Comments (5)
dajiangliu
commented on June 21, 2024
What is the error message?
On Thu, Feb 3, 2022 at 3:50 PM Maxime Boissonneault < ***@***.***> wrote:
Hi,
I was asked to build this software for our cluster. However,
1. The build procedure does not work
2. We already have all of the third parties
Are there instructions on how to build and install this tool without
building all of the vendored dependencies ?
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All the best,
Dajiang
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Co-Chair, Bioinformatics and Genomics Graduate Program
Dept. Public Health Sciences
Institute of Personalized Medicine
Penn State College of Medicine, ASB 4301C
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URL: https://dajiangliu.blog <https://dajiangliu.blog>
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mboisson
commented on June 21, 2024
So, if we let aside that the make command downloads stuff (it should not, make is supposed to be runnable offline, without any internet connection), and builds stuff that is already available (such as zstd, tabix, sqlite, nlopt, gsl, openblas, pcre, samtools), without proper optimizations (we build all of those, but in paritulcar BLAS implementations with specific optimizations for the architectures we run on, for example), it fails in particular with Eigen (which we ALSO have):
echo "obtain Eigen..."
obtain Eigen...
wget --no-check-certificate http://bitbucket.org/eigen/eigen/get/3.3.7.tar.bz2 -O eigen-3.3.7.tar.bz2
URL transformed to HTTPS due to an HSTS policy
--2022-02-03 22:11:11-- https://bitbucket.org/eigen/eigen/get/3.3.7.tar.bz2
Résolution de bitbucket.org… 104.192.141.1, 2406:da00:ff00::3403:4be7, 2406:da00:ff00::22cd:e0db, ...
Connexion à bitbucket.org|104.192.141.1|:443… connecté.
requête HTTP transmise, en attente de la réponse… 404 Not Found
2022-02-03 22:11:11 erreur 404 : Not Found.
make[1]: *** [Makefile:84: eigen-3.3.7.tar.bz2] Error 8
make[1] : on quitte le répertoire « /home/mboisson/tmp/rvtests-2.1.0/third »
make: *** [Makefile.lib:18: /home/mboisson/tmp/rvtests-2.1.0/third/eigen] Error 2
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mboisson
commented on June 21, 2024
The above was an attempt to build manually, without any options specified (just make), which we don't do.
This gist contains the full logs of a build attempted with EasyBuild. It fails to compile nlopt, I guess because somewhere, somehow, in the mess of the build scripts, it passes wrong arguments. Again, it does NOT need to build nlopt, we already have it available.
https://gist.github.com/mboisson/fd82f8585f445148eec2dcaedafa090c
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dajiangliu
commented on June 21, 2024
It looks like the eigen package cannot be found anymore? Can you modify the
script and see if a newer version is available for download? Thank you!
All the best,
Dajiang
--
Associate Professor
Co-Chair, Bioinformatics and Genomics Graduate Program
Dept. Public Health Sciences
Institute of Personalized Medicine
Penn State College of Medicine, ASB 4301C
Email: ***@***.***
URL: https://dajiangliu.blog <https://dajiangliu.blog>
Tel: +1-717-531-4178
…On Thu, Feb 3, 2022 at 5:18 PM Maxime Boissonneault < ***@***.***> wrote:
The above was an attempt to build manually, without any options specified
(just make), which we don't do.
This gist contains the full logs of a build attempted with EasyBuild. It
fails to compile nlopt, I guess because somewhere, somehow, in the mess
of the build scripts, it passes wrong arguments. Again, it does NOT need to
build nlopt, we already have it available.
https://gist.github.com/mboisson/fd82f8585f445148eec2dcaedafa090c
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mboisson
commented on June 21, 2024
I would rather not have to download Eigen at all. As I said, we already have it installed.
I pointed our user to the binary version that you have and will forget about building from source. The binary version won't be optimized for our hardware, but I guess it's gonna be good enough.
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