649. N/EDA in GAMESS. 1. Recompiling GAMESS US with NBO6

I need to do energy decomposition analysis (EDA), but only have licenses for Gaussian and NBO6 (i.e. not ADF, turbomole, QChem etc.). NEDA isn't supported by NBO6 with gaussian (afaik).

NWChem, my usual gaussian alternative, doesn't support NBO6 beyond writing a .47 file.

Enter GAMESS US. I've been trying out gamess every few years, but I've found that it's slow and unreliable (very difficult to get SCF convergence) for the systems I work with (polyanions). Some of this may obviously be down to my lack of familiarity with the code -- there are probably plenty of satisified users of GAMESS US.

Either way, NBO6 suppports NEDA with GAMESS US. Also, GAMESS US does two different types  of   EDA: the common Morokuma-Kitaura (MOROKM) one (although only with HF) and an alternative approach by Su and Li that's referred to by GAMESS as LMOEDA (or CMOEDA).

MOROKM and LMOEDA as supported out of the box by GAMESS, but to get it to do NEDA you need to re-link it against NBO. Luckily it's even easier than the instructions in the NBO gamess file (i.e. no need to edit code).

NOTE: I could only link with gfortran 4.9 (jessie). gfortran 6.3 (stretch) failed to link (messages re -fPIC; recompiling gamess with -fPIC didn't solve it).

To compile gamess, see e.g. http://verahill.blogspot.com/2013/06/4xx-gamess-us-2013-r1-on-debian-wheezy.html

Once you've done the ddi/comp and compall steps, edit lked and search for NBO. Change to

set NBO=true
set NBOLIB="/opt/nbo6/bin/gmsnbo.i8.a"

assuming that this location is correct.

Then do lked as in the post above.

648. Compiling Quantum Espresso 6.2.1 on debian 8

Time has come for me to expand my horizons and skills. As I drift farther and farther away from my origins as an organic chemist and more and more towards inorganic materials science and non-discrete, extended systems, localised orbital DFT (i.e. 'standard' DFT) is not always looking as an appropriate method.

NWChem
Time thus to start using periodic systems and planewave basis sets. I've started working with nwpw and pspw in nwchem, and since I've used nwchem since ca 2002, in terms of setting up jobs and getting results it's been fairly straightforward. Understanding what all the options do and what's appropriate is another issue, but that's something I can work out empirically by comparing with benchmark systems (beginning to discover the importance of simulation cell now...)

Either way, nwchem does not yet afford a way of computing raman spectra for pspw jobs, which is one of the properties I'm interested in. Quantum Espresso, on the other hand, does, and is geared towards materials science in a way that nwchem isn't. Although quantum-espresso is included in the debian repos, I prefer to compile my own version. So, here I am.

I did this on one of my AMD nodes, but will follow up later with a post using intel MKL on my intel nodes. I only used the debian math libs, and not the AMD ACML (now replaced with ACL?), which I probably should've. Maybe I'll do an updated post on that later.

Note: I specify libblas.a instead of -lblas in the configure step since I have a custom openblas package installed as well, but which didn't work during compilation of QE.

Quantum Espresso (on an 8 core AMD processor)

'make' for gwl failed, and I didn't want to figure out why, so I skipped it. You can try doing make all instead of doing make for individual parts as I do below (type make to see what your options are).

---

sudo mkdir /opt/QE
sudo chown $USER /opt/QE
mkdir ~/tmp/QE -p

mkdir $HOME/scratch/QE -p
cd ~/tmp/QE
wget https://gitlab.com/QEF/q-e/-/archive/qe-6.2.1/q-e-qe-6.2.1.tar.gz
tar xvf q-e-qe-6.2.1.tar.gz
cd q-e-qe-6.2.1/

edit environment_variables

20 PREFIX=`/opt/QE`
 21 BIN_DIR=$PREFIX/bin
 22 PSEUDO_DIR=$PREFIX/pseudo
 23 # Beware: everything in $TMP_DIR will be destroyed !
 24 TMP_DIR=$HOME/scratch/QE

sudo apt-get install libblas-dev libfftw3-dev libopenmpi-dev
./configure --prefix=/opt/QE/bin --exec-prefix=/opt/QE/bin/ FC=mpif90 BLAS_LIBS="/usr/lib/libblas/libblas.a" LIBS="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread" CPPFLAGS="-I/usr/lib/openmpi/include"

sudo apt-get install libblas-dev libfftw3-dev libopenmpi-dev

--------------------------------------------------------------------
ESPRESSO can take advantage of several optimized numerical libraries
(essl, fftw, mkl...).  This configure script attempts to find them,
but may fail if they have been installed in non-standard locations.
If a required library is not found, the local copy will be compiled.

