26 May 2015

607. Ping...Topspin and ADF work on debian jessie

My blog post productivity has been getting increasingly poor over the past year and a half, with a precipitous dip occurring at the beginning of this year. The dip is due to teaching and research, and the slow but steady decline preceding it is due to parenthood (the older the little one gets, the less time -- and inclination! -- I have to do extra work. Toddlers can be so much fun.).

I've got a few posts that need a bit of polishing before I publish ('how to set up your own DNS server' and 'how to set up your own mail server' are two examples), but until then, I'll seed your google search results with the following information about something completely different:

* Bruker Topspin 3.2 (https://www.bruker.com/products/mr/nmr/nmr-software/software/topspin/overview.html) -- the NMR program, not the table tennis game -- installs fine on Debian Jessie 64 bit (the only version we tried). Note that:
** you'll need java
** you'll need the 32 bit package with libXtst.so.6, not the 64 bit package. It can be installed via apt-get install libxtst6:i386
** you'll need to enable the root account if you haven't already (the easiest way to do that is to do sudo passwd root, set a password and you're good to go)

* The trial version of the Amsterdam Density Functional package (ADF; http://www.scm.com/Downloads/2014) installs and runs fine* on one of my Debian Jessie 64 bit nodes. 

Installation was quick and painless. I downloaded the package using the instructions in the email, copied the .tgz file to my node, ssh:d with X enabled (ssh -XC) to allow for interactive activation/registration, and to be able to use adfjobs (to draw molecules and set up jobs), and to be able to use adfview.

I untared the adf file:
tar xvf adf2014.07.pc64_linux.intelmpi.tgz

I then moved the folder to /opt and took ownership of it:
sudo mv adf2014.07 /opt/
sudo chown $USER:$USER /opt/adf2014.07 -R

I edited /opt/adf2014.07/adfrc.sh to read:
ADFHOME=/opt/adf2014.07

And then sourced it and ran adfjobs:
source adfrc.sh
bin/adfjobs

I was then asked to provide the username and password from my email, and from that point on it was just a matter of using the program (which has it's own quirks ).

*by default only six cores on a hex core i7-3770k are used. To force 12 cores (hyperthreading) you need to explicitly tell ADF to do so. The manual says not to, however. I haven't done any performance tests, BUT without specifying 12 cores the node is only running at half load.

12 January 2015

606. Downloading programs from iview (Australian Broadcasting Corporation): python-iview

 I did this on debian jessie.

I found the Ep 7 Season 2 episode of The Checkout so well worth watching that I wanted to keep a copy of it, which lead me to search for ways of downloading programs from iview.

Get python-iview from https://github.com/vadmium/python-iview. You can try this direct link: https://github.com/vadmium/python-iview/archive/master.zip

Then unzip and install (you might need to install some of the dependencies listed on the github page first):
me@niobium:~/tmp/python-iview/python-iview-master$ sudo python3 setup.py install
running install
running build
running build_py
running build_scripts
running install_lib
creating /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/comm.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/flvlib.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/config.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/hds.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/parser.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/fetch.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/__init__.py -> /usr/local/lib/python3.4/dist-packages/iview
copying build/lib/iview/utils.py -> /usr/local/lib/python3.4/dist-packages/iview
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/comm.py to comm.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/flvlib.py to flvlib.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/config.py to config.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/hds.py to hds.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/parser.py to parser.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/fetch.py to fetch.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/__init__.py to __init__.cpython-34.pyc
byte-compiling /usr/local/lib/python3.4/dist-packages/iview/utils.py to utils.cpython-34.pyc
running install_scripts
copying build/scripts-3.4/iview-gtk -> /usr/local/bin
copying build/scripts-3.4/iview-cli -> /usr/local/bin
changing mode of /usr/local/bin/iview-gtk to 755
changing mode of /usr/local/bin/iview-cli to 755
running install_data
copying iview-gtk.desktop -> /usr/share/applications
running install_egg_info
Writing /usr/local/lib/python3.4/dist-packages/iview-0.2.egg-info

Start it from within gnome, select your show and download:
 Easy.

08 January 2015

605. Posting your own academic articles on your website (self-archiving)

I've been meaning to put copies of my own articles on my departmental website, but haven't had time to look into the legal aspects until now.

The publishers that matter to me in order are Wiley, ACS, RSC, Elsevier, and Taylor and Francis.

