156. Compiling nwchem 6.1 with internal libs, openmpi, python on debian testing/wheezy

I followed this thread: http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id435/segmentation_fault--running_smal....html

See here for build with external blas: http://verahill.blogspot.com.au/2012/05/building-nwchem-61-on-debian.html

--Start here --
sudo apt-get install libopenmpi-dev python-dev

sudo mkdir /opt/nwchem
sudo chown ${USER} /opt/nwchem
cd /opt/nwchem
wget http://www.nwchem-sw.org/images/Nwchem-6.1-2012-Feb-10.tar.gz
tar xvf Nwchem-6.1-2012-Feb-10.tar.gz
mv nwchem-6.1 nwchem-6.1_internal
cd nwchem-6.1_internal/

Edit src/config/makefile.h and add -lz -lssl to the end of line 1914 (needed by python)

Edit src/tools/GNUmakefile and add two lines as shown below in red (line numbers added by me for illustration only) -- editing needed for compile with internal libs.

355 ifneq ($(BLAS_LIB),)
356     ifeq ($(BLAS_SIZE),4)
357         MAYBE_BLAS = --with-blas4="$(strip $(BLAS_LIB))"
358     else
359         MAYBE_BLAS = --with-blas8="$(strip $(BLAS_LIB))"
360     endif
361 endif

to

355 ifneq ($(BLAS_LIB),)
356     ifeq ($(BLAS_SIZE),4)
357         MAYBE_BLAS = --with-blas4="$(strip $(BLAS_LIB))"
358     else
359         MAYBE_BLAS = --with-blas8="$(strip $(BLAS_LIB))"
360     endif
361 else
362     MAYBE_BLAS = --without-blas
363 endif

Then continue as normal:

export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=`pwd`
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES="all python"
export PYTHONVERSION=2.7
export PYTHONHOME=/usr
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/usr/lib/openmpi/lib
export MPI_INCLUDE=/usr/lib/openmpi/include
export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib/openmpi/lib
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran

**If you get errors relating to openssl etc. at the end of compile, try building without python support by removing anything in blue. You won't need to do make clean so the rebuild will be quick. 

Building takes ages

Edit your ~/.bashrc and add

export NWCHEM_EXECUTABLE=/opt/nwchem/nwchem-6.1_internal/bin/LINUX64/nwchem
export NWCHEM_BASIS_LIBRARY=/opt/nwchem/nwchem-6.1_internal/src/basis/libraries/
export PATH=$PATH:/opt/nwchem/nwchem-6.1_internal/bin/LINUX64

---

Links to this post:
http://chemport.ru/forum/viewtopic.php?f=71&t=98589

155. Gromacs with external fftw3 and blas on debian testing

This is based on http://verahill.blogspot.com.au/2012/03/building-gromacs-with-fftw3-and-openmpi.html

Make sure your build environment is set up:
sudo apt-get install build-essential gfortran libopenmpi-dev

---

fftw
sudo mkdir /opt/fftw/
sudo chown ${USER} /opt/fftw
mkdir ~/tmp
cd ~/tmp
wget ftp://ftp.fftw.org/pub/fftw/fftw-3.3.2.tar.gz
tar xvf fftw-3.3.2.tar.gz
cd fftw-3.3.2/

./configure --enable-float --enable-mpi --enable-threads --with-pic --prefix=/opt/fftw/fftw-3.3.2/single

make && make install

make clean

./configure --disable-float --enable-mpi --enable-threads --with-pic --prefix=/opt/fftw/fftw-3.3.2/double

make && make install

---

openblas
sudo mkdir /opt/openblas
sudo chown ${USER} /opt/openblas
cd ~/tmp
wget http://nodeload.github.com/xianyi/OpenBLAS/tarball/v0.1.1
tar xvf v0.1.1
cd xianyi-OpenBLAS-e6e87a2/
wget http://www.netlib.org/lapack/lapack-3.4.1.tgz
make all BINARY=64 CC=/usr/bin/gcc FC=/usr/bin/gfortran USE_THREAD=0 INTERFACE64=1 1> make.log 2>make.err

make PREFIX=/opt/openblas install
cp lib*.*  /opt/openblas/lib

add

export LD_LIBRARY_PATH:$LD_LIBRARY_PATH:/opt/openblas/lib

to your ~/.bashrc

[for later use with nwchem and ecce, add /opt/openblas/lib to /etc/ld.so.conf and do sudo ldconfig]