The following libraries have been found:
  BLAS_LIBS="/usr/lib/libblas/libblas.a"
  LAPACK_LIBS=-L/opt/ATLAS/lib -llapack -lblas
  FFT_LIBS= -lfftw3 
  
Please check if this is what you expect.

If any libraries are missing, you may specify a list of directories
to search and retry, as follows:
  ./configure LIBDIRS="list of directories, separated by spaces"

Parallel environment detected successfully.\
Configured for compilation of parallel executables.

For more info, read the ESPRESSO User's Guide (Doc/users-guide.tex).
--------------------------------------------------------------------

make -j8 pwall cp ld1 upf xspectra tddft
make couple epw gui gwl

echo 'export PATH=$PATH:/opt/QE/bin' >>~/.bashrc
echo 'export PSEUDO_DIR=/opt/QE/pseudo' >>~/.bashrc
cp * -R /opt/QE/

source ~/.bashrc

To benchmark:

 make test-suite

647. Linda/G16 and ecce + slurm

I had the opportunity to test G16 with Linda on my cluster. Suprisingly, I observed a decent reduction in computational time for geometry optimisation, and a fair reduction for vibrational analysis.

Computational time -- geometry optimisation
1x6 cores: 100%
2x6 cores: 56% (2 nodes)
3x6 cores: 44% (3 nodes)

Computational time -- normal mode computation
1x6 cores: 100%
2x6 cores: 63% (2 nodes)
3x6 cores: 57% (3 nodes)

In no case was the speed up good enough that it actually makes long-term sense to use Linda (need less than 50% for 2 nodes and 33% or less for 3 nodes), but if you're itching for quick results, it might be worth it.

Either way, as part of this I wrote a CONFIG.Linda for ECCE and SLURM:

Gaussian-16: /opt/gaussian/g16a/g16/g16
perlPath: /usr/bin/
qmgrPath: /usr/bin/
xappsPath: /usr/bin/

Slurm {
#!/bin/csh
#SBATCH -p linda
#SBATCH --time=$walltime
#SBATCH --output=slurm.out
#SBATCH --job-name=$submitFile
#SBATCH --nodes=$nodes
#SBATCH --cpus-per-task=$ppn
}

Gaussian-16FilesToRemove{ core }

Gaussian-16Command{
set path = ( /opt/nbo6/bin $path ) 

set nnodes = `scontrol show job $SLURM_JOBID|grep NodeList|sed 's/=/\t/'|gawk '{print $2}'|tail -n 1`
sed -i "2s/^/%LindaWorkers=$nnodes\n/" g16.g16in
sed -i '3s/^/%UseSSH\n/' g16.g16in
sed -i "s/nprocshared.*/nprocshared=$ppn./" g16.g16in

setenv GAUSS_SCRDIR /home/me/scratch
setenv GAUSS_EXEDIR /opt/gaussian/g16a/g16
setenv GAUSS_ARCHDIR /opt/gaussian/g16a/g16/arch
setenv GAUSS_BSDDIR /opt/gaussian/g16a/g16/bsd
setenv GAUSS_LEXEDIR /opt/gaussian/g16a/g16/linda-exe
/opt/gaussian/g16a/g16/g16< $infile > $outfile 
}

The slurm partition linda has all the nodes that has g16.

646. NWChem 6.6 on debian stretch (9)

I've got plenty of posts on how to compile nwchem on this blog. However, as I'm still running debian jessie on my work computers and cluster I have failed to appreciate quite how different things work in debian stretch.

This includes the compilation of ECCE (although owing to updates meant to rectify that at https://github.com/FriendsofECCE/ECCE this isn't necessarily something you'd notice) and NWChem.

