03 August 2016

630. Making MO figures in gabedit using fchk files from gaussian on Windows XP

The goal is to show how to make pretty figures of MOs from Gaussian computations using GabEdit.

This is a write-up for a colleague whom is using Windows. The GabEdit bits work pretty much the same way on linux, although the povray stuff is a lot easier (in my opinion anyway) on that OS.

Anyway, Windows it is.

A. Optional: Install Gaussian (G09W)
If you have G09W you can install it. To use the formchk utility, add the location of your gaussian installation to path.

Do this by right-clicking on My Computer, select the Advanced tab, click on Environment Variables, and then click on the Path entry under System Variables. Click Edit, and add
if that's the correct path for you. The ";" is just to separate your entry from the previous one. If you need to add another entry afterwards (e.g. for povray), put a ";" after c:\g09w

Either way it's optional, as you will likely have access to formchk on the same computer/system that you ran your job on and can do the chk -> fchk conversion there.

Also, using formchk on a windows computer on a .chk file from a linux computer might not work (which was my case)

An alternative is to set up a smallish linux VM: https://verahill.blogspot.com.au/2016/08/631-small-linux-installation-in.html

B. Optional: Add option to open terminal using mouse
Following this: https://stackoverflow.com/questions/378319/windows-explorer-command-prompt-here/379804

Create a plain text file called context.reg

Edit it and put the following in it:

Windows Registry Editor Version 5.00
@="Open Command Prompt Here"
[HKEY_LOCAL_MACHINE\SOFTWARE\Classes\Folder\shell\cmd\command]@="cmd.exe /k pushd %L"

Like so...
Run it (i.e. double-click):
You will now have an "Open Command Prompt Here" option when right-clicking on a folder in the file explorer.
Open terminal here
Why do this? Because it makes it easier to run either formchk or povray in the directory where you have your files.

C. Install gabedit
Got to https://sites.google.com/site/allouchear/Home/gabedit/download and get "The Gabedit installer for Windows (OpenGL)"

Run. It's that easy.

When running gabedit for the first time you may be asked lots of questions. You can probably just accept all the defaults. We'll change some of them below.

D. Install povray
Download http://www.povray.org/redirect/www.povray.org/ftp/pub/povray/Official/povwin-3.7-agpl3-setup.exe and also accept to install the editor dlls at the end of the installation.
Download povray
Once that's done, add povray to path. Go to My Computer, right-click, click on the Advanced tab, select Environment Variables, click on path under System Variables and then Edit. Add
;C:\Program Files\POV-Ray\v3.7\bin

Like So

Let's get going!

1. Optional: Convert chk to fchk using formchk
Didn't work for me, but you can always try (I convert the files under linux)

Either way, you must have the fchk file before going to gabedit

2. Open fchk file in gabedit
You need to do a bit of setting up:

Set path and command for povray

To look at the fchk file:
a) Go to Display
Display Geometry/Orbitals/Density/Vibration

b) unset dipole (because otherwise you'll have an annoying arrow in your figure)
Untick dipole

c) Set desired atom colours.
In particular, I change N from dark blue to light blue so that it doesn't interfere with the orbital colours.
Atom colour

d) Set backgrounds (povray and screen) to white
Povray background

Window background

e) load fchk file
Go to Orbitals/Gaussian fchk

Open your fchk file

f) Set ball/stick parameters
Set Ball and Stick parameters

g) select level/MO
Note that you get the alpha OR beta orbitals. For a spin restricted system these are the same (apart from signage)

You should edit number of points. 65 is the default. 80 is slow but manageable. 90 is pushing it. Higher = smoother.


"Get Isovalue" almost never works properly. Try 0.04-0.06.

Et voilá!
To select a different MO, go back to orbitals and click on Selection.

h) Edit surfaces
You can change colours and transparency
Transparency is an option

Adjust the transparency/opacity here
i) Export pov
To make a publication-worthy figure, export as pov
Export as Povray
Clicking 'Run' occasionally leads to crash, so it's safer to click on save. Make sure that the background in white.

Edit the command to +A0.01 instead of +A0.3 for less 'pixelated' figure on zooming in. Takes a bit longer to render though. The H/W values depend on your window shape.

Select save, not Run

3. Render povray
You now have a pov file (example.pov). The most straight-forward way to render it is to open the command prompt (terminal) in the same folder and run
pvengine +A0.01 +H604 +W620 example.pov

assuming that the H/W values are the ones listed (or multiples of them) when you saved the pov file (it'll be listed in example.bat in the same folder).

