atlas & numpy/scipy

[Gideon Simpson]

I was curious about the possibility of parallelization of numperical linear
algebra routines in numpy/scipy through ATLAS, but I'm getting an error
when I try to install those variants.  Has anyone gotten this to work?

-- 
gideon
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numpy/scipy and mkl

[Gideon Simpson]

I have an intel mkl license, and I know that numpy/scipy can be built against 
it for a performance boost. I was wondering two things:

1.  Is it possible that we could have a variant of numpy/scipy that supports 
mkl, or is that fundamentally at odds with macports, since the mkl is 
commercial?

2.  Has anyone successfully used the macports python environment and a manually 
built numpy/scipy with mkl?  If so, how?

-gideon

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dolfin and vtk

[Gideon Simpson]

dolfin appears to be broken on el capitan because it depends on vtk5, which has 
a built error in 10.11 (see https://trac.macports.org/ticket/49418).  vtk 6, on 
the other hand, installs without a problem.  is there a way to get dolfin to 
use the vtk that does work in place of the one that doesn’t?

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Re: dolfin on el capitan

[Gideon Simpson]

When I run single process, it’s dying at the same point  as in this ticket: 
https://trac.macports.org/ticket/49418
-gideon

> On Feb 8, 2016, at 7:34 PM, Brandon Allbery  wrote:
> 
> 
> On Mon, Feb 8, 2016 at 7:31 PM, Gideon Simpson  <mailto:gideon.simp...@gmail.com>> wrote:
> The log file is 5 megs, should I open a new ticket and post it to the site? 
> Or send it to the list serve?
> 
> Ticket, upload to something like Dropbox --- or:
> 
>   sudo port clean vtk5; sudo port install vtk5 +python +tcltk build.jobs 
> <http://build.jobs/>=1
> 
> which may be slower but won't keep building a bunch of other stuff after the 
> error.
> 
> -- 
> brandon s allbery kf8nh   sine nomine associates
> allber...@gmail.com <mailto:allber...@gmail.com>  
> ballb...@sinenomine.net <mailto:ballb...@sinenomine.net>
> unix, openafs, kerberos, infrastructure, xmonadhttp://sinenomine.net 
> <http://sinenomine.net/>
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Re: dolfin on el capitan

[Gideon Simpson]

The log file is 5 megs, should I open a new ticket and post it to the site? Or 
send it to the list serve?

-gideon

> On Feb 8, 2016, at 7:30 PM, Brandon Allbery  wrote:
> 
> 
> On Mon, Feb 8, 2016 at 7:27 PM, Gideon Simpson  <mailto:gideon.simp...@gmail.com>> wrote:
> :info:build [ 14%] Built target vtkCommon
> :info:build make[1]: Leaving directory 
> `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_graphics_vtk5/vtk5/work/VTK5.10.1'
> :info:build make: *** [all] Error 2
> 
> Full log please; the above is an independent branch of a parallel build 
> finishing, then make exiting because all branches independent of the failing 
> one have completed.
> 
> -- 
> brandon s allbery kf8nh   sine nomine associates
> allber...@gmail.com <mailto:allber...@gmail.com>  
> ballb...@sinenomine.net <mailto:ballb...@sinenomine.net>
> unix, openafs, kerberos, infrastructure, xmonadhttp://sinenomine.net 
> <http://sinenomine.net/>
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Re: dolfin on el capitan

[Gideon Simpson]

I did 

sudo port install vtk5 +python +tcltk

and I get the error in, the log file:

:info:build [ 14%] Built target vtkCommon
:info:build make[1]: Leaving directory 
`/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_graphics_vtk5/vtk5/work/VTK5.10.1'
:info:build make: *** [all] Error 2
:info:build make: Leaving directory 
`/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_graphics_vtk5/vtk5/work/VTK5.10.1'
:info:build Command failed:  cd 
"/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_graphics_vtk5/vtk5/work/VTK5.10.1"
 && /usr/bin/make -j4 -w all VERBOSE=ON 
:info:build Exit code: 2
:error:build org.macports.build for port vtk5 returned: command execution failed
:debug:build Error code: CHILDSTATUS 5350 2
:debug:build Backtrace: command execution failed
while executing
"system -nice 0 $fullcmdstring"
("eval" body line 1)
invoked from within
"eval system $notty $nice \$fullcmdstring"
invoked from within
"command_exec build"
(procedure "portbuild::build_main" line 8)
invoked from within
"portbuild::build_main org.macports.build"
("eval" body line 1)
invoked from within
"eval $procedure $targetname"
:info:build Warning: targets not executed for vtk5: org.macports.activate 
org.macports.build org.macports.destroot org.macports.install
:notice:build Please see the log file for port vtk5 for details:

