[Ifeffit] Installing demeter from source on Yosemite?

George Sterbinsky GeorgeSterbinsky at u.northwestern.edu
Mon Mar 23 11:00:59 CDT 2015


Hi Anders,

Is there a reason you are trying to install from source? Have you tried to
install from macports?

George

On Fri, Mar 20, 2015 at 5:16 PM, Anders Glans <paglans at lbl.gov> wrote:

> Hi again,
>
> I have rebuilt things more carefully but I still have problems.
>
> - I built pgplot following the instructions at
> http://www.iac.es/sieinvens/siepedia/pmwiki.php?n=HOWTOs.PGPLOTMacOSX. It
> works fine and the test produces png files.
>
> - I have been building ifeffit in various ways. The current version of my
> ./configure command looks like this:
> $ ./configure --with-fortran=gfortran --with-pgplot=/usr/local/lib/pgplot
> --with-pgplot-link='-L/usr/local/lib/pgplot -lpgplot -lXaPgplot -lcpgplot'
> CC=gcc-fsf-4.9 CFLAGS=-m64 FFLAGS='-ffixed-line-length-132 -m64'
> LDFLAGS='-L/usr/X11/lib -lX11 -lXt -lXaw3d -I/usr/local/include
> -I/sw10.9/include -L/sw10.9/lib -lpng’
>
> gfortran and gcc are installed via fink. I have also tried Apples stock
> gcc. I have tried with and without the -m64 flags, with just pgplot or by
> also including XaPgplot and cpgplot.
>
> The build seems to include pgplot, part of the output during the make is:
> make[3]: Entering directory '/Users/Anders/ifeffit/ifeffit/src/cmdline'
> gcc-fsf-4.9 -DHAVE_CONFIG_H -I. -I. -I../..     -m64 -c iff_shell.c
> gcc-fsf-4.9  -m64 -L/usr/X11/lib -lX11 -lXt -lXaw3d -I/usr/local/include
> -I/sw10.9/include -L/sw10.9/lib -lpng -o ifeffit  iff_shell.o
> ../lib/libifeffit.a  -L/usr/local/lib/pgplot -lpgplot -lXaPgplot -lcpgplot
> ../../readline/libreadline.a -L/usr/lib -lncurses -L/usr/X11/lib
> -L/sw10.9/lib -L/opt/intel/composer_xe_2015.0.077/compiler/lib
> -L/opt/intel/composer_xe_2015.0.077/mkl/lib
> -L/sw10.9/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.4.0/4.9.2
> -L/sw10.9/lib/gcc4.9/lib/gcc/x86_64-apple-darwin13.4.0/4.9.2/../../.. -lX11
> -lXt -lXaw3d -lpng -lgfortran -lSystem -lgcc_ext.10.5 -lquadmath -lm
> make[3]: Leaving directory '/Users/Anders/ifeffit/ifeffit/src/cmdline’
>
> The test of ifeffit still produces:
> $ ifeffit
>  Ifeffit   1.2.12 Copyright (c) 2005 Matt Newville, Univ of Chicago
>                 command-line shell version 1.1 with GNU Readline
> Ifeffit> testplot
>  %PGPLOT, Unrecognized device type
>  %PGPLOT, Invalid device specification: /AQT
>  %PGPLOT, PGBBUF: selected graphics device is not open
>  %PGPLOT, PGQCI: selected graphics device is not open
>  %PGPLOT, PGQFS: selected graphics device is not open
>  %PGPLOT, PGSCI: selected graphics device is not open
>  %PGPLOT, PGSFS: selected graphics device is not open
>  %PGPLOT, PGSVP: selected graphics device is not open
>  %PGPLOT, PGBBUF: selected graphics device is not open
>  %PGPLOT, PGEBUF: selected graphics device is not open
>  %PGPLOT, PGSVP: selected graphics device is not open
>  %PGPLOT, PGSCI: selected graphics device is not open
>  %PGPLOT, PGSFS: selected graphics device is not open
>  %PGPLOT, PGEBUF: selected graphics device is not open
>   ** plot error: cannot open device:
>  %PGPLOT, Unrecognized device type
>  %PGPLOT, Invalid device specification: /AQT
>   ** plot error: cannot open device:
>
> I have run out of ideas of what to try next.
>
> (The configure script picks up the paths for ifort libraries, could this
> be the problem? I could try to edit these out of all the makefiles… I don’t
> know how to make configure not pick these up.)
>
> Any ideas much appreciated.
>
> Anders
>
>
> On Mar 19, 2015, at 14:55 PM, Bruce Ravel <bravel at bnl.gov> wrote:
>
>
> Anders,
>
> I see two things that look like problems.  I have never built Demeter
> on a Mac myself, so there may be limits to how good my advice can be.
> That said:
>
> You are clearly not linking against the pgplot library you compiled.
> I glean this from the fact that you see this:
>
>   Use of uninitialized value $pgplot_location in substitution (s///)
>   at DemeterBuilder.pm line 191.
>
> and this (from your previous email):
>
>   $ ifeffit
>   Ifeffit   1.2.12 Copyright (c) 2005 Matt Newville, Univ of Chicago
>                  command-line shell version 1.1 with GNU Readline
>   Ifeffit> testplot
>      %PGPLOT, Unrecognized device type
>
> and so on.  You need to make sure that pgplot is someplace that the
> linker/loader knows to look when you build ifeffit.  But I do not know
> how that works on the mac.
>
> The bigger problem is this:
>
> On 03/19/2015 05:42 PM, Anders Glans wrote:
>
> env LD_RUN_PATH=/System/Library/Perl/5.18/darwin-thread-multi-2level/CORE
> cc -mmacosx-version-min=10.10 -arch x86_64 -arch i386 -bundle -undefined
> dynamic_lookup -fstack-protector -o src/Ifeffit.dylib src/ifeffit_wrap.o
> Simple test for presence of gnuplot ---> found it!  Using gnuplot with the
> x11 terminal.
> Building Demeter
> Building Artemis User's Guide
> Building Athena User's Guide
> copying src/Ifeffit.so to /Users/Anders/perl/auto/Ifeffit/Ifeffit.so
>
>
> It seems that my build script is too stupid to know that the shared
> object library built from the ifeffit wrapper is called .dylib and not
> .so.
>
> Try copying "src/Ifeffit.dylib" to "/Users/Anders/perl/auto/Ifeffit/"
> by hand, then doing "./Build" again.
>
> Perhaps oddly, I am not worried about that whole slew of warnings.  I
> don't think they matter.
>
> Hopefully with the .dylib file in the correct location, this
>
>  t/000_ifeffit.t ......... Can't load
> '/Library/Perl/5.18/darwin-thread-multi-2level/auto/Ifeffit/Ifeffit.bundle'
>  for module Ifeffit:
>
> and so on, won't happen.
>
> Fingers crossed!
> B
>
> --
> Bruce Ravel  ------------------------------------ bravel at bnl.gov
>
> National Institute of Standards and Technology
> Synchrotron Science Group at NSLS-II
> Building 535A
> Upton NY, 11973
>
> Homepage:    http://bruceravel.github.io/home/
> Software:    https://github.com/bruceravel
> Demeter:     http://bruceravel.github.io/demeter/
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