17 August 2015

621. Very briefly: comparison of different hardware for a single G09 calculation

And another update:
* I've set up an Amazon EC2/AWS instance and have done some benchmarking there too: http://verahill.blogspot.com.au/2016/01/626-briefly-gaussian-g09d-with-slurm-on.html 
Exciting stuff.

Another update:
* I turned off hyperthreading on the i7-4930K to see whether it improved performance. The geometry optimisation took 2 min (4%) longer but the overall runtime was 2 min (2%) shorter. This is probably within the reproducibility error for the measurement.
* I've also added results for an i7-5820K without hyperthreading


Update: I spotted a few mistakes
* the L5430 job ran on a dual-socket machine, so I've multiplied the passmark by two and have replotted
* the X3480 job use the EM64T version of gaussian, not AMD64. I don't have a license to test that system using AMD64.

Original post:
There are lots of potential flaws when comparing the performance of a computational package on different hardware. Thus, it can be difficult to find examples online comparing different hardware using computational chemistry packages which makes it challenging to decide on what hardware to budget for.

So here's a simple comparison of a few different types of hardware for a geovib calculation in Gaussian.

All systems have spinning (7200 rpm) disks and use debian jessie (64). The systems haven't been optimised in any way.

All systems used G09D rev 01 AMD 64 unless otherwise indicated. The amount of time the geometry optimisation took is given within [].

Performance:
2h 15 min. [1h 14 min.] Intel i7-4930K/ 32 Gb ram/ 12 threads
2h 23 min. [1h 25 min.] Intel i7-5820K/ 32 Gb ram/ 6 threads (HT turned off, NOTE)
3h 49 min. [2h 12 min.] AMD FX 8350/ 8 Gb ram/ 8 threads
4h 12 min. [2h 19 min.] Intel i5-2400/ 16 Gb ram/ 4 threads
4h 16 min. [2h 24 min.] AMD Phenom II X6 1055T/ 8 Gb ram/ 6 threads
4h 28 min. [2h 16 min.] dual-socket Intel Xeon L5430/ 16 Gb ram/ 8 threads-- rev A.02
4h 43 min. [2h 47 min.] AMD FX 8150/ 32 Gb ram/ 8 threads
9h 26 min. [5h 18 min.] AMD Athlon II X3 445/ 8 Gb ram/ 3 threads

I also tried the EM64T version of G09D rev 01 and got:
1h 43 min. [57 min.] i7-4930K/ 32 Gb ram/ 12 threads
3h 03 min. [1h 44 min.] i5-2400/16 Gb ram/ 4 threads
4h 21 min. [2h 27 min.] Xeon X3480/ 8 Gb ram/ 8 threads -- rev B.01

Just by switching from the AMD64 to the EM64T version we thus cut the calculation down to 75% of the time for the i7.

 I also turned off hyperthreading for the i7-4930K and ran with six threads using the EM64T version:
 1h 41 min. [59 min.] i7-4930K/ 32 Gb ram/ 6 threads
 1h 35 min. [58 min.] i7-5820K/ 32 Gb ram/ 6 threads (NOTE)


Here's a plot of the run times vs Passmark benchmarks (I've multiplied the Xeon L5430 passmark by 2):

Note that the Xeon L5430 and Xeon X340 store the job files on an NFS (scratch files are local) and are not using G09 rev D.01.

It'd be tempting to draw a line through the Athlon II to the I7-4930K, in which case the Phenom II X6 and the I5-2400 perform much, much better than they should based on the CPU Passmark alone.

Either way, these are my observations. No interpretations or opinion attached.

So what's  the benchmarking job that I used? I actually prefer not to reveal it, as it'd eventually point towards my identity (and you're not supposed to publish gaussian benchmarks...)

Suffice to say that it uses:
rpbe/def2-svp and 459 functions/759 primitives (46 atoms) with opt=(verytight) and integral(ultrafine)




620. Very Short: Setting up ORCA (comp. chem.) on debian jessie

Nothing odd here, but providing instructions is never a bad idea. Note that ORCA is binaries only i.e. no source code. It's one reason why I wouldn't want to rely on it as my main code for computational chemistry. However, I am interested in using it to compare select results from nwchem and g09, especially in cases where g09 and nwchem produce differing results.

