Archer default GCC 5.1 - outdated dependencies

[ferdinandvanwyk]

As of writing, when changing the PrgEnv on Archer (as per the configuration script) to GNU, the version of GCC that's loaded is gcc/5.1.0.

When compiling HDF5 1.8.9 with this version of gcc, I get the following error:

In file included from ../../../src/hdf5.h:45:0,
                 from gif.h:27,
                 from writehdf.c:19:
../../../src/H5FDlog.h:65:81: warning: ISO C90 does not support 'long long' [-Wlong-long]
 H5_DLL herr_t H5Pset_fapl_log(hid_t fapl_id, const char *logfile, unsigned long long flags, size_t buf_si
                                                                                 ^
make[3]: Leaving directory `/home4/e424/e424/vanwyk1/tmp/hdf5-1.8.9/hl/tools/gif2h5'
make[3]: Entering directory `/home4/e424/e424/vanwyk1/tmp/hdf5-1.8.9/hl/tools'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home4/e424/e424/vanwyk1/tmp/hdf5-1.8.9/hl/tools'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home4/e424/e424/vanwyk1/tmp/hdf5-1.8.9/hl/tools'
make[2]: Entering directory `/home4/e424/e424/vanwyk1/tmp/hdf5-1.8.9/hl'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/home4/e424/e424/vanwyk1/tmp/hdf5-1.8.9/hl'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home4/e424/e424/vanwyk1/tmp/hdf5-1.8.9/hl'
Making all in perform
make[1]: Entering directory `/home4/e424/e424/vanwyk1/tmp/hdf5-1.8.9/perform'
make[1]: *** No rule to make target `../tools/lib/libh5tools.la', needed by `h5perf_serial'.  Stop.
make[1]: Leaving directory `/home4/e424/e424/vanwyk1/tmp/hdf5-1.8.9/perform'
make: *** [all-recursive] Error 1

However, when I revert to gcc/4.8.1 HDF5 compiles fine suggesting we are falling behind when it comes to dependencies and leaving us with major headaches when we start fresh on a system. This issue documents what we use and what needs updating.

What version are we targeting? Helios is using an ancient gcc/4.4.7, whereas Archer now uses gcc/5.1 and will probably move to gcc/5.3 in the near future. Therefore gcc/5.1 is a reasonable target.

What we currently use:

1. HDF5 1.8.9 (newest 1.8.16)
2. NetCDF 4.2.1.1 (newest 4.4.0)
3. GSL 1.16 (newest 2.1)
4. Ruby set version (ideally 2.2.5 or higher)
5. ncurses 5.9 (newest 6.0)
6. readline 6.2 (newest 6.3)
7. YAML 0.1.4 (newest .1.6)

Further comments will deal with updating these one by one using gcc/5.1.

[ferdinandvanwyk]

Updating all the dependencies to the above versions (with Ruby 2.3.0) and compiling from source seems to work fine. Until you load an existing coderunner instance in which case I get the following error:

coderunner im -u
...
/home/e424/e424/vanwyk1/.rvm/gems/ruby-2.3.0/gems/gs2crmod-0.12.16/lib/gs2crmod/gsl_tools.rb:57:in `<top (required)>': uninitialized constant GSL::Matrix (NameError)
Did you mean?  Matrix
               NMatrix
...

I am unable to reproduce this on a local machine and it happens for both GSL 2.1 and 1.16 so doesn't seem related to that.

[edmundhighcock]

OK, so the solution we've worked out is to release coderunner 1.0.x which uses the dependencies at the version we have always been using and then move the master to 1.1.x which will begin the process of moving to all the latest versions of the libraries and compatibility with the SciRuby framework.

[ferdinandvanwyk]

I tried this again and the current status is as above. Using the following set of packages:

netcdf-4.4.0
gsl-2.1
hdf5-1.8.16
yaml-0.1.6
readline-6.3
ncurses-6.0
ruby-2.3.1 (built using RVM)

$ coderunner im -u
CodeRunner (c) 2009-2016. Written by Edmund Highcock & Ferdinand van Wyk. Loading...
Loading libraries...Warning: could not load rbgsl; limited functionality
............
Warning: could not load rbgsl; limited functionality
Loading modules for gs2, nil...
/home/e424/e424/vanwyk1/.rvm/gems/ruby-2.3.1/gems/gs2crmod-0.12.16/lib/gs2crmod/graphs.rb:152: warning: key :t_index is duplicated and overwritten on line 174
/home/e424/e424/vanwyk1/.rvm/gems/ruby-2.3.1/gems/gs2crmod-0.12.16/lib/gs2crmod/gsl_tools.rb:57:in `<top (required)>': uninitialized constant GSL::Matrix (NameError)
Did you mean?  Matrix
               NMatrix
    from /home/e424/e424/vanwyk1/.rvm/gems/ruby-2.3.1/gems/gs2crmod-0.12.16/lib/gs2crmod/gsl_data.rb:20:in `eval'
    from /home/e424/e424/vanwyk1/.rvm/gems/ruby-2.3.1/gems/gs2crmod-0.12.16/lib/gs2crmod/gsl_data.rb:20:in `<class:Gs2>'
    from /home/e424/e424/vanwyk1/.rvm/gems/ruby-2.3.1/gems/gs2crmod-0.12.16/lib/gs2crmod/gsl_data.rb:18:in `<class:CodeRunner>'
    from /home/e424/e424/vanwyk1/.rvm/gems/ruby-2.3.1/gems/gs2crmod-0.12.16/lib/gs2crmod/gsl_data.rb:17:in `<top (required)>'

[ferdinandvanwyk]

Archer have now removed all gcc/4.x versions so the old dependencies lists don't work anymore.

[ferdinandvanwyk]

Did we want to make a new minor version coderunner-1.1 with the updated dependencies?

[ferdinandvanwyk]

Dependencies fixed with PR #11

[ferdinandvanwyk]

https://github.com/SciRuby/nmatrix/wiki/Installation

note that nmatrix doesn't yet support gcc >=5.0

Oh no...

[edmundhighcock]

That is a little unfortunate!