120. Using truecrypt with dropbox

This is not some fancy, automatic solution. This is for people who may not be familiar with truecrypt and how to use it. To most people this will be obvious.

Basically, one way in which you can use truecrypt is to create a file which, when mounted, acts like a device/filesystem. This container is encrypted and the strength of encryption depends on your key or password.

As a solution it also suffers from slow initial syncing.

Setting it up is a piece of cake:
1. Install truecrypt.
Get the correct version e.g. "Standard x64" from http://www.truecrypt.org/downloads.

Install by extracting the file and executing it:
chmod +x truecrypt-7.1a-setup-x64
sudo ./truecrypt-7.1a-setup-x64

2. Start truecrypt and click on Create Volume

Select encrypted file container. The other option is more useful  if you have access to the hardware.

Using a Hidden truecrypt volume means you pay a space penalty, depending on how you distribute the space between the two volumes.

Select location and filename

Pick an algorithm. I don't know much about this, but using a cascade sounds reasonable. I guess there are performance penalties though.

Be aware that the container file will take up all this space -- whether it's empty or not.

 3. Use the container file.

Click on Select File, then mount. You typically need to supply both the container password and your admin password.

This is what the inside of the container file looks like.

And this is what the dropbox folder looks like

119. Installing sun java/Oracle java in debian

Update 23 March 2013:  the java.com file isn't distributed as a .bin file anymore. Just replace all instances of .bin with .tar.gz and it works just as well.

This basically follows http://sylvestre.ledru.info/blog/sylvestre/2012/02/29/java_package_replacement_of_sun_java6

While a few applications (Grix and Grisu) I was playing with which require java 1.5 or better should work fine with openjdk-7 (1.6.0_24), they didnt. I had to run it using binary packages which I downloaded from java.com and then installed locally.

I'd like a better solution, and here it is:

1. sudo apt-get install java-package

2. Download the java files from java.com, e.g. jre-6u31-linux-x64.bin or jre-7u17-linux-x64.tar.gz
http://java.com/en/download/manual.jsp?locale=en

3. Make-jpkg
Run make-jpkg on the downloaded file, whether it's ending in .bin or .tar.gz:

make-jpkg jre-6u31-linux-x64.bin

Create debian package:
    dh_testdir
    dh_testroot
    dh_installchangelogs
    dh_installdocs
    dh_compress
    dh_fixperms
    dh_installdeb
    dh_shlibdeps
dpkg-shlibdeps: warning: Can't extract name and version from library name `libjvm.so'
[..]
dpkg-shlibdeps: warning: Can't extract name and version from library name `libjvm.so'
[..]
dpkg-shlibdeps: warning: Can't extract name and version from library name `libjli.so'
dpkg-shlibdeps: warning: package could avoid a useless dependency if /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/lib/amd64/native_threads/libhpi.so /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/lib/amd64/libjava.so /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/lib/amd64/libdt_socket.so /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/lib/amd64/libnet.so /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/bin/javaws /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/lib/amd64/libhprof.so were not linked against libnsl.so.1 (they use none of the library's symbols).
dpkg-shlibdeps: warning: package could avoid a useless dependency if /tmp/make-jpkg.9XTCruNvKM/install/usr/lib/jvm/j2re1.6-oracle/lib/amd64/libjawt.so was not linked against libmawt.so (it uses none of the library's symbols).
    dh_gencontrol
    dh_md5sums
    dh_builddeb
dpkg-deb: building package `oracle-j2re1.6' in `/tmp/make-jpkg.9XTCruNvKM/oracle-j2re1.6_1.6.0+update31_amd64.deb'.
    copy oracle-j2re1.6_1.6.0+update31_amd64.deb into directory /home/me/Downloads/
The Debian package has been created in the current directory. You can
install the package as root (e.g. dpkg -i oracle-j2re1.6_1.6.0+update31_amd64.deb). 

4. sudo dpkg -i oracle-j2re1.6_1.6.0+update31_amd64.deb 

Selecting previously unselected package oracle-j2re1.6.
(Reading database ... 561777 files and directories currently installed.)
Unpacking oracle-j2re1.6 (from oracle-j2re1.6_1.6.0+update31_amd64.deb) ...
Setting up oracle-j2re1.6 (1.6.0+update31) ...
update-alternatives: using /usr/lib/jvm/j2re1.6-oracle/bin/ControlPanel to provide /usr/bin/ControlPanel (ControlPanel) in auto mode.
update-alternatives: using /usr/lib/jvm/j2re1.6-oracle/lib/amd64/libnpjp2.so to provide /usr/lib/iceweasel/plugins/libjavaplugin.so (iceweasel-javaplugin.so) in auto mode.
update-alternatives: using /usr/lib/jvm/j2re1.6-oracle/lib/amd64/libnpjp2.so to provide /usr/lib/chromium/plugins/libjavaplugin.so (chromium-javaplugin.so) in auto mode.

