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jacopo-chevallard / BEAGLE-general

Basic information to get started with the galaxy spectral modelling tool Beagle
https://www.iap.fr/beagle/
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fit_spectrum_example on a mac #93

Closed codebreaker2 closed 3 years ago

codebreaker2 commented 4 years ago

Hi,

We were able to run the fit_spectrum_example on a friend's PC, but we cannot get it to run on our Mac (OSX 10.14.6) & Docker Platform 19.03.8.

The code appears to finish the sampling, and it finishes without giving an error message. However, it produces an empty *fits.gz file. We noticed that there is still a '.lock' file, and the cpu time is not printed.

Any idea of what's going wrong?

Have others successfully run BEAGLE on a Mac?

Or would you advise purchasing a PC for BEAGLE runs?

Thanks, Crystal

p.s. I attach the output files from the PC (README.guitar-centos) and from the Mac (README.Tango). README.guitar-centos.txt README.Tango.txt

jacopo-chevallard commented 4 years ago

hi @codebreaker2, we mostly run Beagle on mac and linux, so it's surprising that you find this problem... which Beagle version are you running? (can see the version launching Beagle with --version)

It seems that the fitting is running well, but then for some reason the output file is not printed properly... can you provide us the input files you're using?

codebreaker2 commented 4 years ago

Hi Jacopo,

Glad to hear that BEAGLE should work on Mac too. 

Sarah will correct me if I’m wrong, but I believe she generated the output  by running the ‘fit_spectrum_example.param’ input file.

I am wondering if it is a permission problem.  I noticed that Sarah is executing the code as ‘sudo docker run …’.  

I am not familiar with docker, but it surprises me that ‘sudo’ is required.

Crystal Martin & Sarah Polizzotto

From: Jacopo Chevallard notifications@github.com Reply-To: jacopo-chevallard/BEAGLE-general reply@reply.github.com Date: Thursday, October 8, 2020 at 1:11 AM To: jacopo-chevallard/BEAGLE-general BEAGLE-general@noreply.github.com Cc: codebreaker2 cmartin@ucsb.edu, Mention mention@noreply.github.com Subject: Re: [jacopo-chevallard/BEAGLE-general] fit_spectrum_example on a mac (#93)

hi @codebreaker2, we mostly run Beagle on mac and linux, so it's surprising that you find this problem... which Beagle version are you running? (can see the version launching Beagle with --version)

It seems that the fitting is running well, but then for some reason the output file is not printed properly... can you provide us the input files you're using?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

jacopo-chevallard commented 4 years ago

@codebreaker2 can you try to relaunch without sudo, i.e.

docker run --rm -it -v /Applications/BEAGLE-general:/BEAGLE_virtual_workdir --env-file /Applications/BEAGLE-general/env.list --user $(id -u):$(id -g) beagletool/beagle:0.24.4 --parameter-file /BEAGLE_virtual_workdir/params/fit_spectrum_example.param --fit

and, if it doesn't solve, to remove --user $(id -u):$(id -g) while keeping sudo, i.e.

sudo docker run --rm -it -v /Applications/BEAGLE-general:/BEAGLE_virtual_workdir --env-file /Applications/BEAGLE-general/env.list beagletool/beagle:0.24.4 --parameter-file /BEAGLE_virtual_workdir/params/fit_spectrum_example.param --fit

polizzotto12 commented 4 years ago

I'm working with Dr. Martin @codebreaker2 and I tried running both of those commands on the Mac we're using, and got the same error where the program terminated before printing the CPU time without any error messages.

I am running the default fit_spectrum.param file, where I have only changed the paths to TEMPLATES NEBULAR to match what is on our computer.

Thanks, Sarah

eclake commented 4 years ago

Hi @jacopo-chevallard - just a note (it might not be related), if the sampling finished this may be related to https://github.com/jacopo-chevallard/BEAGLE/issues/253 - (sorry @codebreaker2 @polizzotto12, you won't be able to read this one) it was something we've noticed with the dust_HII branch and I haven't worked back yet to see when it was introduced. (Essentially super large memory requirement when writing to files, can be a problem if fitting to spectra because there is a higher memory load when not rebinning the templates). I'll double check if this problem was present in 0.24.4

@codebreaker2 @polizzotto12 - how much memory is available to docker in your runs? Are you fitting to spectra?

polizzotto12 commented 4 years ago

Our goal is to use BEAGLE to fit spectra. Initially I had Docker set to 6 GB of memory, but I increased it to the maximum 16 GB and it appears that this has solved the problem, as fit_spectrum_example.param now runs. Thanks for your help!

The original error (terminating without creating the output file) also occurred for fit_photometry_example.param as well when the memory was set to 6 GB. Is 6 GB the suggested memory only for creating mock spectra (this example worked fine), not fitting?

jacopo-chevallard commented 4 years ago

That's great, thanks @eclake for your suggestion!

The original error (terminating without creating the output file) also occurred for fit_photometry_example.param as well when the memory was set to 6 GB. Is 6 GB the suggested memory only for creating mock spectra (this example worked fine), not fitting?

This is hard to tell, it can be that newer versions of Docker require more memory than older versions... Have you, by chance, tried with some intermediate values, like 8 or 12 GB?