/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_graphics_vtk5/vtk5/main.log
 
Earlier in the log file there is an error similar to the one on ticket 49418
-gideon

> On Feb 8, 2016, at 4:29 PM, Sean Farley  wrote:
> 
> 
> Gideon Simpson  writes:
> 
>> Since vtk5 seems to be broken on el capitan, dolfin won’t install.  Is it 
>> possible to work around that?
> 
> Is there a ticket for this? I have vtk5+python+tcltk installed just fine.

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dolfin on el capitan

[Gideon Simpson]

Since vtk5 seems to be broken on el capitan, dolfin won’t install.  Is it 
possible to work around that?

-gideon

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matplotlib + ipython notebook crashing

[Gideon Simpson]

I’m finding that when I use the OS X backend for matplotlib with ipython 
notebooks, the python application launcher crashes.  Has anyone else had this 
problem?
-gideon

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py-scikits-bvp_solver on el capitan

[Gideon Simpson]

Is there a way to change the gcc dependency of py-scikits-bvp_solver form gcc48 
to something more recent?  Since there’s a bug between gcc48 and el capitan, it 
won’t install.

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Re: installing an older port

[Gideon Simpson]

Got it, that works.  One thing I can’t figure out how to do is to pull an older 
version of swig-python.  I don’t see that as a separate port in the repository.

-gideon

> On Sep 4, 2015, at 10:26 PM, Ryan Schmidt  wrote:
> 
> 
> On Sep 4, 2015, at 9:06 PM, Gideon Simpson wrote:
> 
>> I tried following the directions online to download and install an older 
>> port, but I’m encountering the following problem:
>> 
>> gideon@gs_air:ports$ svn checkout -r 137992 
>> https://svn.macports.org/repository/macports/trunk/dports/devel/swig
>> Error validating server certificate for 'https://svn.macports.org:443':
>> - The certificate is not issued by a trusted authority. Use the
>>   fingerprint to validate the certificate manually!
>> Certificate information:
>> - Hostname: *.macports.org
>> - Valid: from Wed, 11 Feb 2015 19:19:18 GMT until Fri, 01 Apr 2016 01:19:52 
>> GMT
>> - Issuer: GlobalSign nv-sa, BE
>> - Fingerprint: 15:5e:21:55:fe:e3:26:ae:b2:f8:c6:6a:d2:1a:bf:82:74:dd:c9:14
>> (R)eject, accept (t)emporarily or accept (p)ermanently? t
>> Aswig/files
>> Aswig/files/patch-configure.diff
>> Aswig/Portfile
>> Checked out revision 137992.
>> gideon@gs_air:ports$ cd swig/
>> gideon@gs_air:swig$ sudo port install
>> Password:
>> Error: Unable to execute port: Could not open file: 
>> /Users/gideon/Downloads/ports/swig/Portfile
> 
> Read
> 
> https://trac.macports.org/wiki/howto/InstallingOlderPort#Step2:Gettheportdirectory
> 
> to learn why the Downloads directory is not a suitable location for portfiles.
> 
> 

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Re: installing an older port

[Gideon Simpson]

The following still doesn’t work:

gideon@gs_air:swig$ chmod o+x ~
gideon@gs_air:swig$ sudo port install
Error: Unable to execute port: Could not open file: 
/Users/gideon/Downloads/ports/swig/Portfile

-gideon

> On Sep 4, 2015, at 10:17 PM, Brandon Allbery  wrote:
> 
> On Fri, Sep 4, 2015 at 10:06 PM, Gideon Simpson  <mailto:gideon.simp...@gmail.com>> wrote:
> gideon@gs_air:swig$ sudo port install
> Password:
> Error: Unable to execute port: Could not open file: 
> /Users/gideon/Downloads/ports/swig/Portfile
> 
> Make sure that the user "macports" can get to that directory. This usually 
> means "chmod o+x ~" to grant search (only) privilege so that it can traverse 
> ~ to get to the swig subdirectory. (If you are feeling paranoid, you can use 
> "chmod -e" to limit that access to the "macports" user instead of all users; 
> see `man 1 chmod` for how OS X ACLs work.) Likewise ensure that the swig 
> directory grants access to the "macports" user and that that user can read 
> the Portfile and patch.
> 
> MacPorts does not perform all operations as root, but drops to the 
> unprivileged "macports" user for most things.
> 
> -- 
> brandon s allbery kf8nh   sine nomine associates
> allber...@gmail.com <mailto:allber...@gmail.com>  
> ballb...@sinenomine.net <mailto:ballb...@sinenomine.net>
> unix, openafs, kerberos, infrastructure, xmonadhttp://sinenomine.net 
> <http://sinenomine.net/>
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installing an older port

[Gideon Simpson]

I tried following the directions online to download and install an older port, 
but I’m encountering the following problem:

gideon@gs_air:ports$ svn checkout -r 137992 
https://svn.macports.org/repository/macports/trunk/dports/devel/swig
Error validating server certificate for 'https://svn.macports.org:443':
 - The certificate is not issued by a trusted authority. Use the
   fingerprint to validate the certificate manually!
Certificate information:
 - Hostname: *.macports.org
 - Valid: from Wed, 11 Feb 2015 19:19:18 GMT until Fri, 01 Apr 2016 01:19:52 GMT
 - Issuer: GlobalSign nv-sa, BE
 - Fingerprint: 15:5e:21:55:fe:e3:26:ae:b2:f8:c6:6a:d2:1a:bf:82:74:dd:c9:14
(R)eject, accept (t)emporarily or accept (p)ermanently? t
Aswig/files
Aswig/files/patch-configure.diff
Aswig/Portfile
Checked out revision 137992.
gideon@gs_air:ports$ cd swig/
gideon@gs_air:swig$ sudo port install
Password:
Error: Unable to execute port: Could not open file: 
/Users/gideon/Downloads/ports/swig/Portfile


-gideon

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Re: website problem

[Gideon Simpson]

I’m trying to downgrade to an older version of a port.  Is there a way to 
figure that out at the command line?  I used to just use the trac server to 
find the right svn number and then checkout that one.

-gideon

> On Aug 29, 2015, at 7:24 PM, Ryan Schmidt  wrote:
> 
> trac.macports.org has been down for a few days. We have reported the problem 
> to the Mac OS Forge administrator and are awaiting a reply from him. Until 
> it's back up, please feel free to report problems here on this mailing list. 
> Gideon, other ways of looking up a port include the "port search" function on 
> the command line; the database at https://www.macports.org/ports.php ; and 
> the Subversion repository which you can access via a Subversion client 
> (including the command line "svn" program) at 
> https://svn.macports.org/repository/macports .
> 
> 
>> On Aug 29, 2015, at 10:32 AM, Tim Johnson  wrote:
>> 
>> Same problem here (Alaska)
>> Times out at 
>> apple-compu.edge1.sanjose2.level3.net
>> (same as with macports.org earlier)
>> from my server in Provo Utah, times out at
>> 216.156.85.14.ptr.us.xo.ne
>> 
>> * Gideon Simpson  [150829 07:23]:
>>> I’m trying to look up a port and I get an error when navigating to any of 
>>> the trac.macports.org <http://trac.macports.org/> pages.
>>> 
>>> -gideon
> 

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website problem

[Gideon Simpson]

I’m trying to look up a port and I get an error when navigating to any of the 
trac.macports.org  pages.

-gideon

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Re: ipython notebook problem

[Gideon Simpson]

This appears to have something to do with the recent upgrade of py27-jsonschema 
from 2.4.0 to 2.5.1.  As soon as I downgraded this to the earlier version, 
things ran as they had in the past.
-gideon

> On Jun 15, 2015, at 3:11 PM, Lawrence Velázquez  wrote:
> 
> On Jun 15, 2015, at 3:07 PM, Brandon Allbery  wrote:
> 
>> On Mon, Jun 15, 2015 at 3:01 PM, Gideon Simpson  
>> wrote:
>> 
>>> ImportError: No module named functools32
>>> 
>>>IPython notebook format depends on the jsonschema package:
>> 
>> I think the bottom part is boilerplate; functools32 is not part of 
>> jsonschema (and I don't see it in MacPorts offhand).
> 
> Maybe we should add it?
> 
> https://pypi.python.org/pypi/functools32
> 
> vq

