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Comment by gaius | Hacker News Reader

Any HPC language evaluation that doesn't include vs FORTRAN is pointless. It's still king of computation for a reason.

Experiments aren't usually written in FORTRAN.

The programmer is by far the slowest part of HPC. It often makes sense to use the language you're fastest at instead of the language that will run the fastest.

It's very common for experiments to be written in languages not know for their performance (Java, Matlab, Perl, and Python for instance).

For reference, here are some of the packages commonly used in experiments[1]:

    BLAS        Fortran                 http://www.netlib.org/blas/#_software
    NCBI BLAST  C++                     ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.30+-src.zip
    BFAST       C                       http://sourceforge.net/projects/bfast/
    BioPerl     Perl                    https://github.com/bioperl/bioperl-live
    Bowtie      C++, C                  http://sourceforge.net/projects/bowtie-bio/files/bowtie/
    Clustal     C, C++                  http://www.clustal.org/omega/#Download
    cp2k        Fortran                 https://github.com/cp2k/cp2k
    Gromacs     C                       https://github.com/gromacs/gromacs
    HTSeq       Python                  https://pypi.python.org/pypi/HTSeq
    MUSCLE      C++                     http://www.drive5.com/muscle/downloads.htm
    MrBayes     C                       http://sourceforge.net/p/mrbayes/code/HEAD/tree/
    OpenFOAM    C++                     https://github.com/OpenFOAM/OpenFOAM-2.3.x
    SAMtools    C                       https://github.com/samtools/samtools
    SNAP        C                       http://korflab.ucdavis.edu/software.html
    fftw3       C                       https://github.com/FFTW/fftw3

[1]: I went down this list and picked some of the ones I remember using (been out of the HPC world for a couple years): https://portal.tacc.utexas.edu/software It'll be a bit skewed towards genomics.

The list is not just skewed toward bioinformatics; a majority of them is bioinformatics software. I would not call BioPerl or HTSeq high-performance-computing software. Some of the software are written by academic programmers with all attendant baggages. I am not aware of any bioinformatics software written in Fortran, which is not popular in the bioinformatics community. But this is not to say Fortran might not be a good fit. The Broad Institute is rewriting some of its tools in C++ with help from Intel to leverage vector instructions. Who is to say if they had started with Fortran they might not have gotten vector instructions for free earlier.

> fftw3 C

FFTW is C code, but nobody wrote the C code. The C code is generated by code written in OCaml.

http://en.wikipedia.org/wiki/FFTW

... the reason is mostly legacy. All your libraries are written in fortran. Everyone learned fortran in the past and they don't want to switch.

As an example, I've seen physicists use fortran for parsing and transforming the output of a program. The cluster at our department has an awesomely updated ifort but no python2.7 (I think it has 2.2 or 2.3 or something). C++ isn't used directly either.

But yeah, there should have been fortran and some other languages there.

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