Closed apanteli closed 5 years ago
boegel
commented
10 years ago Support for checking MD5 sums (or other checksums) is available since EasyBuild v1.10.
It now comes down to actually providing the checksums in the easyconfig files, so EasyBuild can verify them.
I propose we tackle this together with the collapsing of current easyconfig files into format v2.x easyconfig files though (support for that isn't ready yet right now).
fgeorgatos
commented
10 years ago This was waiting to be submitted for a while, but it's never too late ;-)
$ time find sources/ -type f -exec md5sum {} \; |sort -k2
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87db5f0ca7e1065c5ed5ae7b5172aa1d sources/a/ABINIT/abinit-7.2.1_x86_64_linux_gnu4.5.bz2
5a79f33f828db3c626627c5facd0f712 sources/a/ABySS/abyss-1.3.4.tar.gz
2a2a54222c158e8afce15b0c744f0c08 sources/a/ALLPATHS-LG/allpathslg-46968.tar.gz
51ebe835c93eef9acd39101738b2048c sources/a/AMOS/amos-3.1.0.tar.gz
d2003f7c4a2bfa4f568292814aad9420 sources/a/ASE/python-ase-3.6.0.2515.tar.gz
78753e869231cc1417a92eebaa076718 sources/a/ATLAS/atlas3.10.1.tar.bz2
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781ac3d9b213fa3e1ed0d79f986dc8c7 sources/a/a2ps/a2ps-4.14.tar.gz
4e05e1cc4ea4b56d85bbbc4fe29d1c29 sources/a/ant/apache-ant-1.8.4-src.tar.gz
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9b0574dce903ab83e39e371b0a3bbbc6 sources/b/BFAST/bfast-0.7.0a.tar.gz
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6a1f32d902203ac70fbec78af95b3cf8 sources/b/Boost/boost_1_51_0.tar.gz
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2d924766f6e8b5cf03bd2db81016d821 sources/c/CAP3/cap3.linux.opteron64.tar
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dd9a11d964590dd5f3fd5a3491b2c1ce sources/c/CCfits/CCfits-2.4.tar.gz
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5e0c11a3f3628f58c5948d6d10271f0c sources/c/CGAL/CGAL-4.0.tar.gz
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JensTimmerman
commented
10 years ago I see 3 issues here:
('sources/g/GIMPS/p95v279.linux64.tar.gz', 'c1d50a3da5521c0ee2eb173e87e3c2dc', 'b31e7137a206fc80f0d98ce3f1331434')
('sources/g/g2clib/g2clib-1.4.0.tar', '72b236bad38131dc4997c68761fbe5ec', 'f0cbab4ebbaec6d8dd15da1a36c93675')
('sources/g/g2lib/g2lib-1.4.0.tar', 'd83041e79fa21afad9fa114a4cdb5d84', '739c1197c51da8c5e5675ae1e0b468d7')this rings a bell: GIMPS, at some time they changed the upstream tarball with something that was giving segfaults (in the best case, that was only segfaults ;-) while the others are not entirely surprising, given that earth-scientists have a long-standing bad habit of modifying upstream bits with no warning whatsoever... (bioinformaticians compete with them closely)
JensTimmerman
commented
10 years ago I crossreferenced this with our sources, and I can agree with
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aae4b701ee527c6e4e1a6f9c7399882e sources/t/Tcl/tcl8.6.1-src.tar.gz
6eed09dbd4223ab5b6955378450d228a sources/t/tcsh/tcsh-6.18.01.tar.gz
f245e2405083ea634905875444c7174c sources/t/Tesla-Deployment-Kit/tdk_5.319.43.tar.gz
4a0cfe0d48fc7f0dc3f8ef6223a44c37 sources/t/Theano/Theano-0.5.0.tar.gz
0211ffd7df7855fc48fa30bce2febc86 sources/t/TiCCutils/ticcutils-0.3.tar.gz
f55ea5b91f97879b189fa612952f5256 sources/t/TiMBL/timbl-6.4.3.tar.gz
22d80bdd94c3c8373062761de0d27fde sources/t/TinySVM/TinySVM-0.09.tar.gz