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Re: ipython notebook problem

[Gideon Simpson]

The following ports are currently installed:
  py-ipython @3.1.0_0
  py-ipython @3.1.0_1 (active)
  py-jsonschema @2.5.1_0 (active)
  py27-ipython @3.1.0_0+notebook+parallel+scientific
  py27-ipython @3.1.0_1+notebook+parallel+scientific (active)
  py27-jsonschema @2.4.0_0
  py27-jsonschema @2.5.1_0 (active)

-gideon

> On Jun 15, 2015, at 3:05 PM, Lawrence Velázquez  wrote:
> 
> On Jun 15, 2015, at 3:01 PM, Gideon Simpson  wrote:
> 
>> When I try launching ipython notebook, I get the error:
>> 
>> 
>> ImportError: No module named functools32
>> 
>>IPython notebook format depends on the jsonschema package:
>> 
>>https://pypi.python.org/pypi/jsonschema
>> 
>>Please install it first.
>> 
>> But
>> port installed py-jsonschema
>> The following ports are currently installed:
>>  py-jsonschema @2.5.1_0 (active)
> 
> What Python version is IPython installed against? And do you have the 
> matching jsonschema?
> 
>   % port installed '*-ipython' '*-jsonschema'
> 
> vq

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ipython notebook problem

[Gideon Simpson]

When I try launching ipython notebook, I get the error:


ImportError: No module named functools32

IPython notebook format depends on the jsonschema package:

https://pypi.python.org/pypi/jsonschema

Please install it first.

But
port installed py-jsonschema
The following ports are currently installed:
  py-jsonschema @2.5.1_0 (active)


-gideon

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Re: ipython 3.0 issue

[Gideon Simpson]

py27-ipython @3.0.0_0+notebook+parallel+scientific

Ok, installing mistune through pip solved the problem.  Version 3.0 also 
requires py-jsonschema, which is not a current dependency.
-gideon

> On Mar 2, 2015, at 5:46 PM, Jeremy Lavergne  
> wrote:
> 
> On Mon, March 2, 2015 17:25, Gideon Simpson wrote:
>> I upgraded to ipython 3.0, and when I try to convert an ipython notebook
>> to PDF or HTML, I get the error:
>> 
>> ImportError: No module named mistune
> 
> It's entirely possible. Which python's ipython did you install?
> 
> Once that pythonx.y's pip is installed, I'd recommend using it to install
> mistune.
> 
> The general workflow would be:
> sudo port install pip-X.Y
> sudo port select pip pip-X.Y
> sudo pip-X.Y install mistune
> 
> 

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ipython 3.0 issue

[Gideon Simpson]

I upgraded to ipython 3.0, and when I try to convert an ipython notebook to PDF 
or HTML, I get the error:

ImportError: No module named mistune

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dolfin 1.5.0 and OS X 10.9

[Gideon Simpson]

On one my machines I still have 10.9 installed and with the recent update to 
dolfin (which works fine on my 10.10 machine), I now get errors during the 
build: 

_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build/dolfin/swig/modules/function
 && /opt/local/bin/swig -python -module function -shadow -modern -modernargs 
-fastdispatch -fvirtual -nosafecstrings -noproxydel -fastproxy -fastinit 
-fastunpack -fastquery -nobuildnone -Iinclude/swig -DBOOST_UBLAS_NDEBUG 
-DDOLFIN_SIZE_T=8 -DDOLFIN_LA_INDEX_SIZE=4 -DHAS_UMFPACK -DHAS_CHOLMOD 
-DHAS_ZLIB -DHAS_MPI -DHAS_QT4 -DHAS_VTK -DNUMPY_VERSION_MAJOR=1 
-DNUMPY_VERSION_MINOR=8 -DNUMPY_VERSION_MICRO=2 
-DNPY_NO_DEPRECATED_API=NPY_1_8_API_VERSION -outdir 
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build/dolfin/swig/modules/function
 -c++ 
-I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build
 -I/opt/local/include -I/opt/local/include/QtGui -I/opt/lo
 cal/include/QtCore -I/opt/local/include/vtk-6.1 -I/usr/include/python2.7 
-I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0
 -I/opt/local/include/libxml2 
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include 
-I/opt/local/include/mpich-mp -I/opt/local/include/eigen3 
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include
 
