HPCBIOS_2012-90: Software Tools and Development EnvironmentΒΆ


Software Development environment includes a set of tools which are needed for building and using scientific computing software. The following is an attempt to define which ones are relevant for the HPCBIOS communities and set an action plan.

  • BC Policy: HPCBIOS_2012-90
  • Date of Policy: 2012-12-15

The main objective of this policy is to provide the following common productivity environment across any HPCBIOS resources:

Name Prefered version(s) Compliance level Subcategory
bash sh tcsh ksh csh zsh latest MUST
  1. unix shells
vim emacs nano ed sed latest SHOULD
  1. editors / stream editors
coreutils bc par grep gawk findutils parallel latest SHOULD
  1. GNU variations of common Unix tools
more less screen script tmux latest SHOULD
  1. user interaction
man help2man texinfo par latest SHOULD
  1. online help
zlib openssl openssh latest SHOULD
  1. zlib/openssl are typically required allover
wget curl lynx links rsync unison ftp lftp bbcp latest SHOULD
  1. downloaders / file fetchers
subversion rcs cvs git latest SHOULD
  1. version control
ssh ldap nfs nscd telnet netcat ntp ntpdate latest SHOULD
  1. system interconnection essentials
strace ltrace lsof finger pwgen procps fuser who latest SHOULD
  1. process & user inspection
dstat sysstat iotop htop host ifconfig arp iptraf latest SHOULD
  1. system inspection tools
nmap tcpdump dig bind-utils whois icmpinfo latest SHOULD
  1. network inspection tools
ping traceroute ping6 traceroute6 tcptrace mtr ss latest SHOULD
  1. network diagnostics - basics
iperf nuttcp bwctl ndp ndt thrulay vnstat latest SHOULD
  1. network diagnostics - extras
patch diff diffstat m4 latest SHOULD
  1. patching & macros
bzip2 zip unzip pax arc lzip rzip cpio tar gzip latest SHOULD
  1. archivers
dmidecode lspci blkid fdisk hdparm ethtool latest SHOULD
  1. hardware & devices inspection
make cmake autoconf automake autotools latest SHOULD
  1. build tools
yasm nasm dev86 elfutils latest SHOULD
  1. assembly tools
bison byacc flex latest SHOULD
  1. parsing tools
GMP MPFR MPC PPL antlr expect latest MUST
  1. http://gcc.gnu.org/install/prerequisites.html
gcc g++ v4.4.x OR v4.6.x MUST
  1. gcc compiler: http://gcc.gnu.org
g77 gfortran libf2c libc6-prof libgfortran3 latest SHOULD
  1. compiler related
libtool libltdl-dev ia32-libs latest SHOULD
  1. lib or arch related
gdb valgrind gprof oprofile time objdump latest SHOULD
  1. debugging, profiling, timing
makeself.sh mc latest SHOULD
  1. misc platform
libstdc++ latest MAY
  1. base c++ libraries
ncurses ncurses-dev latest SHOULD
  1. tui development
binutils-dev libssl-dev libtiff4-dev libsm-dev latest SHOULD
  1. devel libs
libmysqlclient-dev libpng12-dev libpq-dev latest SHOULD
  1. devel libs, part II
xutils-dev libx11-dev libxt-dev latest SHOULD
  1. devel, X related
x11proto-xext-dev libxext-dev libqt4-dev latest SHOULD
  1. devel, X related, part II
tk gtk2 QT latest SHOULD
  1. X related
asciidoc doxygen doxygen-doc graphviz latest SHOULD
  1. documentation related
sqlite3 sqlite3-dev latest SHOULD
  1. db
python ruby ri perl ipython ocaml tcl latest SHOULD
  1. scripting & prototyping
pychecker pyflakes pylint latest SHOULD
  1. python code checkers
python-git python-svn latest SHOULD
  1. scripting integration with SCM
python-setuptools latest SHOULD
  1. python-setuptools
openjdk / java v1.6.0 or later MAY
  1. java SDK/Sun JDK
openmpi mpich2 mpich mvapich intelmpi latest MAY
  1. mpi stacks
environment-modules v3.2.10 or later MAY
  1. env. modules (Tcl/C)
lmod v5.9.0 or later MAY
  1. env. modules (lua/lmod)
lsb lsb-release latest MAY
  1. Linux Standard Base

This productivity environment will be supplemented with other related tools.

Potential sources of information for future upgrades of this list include:

Kindly notify -if this policy is inadequate for your work- both your local site technical representative & HPCBIOS maintainers.