Software: Difference between revisions

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===Tutorials===
===Tutorials===


[[http://compbio.chemistry.uq.edu.au/mediawiki/upload/2/2f/GROMOS_tutorial.pdf]]
GROMOS Tutorial July 2008 [[http://compbio.chemistry.uq.edu.au/mediawiki/upload/2/2f/GROMOS_tutorial.pdf]]


===Bioinformatics/Computational Biology/X-ray Crystallography rpm repositories===
===Bioinformatics/Computational Biology/X-ray Crystallography rpm repositories===

Revision as of 23:48, 15 July 2008

Software that is installed or is to be installed on the workstations

This is a listing of the 3rd-party packages are currently installed on the workstations. This list has been compiled by Mitchell Stanton-Cook

Packages tagged From SRC rpm will be added to a local yum repository on compbio
bold = newly added
Related: SEE - yum_repo and building_rpms

LEGEND:
Yes   Have been installed/tested   Maybe   Close to working   No   Have not been installed/tested

???   Need more information   Todo   A MD Group member will need to install this


Package name Version Installed Tested Notes
pgi 7.2

Yes

No

SEE: /opt/pgi on guava and /software/pgi on grape
checkinstall

Yes

No

See checkinstall_patch. SEE: /usr/src/redhat/RPMS/x86_64/checkinstall-1.6.1-1.x86_64.rpm
kile

Yes

No

apbs

Yes

No

src and binary. In /opt
molmol

No

No

Will buy beer if you can get this one working
pymol

Yes

No

src - no up-to-date binaries are provided now without a license
python setup.py build
python setup.py install
python setup2.py install
python setup2.py uninstall
cp ./pymol /usr/local/bin
pdfedit

Yes

No

emacs

Yes

No

gnuplot

Yes

No

gtk

Yes

No

gtk-devel

Yes

No

xplor-nih

Yes

No

binary only

Could not run the test-scripts ! Check !!!

clustalw and clustalx

No

No

Clustalw(INSTALLED): From SRC rpm

/usr/src/redhat/RPMS/x86_64/clustalw-1.83-0.fdr.5.x86_64.rpm

Clustalx: From SRC rpm NCBI-devel is needed by clustalx-1.8.3-2a.x86_64

modeller

No

No

REQUIRES LIC: # env KEY_MODELLER9v2=XXXX rpm -Uvh modeller-9v2-1.i386.rpm
openGL

Yes

No

is this free-glut ?
rasmol

Yes

No

From SRC rpm. /usr/src/redhat/RPMS/x86_64/rasmol-2.7.2.1.1-3.x86_64.rpm
seqview

???

No

Need url please
treeview

No

No

src. In /opt

Requires: wxGTK

Have a compilation error

electric fence library

Yes

No

phylip

No

No

Tried building from SRC rpm.

BUT, EMBOSS-devel = 5.0.0 is needed by PHYLIP-3.6b-6.x86_64

I have built from pure src. in /opt. Have not make links to /usr/local/bin

blast

Yes

No

From binary. In /opt

No DB installed TODO: Install wwwblast on compbio

VMD

Yes

No

From src. In /opt

I will try to create a rpm package for this.

povray

Yes

No

From SRC rpm. /usr/src/redhat/RPMS/x86_64/povray-3.6.1-3.fc7.x86_64.rpm
mead

???

No

Need url please
spdb

No

No

Building from SRC rpm. These are the steps I carried out as I could not rebuild directly
rpm -iUvh spdbv-3.7.5-3.src.rpm
vi /usr/src/redhat/SPECS/spdbv.spec
replace Copyright with License
rpmbuild -ba /usr/src/redhat/SPECS/spdbv.spec

/usr/src/redhat/RPMS/x86_64/spdbv-3.7.5-3.x86_64.rpm

libXm.so.3 is needed by spdbv-3.7.5-3.x86_64 - This is provided by OpenMotif?

rxvt

Yes

No

xterm

Yes

No

GROMACS 3.2.1

3.3.1 3.3.1-CVS

Yes

No

src

3.2.1: in /opt/GROMACS/3.2.1 (All-static fails) [single and doule precision (_d)]

./configure --prefix=/opt/GROMACS/3.2.1 --with-fft=fft F77=/opt/intel/fce/10.0.023/bin/ifort CPPFLAGS=-I/opt/FFTW/2.1.5/include LDFLAGS=-L/opt/FFTW/2.1.5/lib [--disable-float --program-suffix=_d]
(then make and make install)

And an MPI version for mdrun (_mpi and _mpi_d)

