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bilbyfw_install [2022/08/19 07:28]
theoastro 		bilbyfw_install [2022/09/12 15:32] (current)
theoastro
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 It will save you a great amount of pain to use a dedicated python [[https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html|environment]] for your work with bilby. Create it with  It will save you a great amount of pain to use a dedicated python [[https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html|environment]] for your work with bilby. Create it with 
   conda create -n [YOUR_PBILBY_ENVIRONMENT] python=3.7   conda create -n [YOUR_PBILBY_ENVIRONMENT] python=3.7
-and hit  ''%%y%%'' when asked if you want to proceed.  Then activate it by typing+and hit  ''y'' when asked if you want to proceed.  Then activate it by typing
   conda activate [YOUR_PBILBY_ENVIRONMENT]   conda activate [YOUR_PBILBY_ENVIRONMENT]
  
-Python packages are distributed through sometimes conflicting [[https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/channels.html#what-is-a-conda-channel|channels]]. To avoid conflicts, we make sure to use the very common channel  ''%%conda-forge%%'':+Python packages are distributed through sometimes conflicting [[https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/channels.html#what-is-a-conda-channel|channels]]. To avoid conflicts, we make sure to use the very common channel  ''conda-forge'':
   conda config --add channels conda-forge   conda config --add channels conda-forge
   conda config --set channel_priority strict   conda config --set channel_priority strict
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 ==== The Bilby Family ==== ==== The Bilby Family ====
-If you want to work with the ''%%bilby%%'' family in its most recent version, simply use again+If you want to work with the ''bilby'' family in its most recent version, simply use again
   conda install bilby   conda install bilby
   conda install bilby_pipe   conda install bilby_pipe
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 ''parallel_bilby'' uses ''bilby_pipe'' to interact efficiently with ''bilby'' and your computer. ''parallel_bilby'' uses ''bilby_pipe'' to interact efficiently with ''bilby'' and your computer.
  
-If however, you want to include the possibility to sample over Equations of State, you need to install from source as this allows us to include dedicated patches (see below). To do so, (make and) go to a convenient destination directory (''%%cd [YOUR_DESTINATION]%%'') and download the respective package: +If however, you want to include the possibility to sample over Equations of State, you need to install from source as this allows us to include dedicated patches (see below). To do so, (make and) go to a convenient destination directory (''cd [YOUR_DESTINATION]'') and download the respective package: 
   git clone https://git.ligo.org/lscsoft/bilby.git   git clone https://git.ligo.org/lscsoft/bilby.git
   git clone https://git.ligo.org/lscsoft/bilby_pipe.git   git clone https://git.ligo.org/lscsoft/bilby_pipe.git
   git clone https://git.ligo.org/lscsoft/parallel_bilby.git   git clone https://git.ligo.org/lscsoft/parallel_bilby.git
-This should create a folder each in your destination that contains the package's components. The EoS patches require older versions of each package. Therefore execute the following lines:+ 
 +====EoS Patches==== 
 +Patches to handle EoS are available in {{:patches.zip|this zip-file}}. 
 +Copy it to the same directory as the bilby-family, using e.g. the ''scp''-[[https://linuxhandbook.com/scp-command/|command]], and hit ''unzip patches.zip''.  Allocate and apply the patches using these commands:
   cd bilby   cd bilby
 +  git apply ../patches/bilby/* 
   pip install -r requirements.txt   pip install -r requirements.txt
-  git checkout -b branch_1.1.4 1.1.4 
   pip install .   pip install .
- 
   cd ../bilby_pipe   cd ../bilby_pipe
-  git checkout -b branch_1.0.4 1.0.4+  git apply ../patches/pipe/* 
   pip install .   pip install .
- 
   cd ../parallel_bilby   cd ../parallel_bilby
-  git checkout -b branch_1.0.1 1.0.1+  git apply ../patches/pbilby/
   pip install .   pip install .
- 
-====EoS Patches==== 
-Patches to handle EoS are available in {{:patches.zip|this zip-file}}. 
-Copy it to the same directory as the bilby-family, using e.g. the ''scp''-[[https://linuxhandbook.com/scp-command/|command]], and hit ''unzip patches.zip''.  Allocate and apply the patches using these commands: 
-  cd bilby 
-  mv ../patches/bilby/* . 
-  git apply *.patch 
- 
-  cd ../parallel_bilby 
-  mv ../patches/pbilby/*  . 
-  git apply *.patch 
  
