Moses-support Digest, Vol 90, Issue 3

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Today's Topics:

1. Re: yum-installed Boost environment variables for MGIZA++ (Gideon)
2. Installation problems (Jes?s Alberto Alonso Nanclares)
3. 2nd CFP SIGIR Medical Information Retrieval Workshop
(Lorraine Goeuriot)


----------------------------------------------------------------------

Message: 1
Date: Wed, 2 Apr 2014 15:34:22 +0200
From: Gideon <gidi8ster@gmail.com>
Subject: Re: [Moses-support] yum-installed Boost environment variables
for MGIZA++
To: Hieu Hoang <hieuhoang@gmail.com>
Cc: moses-support@mit.edu
Message-ID:
<CALP7mvkt+RJxGPasmmmFbwcF77NFxZrzPmq-9ZDBaHrLzFCkvQ@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Dear Hieu Hoang

Thank you for you reply. I made some changes:

- uncommented out the top variables and commented out the Mac ones
- set BOOST_ROOT to /home/kotzegj/tools/boost_1_54_0 and BOOST_LIBRARYDIR
to /usr/lib64
- set SRC_DIR to /home/kotzegj/tools/mgiza/mgizapp/src

and ran ./compile.sh.

Two issues remain so far:

1) I can't find any MGIZA++/mgiza++/etc. binary (find . -name). Is there a
way to test if MGIZA++ has installed correctly? I did not notice any other
error messages, apart from the files the script tries to remove at the
beginning, which do not exist.

2) When compiling, this warning pops up all the time (you are probably
aware of it)

/usr/include/c++/4.8.2/backward/backward_warning.h:32:2: warning: #warning
This file includes at least one deprecated or antiquated header which may
be removed without further notice at a future date. Please use a
non-deprecated interface with equivalent functionality instead. For a
listing of replacement headers and interfaces, consult the file
backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]

So I assume this is OK for now but there needs to be an update in the
future?

and (just to test)

2) [kotzegj@lt-2433323 manual-compile]$ ./mkcls
ERROR: can not open file train.
Error: Could not read the file 'train'.

But perhaps this is the default?

3) svn checkout http://svn.code.sf.net/p/mgizapp/code/trunk mgizapp-code
--> did not work (timeout). I downloaded 0.7.3 from here instead:
http://www.kyloo.net/software/doku.php/mgiza:overview

svn: E000110: Unable to connect to a repository at URL '
http://svn.code.sf.net/p/mgizapp/code/trunk'
svn: E000110: Error running context: Connection timed out

Thank you for your time.

Best regards,

Gideon



---
gidi8ster@gmail.com
www.gideonkotze.nl
+27 78 739 8923 (Mobile)


On Wed, Apr 2, 2014 at 2:38 PM, Hieu Hoang <hieuhoang@gmail.com> wrote:

> the cmake build system on mgiza is difficult to use.
>
> I create an alternative compile script for mgiza. If you've download mgiza
> via svn, you should find my script in
> mgizapp/manual-compile/compile.sh
> Look at it, change the paths for your own needs
>
>
> On 02/04/2014 11:34, Gideon wrote:
>
> Dear Moses support team
>
> I was wondering if MGIZA++ has been test-compiled on a Fedora Linux
> system where Boost has been installed using yum, as I'm encountering some
> problems. I'm working on a Fedora 20 system with x86_64 architecture. So
> far I have done the following:
>
> yum install boost.x86_64
> yum install boost-devel.x86_64 (version 1.54 was installed)
> yum install gcc
> yum install gcc-c++
> yum install gperftools
> Downloaded and installed IRSTLM
> ./bjam --with-irstlm=/home/kotzegj/tools/irstlm-5.80.03 -j4
> --with-boost=/usr/lib64
> export BOOST_ROOT=/usr/lib64
> export
> BOOST_BUILD_PATH=/home/kotzegj/tools/mosesdecoder/jam-files/boost-build
> ./bjam --with-irstlm=/usr/local/irstlm -j4
>
> I have tested Moses with sample-models and it seems OK.
>
> However, MGIZA++ does not find Boost on its own:
>
> -- Could NOT find Boost
> CMake Error at CMakeLists.txt:59 (MESSAGE):
> Boost not found, please set the BOOST_ROOT and BOOST_LIBRARYDIR
> environment
> variables
>
> I have no success with setting either of these variables to:
>
> - /usr/lib64
> - /usr/include
> - /usr/include/boost
> - /home/kotzegj/tools/mosesdecoder/jam-files/boost-build
> etc.
>
> or if I download Boost manually, set the decompressed directory as
> BOOST_ROOT, and symlink lib64 as a child and set that as BOOST_LIBRARYDIR.
> (I've tried all kinds of stuff.)
>
> I have the feeling (after some Googling) that the yum installation does
> not result in the file structure that cmake is looking for, and that
> instead I should try a manual installation. I hope that I'm wrong?
>
> Thank you for your time.
>
> Best regards,
>
> Gideon Kotz?
>
> ---
> gidi8ster@gmail.com
> www.gideonkotze.nl
>
>
>
> _______________________________________________
> Moses-support mailing listMoses-support@mit.eduhttp://mailman.mit.edu/mailman/listinfo/moses-support
>
>
>
> _______________________________________________
> Moses-support mailing list
> Moses-support@mit.edu
> http://mailman.mit.edu/mailman/listinfo/moses-support
>
>
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Message: 2
Date: Wed, 02 Apr 2014 03:02:07 +0200
From: Jes?s Alberto Alonso Nanclares <jealnan@posgrado.upv.es>
Subject: [Moses-support] Installation problems
To: moses-support@mit.edu
Message-ID: <20140402030207.11021elcipx8l9xr@webmail.upv.es>
Content-Type: text/plain; charset="iso-8859-1"


