Comments (9)
rjbgoudie
commented on June 1, 2024
Sorry to hear you’re having problems. Could you clarify exactly what you mean by "the sampling was not distributed over the three cores” and "the cores are not activated”? What showed to you that this was the case? Since the BUGSWorker.exe show up in the Task Manager, it sounds like MultiBUGS did manage to distribute the computation across cores, so I am unsure what you mean. It may well be that there is no speed-up, even if it did manage to distribute the model — the speed up depends on, in particular, the exact model and the exact computer.
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emmanuellesaffre
commented on June 1, 2024
Dear,
Indeed I see three versions of BUGSworker.exe on Task Manager when I initiate 3 chains and I ask to distribute to 3 cores, but:
- When I ask MultiBUGS for information Info>Distribution then I see that only 1 Logical processor is taken
- Then, when I run 3 chains in parallel and aks for each chain 150,000 iterations to do (for a simple linear regression model), then the time needed by OpenBUGS is exactly the same as for MultiBUGS. This not only happens with me, but also on three other laptops and also happens with a hierarchical logistic regression model
So, my conclusion is that perhaps parallel computing is done but perhaps there is problem with the link between what the BUGSworker.exe programs are doing what we receive as result
Thanks for your help
Kind regards
Emmanuel Lesaffre
…-------------------------------------------------------------------------------------------------------------------------
Professor emeritus Biostatistics
L-Biostat, School of Public Health, KULeuven University of Leuven, Belgium
Kapucijnenvoer 35, 2nd Floor, B-3000 Leuven, BELGIUM
Tel: +32 16 37 33 64| Fax: + 32 16 33 70 15 | Tel secr: +32 16 37 33 89
E-mail: [email protected]<mailto:[email protected]> | Website: https://ibiostat.be
Honorary Professor, Erasmus MC, Rotterdam, the Netherlands
-------------------------------------------------------------------------------------------------------------------------
From: RJB Goudie <[email protected]>
Sent: Thursday, October 24, 2019 1:05 PM
To: MultiBUGS/MultiBUGS <[email protected]>
Cc: Emmanuel Lesaffre <[email protected]>; Author <[email protected]>
Subject: Re: [MultiBUGS/MultiBUGS] Problem with distribute (#33)
Sorry to hear you’re having problems. Could you clarify exactly what you mean by "the sampling was not distributed over the three cores” and "the cores are not activated”? What showed to you that this was the case? Since the BUGSWorker.exe show up in the Task Manager, it sounds like MultiBUGS did manage to distribute the computation across cores, so I am unsure what you mean. It may well be that there is no speed-up, even if it did manage to distribute the model — the speed up depends on, in particular, the exact model and the exact computer.
—
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emmanuellesaffre
commented on June 1, 2024
Hi,
Did you receive my reply?
Kind regards
Emmanuel Lesaffre
…-------------------------------------------------------------------------------------------------------------------------
Professor emeritus Biostatistics
L-Biostat, School of Public Health, KULeuven University of Leuven, Belgium
Kapucijnenvoer 35, 2nd Floor, B-3000 Leuven, BELGIUM
Tel: +32 16 37 33 64| Fax: + 32 16 33 70 15 | Tel secr: +32 16 37 33 89
E-mail: [email protected]<mailto:[email protected]> | Website: https://ibiostat.be
Honorary Professor, Erasmus MC, Rotterdam, the Netherlands
-------------------------------------------------------------------------------------------------------------------------
From: RJB Goudie <[email protected]>
Sent: Thursday, October 24, 2019 1:05 PM
To: MultiBUGS/MultiBUGS <[email protected]>
Cc: Emmanuel Lesaffre <[email protected]>; Author <[email protected]>
Subject: Re: [MultiBUGS/MultiBUGS] Problem with distribute (#33)
Sorry to hear you’re having problems. Could you clarify exactly what you mean by "the sampling was not distributed over the three cores” and "the cores are not activated”? What showed to you that this was the case? Since the BUGSWorker.exe show up in the Task Manager, it sounds like MultiBUGS did manage to distribute the computation across cores, so I am unsure what you mean. It may well be that there is no speed-up, even if it did manage to distribute the model — the speed up depends on, in particular, the exact model and the exact computer.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#33?email_source=notifications&email_token=AMCZQN3OEY6D7LYFKXMVXC3QQF6OVA5CNFSM4JBVAUD2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECEUKLY#issuecomment-545867055>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMCZQNZBVZX6YAJIC4463T3QQF6OVANCNFSM4JBVAUDQ>.
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rjbgoudie
commented on June 1, 2024
Yes, but I’m still puzzled I’m afraid. I have some more questions/comments that might help to isolate the problem.
Just to confirm, you are using MultiBUGS 1.0? Also, do you get results from all 3 chains if you look at the output?
Note that if you run 3 chains, with “num cores”=3, it won’t parallelise WITHIN each chain, regardless of whether it is possible: each chain will use 1 of the 3 cores. Hence why Info>”Show Distribution” is probably showing “Number of processor: 1”. What does Info > Distribution Info say?
The problem could be either (1) MultiBUGS is not setup quite correctly on your computer; (2) your specific model(s) do not parallelise efficiently in MultiBUGS; or (3) a bug in MultiBUGS; or (4) something else..!
To standardise on a model I know about, could you try the Methadone example from Examples > Examples Vol IV > Methadone, and compare run times for "1 chain, with no distribution" (don’t click distribute at all) vs "1 chain, with 2 cores"? I suggest only trying to run a few iterations, since it will be very slow with only 1 or 2 cores. e.g. on my current computer 50 iterations takes ~20s (no distribute) vs ~10s with 2 cores.
Sorry again that you are having problems - hopefully we can figure it out.
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emmanuellesaffre
commented on June 1, 2024
Dear,
When I apply MultiBUGS on your example, then I get for 50 iterations:
15s with 1 core
8s with 2 cores
And Info>Distribution now talks of 2 processors
So the program seems to work.
I then tried 2 chains with
2 cores: 17s
1 core: does not work
4 cores: 9s
So for this example the program appears to work.
Is there a reason why there is no gain when I apply it a simple regression analysis (I include the program) when I run 150000 iterations with 3 chains and distribute =3, compared to 150000 iterations with 3 chains and distribute = 1?
Kind regards
Emmanuel Lesaffre
…-------------------------------------------------------------------------------------------------------------------------
Professor emeritus Biostatistics
L-Biostat, School of Public Health, KULeuven University of Leuven, Belgium
Kapucijnenvoer 35, 2nd Floor, B-3000 Leuven, BELGIUM
Tel: +32 16 37 33 64| Fax: + 32 16 33 70 15 | Tel secr: +32 16 37 33 89
E-mail: [email protected]<mailto:[email protected]> | Website: https://ibiostat.be
Honorary Professor, Erasmus MC, Rotterdam, the Netherlands
-------------------------------------------------------------------------------------------------------------------------
From: RJB Goudie <[email protected]>
Sent: Monday, October 28, 2019 3:30 PM
To: MultiBUGS/MultiBUGS <[email protected]>
Cc: Emmanuel Lesaffre <[email protected]>; Author <[email protected]>
Subject: Re: [MultiBUGS/MultiBUGS] Problem with distribute (#33)
Yes, but I’m still puzzled I’m afraid. I have some more questions/comments that might help to isolate the problem.
Just to confirm, you are using MultiBUGS 1.0? Also, do you get results from all 3 chains if you look at the output?
Note that if you run 3 chains, with “num cores”=3, it won’t parallelise WITHIN each chain, regardless of whether it is possible: each chain will use 1 of the 3 cores. Hence why Info>”Show Distribution” is probably showing “Number of processor: 1”. What does Info > Distribution Info say?
The problem could be either (1) MultiBUGS is not setup quite correctly on your computer; (2) your specific model(s) do not parallelise efficiently in MultiBUGS; or (3) a bug in MultiBUGS; or (4) something else..!
To standardise on a model I know about, could you try the Methadone example from Examples > Examples Vol IV > Methadone, and compare run times for "1 chain, with no distribution" (don’t click distribute at all) vs "1 chain, with 2 cores"? I suggest only trying to run a few iterations, since it will be very slow with only 1 or 2 cores. e.g. on my current computer 50 iterations takes ~20s (no distribute) vs ~10s with 2 cores.
Sorry again that you are having problems - hopefully we can figure it out.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#33?email_source=notifications&email_token=AMCZQN6CYZPK7FGFZ5ADYWDQQ3ZMPA5CNFSM4JBVAUD2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECNCDXY#issuecomment-546972127>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMCZQN4JDJTNDB2S7QOG67LQQ3ZMPANCNFSM4JBVAUDQ>.