5a. sudo update-alternatives --config java

There are 5 choices for the alternative java (providing /usr/bin/java).

  Selection    Path                                            Priority   Status------------------------------------------------------------* 0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      auto mode  1            /usr/bin/gij-4.4                                 1044      manual mode  2            /usr/bin/gij-4.6                                 1046      manual mode  3            /usr/lib/jvm/j2re1.6-oracle/bin/java             314       manual mode  4            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode  5            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1051      manual modePress enter to keep the current choice[*], or type selection number: 3update-alternatives: using /usr/lib/jvm/j2re1.6-oracle/bin/java to provide /usr/bin/java (java) in manual mode.

5b. 

 sudo update-alternatives --config javaws

There are 2 choices for the alternative javaws (providing /usr/bin/javaws).
  Selection    Path                                              Priority   Status
------------------------------------------------------------
* 0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/javaws   1061      auto mode
  1            /usr/lib/jvm/j2re1.6-oracle/bin/javaws             314       manual mode
  2            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/javaws   1061      manual mode
Press enter to keep the current choice[*], or type selection number: 1
update-alternatives: using /usr/lib/jvm/j2re1.6-oracle/bin/javaws to provide /usr/bin/javaws (javaws) in manual mode.
update-alternatives: warning: skip creation of /usr/share/man/man1/javaws.1.gz because associated file /usr/lib/jvm/j2re1.6-oracle/man/man1/javaws.1.gz (of link group javaws) doesn't exist.

6.  Verification
java -version

java version "1.6.0_31"
Java(TM) SE Runtime Environment (build 1.6.0_31-b04)
Java HotSpot(TM) 64-Bit Server VM (build 20.6-b01, mixed mode)

Go to http://java.com/en/download/installed.jsp

Iceweasel worked fine at this stage.

7. To get Chrome to work I did the following:
sudo updatedb
locate libjavaplugin.so

/usr/lib/chromium/plugins/libjavaplugin.so
/usr/lib/iceweasel/plugins/libjavaplugin.so
/usr/lib/mozilla/plugins/libjavaplugin.so

 ls -lah /usr/lib/chromium/plugins/libjavaplugin.so etc.

/usr/lib/chromium/plugins/libjavaplugin.so -> /etc/alternatives/chromium-javaplugin.so
/usr/lib/iceweasel/plugins/libjavaplugin.so -> /etc/alternatives/iceweasel-javaplugin.so
/usr/lib/mozilla/plugins/libjavaplugin.so -> /etc/alternatives/mozilla-javaplugin.so

ls -lah /etc/alternatives/chromium-javaplugin.so etc.

/etc/alternatives/chromium-javaplugin.so -> /usr/lib/jvm/j2re1.6-oracle/lib/amd64/libnpjp2.so
/etc/alternatives/iceweasel-javaplugin.so -> /usr/lib/jvm/j2re1.6-oracle/lib/amd64/libnpjp2.so
/etc/alternatives/mozilla-javaplugin.so -> /usr/lib/jvm/java-6-openjdk-amd64/jre/lib/amd64/IcedTeaPlugin.so

sudo rm /etc/alternatives/mozilla-javaplugin.so

sudo ln -s /usr/lib/jvm/j2re1.6-oracle/lib/amd64/libnpjp2.so /etc/alternatives/mozilla-javaplugin.so

And you're done.

---

Links to this post:
https://www.linuxquestions.org/questions/debian-26/which-java-for-wheezy-4175469043/

118. Solution to nwchem: SHMMAX too small

Update: also see this post: http://verahill.blogspot.com.au/2012/10/shmmax-revisited-and-shmall-shmmni.html

When running nwchem using mpirun I've occasionally encountered this error.

Error:
******************* ARMCI INFO ************************

The application attempted to allocate a shared memory segment of 44498944 bytes in size. This might be in addition to segments that were allocated succesfully previously. The current system configuration does not allow enough shared memory to be allocated to the application.

This is most often caused by:
1) system parameter SHMMAX (largest shared memory segment) being too small or
2) insufficient swap space.
Please ask your system administrator to verify if SHMMAX matches the amount of memory needed by your application and the system has sufficient amount of swap space. Most UNIX systems can be easily reconfigured to allow larger shared memory segments,
see http://www.emsl.pnl.gov/docs/global/support.html
In some cases, the problem might be caused by insufficient swap space.
*******************************************************
0:allocate: failed to create shared region : -1
(rank:0 hostname:boron pid:17222):ARMCI DASSERT fail. shmem.c:armci_allocate():1082 cond:0

Diagnosis:

Check the currently defined shmmax:

cat /proc/sys/kernel/shmmax
33554432

Well, 33554432<44498944, so it seems that it's caused by reason 1 above.

Solution:

http://www.linuxforums.org/forum/red-hat-fedora-linux/17025-how-can-i-change-shmmax.html

Edit /etc/sysctl.conf

Add a line saying

kernel.shmmax=44498944

Save and reboot. The exact value is up to you -- I've set my shmmax to 128*1024*1024=134217728, while our production cluster has 6269961216.

Update: to change it on the fly do
sudo sysctl -w kernel.shmmax=6269961216

117. Sorting out framebuffer in linux (debian)

If you have /dev/fb0 you're fine -- you have a working frame buffer, and that was the case on my laptop and my optiplex 990. However, my homebuilt boxes didn't have any framebuffer devices.

This is how to set up framebuffer:

sudo apt-get install hwinfo
sudo hwinfo --framebuffer

02: None 00.0: 11001 VESA Framebuffer                        
  [Created at bios.464]
  Unique ID: rdCR.fRULN9k9OD4
  Hardware Class: framebuffer
  Model: "Intel(r)Cantiga Graphics Controller"
  Vendor: "Intel Corporation"
  Device: "Intel(r)Cantiga Graphics Controller"
  SubVendor: "Intel(r)Cantiga Graphics Chip Accelerated VGA BIOS"
  SubDevice:
  Revision: "Hardware Version 0.0"
  Memory Size: 127 MB + 960 kB
  Memory Range: 0xd0000000-0xd7feffff (rw)
  Mode 0x0360: 848x480 (+896), 8 bits
  Mode 0x0361: 848x480 (+1728), 16 bits
  Mode 0x0362: 848x480 (+3392), 24 bits
  Mode 0x0305: 1024x768 (+1024), 8 bits
  Mode 0x0317: 1024x768 (+2048), 16 bits
  Mode 0x0318: 1024x768 (+4096), 24 bits  Mode 0x0312: 640x480 (+2560), 24 bits
  Mode 0x0314: 800x600 (+1600), 16 bits
  Mode 0x0315: 800x600 (+3200), 24 bits
  Mode 0x0301: 640x480 (+640), 8 bits
  Mode 0x0303: 800x600 (+832), 8 bits
  Mode 0x0311: 640x480 (+1280), 16 bits
  Config Status: cfg=new, avail=yes, need=no, active=unknown

Pick a mode e.g. 0x0318

Edit your /etc/default/grub

Add vga=0x0318 to the GRUB...DEFAULT line:

GRUB_CMDLINE_LINUX_DEFAULT="quiet nouveau.modeset=0 vga=0x0318"

If there's a nomodeset command, delete it.

Do
sudo update-grub

and reboot. You're done.

There should now be a /dev/fb0 and your resolution when working in a TTY* should be different.

*the terminal you get to by doing alt+f1, alt+f2 etc.

What to do with framebuffers?
Apart from making your ttys look a lot nicer and work at higher resolution, they'll also allow you to use w3m-img for ncurses based browsing with images (w3m+w3m-img; sometimes it's useful), and to take screenshots of the terminal in terminal mode. But mostly, it just makes your terminal experience better through being at higher resolution.


More modes:
02: None 00.0: 11001 VESA Framebuffer                        
  [Created at bios.464]
  Unique ID: rdCR.efxRnBcYXs5
  Hardware Class: framebuffer
  Model: "NVIDIA GF108 Board - 1071v0p1"
  Vendor: "NVIDIA Corporation"
  Device: "GF108 Board - 1071v0p1"
  SubVendor: "NVIDIA"
  SubDevice:
  Revision: "Chip Rev"
  Memory Size: 14 MB
  Memory Range: 0xd7000000-0xd7dfffff (rw)

  Mode 0x0300: 640x400 (+640), 8 bits
  Mode 0x0301: 640x480 (+640), 8 bits
  Mode 0x0303: 800x600 (+800), 8 bits
  Mode 0x0305: 1024x768 (+1024), 8 bits
  Mode 0x0307: 1280x1024 (+1280), 8 bits
  Mode 0x030e: 320x200 (+640), 16 bits
  Mode 0x030f: 320x200 (+1280), 24 bits
  Mode 0x0311: 640x480 (+1280), 16 bits
  Mode 0x0312: 640x480 (+2560), 24 bits
  Mode 0x0314: 800x600 (+1600), 16 bits
  Mode 0x0315: 800x600 (+3200), 24 bits
  Mode 0x0317: 1024x768 (+2048), 16 bits
  Mode 0x0318: 1024x768 (+4096), 24 bits
  Mode 0x031a: 1280x1024 (+2560), 16 bits
  Mode 0x031b: 1280x1024 (+5120), 24 bits
  Mode 0x0330: 320x200 (+320), 8 bits
  Mode 0x0331: 320x400 (+320), 8 bits
  Mode 0x0332: 320x400 (+640), 16 bits
  Mode 0x0333: 320x400 (+1280), 24 bits
  Mode 0x0334: 320x240 (+320), 8 bits
  Mode 0x0335: 320x240 (+640), 16 bits
  Mode 0x0336: 320x240 (+1280), 24 bits
  Mode 0x033d: 640x400 (+1280), 16 bits
  Mode 0x033e: 640x400 (+2560), 24 bits
  Mode 0x0345: 1600x1200 (+1600), 8 bits
  Mode 0x0346: 1600x1200 (+3200), 16 bits
  Mode 0x034a: 1600x1200 (+6400), 24 bits
  Mode 0x0360: 1280x800 (+1280), 8 bits
  Mode 0x0361: 1280x800 (+5120), 24 bits
  Config Status: cfg=new, avail=yes, need=no, active=unknown

---

Links to this post:
http://pinboard.in/u:greppy

116. [Solved] Latex bug -- "tcfmgr: config file `tcfmgr.map' (usually in $TEXMFMAIN/texconfig) not found."

Symptom:
When using latexila or texmaker no dvi/ps/pdf is generated. No outright error is report though

When trying to generate the pdf in the terminal using latex e.g.

me@beryllium:~$ latex nature_draft.tex

This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009/Debian)
kpathsea: Running mktexfmt latex.fmt
tcfmgr: config file `tcfmgr.map' (usually in $TEXMFMAIN/texconfig) not found.
I can't find the format file `latex.fmt'!

But (http://www.mwusers.com/forums/showthread.php?1687-Another-teX-thread)

 kpsewhich -expand-var='$TEXMFMAIN'

gives

/usr/share/texmf/

which is the correct file structure as defined by texmf.cnf

kpsewhich texmf.cnf

/usr/share/texmf/web2c/texmf.cnf

So what the heck is going on? I've written articles, reviews and book in latex and never had a problem until now. Also, it only happens on one computer.

Solution:

I ended up just fooling around. What solved it was doing

sudo texconfig rehash

mktexlsr: Updating /var/lib/texmf/ls-R-TEXMFMAIN...
mktexlsr: Updating /var/lib/texmf/ls-R-TEXLIVE...
mktexlsr: Updating /var/lib/texmf/ls-R...
mktexlsr: Done.

That's all. Really.

Minor note:

you can run texonfig interactively as well. Just make sure to run it using sudo.

---

Links to this post:
http://tex.stackexchange.com/questions/64894/error-i-cant-find-the-format-file-pdflatex-fmt

115. Very Simple Python Queue Manager

I suppose we can call it the VSPQM, which sounds a bit like a Roman initialism, akin to SPQR.

I've spent the past few days trying to get to grips with the Sun Gridengine (SGE) but have given up for now. While it seems capable, it's just overkill for my purposes, especially taking into account the difficulties in simply configuring it. It's a bit similar to my experience with OpenDX, a very capable plotting program, but which I couldn't make work to satisfaction in spite of being one of the lucky few in possession of the "Open DX -- Paths to Visualisation" book.

---

Long story short -- I wrote a small script in python. It
- reads a file, list, with the name of shell scripts
- the shell scripts, job1.sh..jobn.sh, are executed sequentially - when the execution of one script is finished, the next one is executed
- jobs can be added and removed from list during execution

It's a 'dumb' script -- it does not try to balance jobs across nodes or look for idle cpus/cores. It just executes one job after the other, and mark jobs as done after execution.

To test it:
create a file called list and put the following lines in it:

pi40.sh
pi400.sh
pi2000.sh

The scripts are the following:

pi40.sh

echo "pi to 40 decimals"
echo "scale=40; 4*a(1)" | bc -l -q
echo "done"

pi400.sh

echo "scale=400; 4*a(1)" | bc -l -q

pi200.sh

 echo "scale=2000; 4*a(1)" | bc -l -q

The python code for vspqm.py is below

I've aliased my vspqm (edit ~/.bashrc):

alias vspqm='/home/me/work/vspqm/vspqm.py'

Then sourced ~/.bashrc

Launch in the directory you keep your list file using

me@beryllium:~/work/vspqm/jobs$ vspqm list > log &
[1] 23925
me@beryllium:~/work/vspqm/jobs$ cat log

pi to 40 decimals
3.1415926535897932384626433832795028841968
done
3.141592653589793238462643383279502884197169399375105820974944592307\
[..]
3.141592653589793238462643383279502884197169399375105820974944592307\
81640628620899862803482534211706798214808651328230664709384460955058\
[..]

An nwchem example would be
list:

ac.sh
bn.sh

ac.sh:

cd acetone/
mpirun -n 4 nwchem ac.nw>ac.out
cd ../

bn.sh:

cd benzene/
mpirun -n 4 nwchem bn.nw>bn.out
cd ../

---

Our python queue manager (which we'll call vspqm.py and chmod +x to make executable) is below. Don't forget to change #!/usr/bin/python2.4 if necessary -- I use 2.4 on ROCKS and 2.7 on Debian testing/wheezy

#!/usr/bin/python2.4
# rudimentary queue manager. Handles a single node,
# submitting a series of jobs in sequence. use python v2.4-2.7
import os
import time
import sys
infile=sys.argv[1]
print "pyqm v 0.0.3"
def launchjob(job):
        i=0
        print "######"
        job=job.rstrip('\n')
     
        i=os.system("sh "+job)
        if i==0:
                print "Job successful"
        else:
                print "Job failed"
        print "######"
        return i
def remake_list(infile):
        qfile=open(infile,"w")
        bakfile=open(infile+".bak",'r')
        for i in bakfile:
                qfile.write(i)
        return 0
def rewind(infile):
        qfile=open(infile,"w")
        bakfile=open(infile+".bak",'r')
        for i in bakfile:
                qfile.write(i[1:])
        return 0
def get_next_job(infile):
        qfile=open(infile,"r")
        bakfile=open(infile+".bak",'w')
        lines=""
        job=""
        for line in qfile:
                if line[0]=="*":
                        print "Marked as done: ",line[1:]
                if line[0]!="*" and job=="":
                        print "Launching: ", line
                        job=line
                        line="*"+line
                lines+=line
        bakfile.write(lines)
        qfile.close
        bakfile.close
        return job
def main(infile):
        jobs=1
        while (jobs==1):
                newjob=get_next_job(infile)
                remake_list(infile)
                if newjob!="":
                        jobs=1
                        echojob=launchjob(newjob)
                else:
                        print "No more jobs found at "+str(time.asctime())    
                        jobs=0
        return 0

if __name__ == "__main__":
        main(infile)
        rewind(infile)

114. Nwchem 6.0 with openmpi support on debian testing

I still haven't managed to compile a working versin of Nwchem 6.1 on Debian 64 bit regardless of whether I'm using mpich or openmpi. The number of posts relating to compiling nwchem is steadily growing, but I'd rather have post which are almost, but not quite, identical if it makes it's unambiguous for the average user how to build and use nwchem.

Anyway, since I'm using openmpi on my rocks cluster(s), I figure I might as well start using openmpi on debian too. In addition, the only way you can get nwchem 6.0 to work with mpich2 on debian seems to be by using the old v1.2 package which causes problems of its own (see apt-pinning).

Note: See here for information about python support: http://verahill.blogspot.com.au/2012/04/adding-python-support-to-nwchem-under.html

Long story short -- nwchem with openmpi:
mkdir ~/tmp
sudo apt-get install openmpi-bin libopenmpi-dev
wget http://www.nwchem-sw.org/images/Nwchem-6.0.tar.gz
tar -xvf Nwchem-6.0.tar.gz
cd nwchem-6.0/

export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=/home/me/tmp/nwchem-6.0
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all
export USE_MPI=y
export USE_MPIF=y
export MPI_LOC=/usr/lib/openmpi/lib
export MPI_INCLUDE=/usr/lib/openmpi/include
export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib/openmpi/lib
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
cd $NWCHEM_TOP/src
make clean
make nwchem_config
make FC=gfortran

This will take a good 20-30 minutes.


Your binary will be in nwchem-6.0/bin/LINUX64/

Finally, see whether openmpi is already in your LD_LIBRARY_PATH

echo $LD_LIBRARY_PATH

/lib/openmm:/usr/lib/nvidia-cuda-toolkit:/usr/lib/nvidia

If not, edit ~/.bashrc and add
export LD_LIBRARY_PATH=/usr/lib/openmpi/lib:$LD_LIBRARY_PATH
export PATH=$PATH:/home/me/tmp/nwchem-6.0/bin/LINUX64

113. Using ECCE to run nwchem jobs

EDIT: This post is getting messier as I'm hammering things out...but I've gotten everything to work in the end, so please persist.  The workflow described below is not the ideal one, but it'll get you started. I'll link here when I put up a newer, more reasonable tutorial.

EDIT2: I'm really warming to ECCE as I'm learning more about it. I still think it'd be nice if it was open source, and I can't understand why it has to be reliant on csh (which is pretty much broken on ROCKS, and uncomfortable at the best of times), but it's pretty neat once you've got all the details ironed out. Error feedback/report could be better though.

EDIT 3: ECCE is going open source the (northern) summer of 2012! As users we no longer have any excuses to complain.

Here's a quick introduction to getting started with using ECCE as the interface to nwchem, similar to how gaussview can be used to set up gaussian jobs.

This presumes that you've set up ECCE and preferably compiled your own version of nwchem:
http://verahill.blogspot.com.au/2012/03/ecce-on-debian-but-not-on-rockscentos.html
http://verahill.blogspot.com.au/2012/03/nwchem-61-with-openmpi-on-rocks.html
http://verahill.blogspot.com.au/2012/01/debian-testing-64-wheezy-nwhchem.html


##Important##
Once I had figured all of this out I rebuilt nwchem and re-installed ecce in the proper locations. You might want to do the same.

A. If you're going to use several nodes you should put nwchem in the same position in the file system hierarchy on all nodes e.g.
/opt/nwchem/nwchem-6.0/bin/LINUX64/nwchem

Also, make sure you share a folder (see how to use NFS) between the nodes which you can use for run time files e.g. /work

EDIT 4: This (probably) isn't necessary. In fact, using NFS in the wrong way will slow things down.

Set the permissions right (chown your user and set to 777 -- 755 is enough for nfs sharing between debian nodes, but between ROCKS and Debian you seem to need 777), and open your firewall on all ports for communication between the nodes.

B. Make sure that ECCE_HOME has been set in ~/.bashrc e.g.
export ECCE_HOME=/opt/ecce/apps

and in ~/.cshrc
setenv ECCE_HOME=/opt/ecce/apps

C.
edit /opt/ecce/apps/siteconfig/submit.site (location depends on where you install ecce)
Change lines 65+ from

#NWChemCommand {
#  $nwchem $infile > $outfile
#}

to (for multiple nodes)

NWChemCommand {
mpirun -hostfile /work/hosts.list -n $totalprocs --preload-binary /opt/nwchem/nwchem-6.0/bin/LINUX64/nwchem $infile > $outfile
}

to use mpirun for parallel job submissions and assuming you have a hosts file in /work. For running on a single node you can use

NWChemCommand {
mpirun  -n $totalprocs $nwchem  $infile > $outfile
}

user either --preload-binary /opt/nwchem/nwchem-6.0/bin/LINUX64/nwchem or $nwchem -- see what works for you. You probably can't do preload if you're running different linux distros (e.g. debian and centos)

My hosts.list looks like this:

tantalum slots=4 max_slots=4
beryllium slots=4 max_slots=5

Make sure that you don't accidentally put 2 jobs on node 0, then 2 jobs on node 1, then another 2 jobs on node 0, since they won't be consecutively numbered and will crash armci. You can avoid this by setting slots and max_slots to the same number.


D.
You may have to edit /etc/openmpi/openmpi-mca-params.conf if you have several (real or virtual) interfaces and add e.g.


btl=tcp,sm,self
btl_tcp_if_include=eth1,eth2
btl_tcp_if_exclude=eth0,virtbr0


Start ECCE:
First start the server
csh /home/me/tmp/ecce/ecce-v6.2/server/ecce-utils/start_ecce_server
then launch ecce

ecce

This will launch what the ecce people call the 'gateway':

The Gateway

0. Make sure you've got your machine set up
Click on Machine browser

Make sure that you can connect to the node e.g. by clicking on disk usage

Set the application paths. Don't fiddle with nodes -- just change number of processors to the total for all nodes.

1. Draw SiCl₄ 
Click on the Builder in the Gateway, which gives you the following:

The builder window

Click on More to get the periodic table which gives you access to Si

Select Geometry -- here, Tetrahedral

Si -- with four 'nubs' (yup, that's what the ecce ppl call them)

Time to attach Cl atoms to the nubs. Select Cl and pick Terminal geometry.

Click on a 'nub' to replace it with a Cl

And do it until you've replaced all 'nubs'. Hold down right mouse button to rotate

Click on the broom next to the bond menu on the right to pre-optimize  the structure using MM

And save. You will probably be limited to saving your jobs in folders below the ecce  folder.

2. Set up your job
Click on the Organizer icon in the 'gateway', which takes you here:

Click on the first icon, Editor

Focus on selecting Theory and Run type. Here's we'll do a geometry optimisation.

Click on Details for Theory

Click on Details for Run type

Constraints are optional

In the organizer, click on the third icon to set the basis set. Defined atoms for a particular basis set are indicated by a n orange right lower corner

You can get Details about the basis set

If you don't have a Navy Triangle you can't run. Click on Editor and see what might be wrong.

Ready to run. Click on Launch.

4. Running

I'm still working on enabling more than a single core...

Once you've clicked on launch you'll get

 If you click on viewer you can monitor the job

Optimization in progress

5. Re-launch a job at higher theory
In the Organizer, select your last job and then click on Edit, Duplicate Setup with Last Geometry

You then get a copy to edit

Change the basis set, save, then click on Final Edit

This is the nwchem input file in a vim instance

Add a line to the end, saying task scf freq to calculate the vibrations (there's another job option called geovib which does optim+freq , but here we do it by hand)

Launch

Running...

You can now look at the vibrations

And you can visualise MOs -- here's the HOMO which looks like all isolated p orbitals on the chlorine

You can also calculate 'properties'

These include GIAO shielding

---

Performance:
Here's phenol (scf/6-31g*) across three gigabit-linked nodes. The dotted line denotes node boundaries.

Here's a number of alkanes (scf/6-31g) on 4 cores on a single node:

112. Kernel 3.3.x on debian testing

Compiling a kernel on debian is easy. Kernel 3.3 came out today, and here's how to build it for debian testing:
sudo apt-get install kernel-package fakeroot
wget http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.3.tar.bz2
tar -xvf linux-3.3.tar.bz2 
cd linux-3.3/

cat /boot/config-`uname -r`>.config
make oldconfig

EDIT: 3.3.1 is here: http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.3.1.tar.bz2 -- the build instructions are the same
EDIT 2: This has been tried with 3.3.4 as well. All is fine.
EDIT 3: And it's fine with 3.3.5

You'll also be asked about the new inclusions in the kernel. You can pick the default if you don't know - Yes means to compile into the kernel, m mean to provide as a module and no means don't support. Some drivers are better provided as modules -- see e.g. http://justlinux.com/forum/archive/index.php/t-127876.html
"Some things obviously have to be compiled into the kernel - file system support for your / filesys, stuff like that. Most everything else can be modules, if you desire." and "f you hot-swap different usb peripherals then I would recommend compiling those drivers as modules". Same goes for network drivers.

You can also look up the different options here: http://cateee.net/lkddb/web-lkddb/.
Seems like there's a lot of network and touch/screen drivers. And the fabled android drivers are available now:

