem.
I am sure you could also make use of the parallel toolbox to speed the things a bit up.
Let me know if this solves your problem
Cheers
L
… On 5. Dec 2017, at 19:09, Antonius Wiehler ***@***.***> wrote:
Ouch, I could have done that. *facepalm* Great immediate fix!
I will speak to Jean tomorrow, he left already.
Best,
Antonius
On Tue, Dec 5, 2017 at 7:04 PM, Lionel RIGOUX ***@***.***>
wrote:
> So far I’m just doin a close all /clc after each iteration to avoid
> crowding the memory. You should see with Jean (and whoever wrote the MFX
> function) about implementing a proper verbose/display switch.
>
> BTW, could you ask/help Jean to switch his copy of the toolbox to the
> development branch, he’s started pushing frenetically directly to the
> master and that’s not good...
>
>
> > On 5. Dec 2017, at 19:00, Antonius Wiehler ***@***.***>
> wrote:
> >
> > great, thanks for checking! Let me know what the result is. I will try
> the
> > inversion. how did you manage to supress the windows?
> >
> > Best,
> > Antonius
> >
> > On Tue, Dec 5, 2017 at 6:56 PM, Lionel RIGOUX ***@***.***>
> > wrote:
> >
> > > I got the script running with no windows. For me, even the first files
> > > take way more than “few seconds” to run, as I am closer to 3min so
> far. I
> > > will let run overnight while logging the duration this if I can
> reproduce
> > > you bug.
> > > Are you sure the lengthening is due to the repetition and not the
> specific
> > > parametrization you’re testing in later loops? Meaning, if you reverse
> the
> > > order of model inversion, do you still see an increase of duration or
> does
> > > it reverse?
> > >
> > >
> > >
> > > > On 5. Dec 2017, at 15:55, Antonius Wiehler ***@***.***
> >
> > > wrote:
> > > >
> > > > Hi, sorry not for beeing clear enough. Unzip everything.
> > > > "Die-hard-discounting" is the main folder, "main_exp" includes
> > > (simulated)
> > > > log files, "_output" priors for modeling. The main script to run is
> > > > VBA_fit_multi_subject.m. Folder locations in line 21-24 need to be
> > > > adjusted, depending on the location of the folders.
> > > >
> > > > hope this helps.
> > > >
> > > > Best,
> > > > Antonius
> > > >
> > > > On Tue, Dec 5, 2017 at 3:01 PM, Lionel RIGOUX <
> ***@***.***>
> > > > wrote:
> > > >
> > > > > How should I organize all the folders and what should I change to
> run
> > > it?
> > > > >
> > > > > > On 5. Dec 2017, at 14:58, Antonius Wiehler <
> ***@***.***
> > > >
> > > > > wrote:
> > > > > >
> > > > > > done. (sent to your gmail).
> > > > > >
> > > > > > On Tue, Dec 5, 2017 at 2:55 PM, Lionel RIGOUX <
> > > ***@***.***>
> > > > > > wrote:
> > > > > >
> > > > > > > Hey Antonius
> > > > > > >
> > > > > > > This is a Github thread and answering to this email is logged
> into
> > > > > github.
> > > > > > > Because of this (I guess) I could not see the files you
> attached.
> > > > > > > Please send me privately the code, or start a Gist. Please
> ensure
> > > to
> > > > > > > enclose all dependencies.
> > > > > > > I’ll then try to reproduce your bug.
> > > > > > >
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Hi,
so I double checked. You had the right idea, closing the figures in every
loop iteration did the trick. The problem disappeared. I still not fully
understand it, I started Matlab with no graphical display and there was no
more than 1/3 of my RAM used, but anyway...
I could help with setting up a no display option for VBA_MFX if needed.
Thanks again for checking!
Best,
Antonius
On Wed, Dec 6, 2017 at 10:18 AM, Lionel RIGOUX <[email protected]>
wrote:
… Hey Antonius,
Your script ran overnight and is till running. So far I’ve seen no
consistent slowing of the inversion across the ~250 blocs than were
inverted, one bloc taking between 150 and 350s. I guess the accumulation of
windows was indeed the issue (it can be quite memory greedy).