And it looks like this:
A basic POV-Ray generated png

You can also run the .bat file associated with the pov file, but note that you'll have to put paths in "":
You need ""s
You can also render in the povray editor (open the povray with the editor):
Povray editor

Render Settings

The issue becomes the default H/W (resolution) values. Override using command line options: +HXXX +WYYY
You may have to associate .pov files with pvengine manually:

Edit -- but you'll be told that there's no program

Select a program to open


Always use the selected program

06 February 2016

629. Google drive with rclone on debian jessie

My free dropbox account has 6Gb storage, whereas my google drive has 15Gb. Dropbox pro is way too expensive, so here's what you can do to get your google drive to work ok-ish with linux.

To set up rclone, do:
cd ~/Downloads
wget http://downloads.rclone.org/rclone-current-linux-amd64.zip
unzip rclone-current-linux-amd64.zip
cd rclone-v1.27-linux-amd64
sudo cp rclone /usr/bin/
rclone config
No remotes found - make a new one n) New remote q) Quit config n/q> n name> google_drive What type of source is it? Choose a number from below 1) amazon cloud drive 2) b2 3) drive 4) dropbox 5) google cloud storage 6) swift 7) hubic 8) local 9) onedrive 10) s3 11) yandex type> 3 Google Application Client Id - leave blank normally. client_id> Google Application Client Secret - leave blank normally. client_secret> Remote config Use auto config? * Say Y if not sure * Say N if you are working on a remote or headless machine or Y didn't work y) Yes n) No y/n> y If your browser doesn't open automatically go to the following link: Log in and authorize rclone for access Waiting for code... Got code -------------------- [google_drive] client_id = client_secret = token = {"access_token":"y**5","token_type":"Bearer","refresh_token":"1/o**T","expiry":"2016-02-06T18:41:22.167889627+11:00"} -------------------- y) Yes this is OK e) Edit this remote d) Delete this remote y/e/d> y Current remotes: Name Type ==== ==== google_drive drive e) Edit existing remote n) New remote d) Delete remote q) Quit config e/n/d/q> q

Syncing is a bit of an issue as you can't sync based on last changed file. So, my solution is that each device has it's own folder that it syncs up to, and each device syncs down all other folders. For my two devices, nb and be, I have thus set it up like this:

Create new dirs and sync:
mkdir ~/gdrive/nbdrive -p
mkdir ~/gdrive/bedrive

On Nb the crontab looks like this:
*/2 *    * * * rclone sync /home/me/gdrive/nbdrive google_drive:/nbdrive
*/10 *   * * * rclone sync google_drive:/bedrive /home/me/gdrive/bedrive

and on Be it looks like this:
*/10 *    * * * rclone sync google_drive:/nbdrive /home/me/gdrive/nbdrive 
*/2 *   * * * rclone sync /home/me/gdrive/bedrive google_drive:/bedrive 

If I do work on a file on Be I then copy it to bedrive, and edit it. To edit it late on Nb I copy it from bedrive to nbdrive and edit it. Of course I could always sync manually and avoid this, but the above is a solution for people who might not feel comfortable working on the command line or if you want everything automated.

20 January 2016

628. Very briefly: Crystalmaker in debian jessie with wine-staging (1.9)

 I am seeing consistent crashes with files containing multiple structures (e.g. multi-xyz or multi-cif files). They open fine in a virtualbox instance of crystalmaker.

The terminal shows
fixme:shell:check_flags Unsupported flags: 2414
Before buying crystalmaker, make sure to try it extensively first as there is a free demo version available.

Original post:
This is a brief and somewhat incomplete post.
I recently bought a crystalmaker license, knowing that it had no support under linux. I figured that I'd live with running it in an XP VM. My allergies to all things windows made me very unhappy with that solution, however.

So I tried to install crystalmaker using wine in jessie (1.6.2) and the current (1.50.1) version of Crossover. The installation worked fine for both, but running the software lead to crashes.

I then installed the winehq-staging version (1.9):
sudo apt-get install apt-transport-https
wget https://dl.winehq.org/wine-builds/Release.key
sudo apt-key add Release.key

I edited /etc/apt/sources.list
deb https://dl.winehq.org/wine-builds/debian/ jessie main
sudo apt-get update
sudo sudo apt-get install winehq-staging

Same issue.