./configure --prefix=/opt/GROMACS/3.2.1 --with-fft=fft F77=/opt/lam-mpi-7.1.4/bin/mpif77 CC=/opt/lam-mpi-7.1.4/bin/mpicc CXX=/opt/lam-mpi-7.1.4/bin/mpiCC CPPFLAGS=-I/opt/FFTW/2.1.5/include LDFLAGS=-L/opt/FFTW/2.1.5/lib --enable-mpi --program-suffix=_mpi [--disable-float --program-suffix=_mpi_d]

3.3.1: in /opt/GROMACS/3.3.1 (All-static fails) [single and doule precision (_d)]

./configure --prefix=/opt/GROMACS/3.3.1 --with-fft=fftw2 F77=/opt/intel/fce/10.0.023/bin/ifort CPPFLAGS=-I/opt/FFTW/2.1.5/include LDFLAGS=-L/opt/FFTW/2.1.5/lib [--disable-float --program-suffix=_d]

And an MPI version for mdrun (_mpi and _mpi_d)

./configure --prefix=/opt/GROMACS/3.3.1 --with-fft=fftw2 F77=/opt/lam-mpi-7.1.4/bin/mpif77 CC=/opt/lam-mpi-7.1.4/bin/mpicc CXX=/opt/lam-mpi-7.1.4/bin/mpiCC CPPFLAGS=-I/opt/FFTW/2.1.5/include LDFLAGS=-L/opt/FFTW/2.1.5/lib --enable-mpi --program-suffix=_mpi [--disable-float --program-suffix=_mpi_d]

3.3.1 (CVS): in /opt/GROMACS/3.3.1-CVS [single and doule precision, MPI-enabled mdrun]

./bootstrap and then, same commands as 3.3.1
GROMOS

No

No

promd, promd_opt_omp (works for two processors will try for 8 after ice comes across) – Does NOT work! (so-called known problem, but not solved)
/opt/GROMOS/gromos96_24Jun04/LINUX_IFC/bin/ 
gromos++ 14Jul2008

Yes

Yes

Jul 2008 Forcefield files in /software/gromos/forcefield SEE: /software/gromos/gromos++ on grape
PATH=$PATH:/software/libtool/bin
./Config.sh
export FFFLAGS=-I/software/pgi/linux86-64/7.2-2/include
export LDFLAGS=-L/usr/local/lib
./configure 
make
make check
make install
gromosXX 15Jul2008

Yes

Yes

Jul 2008 Forcefield files in /software/gromos/forcefield SEE: /software/gromos/gromosXX on grape
PATH=$PATH:/software/libtool/bin
./Config.sh
./configure --prefix=/software/gromos/gromosXX 
make
make check
make install
gv

Yes

No

xemacs

Yes

No

zsh

Yes

No

vim

Yes

No

LAM/MPI 7.1.4

Yes

No

src - Default settings used (Fortran compiler is Intel ifort /opt/intel/fce/10.0.023/bin/ifort)
./configure --prefix=/opt/lam-mpi-7.1.4 FC=/opt/intel/fce/10.0.023/bin/ifort
mplayer

Yes

No

No codecs installed
vlc

Yes

No

fftw 2.1.5

Yes

No

src - Installed version 2.1.5 (single and double precision). I can't manage to install 3.0.1.
./configure --prefix=/opt/FFTW/2.1.5 --enable-mpi --enable-fortran --enable-threads --enable-type-prefix F77=/opt/lam-mpi-7.1.4/bin/mpif77 CC=/opt/lam-mpi-7.1.4/bin/mpicc FFLAGS=-L/opt/lam-mpi-7.1.4/lib/ CPPFLAGS=-I/opt/lam-mpi-7.1.4/bin [--enable-float]
R

Yes

No

xmms-mp3

Yes

No

installed AUDACIOUS instead
flash

Yes

No

shockwave

???

No

Is this available for linux? Does flash take care of this?
acrobat

Yes

No

xmgrace

Yes

No

Requires: Motif/LessTif

yum install lesstif (note: only i386 available)
yum install grace (note: installs fftw2
firefox

Yes

No

thunderbird

Yes

No

nedit

Yes

No

java

Yes

No

Currently in: /opt/jdk1.6.0_02/ WILL move someone more convenient location SOON.
xine

Yes

No

wxMaxima Yes
nedit Yes
K3b Yes
mutt Yes
rxvt Yes
gsl (GNU Scientific Librairy) >= 1.10 Yes
Anjuta <= 2.2.1 Yes
glade-3 >= 3.0.2 (install before anjuta) Ask me help when you install it cause there is some tricks
g77 GNU FORTRAN77 compiler
Anjuta >= 2.2.2 :) Ask me help when you install it cause there is some tricks
compat-libf2c

Yes

No

DSSP Should be install at /usr/local/bin/dssp for compatibility with GROMACS.


Tutorials

GROMOS Tutorial July 2008 [[1]]

Bioinformatics/Computational Biology/X-ray Crystallography rpm repositories