If you're using nwchem chances are that you've considered using ECCE to parse the output:
http://ecce.emsl.pnl.gov/
First of all you'll need to register at https://eus.emsl.pnl.gov/Portal/ -- and you can only do that if you're faculty. Postdocs and PhD students need not apply. Other than that, it's free, but you'll have to wait a couple of days to get your registration approved.
As much as I like nwchem owing to the clear syntax, I feel less warmly about ecce. Don't get me wrong -- it's pretty. It's just feels archaic and cobbled together. Even worse is that it's not open source and that its workings feel a bit opaque at times. Still, there's no better program for visually parsing nwchem output at this point. Anyway...
--start here --
Debian:
Download the install_ecce.v6.2.rhel5-gcc3.2.3-m32.csh file to ~/tmp/ecce
There's no md5sum supplied but here's what I got:
2ee70cc817dee9f80b11be5eac6e53e5
If you haven't already
sudo apt-get install csh
OK, moving on...
cd ~/tmp/ecce
chmod +x install_ecce.v6.2.rhel5-gcc3.2.3-m32.csh
./install_ecce.v6.2.rhel5-gcc3.2.3-m32.csh
Assuming you've source your ~/.bashrc, start ecce by typing
ecce
...which takes an unreasonably long time (ca 1 min) after which you're greeted by
Type in a password -- any password -- which will be your password from now on.
You're then taken to
Click on Viewer (assuming you've got something to look at)
Have a look at the text box in the bottom right corner..and pay attention. In my particular case I have 6 cores and an mpi aware nwchem 6.0 version compiled. I bet that's better than whatever comes bundled with ecce. Also, the
To change you go to the machine browser (see screen shot #2), click on set up remote access and make sure that everything is working by clicking on e.g. processes:
Then click on the Machine menu (top left), select Register Machine while your machine is selected.
You can now change your options.
Running:
So, before using ecce you always need to
sh /home/me/tmp/ecce/ecce-v6.2/server/ecce-utils/start_ecce_server
first. The server will run until you stop it or reboot.
Next, start ecce
ecce
Integration with nwchem
Most people would probably set up their nwchem jobs by hand, because it's so simple. All you need to do is to include the statement
ecce_print ecce.out
in the beginning, and you'll get an ecce.out file which you can then IMPORT (not open regularly, but import) into ecce.
Click on Viewer, Import Calculation From Output File, select your ecce out and voilá:
If you're running debian, you're done now.
ROCKS 5.4.3/Centos 5.6:
This isn't a fix as much as a rant. The problem with ROCKS 5.4.3 is that csh is so broken that it's a struggle just to install ecce. I mean, I do show how to get ecce running in the end, but ROCKS feels like an unfinished piece of work compared to a normal debian install.
--Demonstration only -- don't do --
First back up ssh-key.sh and ssh-key.csh in /etc/profile.d
So...you start by
chmod +x install_ecce.v6.2.rhel5-gcc3.2.3-m32.csh
./install_ecce.v6.2.rhel5-gcc3.2.3-m32.csh
...and nothing's happening.
You then try just typing in
csh
Turns out there's a bug in ROCKS 5.4.3. You can fix that by:
rpm -Uvh ftp://www.rocksclusters.org/pub/rocks/updates/5.4.3/x86_64/RPMS/rocks-config-server-5.4.3-1.x86_64.rpm
So far so good.
csh
...and nothing. It just exits. Or so you think. But the problem is bigger than that -- try opening a new terminal in e.g. gnome (gnome-terminal or xterm) -- it exits immediately. No error message or anything.
You can get csh to start by moving /etc/csh.cshrc out of the way, but you're still screwed as to opening a new terminal. The only way to get back a working system is to restore ssh-key.sh and ssh-key.csh.
--- Demonstration over ---
--Start here --
You could also get around all this by running
csh -f
But then you don't have any env. variables loading and it can lead to problems of its own.
Anyway:
csh -f install_ecce.v6.2.rhel5-gcc3.2.3-m32.csh
The install starts. Just follow the instructions.
After installation, start the server:
csh -f ecce-v6.2/server/ecce-utils/start_ecce_server
Hit enter until you get a workable prompt back...
Edit your ~/.bashrc and add
http://ecce.emsl.pnl.gov/
First of all you'll need to register at https://eus.emsl.pnl.gov/Portal/ -- and you can only do that if you're faculty. Postdocs and PhD students need not apply. Other than that, it's free, but you'll have to wait a couple of days to get your registration approved.
As much as I like nwchem owing to the clear syntax, I feel less warmly about ecce. Don't get me wrong -- it's pretty. It's just feels archaic and cobbled together. Even worse is that it's not open source and that its workings feel a bit opaque at times. Still, there's no better program for visually parsing nwchem output at this point. Anyway...
--start here --
Debian:
Download the install_ecce.v6.2.rhel5-gcc3.2.3-m32.csh file to ~/tmp/ecce
There's no md5sum supplied but here's what I got:
2ee70cc817dee9f80b11be5eac6e53e5
If you haven't already
sudo apt-get install csh
OK, moving on...
cd ~/tmp/ecce
chmod +x install_ecce.v6.2.rhel5-gcc3.2.3-m32.csh
./install_ecce.v6.2.rhel5-gcc3.2.3-m32.csh
Main ECCE installation menu
===========================
0) Help on main menu options
1) Full install
2) Full upgrade
3) Application software install
4) Application software upgrade
5) Server install
6) Server upgrade
Pick 1 if you're installing on your desktop and there's no server that you know of.
Once the installation is over you get:
***************************************************************
!! You MUST perform the following steps in order to use ECCE !!