Anyway, here's how to build nwchem with openmpi support under debian stretch:

---

1. Download source code and patches

sudo mkdir /opt/nwchem -p
sudo chown $USER:$USER /opt/nwchem
cd /opt/nwchem
mkdir patches6.6
cd patches6.6
for i in Tddft_mxvec20.patch.gz Tools_lib64.patch.gz Config_libs66.patch.gz Cosmo_meminit.patch.gz Sym_abelian.patch.gz Xccvs98.patch.gz Dplot_tolrho.patch.gz Driver_smalleig.patch.gz Ga_argv.patch.gz Raman_displ.patch.gz Ga_defs.patch.gz Zgesvd.patch.gz Cosmo_dftprint.patch.gz Txs_gcc6.patch.gz Gcc6_optfix.patch.gz Util_gnumakefile.patch.gz Util_getppn.patch.gz Gcc6_macs_optfix.patch.gz Xatom_vdw.patch.gz Notdir_fc.patch.gz Hfmke.patch.gz Cdfti2nw66.patch.gz ; do wget http://www.nwchem-sw.org/download.php?f=$i ; done
gunzip *.gz
cat *.patch > consolidated.patch
cd ..
wget http://www.nwchem-sw.org/download.php?f=Nwchem-6.6.revision27746-src.2015-10-20.tar.gz -O Nwchem-6.6.revision27746-src.2015-10-20.tar.gz
tar xvf Nwchem-6.6.revision27746-src.2015-10-20.tar.gz

Apply patches:

cd /opt/nwchem/nwchem-6.6/
cp /opt/nwchem/patches6.6/consolidated.patch .
patch -p0 < consolidated.patch

In addition, you can do the following to print more information so that GabEdit properly shows MOs:

cd nwchem-6.6/
grep -rl "do klo = 0, min(n-1,9), 2"|xargs -I {} sed -i 's/do klo = 0, min(n-1,9), 2/do klo = 0, min(n-1,199), 2/g' {}
grep -rl " 0.15d0,"|grep -v "atomdata"|xargs -I {} sed -i 's/0.15d0/0.01d0/g' {}

---

2. Install dependencies and compile.
 How exactly it is done depends on your compiler and math libs. I've used red for examples with INTEL mkl, blue for AMD acml and orange for the free openblas. ifort is shown in purple and gfortran like this.You should only use one compiler + one math lib.
Hint: also make sure your ld.conf.so.d files contain paths to your math libs.

cd /opt/nwchem/nwchem-6.6
sudo apt-get install build-essential gfortran python2.7-dev libopenmpi-dev openmpi-bin

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

export BLASOPT="-L/opt/intel/composer_xe_2013.4.183/mkl/lib/intel64/ -lmkl_core -lmkl_sequential -lmkl_intel_ilp64"
export LIBRARY_PATH="$LIBRARY_PATH:/opt/intel/composer_xe_2013.4.183/mkl/lib/intel64/"

export BLASOPT="-L/opt/acml/acml5.3.1/gfortran64_int64/lib -lacml"
export LIBRARY_PATH="$LIBRARY_PATH:/opt/acml/acml5.3.1/gfortran64_int64/lib"

export BLASOPT="-L/opt/openblas/lib -lopenblas"
export LIBRARY_PATH="$LIBRARY_PATH:/opt/openblas/lib"


export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export ARMCI_NETWORK=SOCKETS

cd $NWCHEM_TOP/src

make clean
make nwchem_config
make FC=ifort 1> make.log 2>make.err
make FC=gfortran 1> make.log 2>make.err

cd $NWCHEM_TOP/contrib
export FC=ifort
export FC=gfortran
./getmem.nwchem

---

3. Run
mpirun -n 8 /opt/nwchem-6.6/bin/LINUX64/nwchem input.nw > output.nw

645. Moodle on Debian

I want to play around with moodle on my own desktop so I can experiment before making any major commits to a course website.

I first had a look at https://docs.moodle.org/33/en/Installing_Moodle_on_Debian_based_distributions, but, realising that moodle is in sid, decided to build my own .deb package.

This was done on debian jessie (8.9), which has at this point been overtaken by stretch as stable. I'm thus three releases behind sid.

