[hdf5] Update HDF5 to 1.12 #11747

Neumann-A · 2020-06-03T14:27:50Z

and use gitlab live-clones/hdf5 instead of binary download

…ry download

cenit · 2020-06-03T16:28:46Z

Personally, I am not a fan of unofficial urls.
If you want to download from repo, isn't it better to use vcpkg_from_git and point to https://bitbucket.hdfgroup.org/projects/HDFFV/repos/hdf5/browse ?

Neumann-A · 2020-06-03T17:22:21Z

@cenit: give me a working example for vcpkg_from_git for hdf5 with the tag and I will change it. Otherwise I will not spend time on trying to get vcpkg_from_git to work ;)

ports/hdf5/portfile.cmake

cenit · 2020-06-03T17:37:06Z

vcpkg_from_git is working, no need to touch it

I put it as a suggestion in the code review panel, copied also here

vcpkg_from_git(
    OUT_SOURCE_PATH SOURCE_PATH
    URL https://bitbucket.hdfgroup.org/scm/hdffv/hdf5.git
    REF 83385326ef1588167f2b37300313a6e51e51ffca
)

(there it's missing the close bracket in order to continue with your PATCHES keyword

Neumann-A · 2020-06-03T17:49:31Z

@cenit: You actually tried the code?

Starting package 3/3: hdf5:x64-windows-static
Building package hdf5[core,szip,zlib]:x64-windows-static...
-- Fetching https://bitbucket.hdfgroup.org/scm/hdffv/hdf5.git...
CMake Error at scripts/cmake/vcpkg_execute_required_process.cmake:72 (message):
    Command failed: "C:/Program Files/Git/mingw64/bin/git.exe" fetch https://bitbucket.hdfgroup.org/scm/hdffv/hdf5.git 83385326ef1588167f2b37300313a6e51e51ffca --depth 1 -n
    Working Directory: D:/vcpkg_common/downloads/git-tmp
    Error code: 128
    See logs for more information:
      D:\qt2\buildtrees\hdf5\git-fetch-x64-windows-static-err.log

fatal: expected shallow/unshallow, got The client mentioned a shallow object that is missing on the server. This may be due to a rebase or other forced update on the server. You should recreate your shallow clone.
fatal: the remote end hung up unexpectedly

cenit · 2020-06-03T18:01:26Z

Working on my Pc
Anyway, feel free to do what you prefer. Just stating my opinion about unofficial repositories...

Neumann-A · 2020-06-04T22:30:59Z

@NancyLi1013: Can i assume that none of those regressions have anything to do with the changes made in this PR?

NancyLi1013 · 2020-06-05T01:45:13Z

@Neumann-A
Thanks for your kindly reminder. I will rerun this PR and confirm if those regression can be solved.
Currently, I'm not sure how the regression for field3d on x64-linux is caused.

/mnt/vcpkg-ci/buildtrees/field3d/src/v1.7.2-ae08f6d321/src/Field3DFileHDF5.cpp:1138:71: error: too few arguments to function ‘herr_t H5Oget_info_by_name3(hid_t, const char*, H5O_info2_t*, unsigned int, hid_t)’
   status = H5Oget_info_by_name(loc_id, itemName, &infobuf, H5P_DEFAULT);
                                                                       ^
In file included from /mnt/vcpkg-ci/install/x64-linux/include/H5Apublic.h:22:0,
                 from /mnt/vcpkg-ci/install/x64-linux/include/hdf5.h:23,
                 from /mnt/vcpkg-ci/buildtrees/field3d/src/v1.7.2-ae08f6d321/src/Field3DFileHDF5.cpp:50:
/mnt/vcpkg-ci/install/x64-linux/include/H5Opublic.h:188:15: note: declared here
 H5_DLL herr_t H5Oget_info_by_name3(hid_t loc_id, const char *name, H5O_info2_t *oinfo,
               ^~~~~~~~~~~~~~~~~~~~
/mnt/vcpkg-ci/buildtrees/field3d/src/v1.7.2-ae08f6d321/src/Field3DFileHDF5.cpp: In function ‘herr_t Field3D::v1_7::InputFileHDF5::parseLayers(hid_t, const char*, const H5L_info2_t*, void*)’:

   status = H5Oget_info_by_name (loc_id, itemName, &infobuf, H5P_DEFAULT);

NancyLi1013 · 2020-06-05T01:45:28Z

/azp run

azure-pipelines · 2020-06-05T01:45:37Z

Azure Pipelines successfully started running 1 pipeline(s).

