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hdf5 --with-mpi failed to build on OS 10.11.6 #4652

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nbren12 opened this Issue Nov 28, 2016 · 14 comments

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@nbren12

nbren12 commented Nov 28, 2016

Indicate troubleshooting steps taken

  • Ran brew update and retried your prior step?
  • Ran brew doctor, fixed as many issues as possible and retried your prior step?
  • Checked that a similar issue hasn't already been filed?
  • Looked up the software bug tracker if reporting a build error?
  • [NA] If you're seeing permission errors tried running sudo chown -R $(whoami) $(brew --prefix)?

Bug reports / build errors:

Brief summary of issue:

hdf5 fails to configure with mpi. It complains that

checking for gcc... /usr/local/bin/mpicc
checking whether the C compiler works... no
configure: error: in `/private/tmp/hdf5-20161128-9971-9ijs2q/hdf5-1.8.17':
configure: error: C compiler cannot create executables
See `config.log' for more details

Maybe this fails because mpicc is calling clang rather than gcc?

The complete command that you issued:

brew install hdf5 --with-mpi

Gist with output of brew doctor:

https://gist.github.com/bc29646673d6ad67ef3ee20c74efaf1b

Link output by brew gist-logs <formula>:

https://gist.github.com/bc29646673d6ad67ef3ee20c74efaf1b

Output of brew config:

HOMEBREW_VERSION: 1.1.1-95-g84b3c57
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: 84b3c57086d201ea07070a1b4d1b0520e2d7134a
Last commit: 22 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 158decbf79ffbd01893cb78ee6756680a977a9fc
Core tap last commit: 3 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local/Homebrew
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: quad-core 64-bit haswell
Homebrew Ruby: 2.0.0-p648
Clang: 7.3 build 703
Git: 2.9.0 => /usr/local/bin/git
Perl: /usr/bin/perl
Python: /usr/local/bin/python => /usr/local/Cellar/python/2.7.11/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby
Java: 1.8.0_51, 1.6.0_65-b14-468
macOS: 10.11.6-x86_64
Xcode: 8.1
CLT: 7.3.1.0.1.1461711523
X11: 2.7.9 => /opt/X11
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ilovezfs Nov 28, 2016

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I believe this is the same behavior I described here: Homebrew/brew#1130 (comment)

Do you have gcc installed?

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ilovezfs commented Nov 28, 2016

I believe this is the same behavior I described here: Homebrew/brew#1130 (comment)

Do you have gcc installed?

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nbren12 Nov 28, 2016

I do, but I think hdf5 is trying to compile with clang

nbren12 commented Nov 28, 2016

I do, but I think hdf5 is trying to compile with clang

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ilovezfs Nov 28, 2016

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what's the output of

xcode-select -p
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ilovezfs commented Nov 28, 2016

what's the output of

xcode-select -p
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nbren12 Nov 28, 2016

It gives /Library/Developer/CommandLineTools

nbren12 commented Nov 28, 2016

It gives /Library/Developer/CommandLineTools

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ilovezfs Nov 28, 2016

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sudo xcode-select -r

then try the build again

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ilovezfs commented Nov 28, 2016

sudo xcode-select -r

then try the build again

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nbren12 Nov 28, 2016

ha! it works. it successfully configured and is now compiling. thanks so much!

So xcode-select needs to have the "/Applications/Xcode.app/Contents/Developer" directory selected?

nbren12 commented Nov 28, 2016

ha! it works. it successfully configured and is now compiling. thanks so much!

So xcode-select needs to have the "/Applications/Xcode.app/Contents/Developer" directory selected?

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@nbren12 yeah it should no longer be an issue after the 8.2 CLT ships for El Capitan or you upgrade to Sierra. Incidentally, did it end up actually using gcc-6?

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ilovezfs commented Nov 28, 2016

@nbren12 yeah it should no longer be an issue after the 8.2 CLT ships for El Capitan or you upgrade to Sierra. Incidentally, did it end up actually using gcc-6?

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nbren12 Nov 29, 2016

nbren12 commented Nov 29, 2016

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ilovezfs Nov 29, 2016

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How did you stick with clang? Pass --cc= or an envvar or something else?

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ilovezfs commented Nov 29, 2016

How did you stick with clang? Pass --cc= or an envvar or something else?

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nbren12 commented Nov 29, 2016

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ilovezfs Nov 29, 2016

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Mind posting the link from running the following?

brew gist-logs hdf5

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ilovezfs commented Nov 29, 2016

Mind posting the link from running the following?

brew gist-logs hdf5

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nbren12 commented Nov 29, 2016

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Cool thanks. Yes please open a new issue for the problem you're now seeing.

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ilovezfs commented Nov 29, 2016

Cool thanks. Yes please open a new issue for the problem you're now seeing.

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iMichka Feb 7, 2017

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We provide now hdf5 1.10.0-patch1 now. Our CI built it --with-mpi on 10.12, 10.11 and 10.10 with success. Please open a new issue if you still encounter problems.

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iMichka commented Feb 7, 2017

We provide now hdf5 1.10.0-patch1 now. Our CI built it --with-mpi on 10.12, 10.11 and 10.10 with success. Please open a new issue if you still encounter problems.

@iMichka iMichka closed this Feb 7, 2017

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