I suggest that:
- you insert a clc and a close all between each block of MFX inversion
- ask Jean for a more elegant solution using a noDisplay and a verbose
flag in the MFX (and please on the development branch)
- see if you still have the problem.
I am sure you could also make use of the parallel toolbox to speed the
things a bit up.
Let me know if this solves your problem
Cheers
L
> On 5. Dec 2017, at 19:09, Antonius Wiehler ***@***.***>
wrote:
>
> Ouch, I could have done that. *facepalm* Great immediate fix!
>
> I will speak to Jean tomorrow, he left already.
>
> Best,
> Antonius
>
> On Tue, Dec 5, 2017 at 7:04 PM, Lionel RIGOUX ***@***.***>
> wrote:
>
> > So far I’m just doin a close all /clc after each iteration to avoid
> > crowding the memory. You should see with Jean (and whoever wrote the
MFX
> > function) about implementing a proper verbose/display switch.
> >
> > BTW, could you ask/help Jean to switch his copy of the toolbox to the
> > development branch, he’s started pushing frenetically directly to the
> > master and that’s not good...
> >
> >
> > > On 5. Dec 2017, at 19:00, Antonius Wiehler ***@***.***
>
> > wrote:
> > >
> > > great, thanks for checking! Let me know what the result is. I will
try
> > the
> > > inversion. how did you manage to supress the windows?
> > >
> > > Best,
> > > Antonius
> > >
> > > On Tue, Dec 5, 2017 at 6:56 PM, Lionel RIGOUX <
***@***.***>
> > > wrote:
> > >
> > > > I got the script running with no windows. For me, even the first
files
> > > > take way more than “few seconds” to run, as I am closer to 3min so
> > far. I
> > > > will let run overnight while logging the duration this if I can
> > reproduce
> > > > you bug.
> > > > Are you sure the lengthening is due to the repetition and not the
> > specific
> > > > parametrization you’re testing in later loops? Meaning, if you
reverse
> > the
> > > > order of model inversion, do you still see an increase of duration
or
> > does
> > > > it reverse?
> > > >
> > > >
> > > >
> > > > > On 5. Dec 2017, at 15:55, Antonius Wiehler <
***@***.***
> > >
> > > > wrote:
> > > > >
> > > > > Hi, sorry not for beeing clear enough. Unzip everything.
> > > > > "Die-hard-discounting" is the main folder, "main_exp" includes
> > > > (simulated)
> > > > > log files, "_output" priors for modeling. The main script to run
is
> > > > > VBA_fit_multi_subject.m. Folder locations in line 21-24 need to
be
> > > > > adjusted, depending on the location of the folders.
> > > > >
> > > > > hope this helps.
> > > > >
> > > > > Best,
> > > > > Antonius
> > > > >
> > > > > On Tue, Dec 5, 2017 at 3:01 PM, Lionel RIGOUX <
> > ***@***.***>
> > > > > wrote:
> > > > >
> > > > > > How should I organize all the folders and what should I change
to
> > run
> > > > it?
> > > > > >
> > > > > > > On 5. Dec 2017, at 14:58, Antonius Wiehler <
> > ***@***.***
> > > > >
> > > > > > wrote:
> > > > > > >
> > > > > > > done. (sent to your gmail).
> > > > > > >
> > > > > > > On Tue, Dec 5, 2017 at 2:55 PM, Lionel RIGOUX <
> > > > ***@***.***>
> > > > > > > wrote:
> > > > > > >
> > > > > > > > Hey Antonius
> > > > > > > >
> > > > > > > > This is a Github thread and answering to this email is
logged
> > into
> > > > > > github.
> > > > > > > > Because of this (I guess) I could not see the files you
> > attached.
> > > > > > > > Please send me privately the code, or start a Gist. Please
> > ensure
> > > > to
> > > > > > > > enclose all dependencies.
> > > > > > > > I’ll then try to reproduce your bug.
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > —
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Hi,
I'm using VBA_MFX to estimate choice model parameters. Now I tapped into the following issue: I ran multiple simulations and VBA_MFX fits in a row (~ 360 times to test different models and a range of parameters). I noticed that the VBA_MFX inversion is getting slower and slower (starting from a few seconds up to >60min per run). If I restart MATLAB, the problem is gone. 'clear all' or 'close all' do not solve the problem.
Best,
Antonius
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