haddock-2024.12.0b7 :: examples failure #1167
Comments
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How did you install it?
Could you try simply from the cloned GitHub repository:
pip install .
Did you copy the cns executable into the haddock3-2024.12.0b7/bin directory (as simply cns)?
Did you follow the instructions for CNS from varia/cns1.3/README.md?
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python 3.10, virtulal env.
done and same behaviour....
yes.
yes |
Hi @EricDeveaud, I tried my best to reproduce your issue but didn't manage..there must be something wrong with your CNS executable. I suggest you try to get the package simply from pypi Otherwise try deleting the repository folder and re-download it. After that running If none of this works let me know! |
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pip install from pipy problem. with cns binary. see: thats the reason I rebuilt cns, follwing instructions here: https://github.com/haddocking/haddock3/blob/main/docs/CNS.md NB same problem with tagged archive, fresh clone of the repo. i tried to start again the build many times and always had the same failure |
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Hello, dunno if it may helps but I tarcked the flexref job, at least the first one. exported the following: the ran in
and got the bellow attached error log. cns.params.txt NB all file are readable and present. hope we will find a solution |
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I check that all @modules from cns.params.txt are present |
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Try then replacing the cns exec coming from pip in ./lib/python3.10/site-packages/haddock/bin/cns by your compiled version
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Importantly when compiling CNS did you first follow the instructions from the README.md file in varia/cns1.3 from the haddock3 directory? This will replace/add some files that have extended parameter settings (path length might be an issue)
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I think yes ;-) here's my build rule for cns |
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I found the problem. We forgot to update to Recompile and replace the exec. |
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currently building stay tunned ;-) |
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PS: Another solution to this path problem should be to define in the workflow config file: But better to have a recompiled CNS |
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new cns built with WORD_SIZE=264, no luck see: |
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adding self_contained = true in I am abble to run succesfully what does self_contained ? seems more a workaround than a bug fix ? |
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OK see: This option will copy the CNS scripts and executable to the run folder. hummmm makes me think to a problen of path length. sorry, not fluent enough in fortran to dive in cns code // cns patches |
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indeed a problem with the path length accepted by your executable..if you add |
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Hummm. I would prefer to find the culprit to avoid this necessity. in the mean time I guess I can turn self_contained=true for all the users on the cluster by settting |
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I've also been having this problem for protein small molecule docking (although curiously the .psf is made for the protein, just not the ligand, so I'm getting 50% output not generated). I added self_contained=true to my .cfg but now it fails before running topoaa, with a ModuleNotFound error for the clis. Tried a fresh conda environment and install but i'm getting the same error. |
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Yes - that should do.
And the current word length is already max if you indeed modified cns.inc as indicated and copied the CNS exec to the proper location.
There is yet one another thing to try: install haddock3 in development mode. In doing that the files will be located under the build directly on the haddock3 location and might have a shorter path (assuming the path is the issue). For this do:
pip install -e '.[dev,docs]'
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Are you running the default ligand example?
If docking another system, you will have to create and provide the ligand topo/param files.
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Hello. finally abble to sort this path length problem. modification are quite simple, thus I won't create a PR for this
regards Eric |
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Thanks for the time @EricDeveaud, with your suggestion we can hopefully implement a proper fix instead of the previously proposed workarounds 🚀 |
rvhonorato
added
CNS
Hello,
I just installed haddock-2024.12.0b7 from release tag archive
after checking some issues (eg #329) I recompiled cns_solve from
cns_solve_1.3_all.tar.gzusing the CNS installation documentation.tools used of build//installation
cns starts smoothly. see:
when I run the
run.pyfrom examples folder I have some "test" failure. in the form of100.00% of output was not generated for this module and tolerance was set to XX.00%.see for example.
DOCKING-FLEXREF-PROTEIN-GLYCAN-TEST.CFG
same apply to eg
some examples succeed
output of
pip3 freezewhat I'am doing wrong ?
PS attcahed full run log
haddock3.log.txt
log
regards
Eric
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