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emmanuellesaffre
commented on June 1, 2024
Forgot to include the example
Kind regards
Emmanuel Lesaffre
…-------------------------------------------------------------------------------------------------------------------------
Professor emeritus Biostatistics
L-Biostat, School of Public Health, KULeuven University of Leuven, Belgium
Kapucijnenvoer 35, 2nd Floor, B-3000 Leuven, BELGIUM
Tel: +32 16 37 33 64| Fax: + 32 16 33 70 15 | Tel secr: +32 16 37 33 89
E-mail: [email protected]<mailto:[email protected]> | Website: https://ibiostat.be
Honorary Professor, Erasmus MC, Rotterdam, the Netherlands
-------------------------------------------------------------------------------------------------------------------------
From: RJB Goudie <[email protected]>
Sent: Monday, October 28, 2019 3:30 PM
To: MultiBUGS/MultiBUGS <[email protected]>
Cc: Emmanuel Lesaffre <[email protected]>; Author <[email protected]>
Subject: Re: [MultiBUGS/MultiBUGS] Problem with distribute (#33)
Yes, but I’m still puzzled I’m afraid. I have some more questions/comments that might help to isolate the problem.
Just to confirm, you are using MultiBUGS 1.0? Also, do you get results from all 3 chains if you look at the output?
Note that if you run 3 chains, with “num cores”=3, it won’t parallelise WITHIN each chain, regardless of whether it is possible: each chain will use 1 of the 3 cores. Hence why Info>”Show Distribution” is probably showing “Number of processor: 1”. What does Info > Distribution Info say?
The problem could be either (1) MultiBUGS is not setup quite correctly on your computer; (2) your specific model(s) do not parallelise efficiently in MultiBUGS; or (3) a bug in MultiBUGS; or (4) something else..!
To standardise on a model I know about, could you try the Methadone example from Examples > Examples Vol IV > Methadone, and compare run times for "1 chain, with no distribution" (don’t click distribute at all) vs "1 chain, with 2 cores"? I suggest only trying to run a few iterations, since it will be very slow with only 1 or 2 cores. e.g. on my current computer 50 iterations takes ~20s (no distribute) vs ~10s with 2 cores.
Sorry again that you are having problems - hopefully we can figure it out.
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#33?email_source=notifications&email_token=AMCZQN6CYZPK7FGFZ5ADYWDQQ3ZMPA5CNFSM4JBVAUD2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECNCDXY#issuecomment-546972127>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMCZQN4JDJTNDB2S7QOG67LQQ3ZMPANCNFSM4JBVAUDQ>.
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rjbgoudie
commented on June 1, 2024
Glad we’re making a little progress. Across-chain parallelisation should work for any model, so I’m not sure why it isn’t working for you.
I guess you attached the fiels to the email, but it seems that email attachments don’t get passed through via GitHub. Can you please attach the files directly to the issue on GitHub? (Or email direct to me if you don’t want it in the public domain)
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emmanuellesaffre
commented on June 1, 2024
Thanks
What your email address?
Emmanuel
From: RJB Goudie <[email protected]>
Sent: Monday, October 28, 2019 8:31 PM
To: MultiBUGS/MultiBUGS <[email protected]>
Cc: Emmanuel Lesaffre <[email protected]>; Author <[email protected]>
Subject: Re: [MultiBUGS/MultiBUGS] Problem with distribute (#33)
Glad we’re making a little progress. Across-chain parallelisation should work for any model, so I’m not sure why it isn’t working for you.
I guess you attached the fiels to the email, but it seems that email attachments don’t get passed through via GitHub. Can you please attach the files directly to the issue on GitHub? (Or email direct to me if you don’t want it in the public domain)
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub<#33?email_source=notifications&email_token=AMCZQN62KO43C3J7L663ZODQQ44YHA5CNFSM4JBVAUD2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECODUVA#issuecomment-547109460>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMCZQNYCKFYA7ZHO32YDJLLQQ44YHANCNFSM4JBVAUDQ>.
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rjbgoudie
commented on June 1, 2024
Resolved offline but for future reference: each MCMC step of the model is quite fast so if refresh=100, then the communication time dominates everything else.
For 100,000 iterations, with 3 chains, with refresh=100 we get:
3 cores in MultiBUGS: 62 seconds
1 core in MultiBUGS: 62 seconds
With refresh=100000:
3 cores in MultiBUGS: 1 second
1 core in MultiBUGS: 4 seconds
The setting of refresh makes a big difference because at each refresh all the cores must communicate their results to the master process, so that any trace plots etc can be updated. When each MCMC step is quite fast, as here, this communication overhead dominates.
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- Replace link in readme file
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