a01640176845c1f654a412cfc9bab13b sources/t/Tk/tk8.5.12-src.tar.gz
10c13674debec89b3f5cf9c5c780b9c5 sources/t/Tophat/tophat-2.0.4.tar.gz
10c13674debec89b3f5cf9c5c780b9c5 sources/t/TopHat/tophat-2.0.4.tar.gz
b93148df8a205fcf46a27798acc64cfb sources/t/TopHat/tophat-2.0.8.tar.gz
eafdfb5d702b7ae1ce6146db2233bc94 sources/t/Trilinos/trilinos-10.12.2-Source.tar.gz
d706f59b9b00967f88955abac92b36e9 sources/t/Trinity/jellyfish-1.1.10.tar.gz
84f2847831c4cb948620bd2839497aee sources/t/Trinity/trinityrnaseq_r2012-10-05.tgz
3756bf5c7d77d6c609b48db668edd6be sources/t/Trinity/trinityrnaseq_r2013-02-25.tgz
6986545721747a51285c765644dcd9d8 sources/u/UDUNITS/udunits-2.1.24.tar.gz
7edcdd12cbd2d4a0525aa017281771c4 sources/u/UFC/ufc-2.0.5.tar.gz
5996ee68b1b75cb258213735a1297e51 sources/u/UFL/ufl-1.0.0.tar.gz
3005e93f7fff3f980bc364b12be1b17f sources/u/util-linux/util-linux-2.22.2.tar.gz
a60466e5323a6b34221b2e2bb3d1e70b sources/vsc-base-0.95.tar.gz
985044fdef6d1d26f53e32c31141e30b sources/vsc-mympirun-3.0.5.tar.gz
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4a6e1bb04eb37e3f79ba3e23d2fe3dc1 sources/vtune_amplifier_xe_2013_update8.tar.gz
14f486974bbde966f2e473df6b2c0226 sources/vtune_amplifier_xe_2013_update9.tar.gz
288758010b271119a0ffc0183f1d6e38 sources/v/Valgrind/valgrind-3.8.1.tar.bz2
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2e660631a96e1f192cb2f4b483665de9 sources/v/Velvet/velvet_1.2.09.tgz
701962903995e3135a788d53eed194ac sources/v/ViennaRNA/ViennaRNA-2.0.7.tar.gz
4aa7d37934c98e637b45eb9cc7d03cdd sources/v/Viper/viper-1.0.0.tar.gz
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c918b30cb7ec047291e8eda6e636e03f sources/WIEN2k_12.tar
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73a0e40c312af5555c0f2391d1a3c57c sources/x/xcb-proto/xcb-proto-1.7.tar.gz
2f6b89546de5f82e5b7a7d81ac0646ef sources/x/XCrySDen/xcrysden-1.5.53.tar.gz
c5db1c6ba5f588802a5e1a15b5b6d653 sources/x/XML-LibXML/XML-LibXML-2.0018.tar.gz
4d10964e123b76eca36678464daa63cd sources/x/XML-Simple/XML-Simple-2.20.tar.gz
7ab1239930563a352cb3552fd2db4140 sources/x/xproto/xproto-7.0.23.tar.gz
c976bbb3bae2a68ce02699a75bdd0816 sources/y/yaff/yaff-1.0.tar.gz
187ab0b6804941dfdaa21fe28f0b6ffd sources/y/YamCha/yamcha-0.33.tar.gz
8920091e68a078cfa9c42041e5759162 sources/y/YAML-Syck/YAML-Syck-1.27.tar.gz
4cfc0686cf5350dd1305c4d905eb55a6 sources/y/Yasm/yasm-1.2.0.tar.gz
1b11aae09b19d18276d0717b2ea288f6 sources/z/ZeroMQ/zeromq-2.2.0.tar.gz
df68431d9300da84a1a5f9a2784e33de sources/z/ZeroMQ/zeromq-3.2.2.tar.gz
c735eab2d659a96e5a594c9e8541ad63 sources/z/zlib/zlib-1.2.5.tar.gz
60df6a37c56e7c1366cca812414f7b85 sources/z/zlib/zlib-1.2.7.tar.gz
44d667c142d7cda120332623eab69f40 sources/z/zlib/zlib-1.2.8.tar.gz
19466d778777fe7f36e89b3b3c8613c1 sources/z/zsh/zsh-5.0.2.tar.gz
862f90bafda118c4d3c5ee6477e50841 sources/z/zsync/zsync-0.6.2.tar.bz2I will try to add these to the respective easyconfig files.
ocaisa
commented
5 years ago Closing this as we now enforce checksums in easyconfig contributions
Sometimes during build, the sources are corrupted or not properly downloaded. In order to mitigate this issue we can perform an md5sum check on the downloaded sources.
As a first step I am attaching a list with the sources we have at CyI with the respective md5 hashes.
Excuse me for the long post.