Here are their policies:

Wiley (also see this)
Under Wiley copyright, authors are permitted to self-archive the peer-reviewed (but not final) version of a contribution on the contributor's personal website, [..], subject to an embargo period of 12 months for scientific, technical, and medical (STM) journals [..] following publication of the final contribution. Authors should be aware that Wiley’s society partners set policies independently, and authors should refer to individual journal pages as the authority on copyright policy.
Summary: you can post the article version containing improvements following peer-review twelve months after it was published online (my interpretation), but you can't post the galley proof, on your own website.

Elsevier
Accepted Author Manuscript (AAM) Definition: An accepted author manuscript (AAM) is the author’s version of the manuscript of an article that has been accepted for publication and which may include any author-incorporated change s suggested through the processes of submission processing, peer review, and editor-author communications. AAMs do not include other publisher value-added contributions such as copy-editing, formatting, technical enhancements and (if relevant) pagination. Elsevier's AAM Policy: Authors retain the right to use the accepted author manuscript for personal use, internal institutional use and for permitted scholarly posting provided that these are not for purposes of commercial use or systematic distribution. [..] Permitted scholarly posting: Voluntary posting by an author on open websites operated by the author or the author’s institution for scholarly purposes, as determined by the author, or (in connection with preprints) on preprint servers.
Summary: you can post the article version containing improvements following peer-review on your own website as long as it's not for commercial purposes.

Royal Society of Chemistry (RSC)
When the author accepts the exclusive Licence to Publish for a journal article, he/she retains certain rights concerning the deposition of the whole article. He/she may: [..] Make available the PDF of the final published article via the personal website(s) of the author(s) or via the Intranet(s) of the organisation(s) where the author(s) work(s). No embargo period applies. [..] Deposition of the article on any website acting as a collection of personal articles from multiple scientists is explicitly prohibited.
Surprisingly, it sounds like it's actually OK to upload the version which is found on the RSC website -- which sounds too good to be true. Be your own judge.

American Chemical Society (ACS) (but also this)
Note that ACS does not grant permission for these materials or provide the following:
However, on page 6 here:
6. Posting Submitted Works on Websites and Repositories: A digital file of the Submitted Work may be made publicly available on websites or repositories (e.g. the Author’s personal website, preprint servers, university networks or primary employer’s institutional websites, third party institutional or subject-based repositories, and conference websites that feature presentations by the Author(s) based on the Submitted Work) under the following conditions: * The Author(s) have received written confirmation (via letter or email) from the appropriate ACS journal editor that the posting does not conflict with journal prior publication/embargo policies (see http://pubs.acs.org/page/policy/prior/index.html ) * The posting must be for non-commercial purposes and not violate the ACS' "Ethical Guidelines to Publication of Chemical Research" (see http://pubs.acs.org/ethics ). * If the Submitted Work is accepted for publication in an ACS journal, then the following notice should be included at the time of posting, or the posting amended as appropriate: "This document is the unedited Author’s version of a Submitted Work that was subsequently accepted for publication in [JournalTitle], copyright © American Chemical Society after peer review. To access the final edited and published work see [insert ACS Articles on Request author-directed link to Published Work, see http://pubs.acs.org/page/policy/articlesonrequest/index.html ]."
My reading is that it's only ok to post a pre-review version, and only if the above note is included, and only if you have received explicit permission from the editor of the journal. The ACS, which should represent us chemists, have by far the most draconian rules.

[Note that section 7 (which I haven't reproduced) covers 'accepted and published works', which is only permitted in case posting is mandated and only under certain conditions.]

See also item 19 here: http://pubs.acs.org/page/copyright/journals/faqs.html#
 It says pretty much the same thing. Note also that they tell you that you're allowed to link to the journal website, and that you're allowed to use the DOI.

How very generous.

Taylor and Francis
Author’s Original Manuscript (AOM) This is your original manuscript (often called a "preprint"), and you can share this as much or as little as you like. If you do decide to post it anywhere, including onto an academic networking site, we would recommend you use an amended version of the wording below to encourage usage and citation of your final, published article. Accepted Manuscript (AM) As a Taylor & Francis author, you can post your Accepted Manuscript (AM) on your departmental or personal website at any point after publication of your article (this includes posting to Facebook, Google groups, and LinkedIn, and linking from Twitter). Version of Record (VoR) This is your published article. We recommend that you include a link to the VoR from anywhere you have posted your AOM or AM using the text above. Please do not post the PDF of the VoR unless you have chosen to publish your article open access. This also applies to any author who has published with us in the past.
Summary: you can post the accepted manuscript, but not the journal version.