1. Add the sid /src/ repo to sources.list
deb-src http://ftp.au.debian.org/debian/ sid main non-free contrib

2. Get source and build
I don't know exactly what dependencies you'll need. Error messages will tell you.

sudo apt-get update
sudo apt-get install build-essential dpkg-dev mysql-server mysql-client php5-xmlrpc php5-intl
sudo service mysql start
mkdir ~/tmp/moodle -p
cd ~/tmp/moodle
sudo apt-get source moodle

Edit debian/control (necessary if you're on Jessie/8.9 -- newer debian versions may not need this):

14 Depends: ${misc:Depends},
 15  php5, php5-mysql | php5-pgsql, php5-gd, php5-curl, php5-cli,
 16  apache2 | httpd, ucf, postgresql-client | default-mysql-client | virtual-mysql-client,
 17  dbconfig-common, libphp-phpmailer, libphp-adodb, php-htmlpurifier, php-tcpdf,
 18  php-cas (>= 1.3.3-1), libjs-jquery-migrate-1
 19 Pre-Depends: debconf (>= 0.5) | debconf-2.0

Then continue in the terminal:

cd ~/tmp/moodle-2.7.19+dfsg
sudo dpkg-buildpackage -us -uc
cd ..
sudo dpkg -i moodle_2.7.19+dfsg-2_all.deb
sudo apt-get -f install
sudo cp /etc/moodle/apache.conf /etc/apache2/sites-available/moodle.conf
sudo ln -s /etc/apache2/sites-available/moodle.conf /etc/apache2/sites-enabled/moodle.conf
sudo chmod o+r /etc/apache2/sites-available/moodle.conf
sudo chmod go+w /var/lib/moodle
sudo service apache2 reload

Navigate to http://localhost/moodle and follow the prompts

644. Redmine -- project management -- briefly.

I've reached the point in my career that I need to start thinking seriously about how I organise my work. It used to be enough to work with a white board, google calendar (w/ lightning + thunderbird) and lots of post-it notes.

Somehow it's not working anymore, in part because I'm getting older and find it difficult to remember things -- in particular short-term.

Running a group is much like running a company (I imagine):
1. you have to manage your funds
2. you have to manage projects over short, medium and long-term
3. you have employees that need taking care of -- PhD students and Postdocs

I manage my funds using GnuCash. It's not perfect, but once you've set it up it works well enough to keep track of your assets. Of course your university accountants/administrators will do the same, but there's always a lag between you spending your money and getting updated financial reports. It's also nice to be able to 'lean' money in case of future spending. I've found that the financial reports that I've been getting from the different institutions that I've been working at have not dealt well with salaries.  I mean, salaries get taken out monthly, but as they are predictable expenses I as a PI don't want to see the money -- I want it removed from view.

Also, every now and again the accountants make a mistake, and you're much more likely to discover it if you have a means of comparing your financial reports with what you would be expecting to see.

Taking care of and managing employees is a different kettle of fish altogether, and at this point I haven't found any magic bullet in terms of management style. I'm simply being me -- which sounds fine -- but that doesn't always work due to personality clashes etc. Sometimes it's probably better to have a professional persona that you can put on.

Anyway, this post is about project planning -- I need to plan my work and my private life. I've looked at a few solutions. Most of these are serious overkill for what I need. All are free, although their websites heavily advertise paid options.
* TaskCoach
* Project Libre
* RedMine
* Odoo (formerly OpenERP)

I really wanted something like the project tracker in github, but the programs that support that style seems to be cloud based, and I'd much rather have something that I can run locally.

TaskCoach is in the debian repo, as is redmine. Project libre and odoo have debs available from their respective websites.

I failed to get odoo working -- otherwise it looked nice in the screen shots on their website.

TaskCoach was easy to use, but not very pretty, and it just didn't feel 'right' for me in terms of look/layout and workflow. If I hadn't found redmine I probably would've stayed with TaskCoach.

I got lost and confused when looking at ProjectLibre, and gave up.

Redmine has the advantage of the redmine website running on redmine, so you can see exactly what it looks like and how it works. That's what I'm using now, and it seems to work with how I think about things. I like being able to attach files, make lots of short notes that show up and give a good overview what's going on.

I don't need time tracking, Gantt charts etc -- I just need to track the qualitative progress of what I'm doing.

I installed redmine on debian jessie according to https://wiki.debian.org/redmine
I did
sudo cp  /usr/share/doc/redmine/examples/apache2-passenger-alias.conf /etc/apache2/sites-enabled/redmine.conf

I then edited redmine.conf to include
ServerName localhost
but made no other changes.

I could then access redmine at localhost/redmine