Make audit loginuid immutable (AUDIT_LOGINUID_IMMUTABLE) [N/y/?] (NEW) Yes
Memory Resource Controller Kernel Memory accounting (EXPERIMENTAL) (CGROUP_MEM_RES_CTLR_KMEM) [N/y/?] (NEW) No
EFI stub support (EFI_STUB) [N/y/?] (NEW) No
UNIX: socket monitoring interface (UNIX_DIAG) [N/m/y/?] (NEW) m
UDP: socket monitoring interface (INET_UDP_DIAG) [N/m/?] (NEW)  m
Netfilter NFACCT over NFNETLINK interface (NETFILTER_NETLINK_ACCT) [N/m/y/?] (NEW) m
Supply CT list in procfs (OBSOLETE) (NF_CONNTRACK_PROCFS) [Y/n/?] (NEW) Yes
"nfacct" match support (NETFILTER_XT_MATCH_NFACCT) [N/m/?] (NEW) No
IPVS source hashing table size (the Nth power of 2) (IP_VS_SH_TAB_BITS) [8] (NEW)
"rpfilter" reverse path filter match support (IP_NF_MATCH_RPFILTER) [N/m/?] (NEW) No
"rpfilter" reverse path filter match support (IP6_NF_MATCH_RPFILTER) [N/m/?] (NEW) No
Open vSwitch (OPENVSWITCH) [N/m/y/?] (NEW) No
Network priority cgroup (NETPRIO_CGROUP) [N/m/y/?] (NEW) m
ISA Bus based legacy SJA1000 driver (CAN_SJA1000_ISA) [N/m/?] (NEW) No
Bosch CC770 and Intel AN82527 devices (CAN_CC770) [N/m] (NEW) No
NFC LLCP support (EXPERIMENTAL) (NFC_LLCP) [N/y/?] (NEW) No
Block Device Driver for Micron PCIe SSDs (BLK_DEV_PCIESSD_MTIP32XX) [N/m/?] (NEW) No
NVM Express block device (BLK_DEV_NVME) [N/m/y/?] (NEW) No
Ethernet team driver support (EXPERIMENTAL) (NET_TEAM) [N/m/y/?] (NEW) Yes
Calxeda 1G/10G XGMAC Ethernet driver (NET_CALXEDA_XGMAC) [N/m/y/?] (NEW) No
Micrel KS8995MA 5-ports 10/100 managed Ethernet switch (MICREL_KS8995MA) [N/m/y] (NEW) No
Atheros ath9k bluetooth coexistence support (ATH9K_BTCOEX_SUPPORT) [Y/n/?] (NEW) Yes
Hardware support that overlaps with the brcmsmac driver (B43_BCMA_EXTRA) [Y/n] (NEW) Yes
Broadcom IEEE802.11n PCIe SoftMAC WLAN driver (BRCMSMAC) [N/m/?] (NEW) No
iwlwifi experimental P2P support (IWLWIFI_P2P) [N/y/?] (NEW) No
Enable full debugging output in iwlegacy (iwl 3945/4965) drivers (IWLEGACY_DEBUG) [N/y/?] (NEW)  No
TCA8418 Keypad Support (KEYBOARD_TCA8418) [N/m/?] (NEW) No
AUO in-cell touchscreen using Pixcir ICs (TOUCHSCREEN_AUO_PIXCIR) [N/m/?] (NEW) No
EETI eGalax multi-touch panel support (TOUCHSCREEN_EGALAX) [N/m/?] (NEW) No
PIXCIR I2C touchscreens (TOUCHSCREEN_PIXCIR) [N/m/?] (NEW) No
Sharp GP2AP002A00F I2C Proximity/Opto sensor driver (INPUT_GP2A) [N/m/?] (NEW) No
Polled GPIO tilt switch (INPUT_GPIO_TILT_POLLED) [N/m/y/?] (NEW) No
SBS Compliant gas gauge (BATTERY_SBS) [N/m/?] (NEW) No
National Semiconductor LP8727 charger driver (CHARGER_LP8727) [N/m/?] (NEW) No
Battery charger manager for multiple chargers (CHARGER_MANAGER) [N/y/?] (NEW)  No?
VIA Watchdog Timer (VIA_WDT) [N/m/y/?] (NEW) No
Support STMicroelectronics STMPE (MFD_STMPE) [N/y/?] (NEW) No
Support Dialog Semiconductor DA9052/53 PMIC variants with SPI (MFD_DA9052_SPI) [N/y/?] (NEW) No
Enable IR raw decoder for the Sanyo protocol (IR_SANYO_DECODER) [M/n/?] (NEW) No
JL2005B/C/D USB V4L2 driver (USB_GSPCA_JL2005BCD) [N/m/?] (NEW) m
V4L PCI(e) devices (V4L_PCI_DRIVERS) [Y/n/?] (NEW) Yes
V4L ISA and parallel port devices (V4L_ISA_PARPORT_DRIVERS) [N/y/?] (NEW) No
V4L platform devices (V4L_PLATFORM_DRIVERS) [N/y/?] (NEW)  No
Intel GMA5/600 KMS Framebuffer (DRM_GMA500) [N/m/?] (NEW) No
Roccat Isku keyboard support (HID_ROCCAT_ISKU) [N/m/?] (NEW) No
Microsoft Hyper-V mouse driver (HID_HYPERV_MOUSE) [N/m/?] (NEW) No
EHCI support for Marvell on-chip controller (USB_EHCI_MV) [N/y/?] (NEW) No
Inventra Highspeed Dual Role Controller (TI, ADI, ...) (USB_MUSB_HDRC) [N/m/?] (NEW) No
Marvell USB2.0 Device Controller (USB_MV_UDC) [N/m/?] (NEW) No
LED Support for TCA6507 I2C chip (LEDS_TCA6507) [N/m/?] (NEW) No
LED support for the Bachmann OT200 (LEDS_OT200) [N/m/y/?] (NEW) No
InfiniBand SCSI RDMA Protocol target support (INFINIBAND_SRPT) [N/m/?] (NEW) No
Support for rtllib wireless devices (RTLLIB) [N/m/?] (NEW)
Android Drivers (ANDROID) [N/y/?] (NEW) No
Fujitsu Tablet Extras (FUJITSU_TABLET) [N/m/y/?] (NEW) No
Fujitsu-Siemens Amilo rfkill support (AMILO_RFKILL) [N/m/?] (NEW) No
AMD IOMMU Version 2 driver (EXPERIMENTAL) (AMD_IOMMU_V2) [N/m/y/?] (NEW) No
Btrfs with integrity check tool compiled in (DANGEROUS) (BTRFS_FS_CHECK_INTEGRITY) [N/y/?] (NEW) No
NFS server manual fault injection (NFSD_FAULT_INJECTION) [N/y/?] (NEW) No
Kernel memory leak detector (DEBUG_KMEMLEAK) [N/y/?] (NEW) No
NMI Selftest (DEBUG_NMI_SELFTEST) [N/y/?] (NEW) No
Serpent cipher algorithm (x86_64/SSE2) (CRYPTO_SERPENT_SSE2_X86_64) [N/m/y/?] (NEW) 
No

Continuing,
make-kpkg clean
fakeroot make-kpkg -j7 --initrd --revision=3.3.0 --append-to-version=amd64 kernel_image kernel_headers  

The build takes a LONG time. Once it's done:

mv ../linux*3.3.0*.deb .
sudo dpkg -i *.deb

Done.

Linux tantalum 3.3.0-amd64 #1 SMP Tue Mar 20 06:29:46 EST 2012 x86_64 GNU/Linux

---

111. Ecce (nwchem) on Debian, and ROCKS/Centos

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

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

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

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)

Pay attention to the fine print

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:

ECCE: homo (benzene)

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

/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

and

ecce/apps/siteconfig/jndi.properties 

In particular, I had to change references to eccetera.emsl.pnl.gov.