In this document, we describe how to compile QBOX program on wcr.stanford.edu (Linux parallel cluster).
I designed this wiki such that you could in principle copy and paste the code part in your terminal, I encourage to do this to other writers of the group wiki. In any case, be aware of error messages, please report if something it is not working from this instructions or edit this wiki for other obvious typos.
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General Remarks
Based on the Qbox build instructions page we will give some additional details. The difficult part of the installation is to correctly build the dependence libraries. In particular
- BLACS http://www.netlib.org/blacs
- ScaLAPACK http://www.netlib.org/scalapack
- FFTW 2.1.5 http://www.fftw.org
- Apache Xerces-C http://xerces.apache.org/xerces-c
these libraries will have to be installed in your local directory. To achieve this I use to create a directory called ~/usr where libraries and header files will stay:
mk $HOME/usr mk $HOME/usr/local mk $HOME/local/bin
I also use to download software packages to ~/soft. This will make easier to establish absolute compilation paths for BLACS and Scalapack which have a non-standard installation procedure.
mk $HOME/soft
I will assume that
- BLAS (or ATLAS) http://www.netlib.org or http://math-atlas.sourceforge.net
- LAPACK http://www.netlib.org/lapack
are installed system wide already (as they are currently in wcr.stanford).
Install FFTW
The easiest library to install is FFTW 2.1.5 (FFTW3 is available but to the best of my knowledge incompatible with FFTW2). Simple download it from the FFTW download page and decompress it:
cd ~/soft wget http://www.fftw.org/fftw-2.1.5.tar.gz tar -zxvf fftw-2.1.5.tar.gz cd fftw-2.1.5
Then we do the usual configure and make install procedure, also indicating that we want a private installation in our ~/usr directory
./configure --prefix=$HOME/usr make make install
This will install the FFTW2 libraries in ~/usr/include and ~/usr/lib.
Install BLACS
Next download and untar BLACS from BLACS papers page:
cd ~/soft wget http://www.netlib.org/blacs/mpiblacs.tgz tar -zxvf mpiblacs.tgz cd BLACS
We have to have our own version of a file called Bmake.inc in the ~/soft/BLACS directory. The following file will serve for BLACS/Bmake.inc
wget http://micro.stanford.edu/mediawiki-1.11.0/images/BLACS_Bmake.inc.txt -O Bmake.inc
The file is just the same as BMAKES/Bmake.MPI-LINUX with the following changes in the variables definition:
< BTOPdir = $(HOME)/soft/BLACS < MPIdir = /opt/mpich/gnu
Then change to the source directory and make, then copy the compiled libraries to ~/usr/lib/
cd SRC/MPI make cp ~/soft/BLACS/LIB/*.a ~/usr/local/lib
Install Scalapack
Now it is the turn for Scalapack, get it from the Scalapack home page, untar it
cd ~/soft wget http://www.netlib.org/scalapack/scalapack-1.8.0.tgz tar -zxvf scalapack-1.8.0 cd scalapack
and put this compilation input file scalapack/SLmake.inc in the directory
wget http://micro.stanford.edu/mediawiki-1.11.0/images/Scalapack_SLmake.inc.txt -O SLmake.inc
which is just the same as SLmake.inc.example with the following changes:
< home = $(HOME)/soft/scalapack-1.8.0 < F77 = /opt/mpich/gnu/bin/mpif77 < CC = /opt/mpich/gnu/bin/mpicc
then make and copy the resulting library to ~/usr/lib
cp ~/soft/scalapack-1.8.0/libscalapack.a ~/usr/local/lib
Install Xerces
Now the Xerces XML library, get it from the Xerces download page and untar
wget http://apache.mirrors.hoobly.com/xerces/c/sources/xerces-c-src_2_8_0.tar.gz tar -zxvf xerces-c-src_2_8_0.tar.gz cd src/xerces
then run this script and the usual make install
./runConfigure -plinux -cgcc -xg++ -minmem -nsocket -tnative -rpthread -P $HOME/usr make make install
(there are some clues that indicate that we may need to use -rnone but it is not for sure.) This will make xerces installed in ~/usr/lib and ~/usr/include/xerces.
Ready to Install Qbox
Having the previous libraries installed in our own directory ~/usr and the rest of them already installed by the system administrator we shouldn't have any problems compiling Qbox
First step is to get the source code from Qbox download page and decompress it.
cd ~/soft wget http://fpmd.ucdavis.edu/software/qbox/qbox-1.45.0.tgz tar -zxvf qbox-1.45.0.tgz cd qbox-1.45.0/src
We have to have a makefile input file for our own system (wcr) in the current directory; for that we have created qbox-1.45.0/src/wcr.mk, we will also need to specify our target system (according to the filename wcr.mk)
wget http://micro.stanford.edu/mediawiki-1.11.0/images/Qbox_wcr.mk.txt -O wcr.mk export TARGET=wcr
wcr.mk file distributed here is based on x8664_gcc.mk with the following changes:
< MPIDIR=/opt/mpich/gnu < XERCESCDIR=$(HOME)/usr < FFTWDIR=$(HOME)/usr < BLASDIR=$(HOME)/usr/local/lib < LAPACKDIR=$(HOME)/usr/local/lib < CXX=/opt/mpich/gnu/bin/mpicxx < -llapack -lf77blas -latlas -lm \ < -Xlinker -lxerces-c -Bstatic \ < -lc -static-libgcc -lmpich \ < # gfortran < PLAT=LINUX < BLACSdir = $(HOME)/usr/local/lib < SCALAPACK_DIR = $(HOME)/usr/local/lib
The following is not documented but very useful to free us from defining system variables in out rc files such as 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/usr/lib:$HOME/usr/local/lib'. We have to define this variable BEFORE compilation occurs (there is no need to define it before each run of Qbox):
export LD_RUN_PATH=~/usr/lib
This will enforce the compiler to store the absolute location of the libraries (e.g. xerces) in the executable itself. Now we are ready to make
make
This can take a couple of minutes, afterwards we can try to run a small example,
cd ~/soft/qbox-1.45.0/examples/ch4 /opt/mpich/gnu/bin/mpirun -np 2 ~/soft/qbox-1.45.0/src/qb gs.i
If it works we can copy the executable to our bin directory. Since the qbox versions change rather often it is convenient to keep track of the executable version and make a link to the latest version available.
cp ~/soft/qbox-1.45.0/src ~/usr/local/bin/qbox-1.45.0 ln -s ~/usr/local/bin/qbox-1.45.0 ~/usr/local/bin/qbox
(end of compilation tutorial)