Python 2 requirement

[ivan-pi]

Attempting to build this project from source, I noticed the packaged CTemplate version has a Python 2 build/installation requirement:

[ 70%] Performing build step for 'CTemplate'
  File "/home/HemePure-GPU/dep/build/CTemplate-prefix/src/CTemplate/./src/htmlparser/generate_fsm.py", line 309
    print '\n'.join((self._CreateHeader(),

There has only been one new CTemplate release (v2.4), but I haven't yet inspected if it was replaced with Python 3.

[ivan-pi]

Okay, it looks like the switch was made in v2.4 of CTemplate: OlafvdSpek/ctemplate@ee11ba1

Since Python 2 is now unsupported, some environments don't provide it anymore.

Replacing the old tarball (https://github.com/UCL-CCS/HemePure-GPU/blob/master/dep/src/ctemplate-2.3.tar.gz) with the new one (https://github.com/OlafvdSpek/ctemplate/releases/tag/ctemplate-2.4) would be the solution.

[ivan-pi]

Replacing the tarball with the new version or simply using the CTEMPLATE_TARBALL variable doesn't work, because the CMake script expects to find an executable configure:

[ 70%] Creating directories for 'CTemplate'
[ 75%] Performing download step (download, verify and extract) for 'CTemplate'
-- Downloading...
   dst='/home/HemePure-GPU/dep/build/CTemplate-prefix/src/ctemplate-2.4.tar.gz'
   timeout='none'
   inactivity timeout='none'
-- Using src='http://github.com/OlafvdSpek/ctemplate/archive/ctemplate-2.4.tar.gz'
-- Downloading... done
-- extracting...
     src='/home/HemePure-GPU/dep/build/CTemplate-prefix/src/ctemplate-2.4.tar.gz'
     dst='/home/HemePure-GPU/dep/build/CTemplate-prefix/src/CTemplate'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 79%] No update step for 'CTemplate'
[ 83%] Performing patch step for 'CTemplate'
noalign
novacopy
[ 87%] Performing configure step for 'CTemplate'
/bin/sh: /home/HemePure-GPU/dep/build/CTemplate-prefix/src/CTemplate/configure: No such file or directory
make[2]: *** [CMakeFiles/CTemplate.dir/build.make:92: CTemplate-prefix/src/CTemplate-stamp/CTemplate-configure] Error 127
make[1]: *** [CMakeFiles/Makefile2:139: CMakeFiles/CTemplate.dir/all] Error 2
make: *** [Makefile:91: all] Error 2

The configure script is only available after ./autogen.sh has been run, which must have been the case in the current tarball.

To fix this I had to patch this line:

HemePure-GPU/dep/CMakeLists.txt

Line 229 in a398c30

CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CTEMPLATE_CONFIGURE_OPTIONS}

-	CONFIGURE_COMMAND	<SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CTEMPLATE_CONFIGURE_OPTIONS}
+	CONFIGURE_COMMAND	<SOURCE_DIR>/autogen.sh && <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CTEMPLATE_CONFIGURE_OPTIONS} 

[ivan-pi]

I was finally able to build CTemplate now 🚀

[100%] Completed 'CTemplate'
[100%] Built target CTemplate

It did however choke with the NVIDIA nvc/nvc++ compiler, so I switched to gcc for the dependency libraries.

[izacharo]

Hi Ivan, Another alternative is to use python's function 2to3 to convert the python scripts that cause the problem. So when it complains about the python 2 files (there will be 2 in total) you can do the conversion by using 2to3 - w path_to_python_file/python_file.py You will do that twice. I will get back to you in a while with more details regarding these files. Best, Ioannis

…

On Wed, 3 May 2023, 13:21 Ivan Pribec, ***@***.***> wrote: I was finally able to build CTemplate now 🚀 [100%] Completed 'CTemplate' [100%] Built target CTemplate It did however choke with the NVIDIA nvc/nvc++ compiler, so I switched to gcc for the dependency libraries. — Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMNBIMBMHDKFCRAGCFZXX2DXEIWRVANCNFSM6AAAAAAXUEAZKM> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[ivan-pi]

Thanks for the tip, I was not aware of the 2to3 tool. 👍🏻

The environment I'm working in is somewhat restricted, I have no pip access, and only Python 3.9 is available by default. Not even automake/autoreconf were present to build CTemplate, but I got hold of them through a module.

As far as I can see, the only difference in CTemplate v2.4 is the switch to Python 3. It is also used in HemePure-CPU Spack build: https://github.com/compbiomedeu/compbiomed-spack/blob/main/packages/ctemplate/package.py#L33

[izacharo]

I understand what pain this can be... On a different note I got rid of the memory allocations inside the GPU kernels that were causing a problem with porting to oneapi. So I should be able to make progress on that task soon. I just need to finalize a few other things this week with the hipified code first. I will keep you posted Best, Ioannis Sent from my phone-------- Original message --------From: Ivan Pribec ***@***.***>Date: Wed, 3 May 2023, 13:35To: UCL-CCS/HemePure-GPU ***@***.***>Cc: izacharo ***@***.***>, Comment ***@***.***>Subject: Re: [UCL-CCS/HemePure-GPU] Python 2 requirement (Issue #6) Thanks for the tip, I was not aware of the 2to3 tool. 👍🏻 The environment I'm working in is somewhat restricted, I have no pip access, and only Python 3.9 is available by default. Not even automake/autoreconf were present to build CTemplate, but I got hold of them through a module. As far as I can see, the only difference in CTemplate v2.4 is the switch to Python 3. It is also used in HemePure-CPU Spack build: https://github.com/compbiomedeu/compbiomed-spack/blob/main/packages/ctemplate/package.py#L33 —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: ***@***.***>

[ivan-pi]

I think this issue is also resolved by #9? cc @benczaja

[benczaja]

Yes it should be (@ivan-pi). Though I think that the HIP branch (https://github.com/UCL-CCS/HemePure-GPU/tree/HIP) still does not have the merge