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 
-o 
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build/dolfin/swig/modules/function/modulePYTHON_wrap.cxx
 
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build/dolfin/swig/modules/function/module.i
:info:build 
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build/dolfin/swig/modules/la/module.i:137:
 Error: Unable to find 'dolfin/swig/la/docstrings.i'
:info:build 
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build/dolfin/swig/modules/la/module.i:138:
 Error: Unable to find 'dolfin/swig/nls/docstrings.i'
:info:build make[2]: *** [dolfin/swig/modules/la/modulePYTHON_wrap.cxx] Error 1
:info:build make[2]: Leaving directory 
`/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build'
:info:build make[1]: *** [dolfin/swig/modules/la/CMakeFiles/_la.dir/all] Error 2
:info:build make[1]: *** Waiting for unfinished jobs
:info:build 
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build/dolfin/swig/modules/common/module.i:78:
 Error: Unable to find 'dolfin/swig/common/docstrings.i'
:info:build 
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build/dolfin/swig/modules/common/module.i:79:
 Error: Unable to find 'dolfin/swig/parameter/docstrings.i'
:info:build 
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build/dolfin/swig/modules/common/module.i:80:
 Error: Unable to find 'dolfin/swig/log/docstrings.i'
:info:build make[2]: *** [dolfin/swig/modules/common/modulePYTHON_wrap.cxx] 
Error 1
:info:build make[2]: Leaving directory 
`/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build'
:info:build make[1]: *** 
[dolfin/swig/modules/common/CMakeFiles/_common.dir/all] Error 2
:info:build 
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build/dolfin/swig/modules/mesh/module.i:160:
 Error: Unable to find 'dolfin/swig/mesh/docstrings.i'
:info:build 
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build/dolfin/swig/modules/mesh/module.i:161:
 Error: Unable to find 'dolfin/swig/generation/docstrings.i'
:info:build 
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.5.0/build/dolfin/swig/modules/mesh/module.i:162:
 Error: Unable to find 'dolfin/swig/geometry/docstrings.i'
:info:build 
/opt/local/var/macports/build/_opt_local_var_m

dolfin & petsc

[Gideon Simpson]

I have macports petsc 3.5.2 installed, and i tried installing  sudo port 
install dolfin +mpich +suitesparse +petsc +slepc.  I got an error that looks 
like there was some break in the functionality of Petsc, at least with regard 
to dolfin:

_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.4.0/dolfin/la/STLFactory.cpp
:info:build 
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.4.0/dolfin/la/PETScKrylovSolver.cpp:528:62:
 error: use of undeclared identifier 'SAME_PRECONDITIONER'
:info:build ierr = KSPSetOperators(_ksp, _matA->mat(), _matP->mat(), 
SAME_PRECONDITIONER);


The log file is a bit too large to attach.


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Re: dolfin issue

[Gideon Simpson]

I did a port uninstall and a port clean, and I got the same error.

I do have petsc/slepc installed with mpich, if that’s part of the problem.  I 
suspect that petsc is built as a C library, while dolfin is C++.  Perhaps 
that’s the incompatibility?

-gideon

On Sep 30, 2014, at 2:35 AM, Sean Farley  wrote:

> 
> Ryan Schmidt writes:
> 
>> On Sep 29, 2014, at 7:45 PM, Gideon Simpson wrote:
>>> 
>>> I don’t seem to have that file
>> 
>> Ok, looks like the compiler name is just being specified as 
>> "mpicc-mpich-mp", without a path, and cmake is incorrectly inferring that it 
>> is in the build directory.
>> 
>> Do you have any of the mpich ports installed?
>> 
>> port installed name:mpich
>> 
>> Do any of them provide this file?
> 
> The issue is that dolfin needs a clean configure. I don't know why it
> has trouble with this (do any cmake people know?). Try 'port clean
> dolfin' before attempting to build dolfin again.