 Your computer should now be ready to handle Bayesian Inference problems in a gravitational wave context. Your computer should now be ready to handle Bayesian Inference problems in a gravitational wave context.
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 You may also need to update ''pip'' by running ''pip install -U pip'' (with a capital U). You may also need to update ''pip'' by running ''pip install -U pip'' (with a capital U).
  
-On a cluster, you may expect ''zip'' to be available, but it probably is not on your private computer+Essentially, ''pip install . '' is a convenient way to check dependencies and then execute the file ''setup.py'' in your current directory.  
 +This file specifies the routines to be installed. The patches now serve to change some of the files ''setup.py'' refers to //before// installation. As a basic sanity check, the patches contain some lines of the original code //at time of writing// to investigate whether the insertions will happen at the expexted lines.   As all of the bilby family is still under development, there is a good chance this reference content is not matched and ''git apply'' will return  
 +  error:[file]: patch does not apply 
 +You have two options two fix this: 
 +A) //Ressort to that version for which the patches were written.// This can be done by creating [[https://www.atlassian.com/git/tutorials/using-branches/git-checkout|new branches]] of the code. To do so, execute: 
 +  cd  [YOUR_DESTINATION]/bilby 
 +  git checkout -b branch_1.2.1 1.2.1 
 + 
 +  cd  [YOUR_DESTINATION]/bilby_pipe 
 +  git checkout -b branch_1.0.7 1.0.7 
 + 
 +  cd  [YOUR_DESTINATION]/parallel_bilby 
 +  git checkout -b branch_1.1.0 1.1.0 
 +You can then apply the patches as described above. 
 + 
 +B) //Fix the fix.// 
 +If you feel comfortable doing so, you might also fix the patches. This will generally be advantageous as newer programme versions tend to be more efficient, but the patches might also cause some fringe behaviour. For safety, you might want to first do A in a dedicated ''conda'' environment. The patch files look something like this: 
 + 
 +  diff --git a/parallel_bilby/analysis.py b/parallel_bilby/analysis.py 
 +  [...] 
 +  --- a/parallel_bilby/analysis.py 
 +  +++ b/parallel_bilby/analysis.py 
 +  @@ -684,4 +686,6 @@ with MPIPool( 
 +    
 +  +        logger.info(f"Saving posterior samples to {outdir}/{label}_posterior_samples.dat") 
 +  +        result.save_posterior_samples() 
 +           logger.info(f"Saving result to {outdir}/{label}_result.json") 
 +           result.save_to_file(extension="json") 
 +           print(f"Sampling time = {datetime.timedelta(seconds=result.sampling_time)}s") 
 + 
 +Read this as: The content of file a in the 4 lines starting at line 684 and file b in the 6lines starting at line 686 should be  
 +  * exlusive to file b if the line begins with a ''+'' 
 +  * exclusive to file a if the line begins with a ''-'' 
 +  * shared if the line begins with a blank. 
 +Since file a and b are identical, this will effectively result in the addition of the two lines indicated by the '+'. Because the omitted code section had already added two more lines, the linecount for b starts at 686, not 684.  
 +So probably all you need to do is to identify where in the updated version of the respective files //a// and //b// the insertions have to be made and change the corresponding start lines. The addition of ''with MPIPool('' indicates the general context (in many other cases the superior function) in which the respective lines of code were called. 
 +As mentioned, though, this is subject to the extend of changes that have been made to the packages. If you find that this context is no longer present or that the patch causes other errors, you might prefer to ressort to option A. 
 + 
Last modified: le 2022/08/19 07:28

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