139. compiling nwchem with custom ATLAS on debian

I'm not yet sure, but there seems to be something weird with this build. Use the openblas build here preferentially:  http://verahill.blogspot.com.au/2012/05/nwchem-with-openblas.html

i.e. do not use this build without testing it against builds without external blas/atlas and against other libraries.

I am not an expert

The atlas build is pretty much like what was described here:
http://verahill.blogspot.com.au/2012/05/compile-atlas-blas-on-debian-testing.html

---

Build atlas
Check you cpu governor:

cat /sys/devices/system/cpu/cpu1/cpufreq/scaling_governor 

ondemand

Next, set it to performance for all cores (example for three-core AMD)
sudo cpufreq-set -g performance
sudo cp /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor /sys/devices/system/cpu/cpu1/cpufreq/scaling_governor
sudo cp /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor /sys/devices/system/cpu/cpu2/cpufreq/scaling_governor

Prepare the install directory:
sudo mkdir /opt/ATLAS
sudo chown ${USER} /opt/ATLAS

Prepare the compile directory
mkdir ~/tmp
cd ~/tmp
 wget http://downloads.sourceforge.net/project/math-atlas/Developer%20%28unstable%29/3.9.72/atlas3.9.72.tar.bz2
tar xvf atlas3.9.72.tar.bz2
cd ATLAS/
mkdir build/
vim Make.top 
change -V on line 6 to -v

cd build
.././configure --prefix=/opt/ATLAS

There's any level of detail in what you can pass to configure. -A AMD64 would be one option. Look at the bottom for more info.

make
make install
cp lib/lib* /opt/ATLAS/lib

Once it's all done, set the cpu governor back if you so desire.
sudo cpufreq-set -g ondemand
sudo cp /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor /sys/devices/system/cpu/cpu1/cpufreq/scaling_governor
sudo cp /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor /sys/devices/system/cpu/cpu2/cpufreq/scaling_governor

---

nwchem

For python support you need to edit src/config/makefile.h (see http://verahill.blogspot.com.au/2012/04/adding-python-support-to-nwchem-under.html)

export LARGE_FILES=TRUE

export TCGRSH=/usr/bin/ssh

export NWCHEM_TOP=/opt/nwchem/nwchem-6.0

export NWCHEM_TARGET=LINUX64

export NWCHEM_MODULES="all python"

export PYTHONHOME=/usr

export PYTHONVERSION=2.7

export BLASOPT="-L/opt/ATLAS/lib -latlas -lblas -llapack"

export USE_MPI=y

export USE_MPIF=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

Note: don't use HAS_BLAS=y. It gave me no end of grief.

Also, IF you binary executes without a hitch at this point it means that you're libs are not being loaded.  You need to put

export LD_LIBRARY_PATH=/opt/ATLAS/lib:$LD_LIBRARY_PATH

in your ~/.bashrc

Building takes a while, but should go ok. Make sure you have python2.7-dev installed, and if you're using a different python version, make sure to change the options above.

---

Here's also an example ~/.nwchemrc file for no particular reason at all -- if you've got ecce installed you might want to make sure yours is correct.

nwchem_basis_library /opt/nwchem/nwchem-6.0/src/basis/libraries/
nwchem_nwpw_library /opt/nwchem/nwchem-6.0/src/nwps/libraryps/
ffield amber
amber_1 /opt/nwchem/nwchem-6.0/src/data/amber_s/
amber_2 /opt/nwchem/nwchem-6.0/src/data/amber_x/
spce /opt/nwchem/nwchem-6.0/src/data/solvents/spce.rst
charmm_s /opt/nwchem/nwchem-6.0/src/data/charmm_s/
charmm_x /opt/nwchem/nwchem-6.0/src/data/charmm_x/

---

You can get a list over compile options for ATLAS using
make xprint_enums ; ./xprint_enums

after you've done .././configure

See http://sourceforge.net/tracker/index.php?func=detail&aid=3021404&group_id=23725&atid=379483

123. Adding python support to nwchem under debian

I've posted the general build instructions for nwchem 6.0 with mpi support here: http://verahill.blogspot.com.au/2012/03/nwchem-60-with-openmpi-support-on.html

However, those instructions don't include python support.

0. Download,  extract nwchem and install blas etc. as shown in http://verahill.blogspot.com.au/2012/03/nwchem-60-with-openmpi-support-on.html

1. Edit nwchem-6.0/src/config/makefile.h
Change line 1962 from

EXTRA_LIBS +=    -lnwcutil  -lpthread -lutil -ldl

to

EXTRA_LIBS +=    -lnwcutil  -lpthread -lutil -ldl -lz -lssl

2. Install python headers
sudo apt-get install python2.7-dev

3. Execute the following commands (one by one or by putting them in a shell script)

export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=`pwd`
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES="all python"
export PYTHONHOME=/usr
export PYTHONVERSION=2.7
export USE_MPI=y
export USE_MPIF=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

It should work fine and after a long build you'll have python enabled binaries.

4. Testing
You can test whether there's python support by creating test.nw with

python
for n in range(1,6):
        print n, n*2,n**2
end
task python

and running it with 

mpirun -n 1 nwchem test.nw

which gives

  NWChem Input Module
                                -------------------


                               NWChem Python program
                               ---------------------
for n in range(1,6):
        print n, n*2,n**2
1 2 1
2 4 4
3 6 9
4 8 16
5 10 25
1 2 1
2 4 4
3 6 9
4 8 16
5 10 25
 Task  times  cpu:        0.0s     wall:        0.0s

Done.


Note:
for ROCKS/CENTOS it was not necessary to edit src/config/makefile.h


The relevant parts in the the build configuration are

export NWCHEM_MODULES="all python"
export PYTHONHOME=/opt/rocks
export PYTHONVERSION=2.4

Other than that, just follow http://verahill.blogspot.com.au/2012/03/building-nwchem-60-on-rocks-543centos.html

---

Error:
gfortran: error: /usr/include/python2.7/lib/python2.7/config/libpython2.7.a: No such file or directory

make: *** [all] Error 1

locate libpython2.7.a

/usr/lib/libpython2.7.a

/usr/lib/python2.7/config/libpython2.7.a

Reason:
export PYTHONHOME=/usr/include/python2.7

Solution:
export PYTHONHOME=/usr

---

Error:

In function `PyZlib_compress':

(.text+0x1540): undefined reference to `deflateEnd'

Solution:
http://www.emsl.pnl.gov/docs/nwchem/nwchem-support/2012/02/0065.Re:_NWCHEM_undocumented_compilation_flag

Edit nwchem-6.0/src/config/makefile.h
For LINUX64 look at lines 1960-1964

1960      ifeq ($(BUILDING_PYTHON),python)
1961 #   EXTRA_LIBS += -ltk -ltcl -L/usr/X11R6/lib -lX11 -ldl
1962      EXTRA_LIBS +=    -lnwcutil  -lpthread -lutil -ldl
1963   LDOPTIONS = -Wl,--export-dynamic
1964      endif

Change line 1962 to
EXTRA_LIBS +=    -lnwcutil  -lpthread -lutil -ldl -lz -lssl