380. Modifying NWChem code without a full recompile

This isn't a secret trick or anything, but may still not be immediately obvious to most people.

A full compilation of NWChem can easily take 20-40 minutes, depending on your build machine.

Sometimes you need to make changes to the source code, e.g. if you want to use GabEdit to analyse output -- ECCE is a fantastic piece of software and is great for managing computations, but GabEdit has implemented some pretty interesting routines for orbital analyses. In order for you to be able to reliably import NWChem output into GabEdit you need to modify a handful of fortran files.

See e.g. http://verahill.blogspot.com.au/2013/02/3xx-modifying-nwchem-611-to-work-with.html for patching NWChem, and http://verahill.blogspot.com.au/2012/11/visualising-nwchem-output-with-gabedit.html for how to run your nwchem jobs and how to visualize them in gabEdit (you need to explicitly define your basis sets).

Angelo Rossi made this comment:

Hello:

Thank you so much for this valuable information.

But under the heading of "Compilation" above, the directions lead to a pointer to compile the entire NWChem source. But only one or two subroutines are modified. Shouldn't there be a more surgical way of proceeding after making the suggested changes? Actually this would make a great separate post. That is, provide a procedure to recompile and link when small changes to NWChem are made. I've done this, but I can't remember.

Kind regards,

Angelo

The answer was on this page: http://xray.isc.kharkov.com/ext_docs/NWChem/prog/node12.html
So here we go:

---

Partial recompile/relinking of NWChem

1. Environmental variables
Define your environmental variable like you would during a normal compile

export LARGE_FILES=TRUE
export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=`pwd`
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES="all python"
export PYTHONVERSION=2.7
export PYTHONHOME=/usr
export BLASOPT="-L/opt/openblas/lib -lopenblas"
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/usr/lib/openmpi/lib
export MPI_INCLUDE=/usr/lib/openmpi/include
export LIBRARY_PATH=$LIBRARY_PATH:/usr/lib/openmpi/lib:/opt/acml/acml5.2.0/gfortran64_int64/lib:/opt/openblas/lib
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
export FC=gfortran

2. Run make in modified directories
In the GabEdit example we made changes to files in src/ddscf, src/nwdft/scf_dft, and src/mcscf

cd $NWCHEM_TOP/src/ddscf
make
cd $NWCHEM_TOP/src/nwdft/scf_dft
make
cd $NWCHEM_TOP/src/mcscf
make

3. Run make link in the src directory

cd $NWCHEM_TOP/src
make link

4. Do your usual post-compilation memory magic

cd $NWCHEM_TOP/contrib
./getmem.nwchem

Done!

---

This all in all took around 6 seconds instead of 30-odd minutes.

379. [Solved] Debian Wheezy -- Thinkpad SL410: reboot instead of shutdown when on battery

Solved: it was down to laptop-mode-tools, which I installed as part of this post two weeks ago. I uninstalled that package and my laptop is shutting down properly again.

Original post:
Since today[*], with Debian Wheezy stock kernel (3.2), my Thinkpad SL410 reboots instead of shutting down when it's running on battery. Works fine when on mains power. During shutdown it says 'Will now halt', then reboots.

Similar to what's seen in this thread: http://forums.debian.net/viewtopic.php?f=7&t=86316&start=15, but shutting down X seems to have no effect. Googling seems to yield a lot of hits for thinkpads and ideapads.

Annoying and no idea why.

The support for SL410 under Debian Wheezy has actually gotten worse during the past year -- now 'mute' doesn't work anymore, and from today it doesn't shutdown on issuing e.g. sudo shutdown -h now.Finally, recently the behaviour of the kernel (3.8) has lead to slowdowns on computer with i915 (intel) graphics, which would include a majority of laptops (a fix is on the way though).

Looking at /var/log/apt/history.log my kernel was updated (not a new version, so a bit confused), two days ago. Nothing else looks important enough.

[*] Given that removing laptop-mode-tools solved it, and that I installed that on the 23rd of March, I must've been running my laptop off of mains power for the past two weeks...alternatively, newer kernels fix this (supposed to be due to the combination of laptop-mode-tools and an apci bug in the kernel) since I've been running 3.7.10 for the past two weeks, and only switched back to 3.2 yesterday.

378. Briefly: Windows/Dialogues that are too large for a laptop screen

Short post which is probably just revealing something which a lot of people are already familiar with.

A really annoying thing with Evolution (and ECCE as well, actually) is that it doesn't play well with notebook screen. I have a Lenovo Thinkpad SL410 which has a 1366x768 screen and this is what I see when e.g. editing an account in Evolution:

Note the lack of buttons to click -- the Close and Apply dialogues don't show on the screen

I might be imagining, but I get the impression that GNOME projects don't like you to resize windows -- and you can't resize this dialogue.

The workaround:
In gnome, use alt+click and drag to move the window so that the buttons are revealed.