-- Unless only the user 'me' will be running ECCE,
start the ECCE server as 'me' with:
/home/me/tmp/ecce/ecce-v6.2/server/ecce-utils/start_ecce_server
-- To register machines to run computational codes, please see
the installation and compute resource registration manuals
at http://ecce.pnl.gov/using/installguide.shtml
-- To run ECCE each user must source either the runtime_setup
(csh/tcsh) or runtime_setup.sh (sh/bash/ksh) script in the
directory /home/me/tmp/ecce/ecce-v6.2/apps/scripts
from their shell environment setup script. For example,
with csh or tcsh, add the following to ~/.cshrc:
if (-e /home/me/tmp/ecce/ecce-v6.2/apps/scripts/runtime_setup) then
source /home/me/tmp/ecce/ecce-v6.2/apps/scripts/runtime_setup
endif
***************************************************************
Which translates to:
1. sh /home/me/tmp/ecce/ecce-v6.2/server/ecce-utils/start_ecce_server
2. Sourcing that file makes no sense. Instead, add the following to your ~/.bashrc
1. sh /home/me/tmp/ecce/ecce-v6.2/server/ecce-utils/start_ecce_server
2. Sourcing that file makes no sense. Instead, add the following to your ~/.bashrc
export ECCE_HOME=/home/me/tmp/ecce/ecce-v6.2/apps
export PATH=${ECCE_HOME}/scripts:${PATH}
Assuming you've source your ~/.bashrc, start ecce by typing
ecce
...which takes an unreasonably long time (ca 1 min) after which you're greeted by
 |
| Press Any Key |
You're then taken to
 |
| Pay attention to the fine print |
To change you go to the machine browser (see screen shot #2), click on set up remote access and make sure that everything is working by clicking on e.g. processes:
Then click on the Machine menu (top left), select Register Machine while your machine is selected.
Running:
So, before using ecce you always need to
sh /home/me/tmp/ecce/ecce-v6.2/server/ecce-utils/start_ecce_server
first. The server will run until you stop it or reboot.
Next, start ecce
ecce
Integration with nwchem
Most people would probably set up their nwchem jobs by hand, because it's so simple. All you need to do is to include the statement
ecce_print ecce.out
in the beginning, and you'll get an ecce.out file which you can then IMPORT (not open regularly, but import) into ecce.
Click on Viewer, Import Calculation From Output File, select your ecce out and voilá:
 |
| ECCE: homo (benzene) |
ROCKS 5.4.3/Centos 5.6:
This isn't a fix as much as a rant. The problem with ROCKS 5.4.3 is that csh is so broken that it's a struggle just to install ecce. I mean, I do show how to get ecce running in the end, but ROCKS feels like an unfinished piece of work compared to a normal debian install.
--Demonstration only -- don't do --
First back up ssh-key.sh and ssh-key.csh in /etc/profile.d
So...you start by
chmod +x install_ecce.v6.2.rhel5-gcc3.2.3-m32.csh
./install_ecce.v6.2.rhel5-gcc3.2.3-m32.csh
...and nothing's happening.
You then try just typing in
csh
/etc/profile.d/ssh-key.sh: line 211: return: can only `return' from a function or sourced script
It appears that you have not set up your ssh key.
This process will make the files:
/export/home/me/.ssh/id_rsa.pub
/export/home/me/.ssh/id_rsa
/export/home/me/.ssh/authorized_keys
Generating public/private rsa key pair.
/export/home/me/.ssh/id_rsa already exists.
Overwrite (y/n)?
Turns out there's a bug in ROCKS 5.4.3. You can fix that by:
rpm -Uvh ftp://www.rocksclusters.org/pub/rocks/updates/5.4.3/x86_64/RPMS/rocks-config-server-5.4.3-1.x86_64.rpm
So far so good.
csh
...and nothing. It just exits. Or so you think. But the problem is bigger than that -- try opening a new terminal in e.g. gnome (gnome-terminal or xterm) -- it exits immediately. No error message or anything.
You can get csh to start by moving /etc/csh.cshrc out of the way, but you're still screwed as to opening a new terminal. The only way to get back a working system is to restore ssh-key.sh and ssh-key.csh.
--- Demonstration over ---
--Start here --
You could also get around all this by running
csh -f
But then you don't have any env. variables loading and it can lead to problems of its own.
Anyway:
csh -f install_ecce.v6.2.rhel5-gcc3.2.3-m32.csh
The install starts. Just follow the instructions.
After installation, start the server:
csh -f ecce-v6.2/server/ecce-utils/start_ecce_server
Hit enter until you get a workable prompt back...
Edit your ~/.bashrc and add
export ECCE_HOME=/home/me/tmp/ecce/ecce-v6.2/apps
export PATH=${ECCE_HOME}/scripts:${PATH}
Don't bother sourcing your ~/.bashrc. It's easier to just open a new terminal.
Type
ecce
and you should be up and running...sort of. Under ROCKS I had problems importing ecce.out files since I had problems actually connecting to the server. Don't know why, but it came down to not being able to open a remote shell on the host.
NOTE:
this worked fine on one box, but not on another one which I was setting up remotely. On that one I had to edit
ecce/apps/siteconfig/Dataservers
Don't bother sourcing your ~/.bashrc. It's easier to just open a new terminal.
Type
ecce
and you should be up and running...sort of. Under ROCKS I had problems importing ecce.out files since I had problems actually connecting to the server. Don't know why, but it came down to not being able to open a remote shell on the host.
NOTE:
this worked fine on one box, but not on another one which I was setting up remotely. On that one I had to edit
ecce/apps/siteconfig/Dataservers
and
ecce/apps/siteconfig/jndi.properties
In particular, I had to change references to eccetera.emsl.pnl.gov.
This is dummy text. It is not meant to be read. Accordingly, it is difficult to figure out when to end it. But then, this is dummy text. It is not meant to be read. Period.
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