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Re: dolfin issue

[Gideon Simpson]

I don’t seem to have that file
-gideon

On Sep 29, 2014, at 8:00 PM, Ryan Schmidt  wrote:

> 
> On Sep 29, 2014, at 3:48 PM, Gideon Simpson wrote:
> 
>> The following combination generated an error:
>> sudo port install dolfin +mpich +petsc +slepc +suitesparse
>> --->  Computing dependencies for libgcc
>> --->  Cleaning libgcc
>> --->  Computing dependencies for dolfin
>> --->  Configuring dolfin
>> Error: org.macports.configure for port dolfin returned: configure failure: 
>> command execution failed
>> Please see the log file for port dolfin for details:
>>
>> /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/main.log
>> To report a bug, follow the instructions in the guide:
>>http://guide.macports.org/#project.tickets
>> Error: Processing of port dolfin failed
>> 
> 
> Hmm, it says:
> 
> 
> :info:configure   The CMAKE_CXX_COMPILER:
> :info:configure 
> :info:configure 
> /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.4.0/build/mpicxx-mpich-mp
> :info:configure 
> :info:configure   is not a full path to an existing compiler tool.
> 
> 
> Does 
> /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_dolfin/dolfin/work/dolfin-1.4.0/build/mpicxx-mpich-mp
>  exist? Does it work? Is it perhaps a broken symlink?
> 
> 

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Re: 64 bit linking error

[Gideon Simpson]

This is 10.8, not mavericks.

-gideon

On Nov 26, 2013, at 7:42 PM, Ryan Schmidt  wrote:

> 
> On Nov 26, 2013, at 09:10, Gideon Simpson wrote:
> 
>> I'm trying to compile something using the macports openmpi (built on 
>> macports gcc48), and am getting the following linking error:
>> 
>> openmpicxx -I/Users/gideon/software/sprng4.4/include -o sprng_mpi 
>> sprng_mpi.cpp  -L/Users/gideon/software/sprng4.4/lib -lsprng  
>> -I/opt/local/include/openmpi -L/opt/local/lib -lmpi_cxx -lmpi
>> Undefined symbols for architecture x86_64:
>> "std::ctype::_M_widen_init() const", referenced from:
>> mult_48_32(int*, int*, int*) in libsprng.a(libsprng_a-lcg.o)
>> operator<<(std::ostream&, BigNum const&) in 
>> libsprng.a(libsprng_a-bignum.o)
>> ld: symbol(s) not found for architecture x86_64
>> clang: error: linker command failed with exit code 1 (use -v to see 
>> invocation)
>> make: *** [sprng_mpi] Error 1
>> 
>> This is using a library called SPRNG (http://www.sprng.org), which I built 
>> on the macports gcc 48.
>> 
>> Going through the listserv archives, there was something about this over 2 
>> yeas ago, but it was unclear to me how/if it was resolved.
> 
> What version of OSX? If Mavericks, you may be having the problem that you 
> cannot mix software compiled with libc++ (i.e. anything compiled with clang) 
> with software compiled with libstdc++ (i.e. anything compiled with FSF GCC).
> 

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64 bit linking error

[Gideon Simpson]

I'm trying to compile something using the macports openmpi (built on macports 
gcc48), and am getting the following linking error:

openmpicxx -I/Users/gideon/software/sprng4.4/include -o sprng_mpi sprng_mpi.cpp 
 -L/Users/gideon/software/sprng4.4/lib -lsprng  -I/opt/local/include/openmpi 
-L/opt/local/lib -lmpi_cxx -lmpi
Undefined symbols for architecture x86_64:
 "std::ctype::_M_widen_init() const", referenced from:
 mult_48_32(int*, int*, int*) in libsprng.a(libsprng_a-lcg.o)
 operator<<(std::ostream&, BigNum const&) in libsprng.a(libsprng_a-bignum.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [sprng_mpi] Error 1

This is using a library called SPRNG (http://www.sprng.org), which I built on 
the macports gcc 48.

Going through the listserv archives, there was something about this over 2 yeas 
ago, but it was unclear to me how/if it was resolved.

