{bio}[intel/2018a] AFNI v18.1.09 + deps by boegel · Pull Request #6266 · easybuilders/easybuild-easyconfigs

boegel · 2018-05-02T18:55:21Z

(created using eb --new-pr)

…5.10.1-intel-2018a-Python-3.6.4.eb, SIP-4.19.8-intel-2018a-Python-3.6.4.eb, tcsh-6.20.00-GCCcore-6.4.0.eb

boegel · 2018-05-02T21:11:08Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
node2578.golett.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/8a9b665965a03c30d64aa2c4b26a5fb1 for a full test report.

boegel · 2018-05-02T21:17:30Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
node2065.delcatty.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/56a3fcad2b1d95d3ef0a7b316bc0d30b for a full test report.

easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb

boegel · 2018-05-05T09:35:28Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
node2413.golett.os - Linux centos linux 7.4.1708, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/ea99fec870dd7168868d6a5a1d35cd23 for a full test report.

vanzod · 2018-05-10T14:21:08Z

Test report by @vanzod
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in this PR)
cermis - Linux debian 9.4, Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, Python 2.7.13
See https://gist.github.com/bc50aefa4d7888e116c62c9602888f12 for a full test report.

vanzod · 2018-05-10T14:22:39Z

@boegel It looks like the checksum is different than the source file currently hosted in the AFNI repo URL...

boegel · 2018-05-10T18:22:34Z

Hmm, a fresh download indeed also gives me another checksum:

sha256sum ~/Downloads/afni_src.tgz
bd4cbc41d72c51006c165de5e12e3db45995fba330b16df812dc41f2970eaaf4  /Users/kehoste/Downloads/afni_src.tgz

Looking at a diff of the unpacked source tarballs shows that afni_src.tgz is being updated in place, but somehow the timestamp in the directory listing at https://afni.nimh.nih.gov/pub/dist/tgz/ stays the same... Grrrrrr

diff -u afni_src-20180104/1dplot.c afni_src/1dplot.c
--- afni_src-20180104/1dplot.c  2018-05-01 05:07:21.000000000 +0200
+++ afni_src/1dplot.c   2018-05-08 22:51:26.000000000 +0200
@@ -192,6 +192,11 @@
      "             [before the program scans the command line for options]\n"
      #endif
      "\n"
+     " -naked     = Do NOT plot axes or labels, just the graph(s).\n"
+     "              You might want to use '-nopush' with '-naked'.\n"
+     " -aspect A  = Set the width-to-height ratio of the plot region to 'A'.\n"
+     "              Default value is 1.3. Larger 'A' means a wider graph.\n"
+     "\n"
      " -stdin     = Don't read from tsfile; instead, read from\n"
      "              stdin and plot it. You cannot combine input\n"

Note how in afni_src-20180104 the timestamp on the file is already May 1st 2018...

boegel · 2018-05-10T18:41:32Z

@vanzod I've reached out to the AFNI developers via https://afni.nimh.nih.gov/contact, let's see if that changes anything...

boegel · 2018-05-23T11:47:15Z

No response from AFNI developers, I'm not sure how to continue with this...

boegel · 2018-10-10T20:08:35Z

Oh look what I found! https://github.com/afni/afni/releases

boegel · 2018-10-11T09:08:09Z

@vanzod Please retest?

boegel · 2018-10-11T10:26:14Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
node2601.swalot.os - Linux centos linux 7.5.1804, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/8447ca903bc983d9baae8dbe72e407e9 for a full test report.

boegel · 2018-10-11T10:46:55Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
node2013.delcatty.os - Linux centos linux 7.5.1804, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/d08132289c7f19cc2c9f4ac46bd5ab95 for a full test report.

vanzod · 2018-10-18T14:31:07Z

Test report by @vanzod
FAILED
Build succeeded for 3 out of 4 (4 easyconfigs in this PR)
cermis - Linux debian 9.5, Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, Python 2.7.13
See https://gist.github.com/afd675466da6b282f742837aa62c0a86 for a full test report.

vanzod · 2018-10-18T14:50:46Z

It looks like it needs M4 as builddep:

m4 -B10000 putget.m4 >putget.c
/bin/sh: 1: m4: not found
../rules.make:45: recipe for target 'putget.c' failed

vanzod · 2018-10-19T13:30:59Z

easybuild/easyconfigs/a/AFNI/AFNI-18.1.09-intel-2018a-Python-3.6.4.eb

    '8b739ddc09d6e398ac7fa86d89f6a02f26f2b58b17caea627d5c07de5282aab2',  # AFNI-18.1.09_omp-pragma-statement-fix.patch
 ]

+builddependencies = [('M4', 'M4-1.4.18')]


There is a typo in the version...

