On 05/12/2019 10:33, Ricardo Gregorio wrote:
Hi Ake
Thank you for taking your time to reply.
As I had mentioned, this is all new to me and I am trying to understand the
concept and mechanisms of EasyBuild.
You said you are working to fix the current 3.3.2 version of AUGUSTUS. Would it
be possible for me to contact you via email directly to understand what you are
doing and get some further insight (apologies for this request, if you would
rather not)?
I think Åke was referring to this open pull request:
https://github.com/easybuilders/easybuild-easyconfigs/pull/9396/files .
regards,
Kenneth
Regards,
Ricardo Gregorio
Research and Systems Administrator
Operations ITS
Rothamsted Research | West Common | Harpenden | Hertfordshire | AL5 2JQ
tel: +44 (0)1582 938422 | email: [email protected] |
http://www.rothamsted.ac.uk
When there are patches involved and you're going to a newer version of the
source, you have to check if the patches still apply and if they are still
needed.
If they still seem to be needed, but don't apply any longer, you have to create
a new patch for the new version.
And as can be seen in your output below, the patches fails to apply.
We're also working to fix the current 3.3.2 version of AUGUSTUS in EasyBuild.
There are a couple of small changes to the easyconfig to make the resulting
installation work better.
You are also doing a couple of mistakes below.
You should normally not set optarch, unless you're building for a different
architecture then the one you're building on.
And when using a intel based easyconfig you should use intel compatible
options, -march=xxxx is in principle only for GCC.
On 12/4/19 12:25 PM, [email protected] wrote:
hi all [absolute beginner to eb]
struggling a bit trying to build AUGUSTUS 3.3.3 (source code changes:
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffoss
ies.org%2Fdiffs%2Faugustus%2F3.3.2_vs_3.3.3%2F&data=01%7C01%7Crica
rdo.gregorio%40rothamsted.ac.uk%7C04e952efd3a9411d15b908d778df9839%7Cb
688362589414342b0e37b8cc8392f64%7C1&sdata=NWlpUyvThTX16BmkRuKoQprV
RkqzRO7eohQPHj3OS2s%3D&reserved=0)
I have used the previous version 3.3.2 and then $ eb
AUGUSTUS-3.3.3-intel-2019a.eb --inject-checksums --force
reviewed, replaced (3.2 to 3.3 >>> %s/3.2/3.3/g) and renamed the files:
AUGUSTUS-3.3.2_fix-hardcoding.patch >>>
AUGUSTUS-3.3.3_fix-hardcoding.patch
AUGUSTUS-3.3.2_additional_fix_hardcoding.patch >>>
AUGUSTUS-3.3.3_additional_fix_hardcoding.patch
confirmed files sha256sum and replaced them on file AUGUSTUS-3.3.3-
intel-2019a.eb
$ eb --buildpath=/tmp --job-cores=32 --optarch=march=skylake-avx512
--dry-run AUGUSTUS-3.3.3-intel-2019a.eb -r $ eb --buildpath=/tmp
--job-cores=32 --optarch=march=skylake-avx512
AUGUSTUS-3.3.3-intel-2019a.eb -r
Log throws this errors:
# '-fgnu89-inline' is required to avoid linking errors with older
glibc's, == 2019-12-04 10:33:19,174 run.py:587 INFO
parse_log_for_error msg: Command
used: patch -b -p1 -i
/home/apps/eb/software/EasyBuild/4.0.1/easybuild/
easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch
== 2019-12-04 10:33:19,175 run.py:589 INFO parse_log_for_error (some
may be
harmless) regExp (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?
\w) found:
== 2019-12-04 10:33:19,175 run.py:546 WARNING Found 2 errors in
command output
(output: Hunk #1 FAILED at 15., 1 out of 1 hunk FAILED -- saving
rejects to file auxprogs/bam2wig/Makefile.rej) == 2019-12-04
10:33:19,225 build_log.py:164 ERROR EasyBuild crashed with an error
(at easybuild/base/exceptions.py:124 in __init__): Couldn't apply
patch file
/home/apps/eb/software/EasyBuild/4.0.1/easybuild/easyconfigs/a/AUGUSTU
S/ AUGUSTUS-3.3.3_fix-hardcoding.patch. Process exited with code 1:
patching file auxprogs/bam2wig/Makefile == 2019-12-04 10:33:19,227
build_log.py:164 ERROR EasyBuild crashed with an error (at
easybuild/base/exceptions.py:124 in __init__): build failed (first
300 chars): Couldn't apply patch file
/home/apps/eb/software/EasyBuild/4.0.1/
easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch.
Process exited with code 1: patching file auxprogs/bam2wig/Makefile ==
2019-12-04 10:33:19,227 build_log.py:164 ERROR EasyBuild crashed with
an error (at easybuild/base/exceptions.py:124 in __init__): Build of
/home/apps/
eb/software/EasyBuild/4.0.1/easybuild/easyconfigs/a/AUGUSTUS/AUGUSTUS-
3.3.3- intel-2019a.eb failed (err: "build failed (first 300 chars):
Couldn't apply patch file
/home/apps/eb/software/EasyBuild/4.0.1/easybuild/easyconfigs/a/
AUGUSTUS/AUGUSTUS-3.3.3_fix-hardcoding.patch. Process exited with code 1:
patching file auxprogs/bam2wig/Makefile\nHunk #1 FAILED at 15.\n1 out
of 1 hunk FAILED -- saving rejects to file
auxprogs/bam2wig/Makefile.") (at
easybuild/main.py:147 in build_and_install_software)
The only diffs I can see from the new 3.3.3 auxprogs/bam2wig/Makefile
are
(https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffos
sies.org%2Fdiffs%2Faugustus%2F3.3.2_vs_3.3.3%2Fauxprogs%2Fbam2wig%2FMa
kefile-diff.html&data=01%7C01%7Cricardo.gregorio%40rothamsted.ac.u
k%7C04e952efd3a9411d15b908d778df9839%7Cb688362589414342b0e37b8cc8392f6
4%7C1&sdata=SHKl5THH0D14iFn3jWEkRagf7VQGo7RJKBkItGYLwZI%3D&res
erved=0)
- removes TABIX (which the patch files hashes out anyway) ---
https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgith
ub.com%2Feasybuilders%2Feasybuild-easyconfigs%2Fblob%2F4.0.x%2Feasybui
ld%2Feasyconfigs%2Fa%2FAUGUSTUS%2FAUGUSTUS-3.3.2_fix-hardcoding.patch&
amp;data=01%7C01%7Cricardo.gregorio%40rothamsted.ac.uk%7C04e952efd3a94
11d15b908d778df9839%7Cb688362589414342b0e37b8cc8392f64%7C1&sdata=c
zqzle6SRXCR9O8MXQH9c4yMLEn%2BOD6MzkBjjg%2FWODs%3D&reserved=0
- mkdir -p ../../bin
Would you guys be able to point me in the direction to debugging this further?
Apologies if it is something obvious that I am completely missing.
Thanks in advance
--
Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: [email protected] Phone: +46 90 7866134 Fax: +46 90-580 14
Mobile: +46 70 7716134 WWW:
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Rothamsted Research is a company limited by guarantee, registered in England at
Harpenden, Hertfordshire, AL5 2JQ under the registration number 2393175 and a
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