340. Issues when compiling Nwchem 6.1.1 -- missing *.fh in src/include

The problem:
If you modify the nwchem sources, build, do a make realclean and then pack them up to export your patched sources to other nodes you might find that compiling doesn't work that well, yielding errors such as (I'll list them all to help google):

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/stdio.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(basis.o)'.  Stop.
make: *** [libraries] Error 1

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/nwc_const.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(basis.o)'.  Stop.
make: *** [libraries] Error 1
nwchem.F:3:0: fatal error: errquit.fh: No such file or directory
compilation terminated.
stubs.F:15:0: fatal error: errquit.fh: No such file or directory

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/errquit.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(basis.o)'.  Stop.
make: *** [libraries] Error 1

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/util.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(bas_input.o)'.  Stop.

and

/opt/nwchem/nwchem-6.1.1-src_mod/src/include/util.fh:1:0: fatal error: printlevels.fh: No such file or directory
compilation terminated.
make[1]: *** [/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(bas_input.o)] Error 1
make[1]: *** Waiting for unfinished jobs....

and

basisP.F: In function 'nbf_from_ucont':
basisP.F:427:0: warning: '__result_nbf_from_ucont' may be used uninitialized in this function [-Wmaybe-uninitialized]
make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[1]: warning: -jN forced in submake: disabling jobserver mode.
make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/msgids.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(geom.o)'.  Stop.

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/bitops.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(pstat_alloc.o)'.  Stop.

and

In file included from pstat_alloc.F:12:0:
/opt/nwchem/nwchem-6.1.1-src_mod/src/include/bitops.fh:11:0: fatal error: bitops_decls.fh: No such file or directory
compilation terminated.
make[1]: *** [/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(pstat_alloc.o)] Error 1

and

In file included from pstat_alloc.F:12:0:
/opt/nwchem/nwchem-6.1.1-src_mod/src/include/bitops.fh:12:0: fatal error: bitops_funcs.fh: No such file or directory
compilation terminated.
make[1]: *** [/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(pstat_alloc.o)] Error 1

and

make[2]: warning: -jN forced in submake: disabling jobserver mode.
make[2]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/itri.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwcutil.a(sym_sh_pair.o)'.  Stop.
make[2]: *** Waiting for unfinished jobs....

and

make[2]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/bgj.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libnwints.a(exactd_mem.o)'.  Stop.

and

make[1]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/numerical_constants.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/librimp2.a(rimp2_v_e2.o)'.  Stop.

and

make[2]: *** No rule to make target `/opt/nwchem/nwchem-6.1.1-src_mod/src/include/util_sgroup.fh', needed by `/opt/nwchem/nwchem-6.1.1-src_mod/lib/LINUX64/libdntmc.a(gibbs.o)'.  Stop.

and

nwchem.F:11:0: fatal error: bgj_common.fh: No such file or directory

---

Solution:
This has been mentioned before on the nwchem forum, but not in explicit enough detail.
The solution is to copy a series of files from src/util and to remove make realclean from your build instructions (or at least do the copying after the make realclean step).

Copy these files

cp src/util/stdio.fh src/include/
cp src/util/nwc_const.fh src/include/
cp src/util/errquit.fh src/include/
cp src/util/util.fh src/include/
cp src/util/printlevels.fh src/include/
cp src/util/msgids.fh src/include/
cp src/util/bitops.fh src/include/
cp src/util/bitops_decls.fh src/include/
cp src/util/bitops_funcs.fh src/include/
cp src/util/itri.fh src/include/
cp src/util/bgj.fh src/include/
cp src/util/numerical_constants.fh src/include/
cp src/util/util_sgroup.fh src/include/
cp src/util/bgj_common.fh src/include/

Then build, using e.g.

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/openblas/lib
export LIBMPI="-lmpi -lopen-rte -lopen-pal -ldl -lmpi_f77 -lpthread"
cd $NWCHEM_TOP/src
make nwchem_config
make FC=gfortran 1>make.log 2>make.err
export FC=gfortran
cd ../contrib
./getmem.nwchem

339. Compiling ncdu on ROCKS 5.4.3/Centos 5.6

du is nice, but ncdu gives a better overview. Nothing odd about building it though:

mkdir ~/tmp
cd ~/tmp
wget http://dev.yorhel.nl/download/ncdu-1.9.tar.gz
tar xvf ncdu-1.9.tar.gz
cd ncdu-1.9/
sudo mkdir /share/apps/tools/ncdu -p
sudo chown $USER /share/apps/tools/ncdu
./configure --prefix=/share/apps/tools/ncdu
make
make install
echo 'export PATH=$PATH:/share/apps/tools/ncdu/bin' >> ~/.bashrc
source ~/.bashrc

Start by running

ncdu

338. Annotating PDFs in linux -- revisited. Still no obvious solution

Update 28/02/2014: I've had a look at I, Librarian and Master PDF Editor here: http://verahill.blogspot.com.au/2014/02/558-more-options-for-pdf-annotation.html

There are a a few main reasons why even platform agnostic people have trouble moving to linux. One of them is poor compatibility of open solutions with MS Office (incompatibility between MS Equations and libre/openoffice is my main gripe, and some may find the lack of native EndNote an issue), and one quite particular to academics is the lack of proper pdf annotation (traditionally you edit your galley proofs by making annotations on the pdf -- my latest paper from Wiley came back with a doc file though, which was a bit surprising, but promising)

I've gotten by in the past by using 'pdf x-change viewer', which is a windows program, under wine. However, there are a lot of things I don't like about that solution, and the search for a native solution has continued to the point where I'm willing to throw money at it.

