hdf5 @1.10.0-patch1: update to 1.10.1

[Dave-Allured (Dave Allured)]

hdf5 1.10.1 released 2017 April 27: ​​https://support.hdfgroup.org/HDF5/

Includes improved solution for flock problem with network mounted files.

[Dave-Allured (Dave Allured)]

In this update, please include a prominent note that Mac users may need to set the environment variable "HDF5_USE_FILE_LOCKING" to the five-character string "FALSE" when accessing network mounted files. This is an application run-time setting, not a configure or build setting. Otherwise errors such as "unable to open file" or "HDF5 error" may be encountered.

See the HDF5 release notes for more details about HDF5_USE_FILE_LOCKING:

​https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1-RELEASE.txt

[mf2k (Frank Schima)]

@Dave-Allured: Can you attach a tested Portfile patch for the update?

[Dave-Allured (Dave Allured)]

@mf2k: Sorry, I do not currently have the experience to work on Portfiles. I am relying on the port owner.

[mf2k (Frank Schima)]

I tried a simple version & checksum update but it failed in the configure stage for me. Hopefully the maintainer will respond soon with an update.

[Dave-Allured (Dave Allured)]

@mf2k: My private build on Mac went smoothly a couple weeks ago. If you post your configure output or error messages, I may be able to spot the problem.

[mf2k (Frank Schima)]

--->  Configuring hdf5
Error: reinplace: couldn't read file "/opt/local/var/macports/build/_opt_local_var_macports_sources_github.com_macports_macports-ports_science_hdf5/hdf5/work/hdf5-1.10.1/tools/misc/h5cc": no such file or directory

[Dave-Allured (Dave Allured)]

Short answer, I do not have a fix. My build was a simple autotools-based local build on Mac. Yours was in a Macports context which I do not understand.

My build was for pre-release version 1.10.1-pre2, yours was for the final 1.10.1 version. My guess is that doesn't matter.

Your configure got as far as mine, line 646 in main.log, "Optimization instrumentation: no". My configure ended successfully, right there. Yours went on to Macports post-processing starting at line 647. You apparently failed at h5cc not found. This is odd because up at line 479 you got "creating tools/src/misc/h5cc" and no error message. This feels like some kind of path mixup in the post-processing.

Well that is enough gueswork for me. I hope you and MIke solve this without much further trouble.

[mamoll (Mark Moll)]

I have attached a Portfile patch. This cannot be committed directly, because (as usual) all ports that depend on hdf5 need to be rev-bumped at the same time.

[mf2k (Frank Schima)]

That is timely, I just figured out how to fix it too by updating the replaces. I noticed that nothing actually get changed though. Are they still needed?

[mamoll (Mark Moll)]

The reinplace of arch flags still does something. The reinplace of ccache does nothing for most people, but is still needed.

As a side note, I have a draft Portfile that uses the alternative crake-based build infrastructure. This would eliminate the need for most of this stuff, I believe. Unfortunately, the last time I tested this, the cmake build system didn't install the same file (or used slightly different location; I don't remember). This would cause too much breakage in ports that depend on hdf5.

[Dave-Allured (Dave Allured)]

Replying to mamoll:

I have attached a Portfile patch. This cannot be committed directly, because (as usual) all ports that depend on hdf5 need to be rev-bumped at the same time.

Mark, what is the purpose of rev-bumping all the other ports? This ticket is only hdf5 1.10.0-patch1 --> 1.10.1. There should be no functional or API incompatibilities. This is not the same as hdf5-18 --> hdf5.

I checked a typical portfile, e.g. h5utils. I found only this, and nothing to be changed for 1.10.0-patch1 --> 1.10.1:

depends_lib port:hdf5

If there is history on this requirement, please point me in that direction. Thanks.

[mamoll (Mark Moll)]

hdf5 is very particular about versioning. If you look at other ports (e.g., py-tables), you see this is done regularly.

[mamoll (Mark Moll)]

In 1aac7783b31477b5811b4e775d1183bda7d030e6/macports-ports:

science/hdf5: update to version 1.10.1; rev. bump ports that depend on hdf5, since hdf5 is very picky about this; closes #54139