{bio}[GCCcore/12.3.0] AreTomo2 v1.1.2 w/ CUDA 12.1.1

[ThomasHoffmann77]

(created using eb --new-pr)
fix: rebuild shipped libmrcfile.a and libutil.a from source.

[verdurin]

Test report by @verdurin
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/728f6a8c6a991481e35ae586d9d3e65f for a full test report.

[ThomasHoffmann77]

Test report by @verdurin FAILED Build succeeded for 0 out of 1 (1 easyconfigs in total) easybuild-el8.cloud.in.bmrc.ox.ac.uk - Linux Rocky Linux 8.10, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8 See https://gist.github.com/verdurin/728f6a8c6a991481e35ae586d9d3e65f for a full test report.

sanity check command "AreTomo2 -h" requires libcuda.so.1

[sassy-crick]

@ThomasHoffmann77 You might want to sync your PR with development, something like this:

eb --sync-pr-with-develop NUMBER_OF_PR

[github-actions]

Updated software AreTomo2-1.1.2-GCCcore-12.3.0-CUDA-12.1.1.eb

Diff against AreTomo2-1.0.0-GCCcore-12.3.0-CUDA-12.1.1.eb

easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0-GCCcore-12.3.0-CUDA-12.1.1.eb

diff --git a/easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.1.2-GCCcore-12.3.0-CUDA-12.1.1.eb
index d59d99cda1..b72be8afec 100644
--- a/easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0-GCCcore-12.3.0-CUDA-12.1.1.eb
+++ b/easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.1.2-GCCcore-12.3.0-CUDA-12.1.1.eb
@@ -2,22 +2,22 @@
 easyblock = 'MakeCp'
 
 name = 'AreTomo2'
-version = '1.0.0'
+version = '1.1.2'
 versionsuffix = '-CUDA-%(cudaver)s'
 
 homepage = 'https://github.com/czimaginginstitute/AreTomo2'
 
-description = """AreTomo2, a multi-GPU accelerated software package that fully automates motion-
-corrected marker-free tomographic alignment and reconstruction, now includes
-robust GPU-accelerated CTF (Contrast Transfer Function) estimation in a single
-package. AreTomo2 is part of our endeavor to build a fully-automated high-
-throughput processing pipeline that enables real-time reconstruction of
-tomograms in parallel with tomographic data collection. It strives to be fast
-and accurate, as well as provides for easy integration into subtomogram
-processing workflows by generating IMod compatible files containing alignment
-and CTF parameters needed to bootstrap subtomogram averaging. AreTomo2 can also
-be used for on-the-fly reconstruction of tomograms and CTF estimation in
-parallel with tilt series collection, enabling real-time assessment of sample
+description = """AreTomo2, a multi-GPU accelerated software package that fully automates motion- 
+corrected marker-free tomographic alignment and reconstruction, now includes    
+robust GPU-accelerated CTF (Contrast Transfer Function) estimation in a single  
+package. AreTomo2 is part of our endeavor to build a fully-automated high-      
+throughput processing pipeline that enables real-time reconstruction of         
+tomograms in parallel with tomographic data collection. It strives to be fast   
+and accurate, as well as provides for easy integration into subtomogram         
+processing workflows by generating IMod compatible files containing alignment   
+and CTF parameters needed to bootstrap subtomogram averaging. AreTomo2 can also 
+be used for on-the-fly reconstruction of tomograms and CTF estimation in        
+parallel with tilt series collection, enabling real-time assessment of sample   
 quality and adjustment of collection parameters"""
 
 toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
@@ -25,15 +25,16 @@ toolchainopts = {'cstd': 'c++11'}
 
 source_urls = [GITHUB_SOURCE]
 sources = ['v%(version)s.tar.gz']
-patches = ['%(name)s-%(version)s_makefile.patch']
+patches = ['%(name)s-%(version)s_makefile_lib.patch']
 checksums = [
-    {'v1.0.0.tar.gz': '5518cd5d7bc13a6dbb6d9310b22c301e73a0c91dc059da403445d79ca0ff8892'},
-    {'AreTomo2-1.0.0_makefile.patch': '8595b2fc55e0b5e1bf7c077c93c09503b4e8f95123c6aaf0a5fbe44dda871c73'},
+    {'v1.1.2.tar.gz': '4cbb4d25d28778041d80ef2c598519b17b9a40aa84e1e99daf48ad5a90d946b4'},
+    {'AreTomo2-1.1.2_makefile_lib.patch': '53b3694104c4149d2714e503fb2a7cb9be7cbb0e500ee6991a606faa1c10a314'},
 ]
 
 github_account = 'czimaginginstitute'
 
-build_cmd = 'make exe -f makefile11 CUDAHOME=$CUDA_HOME CUDACC="%(cuda_cc_cmake)s"'
+prebuildopts = 'rm -rf LibSrc/Lib/*.a && '
+build_cmd = 'make clean -f makefile11 && make exe -f makefile11 CUDAHOME=$CUDA_HOME CUDACC="%(cuda_cc_cmake)s"'
 
 builddependencies = [
     ('binutils', '2.40')

[akesandgren]

This should come before source_urls, please fix

[akesandgren]

dirs can be just "[]" since bin is already checked due to files

[akesandgren]

Why not just remove the "@" in front of the compile line if you want it to print what it does.

[akesandgren]

Same here but for the rm line

[akesandgren]

The $(CC) is printed by make anyway

[akesandgren]

This should use $(CXX) not g++

[akesandgren]

Here to, just drop the @

[ThomasHoffmann77]

Thanks @akesandgren, i was not aware of the meaning of @.
I'll have on your suggestions next week.

[akesandgren]

There is also a bunch of trailing whitespace that needs to be removed.