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

643. 'Hacking' a windows 10 computer w/o password

The scenario: a colleague's masters student had finished, and returned his university issued laptop. He didn't write down the password, and no he can't remember it. It's running Windows 10.

My colleague wants to use the laptop for a bit of testing. No IT support around, so can't reinstall windows.

It has Ubuntu installed as well.We have the password for it.

The local admin account in windows was not activated.

Solution:
I looked at http://www.hackcave.net/2015/10/hack-windows-10-login-password-in-2.html, https://www.ghacks.net/2014/11/12/how-to-enable-the-hidden-windows-10-administrator-account/ and http://webcache.googleusercontent.com/search?q=cache:XXlk7evcUggJ:www.thewindowsclub.com/net-user-command-windows+&cd=4&hl=en&ct=clnk&gl=us

1. Boot into windows 10. Hold 'shift' while clicking on 'Shutdown', in order to force a proper shutdown rather than hibernation.

2. Boot into Linux (in this case it was a dual boot setup, but you could boot from a linux cd or usb stick). Mount the windows partition, open a terminal and navigate to Windows/System32. Rename cmd.exe to sethc.exe and sethc.exe to cmd.exe. Restart.

3. Boot into windows. When you get the log in screen, hit 'shift' 5-6 times. You'll now get a terminal with admin powers!

4. Activate the administrator account so that safe mode becomes useful:
net user administrator /active:yes
net user administrator *

Set the password.

5. Add a new user (users: john, password: b3ngalt0r1n.) and give it admin capabilities:
net user john b3ngalt0r1n. /add
net localgroup administrators john /add
exit

Hold 'shift' while clicking on Shutdown

6. Boot into linux, and swap cmd.exe and sethc.exe back.

7. Boot into windows.

642. Garmin GPSMap 64S and the weirdest hardware bug...

Last year I bought a Garmin GPSMap 64S (https://www.ryda.com.au/garmin-gpsmap-64s-handheld-gps) and while it has objectively made my life a lot more amazing (being able to just walk, without having to look for often hard-to-find maps before and printing them, gives you a great sense of freedom), it comes with a weird bug.

If you change the batteries (runs on 2xAA), you might not be able to turn it back on. I did some troubleshooting:
* If you change the batteries quickly -- within 5-10 minutes -- it would turn back on
* Otherwise the only way to turn the GPS back on was to plug it into your computer -- or another power source such as a phone battery bank -- using the USB cable

I sent the device back to Ryda, but when they tested it they had no issues turning it back on. Egg + Face.

Well, I finally figured it out -- it all comes down to how you put the batteries back in.

Right before Left

If you put the device face down as shown in the photo, you need to put the RIGHT battery in BEFORE the LEFT one, and the device will start fine.

If you put the left battery in before the right one, you'll need to hook the GPS up via the USB cable to a power source to start it.

WHY it's like that, and whether it's a manufacturing defect only present in my device, I don't know. I'm just happy that it's working consistently now.

641. Rant: Why is it so hard to comment on blogspot?

I'd like to respond to people who leave comments on my posts, but for some reason it's become so difficult that I normally never get around to it.

Although firefox and chrome hasn't worked for commenting for a long time (in spite of turning off adblockers, cookie blockers etc.) Epiphany ('Web' in Gnome 3) used to do the trick. Not even that works properly anymore -- I was forced to post as anonymous in the end, rather than using my google account.

The steady march of progress...

PS Thanks to everyone who posts feedback. I do read everything and appreciate that you take the time to leave comments. I just might not be able to respond...

640. nordvpn with network-manager-openvpn-gnome (on debian 8), and speeds

So you've signed up for nordvpn, e.g. because you can't live without ABC for Kids and you're exiled to Europe. Unfortunately, while you can connect to a server using

sudo openvpn au35.nordvpn.com.udp1194.ovpn

you're having little luck using network-manager-openvpn-gnome, and the nordvpn official step-by-step guide isn't bleeding working.

Well, here's how to do it:
1. Go to network settings and add a new connection. Click on VPN:

The select import from file.

Select the file:

This will import some, but not all, of the settings.

You'll need to select the .crt file:

And then click on advanced. Got to the TLS Authentication tab:

You need to select 'Use additional TLS authentication' and select the tls.key. The key direction should be 1 (it's in the ovpn file)

Either way, the connection using the gnome network manager seems a lot less stable than what you get using openvpn in the terminal.

So, will it work for streaming? Not really, from what I can see. I do admittedly have a really crappy connection even w/o vpn, and I'm doing this over wifi. Here are results using google speed test:

No VPN: 6.36/9.75 Mbps Up/Down
uk32 (udp): 1.79/7.89
au10 (udp): 3.94/2.85 -- first try
au32 (tcp): 0.86(!)/0.96
us621 (udp): 0.47(!)/3.22
au10 (udp): 1.13/1.45 -- second try

No VPN: 7.53/2.96 -- second try

These are just random servers. There may be higher speed ones out there. Also, note how living in an area with a high concentration of students can cause large variations in your speeds in general.
****
Update: I ran a couple of tests from work where I have a /fast/ ethernet connection. I did it using Okla:
No VPN: 94.09/94.08 -- first try
No VPN: 94.10/94.02 -- second try
ch7 (udp): 87.95/87.87
au10(udp): 0.53/0.75 -- even just running the test took ages


****
Another fun little trick when using openvpn in the terminal is -- if you're not concerned about protecting your username/password -- to follow this post: https://my.hostvpn.com/knowledgebase/22/Save-Password-in-OpenVPN-for-Automatic-Login.html

After creating your auth.txt file, in the folder with your .ovpn files, do

sed -i 's/auth-user-pass/auth-user-pass auth.txt/' *.ovpn

Now you can switch vpns quickly and happily.