---

gromacs


sudo mkdir /opt/gromacs
sudo chown ${USER} /opt/gromacs
cd ~/tmp
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz

tar xvf gromacs-4.5.5.tar.gz

cd gromacs-4.5.5/

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/openblas/lib

single
export LDFLAGS="-L/opt/fftw/fftw-3.3.2/single/lib -L/opt/openblas/lib -lopenblas"
export CPPFLAGS="-I/opt/fftw/fftw-3.3.2/single/include -I/opt/openblas/include"

./configure --disable-mpi --enable-float --with-fft=fftw3 --with-external-blas --with-external-lapack --program-suffix=_sp --prefix=/opt/gromacs/gromacs-4.5.5
make -j3
make install

double
make distclean
export LDFLAGS="-L/opt/fftw/fftw-3.3.2/double/lib -L/opt/openblas/lib -lopenblas" 
export CPPFLAGS="-I/opt/fftw/fftw-3.3.2/double/include -I/opt/openblas/include"

./configure --disable-mpi --disable-float --with-fft=fftw3 --with-external-blas --with-external-lapack --program-suffix=_dp --prefix=/opt/gromacs/gromacs-4.5.5
make -j3
make install

single + mpi
make distclean
export LDFLAGS="-L/opt/fftw/fftw-3.3.2/single/lib -L/opt/openblas/lib -lopenblas"
export CPPFLAGS="-I/opt/fftw/fftw-3.3.2/single/include -I/opt/openblas/include"

./configure --enable-mpi --enable-float --with-fft=fftw3 --with-external-blas --with-external-lapack --program-suffix=_spmpi --prefix=/opt/gromacs/gromacs-4.5.5
make -j3
make install


double + mpi
make distclean
export LDFLAGS="-L/opt/fftw/fftw-3.3.2/double/lib -L/opt/openblas/lib -lopenblas"
export CPPFLAGS="-I/opt/fftw/fftw-3.3.2/double/include -I/opt/openblas/include"

./configure --enable-mpi --disable-float --with-fft=fftw3 --with-external-blas --with-external-lapack --program-suffix=_dpmpi --prefix=/opt/gromacs/gromacs-4.5.5
make -j3
make install

Make sure to put this in your ~/.bashrc

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/openblas/lib
export PATH=$PATH:/opt/gromacs/gromacs-4.5.5/bin

 You now have four versions of each binary -- with and without mpi, with single and with double precision.

---

154. Vim -- weird pasting behaviour

The problem:
Get this

 when you want this?

The solution:

This is perhaps a bit superfluous as it comes from the vim wiki, but it might help someone: 

Edit your ~/.vimrc and add

set pastetoggle=<F3>

Now, before you paste, hit F3 and you can paste as usual (notice the little 'paste' after the 'insert' in the screenshot below).

My full ~/.vimrc is now

set number
set pastetoggle=
set spell
set wrap
nnoremap  :set nonumber!<

Other cool stuff:

* Line number toggle -- nnoremap <F4> :set nonumber!<CR> will map line numbering on /off to F4.

* Substituting only within selection. Go to visual mode and select the text.
Then hit  : which brings up '<,'>.  Anyway, the key is \%V which confines the substitution to the visually selected area.

:'<,'>s/\%Voldphrase/newphrase/g

* Commenting out lines -- the key is ^

: %s/^/#/g 

or

 :'<,'>s/\%V^/#/g

---

I previously had a bigger ~/.vimrc posted here, but now, a year later, I've reduced it to what I've posted above.
Anyway, the old one is here:

set number
filetype plugin on
filetype indent on
set expandtab
set shiftwidth=4
set tabstop=4
set smarttab
set spell
set lbr
set ai "Auto indent
set si "Smart indent
set wrap "Wrap lines
set grepprg=grep\ -nH\ $*
let g:tex_flavor='latex'
highlight Cursor guifg=white guibg=black
highlight iCursor guifg=white guibg=steelblue
set guicursor=n-v-c:block-Cursor
set guicursor+=i:ver100-iCursor
set guicursor+=n-v-c:blinkon0
set guicursor+=i:blinkwait10
set pastetoggle=<F3>
nnoremap <F4> :set nonumber!<CR>