-gideon


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slepc problem

[Gideon Simpson]

I got the following error while trying to install slepc:

version:1
:msg:main --->  Computing dependencies for slepc:info:main .:debug:main slepc 
has no conflicts
:debug:main Searching for dependency: petsc
:debug:main Didn't find receipt, going to depspec regex for: petsc
:debug:main Changing to port directory: 
/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/math/petsc
:debug:main OS darwin/12.2.0 (Mac OS X 10.8) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing 
procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing 
procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a 
pre-existing procedure. Target override will not be provided
:debug:main Using group file 
/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/conflicts_build-1.0.tcl
:debug:main Using group file 
/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/group/active_variants-1.1.tcl
:debug:main universal_variant is false, so not adding the default universal 
variant
:debug:main Executing variant openmpi provides openmpi
:debug:main Executing variant accelerate provides accelerate
:info:main .:debug:main petsc has no conflicts
:debug:main Searching for dependency: cmake
:debug:main Found Dependency: receipt exists for cmake
:debug:main Searching for dependency: hdf5-18
:debug:main Found Dependency: receipt exists for hdf5-18
:debug:main Searching for dependency: libyaml
:debug:main Found Dependency: receipt exists for libyaml
:debug:main Searching for dependency: openmpi
:debug:main Found Dependency: receipt exists for openmpi
:msg:main 
:msg:main --->  Dependencies to be installed: petsc
:debug:main Starting logging for petsc
:debug:main Executing org.macports.main (slepc)
:debug:main changing euid/egid - current euid: 0 - current egid: 0
:debug:main egid changed to: 501
:debug:main euid changed to: 502
:debug:archivefetch archivefetch phase started at Fri Mar  8 23:48:58 GMT 2013
:msg:archivefetch --->  Fetching archive for slepc
:debug:archivefetch Executing org.macports.archivefetch (slepc)
:debug:archivefetch euid/egid changed to: 0/0
:debug:archivefetch chowned /opt/local/var/macports/incoming to macports
:debug:archivefetch euid/egid changed to: 502/501
:info:archivefetch --->  slepc-3.3-p3_0.darwin_12.x86_64.tbz2 doesn't seem to 
exist in /opt/local/var/macports/incoming/verified
:msg:archivefetch --->  Attempting to fetch 
slepc-3.3-p3_0.darwin_12.x86_64.tbz2 from 
http://mse.uk.packages.macports.org/sites/packages.macports.org/slepc
:debug:archivefetch Fetching archive failed:: The requested URL returned error: 
404
:msg:archivefetch --->  Attempting to fetch 
slepc-3.3-p3_0.darwin_12.x86_64.tbz2 from 
http://lil.fr.packages.macports.org/slepc
:debug:archivefetch Fetching archive failed:: The requested URL returned error: 
404
:msg:archivefetch --->  Attempting to fetch 
slepc-3.3-p3_0.darwin_12.x86_64.tbz2 from http://packages.macports.org/slepc
:debug:archivefetch Fetching archive failed:: The requested URL returned error: 
404
:debug:archivefetch Privilege de-escalation not attempted as not running as 
root.
:debug:fetch fetch phase started at Fri Mar  8 23:48:59 GMT 2013
:notice:fetch --->  Fetching distfiles for slepc
:debug:fetch Can't run fetch on this port without elevated privileges. 
Escalating privileges back to root.
:debug:fetch euid changed to: 0. egid changed to: 0.
:debug:fetch changing euid/egid - current euid: 0 - current egid: 0
:debug:fetch egid changed to: 501
:debug:fetch euid changed to: 502
:debug:fetch Executing org.macports.fetch (slepc)
:info:fetch --->  slepc-3.3-p3.tar.gz doesn't seem to exist in 
/opt/local/var/macports/distfiles/slepc
:notice:fetch --->  Attempting to fetch slepc-3.3-p3.tar.gz from 
http://mse.uk.distfiles.macports.org/sites/distfiles.macports.org/slepc
:debug:fetch Privilege de-escalation not attempted as not running as root.
:debug:checksum checksum phase started at Fri Mar  8 23:49:00 GMT 2013
:notice:checksum --->  Verifying checksum(s) for slepc
:debug:checksum Executing org.macports.checksum (slepc)
:info:checksum --->  Checksumming slepc-3.3-p3.tar.gz
:debug:checksum Correct (md5) checksum for slepc-3.3-p3.tar.gz
:debug:checksum Correct (sha1) checksum for slepc-3.3-p3.tar.gz
:debug:checksum Correct (rmd160) checksum for slepc-3.3-p3.tar.gz
:debug:checksum Privilege de-escalation not attempted as not running as root.
:debug:extract extract phase started at Fri Mar  8 23:49:00 GMT 2013
:notice:extract --->  Extracting slepc
:debug:extract Executing org.macports.extract (slepc)
:info:extract --->  Extracting slepc-3.3-p3.tar.gz
:debug:extract setting option extract.args to 
'/opt/local/var/macports/distfiles/slepc/slepc-3.3-p3.tar.gz'
:debug:extract Environment: CPATH='/opt/local/include' 
CC_PRINT_OPTIO

texi2html problem

[Gideon Simpson]