Why the exercise is unfair
The problem is that our definition of what 'works' and what doesn't is based on what we expect it to look like -- and that's based on our experience. I have colleagues that consider libreoffice 'crap' because it behaves or looks different from MS Office. While I agree that it's not viable as a replacement to office when collaborating with Office users who refuse to use libreoffice, it works fine if libreoffice is all you use. Anyway, it's unfair. Same goes for pdf annotation -- we expect it to look and function like adobe acrobat, simply because that's what we're used to. Any deviation is akin to a bug.

So keep that in mind when I write off some of the alternatives that actually do work -- just not in the way I expect them to.

I've found a lot of people (online) swearing by e.g.  Xournal, so even if it doesn't work for me, you may decide differently.

Commercial software in academia

I don't normally like buying software which is critical to my work. There are many reasons for it, and cost is only a minor one (although I don't like spending tax payer money on overpriced software).

Instead, if the software is critical to the science that I'm doing, I prefer to write my own algorithms in octave or python, and if it's a bit more peripheral I'm still wary of becoming reliant on a piece of software that may one day disappear -- either because I'm forced to upgrade through planned obsolescence, or because the company goes bankrupt/discontinues the software without releasing it as open source.

I cannot recommend Mendeley. And that's for two reasons:
1. it installs a list file in /etc/apt/sources.list.d/ without asking. That's the way malware (and google...) behaves!
2. There's plenty of mention about how it's 'free', but the free version is very restrictive, and if you create a private group you're stuck with a nagging message saying that you "must" upgrade if you want to add more users/groups. A simple one-time message would suffice.

Maybe I'm overreacting, but I don't appreciate this behaviour at all. Beyond that the annotation function works fine, so you decide for yourself.

Anyway, here's a short list of programs I've considered:

(and FOSS= Free and Open Source Software)

---

Evince
Evince is FOSS and now (since when?) supports adding annotations. It's not working very well (sometimes doesn't save annotation, slow), and you can't delete annotations, so be careful what you're saving.

Evince

pdfedit
pdfedit is another standard linux package. It does highlighting well, but annotates by adding text on top of the document -- not as a sticky note. FOSS.

pdfedit

flpsed
Does annotation, but as text superimposed on the pdf document, not as a collapsible sticky note. FOSS..

Qoppa PDF Studio
This is java based, and runs on Linux. I must already now say that there's one aspect of it that I really don't like: it's available in a Standard and a Professional version. That's the kind of artificial crippling of software that Microsoft likes to engage in, but I though we were beyond that on Linux...the price, $89, is too steep for something that I'd only use for annotations. Note also that the trial version puts a big nasty watermark over everything -- but you can hardly fault them for that, since it's not free. Closed source. Commercial.
Other than that it works, although it's not as pretty as mendeley.

Qoppa PDF studio

Xournal
Xournal can export annotated PDFs, but it doesn't do annotation in the same way as the other programs i.e. using sticky notes. Instead you can simply add text on top of the pdf, and it doesn't really do it for me. FOSS..

Xournal -- the annotations are not easy to spot

Whyteboard
It draws on top of PDF using imagemagick. FOSS.

Mendeley
While it's meant mainly for reference management, this does proper PDF annotation as well, and is platform agnostic. However, it is closed source, requires you to log in (even if you're using the desktop client) every time you use it, and needs you to explicitly keep documents (at least their titles etc.) out of the shared web catalogue. Other than that the pdf annotation works beautifully. I get really annoyed by the requirement to log in even when working offline though. It's free in the sense of gratis though -- but only up to 100 Mb of shared document space, you can only have one private group, and it can only have two members (+you). If you want more you need to pay (see e.g. here).
In practical terms, it seems to use GMT to time stamp annotationsand I haven't found an obvious way
of changing that (without going online). Also, it installs a file into /etc/apt/sources.list.d/ without asking.

Mendeley

Misc
Other 'solutions' that pop up is Okular which work in a roundabout way -- i.e the annotations aren't stored as part of the pdf. Again, it looks pretty, but the annotations are not exported with the pdf.
UPDATE: Note that this doesn't seem to be an issue anymore -- see comments below and this post: https://groakat.wordpress.com/2013/08/27/annotating-pdf-with-okular/ -- note that the new version is NOT in either wheezy or jessie i.e. they won't work.

okular

I tried FoxIt reader as well which claims to do annotation but doesn't on Linux -- and the windows version is not functional under linux/wine.

PDF X-change viewer/wine pops up so often as a suggested solution that it's beginning to look like spam. It does work though:

PDF Xchange viewer

An online only option is http://www.pdfescape.com -- but the paranoid part of me doesn't like the idea of uploading documents that are meant to be private.