Either way,. to download ORCA you need to join the ORCA forum:
https://orcaforum.cec.mpg.de/portal.php

Once you've joined you can go to Downloads and, well, download. I went for https://orcaforum.cec.mpg.de/downloads.php?view=detail&df_id=43

sudo mkdir /opt/orca
sudo chown $USER /opt/orca
cp ~/Downloads/orca_3_0_3_linux_x86-64.tbz /opt/orca
cd /opt/orca
tar xvf orca_3_0_3_linux_x86-64.tbz
cd orca_3_0_3_linux_x86-64
ln -s orca orca_cc

The symmlink is there because debian already has a binary called orca.
And that's that installed. To add /opt/orca/orca_3_0_3_linux_x86-64 to PATH do

echo 'export PATH=$PATH:/opt/orca/orca_3_0_3_linux_x86-64' >> ~/.bashrc

To test, try one of the jobs on https://www.sharcnet.ca/help/index.php/ORCA#Parallel_ORCA_job and run using
/opt/orca/orca_3_0_3_linux_x86-64/orca_cc test.inp
***************** * O R C A * ***************** --- An Ab Initio, DFT and Semiempirical electronic structure package --- ####################################################### # -***- # # Department of molecular theory and spectroscopy # # Directorship: Frank Neese # # Max Planck Institute for Chemical Energy Conversion # # D-45470 Muelheim/Ruhr # # Germany # # # # All rights reserved # # -***- # ####################################################### Program Version 3.0.3 - RELEASE - [..] ************************************************************ * Program running with 2 parallel MPI-processes * * working on a common directory * ************************************************************ ------------------------------------------------------------------------------ [..] ------------------------------------------------------------------------------ ORCA ELECTRIC PROPERTIES CALCULATION ------------------------------------------------------------------------------ Dipole Moment Calculation ... on Quadrupole Moment Calculation ... off Polarizability Calculation ... off GBWName ... test.gbw Electron density file ... test.scfp.tmp ------------- DIPOLE MOMENT ------------- X Y Z Electronic contribution: 0.00000 -0.00000 -0.00000 Nuclear contribution : -0.00000 0.00000 -0.00000 ----------------------------------------- Total Dipole Moment : -0.00000 0.00000 -0.00000 ----------------------------------------- Magnitude (a.u.) : 0.00000 Magnitude (Debye) : 0.00000 Timings for individual modules: Sum of individual times ... 45.891 sec (= 0.765 min) GTO integral calculation ... 5.511 sec (= 0.092 min) 12.0 % SCF iterations ... 26.269 sec (= 0.438 min) 57.2 % SCF Gradient evaluation ... 13.957 sec (= 0.233 min) 30.4 % Geometry relaxation ... 0.154 sec (= 0.003 min) 0.3 % ****ORCA TERMINATED NORMALLY**** TOTAL RUN TIME: 0 days 0 hours 0 minutes 50 seconds 359 msec

01 August 2015

619. Making libreoffice look a bit nicer

...and by the title I actually refer to making it look like MS office...we can discuss the merits or lack thereof of that, but not here and now.

NOTE: you can install a few alternative icons themes directly from the debian repos by installing the libreoffice-style-* packages.

Anyway, we're commiting sacriledge by making our libreoffice look like MS office. You can obviously use the instructions here to pick a less controversial look.

Icons:
First go to http://charliecnr.deviantart.com/art/Office-2013-theme-for-LibreOffice-512127527 or use wget:

wget http://orig11.deviantart.net/e10d/f/2015/059/7/3/office_2013_theme_for_libreoffice_by_charliecnr-d8gwo4n.zip
mv office_2013_theme_for_libreoffice_by_charliecnr-d8gwo4n.zip images_office2013.zip
sudo mv images_office2013.zip /usr/lib/libreoffice/share/config/

Then in libreoffice go to Tools/Options/Libreoffice:view and pick your theme:
 Menu bar:
This is a weird one. Go to Tools/Options/Libreoffice:personalisation and under Firefox themes select own theme, and Visit Firefox Themes.



Then paste the URL of the theme you want. I used this URL: https://addons.mozilla.org/en-US/firefox/addon/office2010-edit/

And this is how libreoffice writer looks now: