The OPAL Discussion Forum

[Nicole R Neveu <nneveu AT stanford.edu>]

Hi Achim, 

Sorry for my late reply.

I was able to get rid of the H5 errors with the newer version of H5hut and enabling dynamic libraries.

(I didn't realize the default on Cori was static).

Now I'm back to boost errors (the usual culprit). 

I've tried the version 1.67 and 1.69 modules that they provide.

I thought the later had a chance (failed at 100% link step).

The only warning I got before the failure was this:

/usr/common/software/boost/1.69.0/intel/haswell/include/boost/pending/integer_log2.hpp(7): note: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.

Then later, I got the typical boost soup:

/usr/bin/ld: libOPAL.a(Util.cpp.o): in function `boost::re_detail_106900::perl_matcher<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, boost::regex_traits<char, boost::cpp_regex_traits<char> > >::match_prefix()':/usr/common/software/boost/1.69.0/intel/haswell/include/boost/regex/v4/perl_matcher_common.hpp:346: undefined reference to `boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > const&)'

I will try building boost my self now, and using that instead.

Thanks, 

Nicole

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From: Gsell Achim (PSI) <achim.gsell AT psi.ch>
Sent: Wednesday, March 6, 2019 1:10 AM
To: Nicole R Neveu
Cc: opal AT lists.psi.ch
Subject: Re: [Opal] NERSC build and H5Hut

 

Hi Nicole

On 6 Mar 2019, at 00:37, Nicole R Neveu <nneveu AT stanford.edu> wrote:

Hi OPAL developers, 

I'm trying to build on NERSC and ran into H5 issues when I used their H5hut module.

Which version of h5hut are you using?

I asked support about this and they had a question for you: 

Could you ask the opal developers if they updated the HDF5 file open call to take 64 bit integer instead of 32 bit? See this API change: https://gitlab.psi.ch/H5hut/src/wikis/Documentation/API-Changes 

This shouldn't be a problem. Which issues you are running into?

Best

Achim