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bilbyfw_install [2022/08/23 15:42]
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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   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: 
-  cd bilby 
-  pip install -r requirements.txt 
-  git checkout -b branch_1.1.4 1.1.4 
-  pip install . 
- 
-  cd ../bilby_pipe 
-  git checkout -b branch_1.0.4 1.0.4 
-  pip install . 
- 
-  cd ../parallel_bilby 
-  git checkout -b branch_1.0.1 1.0.1 
-  pip install . 
  
 ====EoS Patches==== ====EoS Patches====
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 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: 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
-  mv ../patches/bilby/* . +  git apply ../patches/bilby/* 
-  git apply *.patch+
   pip install -r requirements.txt   pip install -r requirements.txt
   pip install .   pip install .
 +  cd ../bilby_pipe 
 +  git apply ../patches/pipe/*  
 +  pip install .
   cd ../parallel_bilby   cd ../parallel_bilby
-  mv ../patches/pbilby/*  . +  git apply ../patches/pbilby/
-  git apply *.patch+
   pip install .   pip install .
  
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 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: 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   cd  [YOUR_DESTINATION]/bilby
-  git checkout -b branch_1.2.0 1.2.0 +  git checkout -b branch_1.2.1 1.2.1
-  pip install .+
  
   cd  [YOUR_DESTINATION]/bilby_pipe   cd  [YOUR_DESTINATION]/bilby_pipe
-  git checkout -b branch_1.0.6 1.0.6 +  git checkout -b branch_1.0.7 1.0.7
-  pip install .+
  
   cd  [YOUR_DESTINATION]/parallel_bilby   cd  [YOUR_DESTINATION]/parallel_bilby
-  git checkout -b branch_1.0.1 1.0.1 +  git checkout -b branch_1.1.0 1.1.0 
-  pip install .+You can then apply the patches as described above.
  
 B) //Fix the fix.// B) //Fix the fix.//
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            print(f"Sampling time = {datetime.timedelta(seconds=result.sampling_time)}s")            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 six lines starting at line 686 should be  +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 ''+'' +  * exlusive to file b if the line begins with a ''+'' 
-- exclusive to file a if the line begins with a ''-'' +  * exclusive to file a if the line begins with a ''-'' 
-- shared if the line begins with a blank. +  * 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 had already added two more lines, the linecount for b starts at 686, not 684.  +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 line for file these. 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. +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 done 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.+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 2022/08/23 15:42

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