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libxml2 dependency on HDF5 #3759

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boegel merged 5 commits intoeasybuilders:developfrom
rug-cit-hpc:HDF5-libxml
Feb 1, 2017
Merged

libxml2 dependency on HDF5 #3759
boegel merged 5 commits intoeasybuilders:developfrom
rug-cit-hpc:HDF5-libxml

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@RvDijk
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@RvDijk RvDijk commented Nov 6, 2016

If libxml2 is not installed on OS, the following error occurs:

/software/software/binutils/2.25-GCCcore-4.9.3/bin/ld.gold: error: cannot find -lxml2
collect2: error: ld returned 1 exit status

@boegel if this is OK, should I include libxml2 as a dependency in all other HDF5 easyconfigs?

@boegel boegel added this to the 3.0 milestone Nov 6, 2016
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boegel commented Nov 6, 2016

@RvDijk urgh, as you maybe noticed, including libxml2 as a dep now is an issue because this HDF5 is used as a dep in places where libxml2 is already a dependency too, so both the version and versionsuffix of libxml2 must match.

There are a handful of easyconfigs that seem to depend both on this HDF5 and libxml2 2.9.3 with -Python-2.7.11 as versionsuffix, i.e.:

  • MDSplus-7.0.67-foss-2016a-Java-1.7.0_79-Python-2.7.11.eb
  • NCO-4.6.0-foss-2016a.eb
  • libdap-3.18.1-foss-2016a-Python-2.7.11.eb

So, if you want to go through with this, you'll need to see what the libxml2 with Python bindings is really required for these, and if not, drop the versionsuffix for libxml2 in them...

With this in mind, it's probably going to be very painful to add libxml2 as dep in all existing HDF5 easyconfigs, but we should try and do it for at least the most recent ones...

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RvDijk commented Nov 14, 2016

@boegel this seems to work on Travis, except for the newer lmod versions. If this is what you had in mind, then I'll also change this in other versions of HDF5.

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boegel commented Nov 14, 2016

(close/open to retrigger Travis with correct config)

@boegel boegel closed this Nov 14, 2016
@boegel boegel reopened this Nov 14, 2016
@boegel boegel modified the milestones: 3.1, 3.0 Nov 14, 2016
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boegel commented Feb 1, 2017

Test report by @boegel
SUCCESS
Build succeeded for 8 out of 8 (3 easyconfigs in this PR)
node2044.delcatty.os - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/c5b33432c80b3462c2720ab529659396 for a full test report.

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boegel commented Feb 1, 2017

Test report by @boegel
SUCCESS
Build succeeded for 10 out of 10 (3 easyconfigs in this PR)
node2693.swalot.os - Linux centos linux 7.3.1611, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/e4ac1147164e9844237af29001c926e3 for a full test report.

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boegel commented Feb 1, 2017

lgtm

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boegel commented Feb 1, 2017

Going in, thanks @RvDijk!

@boegel boegel merged commit eb0667b into easybuilders:develop Feb 1, 2017
@RvDijk RvDijk deleted the HDF5-libxml branch February 3, 2017 10:25
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