NancyLi1013 · 2020-06-05T01:59:21Z

@Neumann-A
Seems the regression is related with this hdf5.
Could you please look into this?

…nce the cmakelists tries to support windows

Neumann-A · 2020-06-05T14:43:46Z

@NancyLi1013: TODO for the future: Fix field3d hidden MPI dependency

JackBoosY · 2020-06-09T07:00:33Z

/azp run

azure-pipelines · 2020-06-09T07:00:41Z

Azure Pipelines successfully started running 1 pipeline(s).

cenit · 2020-06-09T11:28:28Z

@NancyLi1013: TODO for the future: Fix field3d hidden MPI dependency

It’s already almost done in my opencv 4.3 pr

JackBoosY · 2020-06-10T06:08:09Z

@cenit So, should we waiting for your PR #11130?

cenit · 2020-06-10T07:39:52Z

yes please. I just pushed the patch for field3d there.
Waiting for CI results, hoping for that PR to be done...

ports/field3d/portfile.cmake

ports/hdf5/portfile.cmake

NancyLi1013 · 2020-06-11T03:07:17Z

@cenit
Thanks for your attention and kindly reminder. Actually, we always recommend to use official repos except for some specific reasons. And now I noticed that @Neumann-A has updated as official repo for hdf5 in this PR. Really appreciate.

NancyLi1013 · 2020-06-11T06:04:14Z

@Neumann-A
Is there anything else to be done for this PR? If not, I will try to test these features.

Neumann-A · 2020-06-11T20:01:53Z

@NancyLi1013: Nothing to add. Feel free to resolve the conflict with the baseline.

JackBoosY · 2020-06-12T05:45:23Z

Can you merge the latest changes into this branch and use this to replace ci.baseline.txt?

# Conflicts: # scripts/ci.baseline.txt

… update_hdf5 # Conflicts: # scripts/ci.baseline.txt

Neumann-A · 2020-06-12T08:02:56Z

@JackBoosY: I cleaned the baseline. If you need more changes than that those should probably be in another PR.

NancyLi1013 · 2020-06-16T07:43:55Z

All features have passed with the following triplets:

x86-windows
x64-windows
x64-windows-static

Note: Feature fortran has not been supported yet.

Neumann-A · 2020-06-23T08:26:54Z

@JackBoosY @NancyLi1013´: Is there something blocking the merge of this PR?

JackBoosY · 2020-06-23T10:14:00Z

@Neumann-A See #11747 (comment)

Waiting for merge #11130.

dan-shaw · 2020-06-23T17:23:28Z

LGTM, just waiting for #11130 as suggested above. @Neumann-A Let us know if it makes more sense to merge this PR first.

Neumann-A · 2020-06-23T18:25:27Z

@dan-shaw: seems like #11130 is still not finished so merging this one first seems more reasonable

cenit · 2020-06-23T20:51:21Z

#11130 is finished...

