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.
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]:
[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.