Date: Thu, 7 Jun 2012 17:14:58 -0400 (EDT)
From: Jun-Hui Zhao 
To: Jun-Hui Zhao 
Cc: Berengere Parise , Tyler Bourke , pmailhot@cfa, smamiriad@cfa.harvard.edu
Subject: Re: Miriad on Ubuntu for SMA data reduction

Hints for Miriad installation on Ubuntu:
http://www.cfa.harvard.edu/sma/miriad/download/QandA/ubuntu2012.html

On Thu, 7 Jun 2012, Jun-Hui Zhao wrote:

>
>
> Dear Berengere,
>      Somehow, the new dell comes with Ubuntu 10.10 32bit OS.
> Pat has asked our purchasing department and Dell to change the OS to
> 64bit. While waiting for 64bit software, I have debugged
> SMA Miriad with Ubuntu 10.10 32bit OS.
>      We have made a binary release beta 1.4.4 for Ubuntu 10 32bit
> (http://www.cfa.harvard.edu/sma/miriad/download/) and installation
> notes. The 32bit binary package should be fine with the current SMA
> data size (2Gbyte) but will be problem for a larger size data file.
>      You may try to compile the 32bit binary package on your
> Ubuntu 64 bit computer. The codes now should work for Ubuntu 64 bit
> computer too. Please let us know if you run into any problems.
> Also here is a webpage with some hints for Miriad installation on Ubuntu.
>      Jun-Hui
>
> On Wed, 6 Jun 2012, Jun-Hui Zhao wrote:
>
> >
> > Dear Berengere,
> >      Thank you for trying to install SMA Miriad on ubuntu.
> > Your error messages are valuable, which confirm that there
> > are some problems of the SMA code in Miriad with ubundu.
> >      Do you use ubuntu version 10 and higher?  We have seen
> > similar error report from our users who
> > tried ubuntu 10.?? although some of users reported they have
> > successfully used the SMA code with the older version ubuntu.
> >      A new Dell computer with ubuntu just arrived. We have
> > arranged our system adm to setup the new machine and will
> > debug the codes with ubuntu.
> >      We will contact you as soon as we have a solution.
> >      Jun-Hui
> >
> > On Wed, 6 Jun 2012, Berengere Parise wrote:
> >
> > > Dear Jun-Hui,
> > >
> > > I have tried to install the MiriadBeta version on my Ubuntu 64-bit computer.
> > > I changed the default compiler to gfortran.
> > > The compilation went through, although with some error messages (see
> > > below the history).
> > > But when launching miriad and  reading in the data, I get a similar
> > > error message compared to
> > > yesterday:
> > >
> > > Miriad% smalod in=rawdata/110622_03:13:48 out=110622a rxif=0 sideband=0
> > > nscans=1
> > > SmaLod: version 3.7-beta 25-May-2012
> > > ### Warning [smalod]:  #############################################
> > > ### Warning [smalod]:  Miriad needs updating for SMA data reduction.
> > > ### Warning [smalod]:  #############################################
> > > ### Warning [smalod]:  Number of antennas exceeded the limit 8.
> > > Loading standard SMA data ...
> > > User's input vSource = 0.000000 km/s
> > > User's input RestFrequency =
> > >
88878069510705861413187878106510023551843021571438998157738321667215620738916908041426746766699315571143877093705489184988891277194328249722
35716951376704502669292536153566255040247434261242623862057516265580053298344488998881568936278755777720514248704.000000
> > > GHz
> > > Processing file rawdata/110622_03:13:48/
> > > *** buffer overflow detected ***: smalod terminated
> > > ======= Backtrace: =========
> > > /lib/libc.so.6(__fortify_fail+0x37)[0x2b25cad7d7e7]
> > > /lib/libc.so.6(+0xfe6a0)[0x2b25cad7c6a0]
> > > /aux/pc166a/bparise/app/smaMiriadBeta/miriad_cvs/lib/linux/libmir.so(rsmir_Read+0x16b)[0x2b25c1ab984b]
> > > ======= Memory map: ========
> > > 00400000-0040a000 r-xp 00000000 08:06 43134399
> > > /aux/pc166a/bparise/app/smaMiriadBeta/miriad_cvs/bin/linux/smalod
> > > 00609000-0060a000 r--p 00009000 08:06 43134399
> > > /aux/pc166a/bparise/app/smaMiriadBeta/miriad_cvs/bin/linux/smalod
> > > 0060a000-0060b000 rw-p 0000a000 08:06 43134399
> > > /aux/pc166a/bparise/app/smaMiriadBeta/miriad_cvs/bin/linux/smalod
> > > [...]
> > >
> > >
> > > Do you have any idea where the problem is? I am missing an update
> > > somewhere?
> > > In the compilation message, I spotted:
> > > [...]
> > > Found 420 entries in MIRBIN