Having some problems with Moses installing. The command I used is:

./bjam --with-srilm=/home/usuario/TA/moses/tools/srilm/
--with-giza=/home/usuario/TA/moses/tools/bin -j2

Thanks in advance!
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Message: 3
Date: Wed, 2 Apr 2014 15:08:05 +0100
From: Lorraine Goeuriot <lorraine.goeuriot@gmail.com>
Subject: [Moses-support] 2nd CFP SIGIR Medical Information Retrieval
Workshop
To: Lorraine Goeuriot <lorraine.goeuriot@gmail.com>
Message-ID:
<CALwc3gjMQ6MPtG30Gp0009MuN5KpPYwCbMKZ25e75kVgvDYhEA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

==============================================
MEDICAL INFORMATION RETRIEVAL (MedIR) WORKSHOP
http://medir.dcu.ie/

At SIGIR 2014, July 11 2014, Gold Coast, Australia
=======================================
Call for Papers (2 & 4 page)
--------------------------------------

**Submission deadline: April 28**

Medical information search refers to methodologies and technologies that
seek to improve access to medical information archives via a process of
information retrieval (IR). Such information is now potentially accessible
from many sources including the general web, social media, journal
articles, and hospital records.

Medical information is of interest to a wide variety of users, including
patients and their families, researchers, general practitioners and
clinicians, and practitioners with specific expertise such as radiologists.
Despite the popularity of the medical domain for users of search engines,
and current interest in this topic within the information retrieval
research community, development of search and access technologies remains
particularly challenging. One of the central issues in medical information
search is diversity of the users of these services. In particular, they
will have varying categories of information needs, varying levels of
medical knowledge, and varying language skills. In addition, the format,
reliability, and quality of biomedical and medical information varies
greatly. A single health record can contain clinical notes, technical
pathology data, images, and patient-contributed histories, and may be
linked by a physician to research papers. The importance of health and
medical topics and their impact on people's everyday lives makes the need
for retrieval of accurate and reliable information especially important.
Determining the likely reliability of available information is challenging.
Finally, as with information retrieval in general, the evaluation of
medical search tools is vital and challenging. For example, there are no
established or standardized baselines or evaluation metrics, and limited
availability of test collections.

This workshop aims to bring together researchers interested in medical
information search with the goal of identifying specific research
challenges that need to be addressed to advance the state-of-the-art and to
foster interdisciplinary collaborations towards the meeting of these
challenges. To enable this, we encourage participation from researchers in
all fields related to medical information search including mainstream
information retrieval, but also natural language processing, multilingual
text processing, and medical image analysis.

Topics of interest include but are not limited to:
- Users and information needs
- Semantics and NLP for medical IR
- Reliability and trust in medical IR
- Personalised search
- Evaluation of medical IR
- Multilingual issues in medical IR
- Multimedia technologies in medical IR
- The role of social media in medical IR

====================================
Paper Submissions
---------------------------
The workshop is now accepting paper submissions. Short papers (4 pages) and
short position papers (2 pages) describing approaches or ideas / challenges
on the topics of the workshop are invited. Submissions should be in ACM
SIGS format. LaTeX and Word templates are available at
http://www.acm.org/sigs/publications/proceedings-templates (for LaTeX, use
the "Option 2" style).

Papers should be anonymised for double blind review and submitted in pdf
format through the EasyChair system
https://www.easychair.org/conferences/?conf=medir2014 no later than
midnight Pacific Daylight Time on April 28, 2014. Submissions will be
reviewed by members of the workshop program committee. Accepted papers will
be included in the SIGIR 2014 Medical Information Search Workshop
proceedings.

====================================
Important Dates
----------------------
April 28, 2014: Deadline for paper submission (midnight Pacific Daylight
Time)
May 10, 2014: Notification to authors
May 17, 2014: Camera-ready papers due
July 11, 2014: Workshop

====================================
Further Information
--------------------------
Further information is available on the workshop website at
http://medir.dcu.ie/ or by emailing the workshop organisers.

====================================
Workshop Organisers
------------------------------
Lorraine Goeuriot, Dublin City University, Ireland
Gareth J.F. Jones, Dublin City University, Ireland
Liadh Kelly, Dublin City University, Ireland
Henning M?ller, University of Applied Sciences Western Switzerland
Justin Zobel, University of Melbourne, Australia
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