19 May 2013

421. NWChem 6.3 on ROCKS 5.4.3/CentOS 5.6

Update 23 May 2013: The execution times are pretty much the same as for 6.1.1 with a new patch. I've updated the instructions below to incorporate this new patch (http://www.nwchem-sw.org/images/Iswtch.patch.gz)

Update 21 May 2013:
The execution times can be improved considerably by setting

They are still ca 30% longer than 6.1.1 though due to slower SCF convergence.
See http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id834/Nwchem_6.3_running_2-5_times_slo....html

UPDATE 20 May 2013:
Nwchem 6.3 is very slow compared to 6.1.1. A six-core run (out of eight cores available) was 121 s using 6.1.1 but 254 seconds on 6.3!

I observed this on debian as well: 6.3 on debian is five times slower (190s vs 40 s for example at 8 cores in http://verahill.blogspot.com.au/2013/05/414-frequency-vs-cores-crude.html) than 6.1.1. Not sure why that is.

NWChem 6.3 is out now. Here's how to build it on ROCKS 5.4.3 (based on Centos 5.6) for CPU-based calculations (currently only CCSD(T) can take advantage of GPU/CUDA anyway).

To build on debian, see http://verahill.blogspot.com.au/2013/05/424-nwchem-63-on-debian-wheezy.html

This assumes that you've got a proper build environment (gcc, fortran, openmpi) installed.

I've added all users who do computations to the group compchem.
sudo mkdir /share/apps/openblas
sudo chown $USER:compchem /share/apps/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=/share/apps/openblas install
cp lib*.*  /share/apps/openblas/lib
sudo chmod 755 /share/apps/openblas -R

For later use with nwchem and ecce, add /share/apps/openblas/lib to /etc/ld.so.conf and do
sudo ldconfig

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/apps/openblas/lib
in ~/.bashrc and/or queue files.

I've added all users who do computations to the group compchem.
sudo mkdir /share/apps/nwchem/
sudo chown $USER:compchem /share/apps/nwchem/

cd /share/apps/nwchem
wget http://www.nwchem-sw.org/download.php?f=Nwchem-6.3-src.2013-05-17.tar.gz
tar xvf Nwchem-6.3-src.2013-05-17.tar.gz 
cd nwchem-6.3-src.2013-05-17/
cd src/
wget http://www.nwchem-sw.org/images/Iswtch.patch.gz
gzip -d Iswtch.patch
patch -p0 < Iswtch.patch
cd ../
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=`pwd`
export NWCHEM_MODULES="all python"
export PYTHONHOME=/opt/rocks
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/opt/openmpi
export MPI_INCLUDE=/opt/openmpi/include
export LIBRARY_PATH=$LIBRARY_PATH:/opt/openmpi/lib:/share/apps/openblas
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
export BLASOPT="-L/share/apps/openblas/lib -lopenblas -lopenblas_nehalem-r0.1.1 -lopenblas_nehalemp-r0.1.1"


cd $NWCHEM_TOP/src
export FC=gfortran
make clean
make  nwchem_config
make  FC=gfortran
cd ../contrib
 sudo chmod 755 /share/apps/nwchem/nwchem-6.3-src.2013-05-17 -R

Create a default.nwchemrc in /share/apps/nwchem
nwchem_basis_library /share/apps/nwchem/nwchem-6.3-src.2013-05-17/src/basis/libraries/ ffield amber amber_1 /share/apps/nwchem/nwchem-6.3-src.2013-05-17/src/data/amber_s/ amber_2 /share/apps/nwchem/nwchem-6.3-src.2013-05-17/src/data/amber_x/ amber_3 /share/apps/nwchem/nwchem-6.3-src.2013-05-17/src/data/amber_q/ amber_4 /share/apps/nwchem/nwchem-6.3-src.2013-05-17/src/data/amber_u/ amber_5 /share/apps/nwchem/nwchem-6.3-src.2013-05-17/src/data/custom/ spce /share/apps/nwchem/nwchem-6.3-src.2013-05-17/src/data/solvents/spce.rst charmm_s /share/apps/nwchem/nwchem-6.3-src.2013-05-17/src/data/charmm_s/ charmm_x /share/apps/nwchem/nwchem-6.3-src.2013-05-17/src/data/charmm_x/
and put symmlinks to it in the users' home directories, e.g.
cd ~
ln -s /share/apps/nwchem/default.nwchemrc .nwchemrc

1 comment:

  1. RE: CUDA
    Does the CUDA run only works with CCSD(T) for single point energy only? Will nwchem uses CUDA for other type of jobs, for example optimization?