> > > Found 2 / 372 binaries missing:
> > > atlod
> > > velplotc
> > > [...]
> > >
> > > Is smalod related to atlod, therefore not working?
> > >
> > > Thanks!
> > >
> > > Berengere
> > >
> > >
> > > PS: FYI, the full log of the compilation:
> > >
> > >
> > > pc166 47: ./install.miriad
> > > MIRIAD installation 3-nov-2010, for linux
> > > Running configure, telescope=sma, logfile in configure.LOG:
> > > OK.
> > > Using internal build with
> > > mirroot=/aux/pc166a/bparise/app/smaMiriadBeta/miriad_cvs
> > > mir.mkdirs /aux/pc166a/bparise/app/smaMiriadBeta/miriad_cvs
> > > Fixing gidriv.f from INTEGER*4 PIXMAP to INTEGER*8 PIXMAP for 64 bit
> > > Fixing ppdriv.f from INTEGER*4 PIXMAP to INTEGER*8 PIXMAP for 64 bit
> > > Fixing wddriv.f from INTEGER*4 PIXMAP to INTEGER*8 PIXMAP for 64 bit
> > > make_miriad_starts: using
> > > MIR=/aux/pc166a/bparise/app/smaMiriadBeta/miriad_cvs
> > > CARMA style
> > >
> > > MIRIAD version < beta 1.4.4. 2012-05-30 for handling SMA 4GHz and 2GHz
> > > mode data >  [CVS] loaded from
> > > MIR=/aux/pc166a/bparise/app/smaMiriadBeta/miriad_cvs
> > >   Optimized for telescope=sma
> > >
> > > Using gfortran compiler for linux
> > > Making the MIR tree writable
> > > Installing scripts....
> > > Yuck, resetting xbit in MIRBIN
> > > Warning: you have /usr/lib/libbsd-compat.a
> > > Warning: you do not have /usr/lib/libbsd.a
> > > Borrowing the system version of libreadline.a for linux from /usr/lib64
> > > LIB: linpack wcslib subs
> > > /aux/pc166a/bparise/app/smaMiriadBeta/miriad_cvs/lib/linux
> > > /aux/pc166a/bparise/app/smaMiriadBeta/miriad_cvs
> > > /aux/pc166a/bparise/app/smaMiriadBeta/miriad_cvs
> > > PGM: prog wip rad
> > > Compiling UVIO:
> > > Output file of module in already present; existing file overwritten.
> > > Output file of module out already present; existing file overwritten.
> > > Output file of module vis already present; existing file overwritten.
> > > Output file of module line already present; existing file overwritten.
> > > Output file of module select already present; existing file overwritten.
> > > Output file of module window already present; existing file overwritten.
> > > Output file of module stokes already present; existing file overwritten.
> > > Output file of module region already present; existing file overwritten.
> > > Output file of module server already present; existing file overwritten.
> > > Output file of module device already present; existing file overwritten.
> > > Output file of module options already present; existing file overwritten.
> > > LOCAL install patches for CVS
> > > Updating /aux/pc166a/bparise/app/smaMiriadBeta/miriad_cvs with UMD
> > > patches for version miriad_cvs
> > > Keeping log in
> > > /aux/pc166a/bparise/app/smaMiriadBeta/miriad_cvs/tmp/mir.genman.log
> > > Sometimes this program can hang on linux man page updates.....
> > > [1] 5317
> > > Could not find libforms.a to compile velplotc, trying system libforms.so
> > > Warning: problems compiling velplotc
> > > mv: cannot stat `velplotc': No such file or directory
> > > Compiling rpfits
> > > rm -f *.o core test.tmp
> > > Compiling atnf code: atlod
> > > Problems compiling ATLOD
> > > mv: cannot stat `atlod': No such file or directory
> > > Checking binaries:
> > > Found 420 entries in MIRBIN
> > > Found 2 / 372 binaries missing:
> > > atlod
> > > velplotc
> > > The ones you should not worry about are: atlod, xcorf and velplotc.
> > > Running basic: OK
> > > Running xyio: OK
> > > Running uvio: OK
> > > Running map: OK
> > > Running rad: OK
> > > Creating logfile for baseline check:
> > > Record date and version etc.
> > > few SANITY TESTS:
> > > Imgen: version 27-oct-08
> > > Endianism correct.
> > > === testing pgplot/null:
> > > ImPlot version 1.0 02-Aug-99
> > >  Plots multiple panels for a Miriad Image
> > > Map:    1no axis 3
> > > === testing pgplot/ps:
> > > ImPlot version 1.0 02-Aug-99
> > >  Plots multiple panels for a Miriad Image
> > > Map:    1no axis 3
> > > === testing pgplot/gif:
> > > ImPlot version 1.0 02-Aug-99
> > >  Plots multiple panels for a Miriad Image
> > > Map:    1no axis 3
> > >
> > >
> >
>