I then finally actually read the crash message, which mentioned that
wine: Unimplemented function msvcp120.dll.?_Throw_C_error@std@@YAXH@Z called at address 0x7b83a70c (thread 004e), starting debugger...
That lead me to install vcrun2013 using winetricks:
winetricks -q vcrun2013 gdiplus

Crystalmaker now works perfectly (as far as I can see) under wine. Saving graphics as PNG works too. I haven't tried anything else as I'm not familiar with crystalmaker.

[NOTE: by running WINEPREFIX=~/.cxoffice/crystalmaker winetricks vcrun2013 I later got it to work in crossover. I haven't tried wine 1.6.2 again.]

[Note 2: gdiplus is needed to fix messages of the type
fixme:gdiplus:Gdip<...> graphics object has no HDC]

19 January 2016

627. Very briefly: Turn off screen blanking in GNOME/debian jessie

The only thing that worked for turning off screen-blanking when using youtube or vlc was an ugly little hack:
I installed xdotool and ran crontab -e and added:
*/2 * * * * DISPLAY=:0 XAUTHORITY=/home/andy/.Xauthority xdotool key Ctrl

Original post
In spite of not having any screen saver activate and in spite of setting "Blank Screen" to "Never' under Power options, my screen kept on blanking out after 1-3 minutes of watching TV using mythtv. I tried a lot of things, including using xset, but the only thing that worked in the end was editing my /etc/X11/xorg.conf (I use an nvidia driver) and adding the bits in red:
Section "ServerLayout"
    Identifier     "X.org Configured"
    Screen      0  "Screen0" 0 0
    Screen      1  "Screen1" RightOf "Screen0"
    Screen      2  "Screen2" RightOf "Screen1"
    InputDevice    "Mouse0" "CorePointer"
    InputDevice    "Keyboard0" "CoreKeyboard"
    Option "BlankTime" "0"
    Option "StandbyTime" "0"
    Option "SuspendTime" "0"
    Option "OffTime" "0"
    Option "DPMS" "0"
Now the screen never blanks when watching TV using mythtv. On the other hand, it still blanks when watching DVDs in VLC...

18 January 2016

626. Briefly: Gaussian and cloud computing -- Gaussian G09D with Slurm on aws/ec2

Note: you may want to install awscli and euca2ools. I didn't, so I don't actually know whether they are useful.

My instructions are quite rudimentary since I don't have much time to write these blog posts anymore. Hopefully there's enough information to get you through.

Either way, sign up for AWS. If you already have an amazon ID I think you can use that. Go to https://aws.amazon.com/

Select Launch an Instance and pick the ubuntu AIM and do Launch and Review. I launched it as a t2.micro instance type, as it is free and it's sufficient for set up but not to run jobs.

Hit launch, and create a new key pair. I called mine myfirstkeypair and saved the pem file in my ~/Downloads folder

In my Downloads folder:
ssh -i "myfirstkeypair.pem" ubuntu@ec2-11-222-33-444.us-west-2.compute.amazonaws.com
I then set a password in the ubuntu AWS image:
sudo passwd ubuntu

I added my id_rsa.pub to ~/.ssh/authorized_keys on the ubuntu AWS image to make logging in via ssh easier -- that way I won't need the pem file.

Set up Gaussian
I then connected with SCP and uploaded my gaussian files -- I went straight for EM64T G09D. It went quite fast at +5 MB/s

scp E6L-103X.tgz ubuntu@ec2-00-111-22-333.us-west-2.compute.amazonaws.com:/home/ubuntu/E6L-103X.tgz

Once that was done, on the ubuntu AWS instance I did:
sudo apt-get install csh 
sudo mkdir /opt/gaussian
cd /opt 
sudo chown ubuntu gaussian -R
cd /opt/gaussian
cp ~/E6L-103X.tgz .
tar xvf E6L-103X.tgz
cd g09
csh bsd/install

echo 'export GAUSS_EXEDIR=/opt/gaussian/g09/bsd:/opt/gaussian/g09/local:/opt/gaussian/g09/extras:/opt/gaussian/g09' >> ~/.bashrc
echo 'export GAUSS_SCRDIR=/home/ubuntu/scratch' >> ~/.bashrc
echo 'export PATH=$PATH:/opt/gaussian/g09' >> ~/.bashrc
source ~/.bashrc 
mkdir ~/scratch ~/jobs

NOTE that you can't run any gaussian jobs under a t2.micro instance. You will have to stop and relaunch as at least a t2.small instance or the jobs will be 'Killed' (that's what is echoed in the terminal when you try to run)
Note that if you terminate an image it will be deleted.

Stop the image and then create a snapshot or an image from it to keep everything you've installed.

