531. Briefly: NWChem 6.3 -- issues with planewave (PSPW) module and AMD FX8150 and 8350 CPUs

This is more of an announcement or warning than a proper blog post:

Both FX8350 and FX8150 have trouble running the pspw module causing the calculation to lead to exploding structures:
http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id1059/Issue_with_pspw_using_nwchem_6.3....html

My other nodes have no trouble running the job in question. Also, the issue was only found in nwchem 6.3 -- nwchem 6.1.1 worked fine. So it's not an FX83x50 related fault per se.

Again, see the post at the nwchem-sw.org site for more information.

340. Issues when compiling Nwchem 6.1.1 -- missing *.fh in src/include

The problem:
If you modify the nwchem sources, build, do a make realclean and then pack them up to export your patched sources to other nodes you might find that compiling doesn't work that well, yielding errors such as (I'll list them all to help google):

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/stdio.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(basis.o)'.  Stop.
make: *** [libraries] Error 1

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/nwc_const.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(basis.o)'.  Stop.
make: *** [libraries] Error 1
nwchem.F:3:0: fatal error: errquit.fh: No such file or directory
compilation terminated.
stubs.F:15:0: fatal error: errquit.fh: No such file or directory

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/errquit.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(basis.o)'.  Stop.
make: *** [libraries] Error 1

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/util.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(bas_input.o)'.  Stop.

and

/opt/nwchem/nwchem-6.1.1-src_mod/src/include/util.fh:1:0: fatal error: printlevels.fh: No such file or directory
compilation terminated.
make[1]: *** [/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(bas_input.o)] Error 1
make[1]: *** Waiting for unfinished jobs....

and

basisP.F: In function 'nbf_from_ucont':
basisP.F:427:0: warning: '__result_nbf_from_ucont' may be used uninitialized in this function [-Wmaybe-uninitialized]
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[1]: warning: -jN forced in submake: disabling jobserver mode.
make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/msgids.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(geom.o)'.  Stop.

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/bitops.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(pstat_alloc.o)'.  Stop.

and

In file included from pstat_alloc.F:12:0:
/opt/nwchem/nwchem-6.1.1-src_mod/src/include/bitops.fh:11:0: fatal error: bitops_decls.fh: No such file or directory
compilation terminated.
make[1]: *** [/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(pstat_alloc.o)] Error 1

and

In file included from pstat_alloc.F:12:0:
/opt/nwchem/nwchem-6.1.1-src_mod/src/include/bitops.fh:12:0: fatal error: bitops_funcs.fh: No such file or directory
compilation terminated.
make[1]: *** [/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(pstat_alloc.o)] Error 1

and

make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[2]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/itri.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(sym_sh_pair.o)'.  Stop.
make[2]: *** Waiting for unfinished jobs....

and

make[2]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/bgj.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwints.a(exactd_mem.o)'.  Stop.

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/numerical_constants.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/librimp2.a(rimp2_v_e2.o)'.  Stop.

and

make[2]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/util_sgroup.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libdntmc.a(gibbs.o)'.  Stop.

and

nwchem.F:11:0: fatal error: bgj_common.fh: No such file or directory

---

Solution:
This has been mentioned before on the nwchem forum, but not in explicit enough detail.
The solution is to copy a series of files from src/util and to remove make realclean from your build instructions (or at least do the copying after the make realclean step).

Copy these files

cp src/util/stdio.fh src/include/
cp src/util/nwc_const.fh src/include/
cp src/util/errquit.fh src/include/
cp src/util/util.fh src/include/
cp src/util/printlevels.fh src/include/
cp src/util/msgids.fh src/include/
cp src/util/bitops.fh src/include/
cp src/util/bitops_decls.fh src/include/
cp src/util/bitops_funcs.fh src/include/
cp src/util/itri.fh src/include/
cp src/util/bgj.fh src/include/
cp src/util/numerical_constants.fh src/include/
cp src/util/util_sgroup.fh src/include/
cp src/util/bgj_common.fh src/include/

Then build, using e.g.

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 BLASOPT="-L/opt/openblas/lib -lopenblas"
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:/opt/openblas/lib
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
cd $NWCHEM_TOP/src
make nwchem_config
make FC=gfortran 1>make.log 2>make.err
export FC=gfortran
cd ../contrib
./getmem.nwchem

334. Compiling nwchem with openmpi and python on Arch linux

Here's the reason why I gave my virtual machine 30 Gb in post 333 -- to be able to evaluate whether I can figure out how to build all the software that I need on Arch.

Behold my surprise when I realised that there's no need for separate -dev packages, as is the case on Debian i.e. the headers are generally installed together with the package (so e.g. python is enough -- you don't need python-dev as well).

While debian is probably the best choice for my nodes (I want stability -- not the latest flashiest stuff), nwchem is a good test case since I've been playing with it for years, and it's not available in the pacman or AUR repos.