…tarball

boegel · 2018-10-19T14:58:37Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
node2010.delcatty.os - Linux centos linux 7.5.1804, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/95fb229b93bb26ba03b6b5e3a967b768 for a full test report.

vanzod · 2018-10-19T15:38:41Z

Test report by @vanzod
FAILED
Build succeeded for 3 out of 4 (4 easyconfigs in this PR)
cermis - Linux debian 9.5, Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, Python 2.7.13
See https://gist.github.com/dd4e352d495f24e97f08e6579e15fd77 for a full test report.

vanzod · 2018-10-19T15:42:53Z

Now what is missing is libXp in X11...

boegel · 2018-10-19T15:55:11Z

@vanzod Looks like we'll need to backport #6873 to X11-20180131-GCCcore-6.4.0.eb for that...

boegel · 2018-10-19T16:44:10Z

@vanzod libXp is added to X11 bundle used by 2018a easyconfigs in #7062...

vanzod · 2018-10-21T00:37:56Z

Test report by @vanzod
FAILED
Build succeeded for 3 out of 4 (4 easyconfigs in this PR)
cermis - Linux debian 9.5, Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, Python 2.7.13
See https://gist.github.com/baaf96033d17248fe69073d601fdbf46 for a full test report.

vanzod · 2018-10-22T12:36:14Z

It looks like the error is now due to the lack of libtracktools.
Also, does your build produce 3dkmeans? It is missing in mine.

verdurin · 2018-10-22T13:35:29Z

Test report by @verdurin
SUCCESS
Build succeeded for 6 out of 6 (4 easyconfigs in this PR)
rescomp2 - Linux centos linux 7.3.1611, Intel(R) Xeon(R) Gold 6126 CPU @ 2.60GHz, Python 2.7.11
See https://gist.github.com/c709caad1b08a280ea89a8f439c402c6 for a full test report.

boegel · 2018-10-27T16:25:40Z

@vanzod libtracktools.a is supposed to get built as a part of AFNI, so the actual error must be higher up in the log? Can you share a full (debug) log?

boegel · 2018-12-08T13:38:58Z

@vanzod Ping on a detailed build log for this?

vanzod · 2018-12-11T15:06:40Z

Test report by @vanzod
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
cermis - Linux debian 9.5, Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, Python 2.7.13
See https://gist.github.com/cf0f01c24fe6e8d6e4408354ee122a80 for a full test report.

vanzod · 2018-12-11T15:18:49Z

Going in, thanks @boegel!

adding easyconfigs: AFNI-20180104-intel-2018a-Python-3.6.4.eb, PyQt5-…

5245005

…5.10.1-intel-2018a-Python-3.6.4.eb, SIP-4.19.8-intel-2018a-Python-3.6.4.eb, tcsh-6.20.00-GCCcore-6.4.0.eb

boegel added the update label May 2, 2018

add missing patch for AFNI built with intel/2018a

c41dc2a

easybuilders deleted a comment from boegelbot May 2, 2018

boegel added this to the 3.6.1 milestone May 2, 2018

boegel requested a review from vanzod May 2, 2018 20:22

boegel requested a review from migueldiascosta May 3, 2018 06:39

vanzod reviewed May 4, 2018

View reviewed changes

easybuild/easyconfigs/t/tcsh/tcsh-6.20.00-GCCcore-6.4.0.eb Show resolved Hide resolved

add missing checksum in tcsh easyconfig

31bd526

boegel modified the milestones: 3.6.1, 3.x May 23, 2018

boegel added 2 commits October 11, 2018 09:37

Merge branch 'develop' into 20180502205510_new_pr_AFNI20180104

726e0ac

fix version & download location for AFNI 18.1.09

6316c78

boegel changed the title ~~{bio}[intel/2018a] AFNI v20180104 + deps~~ {bio}[intel/2018a] AFNI v18.1.09 + deps Oct 11, 2018

boegel added 2 commits October 19, 2018 14:51

remove unused AFNI patch

1dc99e1

add missing M4 dependency for AFNI 18.1.09

a0624e0

vanzod reviewed Oct 19, 2018

View reviewed changes

fix typo in build deps + remove outdated comments w.r.t. AFNI source …

35abcf7

…tarball

boegel mentioned this pull request Oct 19, 2018

{bio}[foss/2018b] AFNI v18.3.00, tcsh v6.20.00 #7058

Merged

boegel mentioned this pull request Oct 19, 2018

add libXp component to X11 bundle for GCCcore 6.4.0 #7062

Merged

vanzod approved these changes Dec 11, 2018

View reviewed changes

vanzod merged commit 0957d6c into easybuilders:develop Dec 11, 2018

boegel deleted the 20180502205510_new_pr_AFNI20180104 branch December 11, 2018 17:35

boegel modified the milestones: 3.x, 3.8.0 Dec 11, 2018

boegel mentioned this pull request Dec 11, 2018

stick to PyQt5 5.9.2 as dep for AFNI 18.1.09 #7294

Merged

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