Set up Slurm
You'll want a queue manager so that you can launch several jobs in serial. Also, you can set up your script so that it shuts down the image when your job is done to save money.

sudo apt-get update
sudo apt-get install slurm-llnl

ControlMachine=localhost ControlAddr= MpiDefault=none ProctrackType=proctrack/pgid ReturnToService=2 SlurmctldPidFile=/var/run/slurm-llnl/slurmctld.pid SlurmdPidFile=/var/run/slurm-llnl/slurmd.pid SlurmdSpoolDir=/var/lib/slurm-llnl/slurmd SlurmUser=slurm StateSaveLocation=/var/lib/slurm-llnl/slurmctld SwitchType=switch/none TaskPlugin=task/none FastSchedule=1 SchedulerType=sched/backfill SelectType=select/linear AccountingStorageType=accounting_storage/none ClusterName=rupert JobAcctGatherType=jobacct_gather/none SlurmctldLogFile=/var/log/slurm-llnl/slurmctld.log SlurmdLogFile=/var/log/slurm-llnl/slurmd.log NodeName=localhost NodeAddr= PartitionName=All Nodes=localhost
sudo /usr/sbin/create-munge-key
Edit /etc/default/munge:
Then run
sudo service slurm-llnl restart
sudo service munge restart 
Test using slurm.batch
#!/bin/bash # #SBATCH -p All #SBATCH --job-name=test #SBATCH --output=res.txt # #SBATCH --ntasks=1 #SBATCH --time=10:00 srun hostname srun sleep 60
and submit with
sbatch slurm.batch
                 2       All     test   ubuntu  R       0:08      1 localhost

#!/bin/csh #SBATCH -p All #SBATCH --time=9999999 #SBATCH --output=slurm.out #SBATCH --job-name=benchmark setenv GAUSS_SCRDIR /home/ubuntu/scratch setenv GAUSS_EXEDIR /opt/gaussian/g09/bsd:/opt/gaussian/g09/local:/opt/gaussian/g09/extras:/opt/gaussian/g09 /opt/gaussian/g09/g09< benchmark.in > benchmark.out
Using the same opt/freq benchmark as in post 621.

c4.2xlarge 2h 11 min [1h 20 min] 8 vcpu/16 Gb
c4.4xlarge 1h 15 min [     44 min] 16 vcpu/32 Gb
c4.8xlarge      41 min [     25 min] 36 vcpu/60 Gb

It scales surprisingly well, although not perfectly linearly. It's clear that it's cheaper to use a smaller instance, so if time isn't critical or the larger memory isn't needed, c4.8xlarge is not the first choice.

You might want to use dropbox to transfer files back and forth, especially finished job files (useful if you shut down the machine using a slurm script as shown below)

cd ~ && wget -O - "https://www.dropbox.com/download?plat=lnx.x86_64" | tar xzf -
This computer isn't linked to any Dropbox account... Please visit https://www.dropbox.com/cli_link_nonce?nonce=0011223344556677889900aabbccddeef to link this device. This computer isn't linked to any Dropbox account...

Open that link in a browser, then go back to the terminal.
wget -O - https://www.dropbox.com/download?dl=packages/dropbox.py > dropbox.py
sudo mv dropbox.py /usr/local/bin
sudo chmod +x d/usr/local/bin/dropbox.py
dropbox.py autostart y

Now, since you don't want to use up space unnecessarily (you're paying for it after all), exclude as many directories as possible. To exclude all existing dropbox dirs, do
cd ~/Dropbox
dropbox.py exclude add `ld -d */`
dropbox.py exclude add `ld *.*`
dropbox.py exclude list

Note that it can't handle directories with spaces in the name, so you'll need to polish the list by hand. Next create a directory where you want to run and store your jobs,e .g.
mkdir ~/Dropbox/aws_jobs

When you run a gaussian job, make sure to specify where the .chk files should end up, e.g.
so that you don't use up space/bandwidth for your chk files (unless of course you want to).

Stop after execution:
Use a batch script along these lines:
#!/bin/csh #SBATCH -p All #SBATCH --time=9999999 #SBATCH --output=slurm.out #SBATCH --job-name=benchmark setenv GAUSS_SCRDIR /home/ubuntu/scratch setenv GAUSS_EXEDIR /opt/gaussian/g09/bsd:/opt/gaussian/g09/local:/opt/gaussian/g09/extras:/opt/gaussian/g09 /opt/gaussian/g09/g09< benchmark.in > benchmark.out rm /home/ubuntu/scratch/*.* sudo shutdown -h now