Your mileage with openblas will vary depending on your hardware. ACML is an alternative on e.g. FX-8150. ATLAS doesn't seem to work with NWChem when I try it, but I'm not sure what I'm doing wrong. See the original post for examples on how to link to other math libs.

I'm mainly looking at this post: http://verahill.blogspot.com.au/2012/09/briefly-compiling-nwchem-611-with.html

---

Dependencies:

pacman -S wget base-devel gcc-fortran tcsh openmpi

Openblas:
Download from http://github.com/xianyi/OpenBLAS/tarball/v0.1.1

sudo mkdir /opt/openblas
sudo chown $USER /opt/openblas
tar xvf xianyi-OpenBLAS-v0.1.1-0-g5b7f443.tar.gz
cd xianyi-OpenBLAS-e6e87a2/
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

Nwchem:

sudo mkdir /opt/nwchem
sudo chown $USER /opt/nwchem
cd /opt/nwchem
wget http://www.nwchem-sw.org/images/Nwchem-6.1.1-src.2012-06-27.tar.gz
tar xvf Nwchem-6.1.1-src.2012-06-27.tar.gz
cd nwchem-6.1.1-src/

Edit nwchem-6.1.1-src/src/config/makefile.h and edit line 1957 as shown in this post.

Then continue:

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 BLASOPT="-L/opt/openblas/lib -lopenblas"
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/usr/lib/openmpi
export MPI_INCLUDE=/usr/include
export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib/openmpi:/opt/openblas/lib
export LIBMPI="-L/usr/lib/openmpi -lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran 1> make.log 2>make.err
export FC=gfortran
cd ../contrib
./getmem.nwchem

Note that some of the locations are a little bit different from debian.

Edit your ~/.bashrc and add:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/openblas/lib
export PATH=$PATH:/opt/nwchem/nwchem-6.1.1-src/bin/LINUX64

You can now test your new binary by running a job, e.g. co.nw:

title "co nmr"
geometry
c   0   0   0
o   0   0   1.13
end
basis 
* library "6-311+g*"
end
dft
 direct
 grid fine
 mult 1
 xc HFexch 0.05 slater 0.95 becke88 nonlocal 0.72 vwn_5 1 perdew91 0.81
end
task dft optimize

Run:

nwchem co.nw

or

mpirun -n 2 nwchem co.nw

242. Briefly: Compiling NWChem 6.1.1 with Python on Debian Testing (Wheezy)

Back at the end of June a minor version of NWChem (bug fixes) was released.

There isn't much difference between compiling 6.1.1 and 6.1. Mainly, the difference is in what line to edit for python compatibility (NWChem 6.1 here:http://verahill.blogspot.com.au/2012/05/building-nwchem-61-on-debian.html )

---

1. Install dev packages
sudo apt-get install libopenmpi-dev openmpi-bin python2.7-dev zlib1g-dev libssl-dev

2. Compile openblas  or download e.g. acml.
(compiles fine, but doesn't run, with atlas)

3. NWchem goodness:

sudo mkdir /opt/nwchem
sudo chown $USER /opt/nwchem
cd /opt/nwchem
wget http://www.nwchem-sw.org/images/Nwchem-6.1.1-src.2012-06-27.tar.gz
(or go here http://www.nwchem-sw.org/index.php/Download)

tar xvf Nwchem-6.1.1-src.2012-06-27.tar.gz
cd nwchem-6.1.1-src/src/config/

Edit makefile.h and hange (line numbers are just for convenience -- don't add them)

1956 #   EXTRA_LIBS += -ltk -ltcl -L/usr/X11R6/lib -lX11 -ldl
1957      EXTRA_LIBS +=    -lnwcutil  -lpthread -lutil -ldl
1958   LDOPTIONS = -Wl,--export-dynamic

to

1956 #   EXTRA_LIBS += -ltk -ltcl -L/usr/X11R6/lib -lX11 -ldl
1957      EXTRA_LIBS +=    -lnwcutil  -lpthread -lutil -ldl -lssl -lz
1958   LDOPTIONS = -Wl,--export-dynamic

cd to /opt/nwchem/nwchem-6.1.1-src/ Create a file called buildconf.sh with the following content:

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 BLASOPT="-L/opt/openblas/lib -lopenblas"

#export BLASOPT="-L/opt/acml/acml5.2.0/gfortran64_int64/lib -lacml"

#export BLASOPT="-L/opt/ATLAS/lib -lsatlas -ltatlas"
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:/opt/openblas/lib

#export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/acml/acml5.2.0/gfortran64_int64/lib

#export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/ATLAS/lib
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran 1> make.log 2>make.err
export FC=gfortran
cd ../contrib
./getmem.nwchem

Start the compilation:
time sh buildconf.sh 

 On a quadcore i5-2400 it took 18 minutes.