BillyONeal · 2020-06-25T18:02:24Z

This change broke a lot of stuff :(

Neumann-A · 2020-06-25T18:48:24Z

@BillyONeal. Instead of patching the sources use the following in the CMakeLists.txt:

add_definitions(-UH5_USE_112_API_DEFAULT)
add_definitions(-DH5_USE_110_API_DEFAULT)

there is probably also a way to set those via an environment variable from the portfile or using VCPKG_CXX_FLAGS

[hdf5] Update HDF5 to 1.12 and use github live-clones instead of bina…

035f484

…ry download

Neumann-A marked this pull request as draft June 3, 2020 15:18

cenit reviewed Jun 3, 2020

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ports/hdf5/portfile.cmake Outdated Show resolved Hide resolved

[hdf5] bump control

7ad20e3

NancyLi1013 self-assigned this Jun 4, 2020

Neumann-A added 4 commits June 4, 2020 17:38

Merge remote-tracking branch 'upstream/master' into update_hdf5

7f24353

[hdf5] fix szip and typo about linkage

a3d626f

[hdf5] add missing package namespace.... they somehow missed to set it?

2d11c63

[hdf5] retry without "

0fe270a

Neumann-A marked this pull request as ready for review June 4, 2020 19:19

[field3d] fix regression and update. Remove windows as unsupported si…

6fcc963

…nce the cmakelists tries to support windows

fix typo

31c9daa

NancyLi1013 added the category:port-update The issue is with a library, which is requesting update new revision label Jun 8, 2020

NancyLi1013 suggested changes Jun 10, 2020

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JackBoosY added the depends:different-pr This PR or Issue depends on a PR which has been filed label Jun 11, 2020

NancyLi1013 approved these changes Jun 11, 2020

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Merge branch 'master' into update_hdf5

eeb1014

Neumann-A added 3 commits June 12, 2020 09:58

Merge remote-tracking branch 'upstream/master' into update_hdf5

fc12c68

# Conflicts: # scripts/ci.baseline.txt

Merge branch 'update_hdf5' of https:/Neumann-A/vcpkg into…

360094b

… update_hdf5 # Conflicts: # scripts/ci.baseline.txt

clean baseline

861fe97

JackBoosY approved these changes Jun 16, 2020

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JackBoosY added requires:testing Needs tests added before merging and removed requires:author-response labels Jun 16, 2020

NancyLi1013 added info:reviewed Pull Request changes follow basic guidelines and removed requires:testing Needs tests added before merging labels Jun 16, 2020

dan-shaw approved these changes Jun 23, 2020

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dan-shaw merged commit 23eadea into microsoft:master Jun 23, 2020

Neumann-A deleted the update_hdf5 branch June 23, 2020 20:00

BillyONeal added a commit to JackBoosY/vcpkg that referenced this pull request Jun 25, 2020

[paraview] Fix HDF5 regressions from microsoft#11747

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[hdf5] Update HDF5 to 1.12 #11747

[hdf5] Update HDF5 to 1.12 #11747

Neumann-A commented Jun 3, 2020

cenit commented Jun 3, 2020

Neumann-A commented Jun 3, 2020

cenit commented Jun 3, 2020

Neumann-A commented Jun 3, 2020

cenit commented Jun 3, 2020

Neumann-A commented Jun 4, 2020

NancyLi1013 commented Jun 5, 2020

NancyLi1013 commented Jun 5, 2020

azure-pipelines bot commented Jun 5, 2020

NancyLi1013 commented Jun 5, 2020

Neumann-A commented Jun 5, 2020

JackBoosY commented Jun 9, 2020

azure-pipelines bot commented Jun 9, 2020

cenit commented Jun 9, 2020

JackBoosY commented Jun 10, 2020

cenit commented Jun 10, 2020

NancyLi1013 commented Jun 11, 2020

NancyLi1013 commented Jun 11, 2020

Neumann-A commented Jun 11, 2020

JackBoosY commented Jun 12, 2020

Neumann-A commented Jun 12, 2020

NancyLi1013 commented Jun 16, 2020

Neumann-A commented Jun 23, 2020

JackBoosY commented Jun 23, 2020

dan-shaw commented Jun 23, 2020

Neumann-A commented Jun 23, 2020

cenit commented Jun 23, 2020

BillyONeal commented Jun 25, 2020

Neumann-A commented Jun 25, 2020

[hdf5] Update HDF5 to 1.12 #11747

[hdf5] Update HDF5 to 1.12 #11747

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Neumann-A commented Jun 3, 2020

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