I'm on Mountain Lion and did a port upgrade outdated.  I am getting the 
following error:

gideon@~$ sudo port clean --all texi2html
--->  Cleaning texi2html
gideon@~$ sudo port install texi2html
--->  Computing dependencies for texi2html
--->  Fetching archive for texi2html
--->  Attempting to fetch texi2html-5.0_0.darwin_12.noarch.tbz2 from 
http://packages.macports.org/texi2html
--->  Fetching distfiles for texi2html
--->  Attempting to fetch texi2html-5.0.tar.bz2 from 
http://mirror.cinquix.com/pub/savannah/texi2html
--->  Verifying checksum(s) for texi2html
Error: Checksum (md5) mismatch for texi2html-5.0.tar.bz2
Error: Checksum (sha1) mismatch for texi2html-5.0.tar.bz2
Error: Checksum (rmd160) mismatch for texi2html-5.0.tar.bz2
***
The non-matching file appears to be HTML. See this page for possible reasons
for the checksum mismatch:

***
Error: org.macports.checksum for port texi2html returned: Unable to verify file 
checksums
Please see the log file for port texi2html for details:

/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_textproc_texi2html/texi2html/main.log
To report a bug, follow the instructions in the guide:
http://guide.macports.org/#project.tickets
Error: Processing of port texi2html failed

and this is what's in the log file:

gideon@~$ cat 
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_textproc_texi2html/texi2html/main.log
version:1
:debug:main epoch: in tree: 0 installed: 0
:debug:main perl5 5.12.4_0 exists in the ports tree
:debug:main perl5 5.12.4_0 +perl5_12 is the latest installed
:debug:main perl5 5.12.4_0 +perl5_12 is active
:debug:main Merging existing variants '+perl5_12' into variants
:debug:main new fully merged portvariants: perl5_12 +
:debug:main Changing to port directory: 
/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/lang/perl5
:debug:main OS darwin/12.0.0 (Mac OS X 10.8) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing 
procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing 
procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a 
pre-existing procedure. Target override will not be provided
:debug:main universal_variant is false, so not adding the default universal 
variant
:debug:main Executing variant perl5_12 provides perl5_12
:debug:main No need to upgrade! perl5 5.12.4_0 >= perl5 5.12.4_0
:debug:main epoch: in tree: 0 installed: 0
:debug:main perl5.12 5.12.4_1 exists in the ports tree
:debug:main perl5.12 5.12.4_1  is the latest installed
:debug:main perl5.12 5.12.4_1  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: 
/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/lang/perl5.12
:debug:main OS darwin/12.0.0 (Mac OS X 10.8) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing 
procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing 
procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a 
pre-existing procedure. Target override will not be provided
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from 
/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main No need to upgrade! perl5.12 5.12.4_1 >= perl5.12 5.12.4_1
:debug:main epoch: in tree: 0 installed: 0
:debug:main gdbm 1.10_2 exists in the ports tree
:debug:main gdbm 1.10_2  is the latest installed
:debug:main gdbm 1.10_2  is active
:debug:main Merging existing variants '' into variants
:debug:main new fully merged portvariants: 
:debug:main Changing to port directory: 
/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/databases/gdbm
:debug:main OS darwin/12.0.0 (Mac OS X 10.8) arch i386
:debug:main org.macports.load registered provides 'load', a pre-existing 
procedure. Target override will not be provided
:debug:main org.macports.unload registered provides 'unload', a pre-existing 
procedure. Target override will not be provided
:debug:main org.macports.distfiles registered provides 'distfiles', a 
pre-existing procedure. Target override will not be provided
:debug:main adding the default universal variant
:debug:main Reading variant descriptions from 
/opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/_resources/port1.0/variant_descriptions.conf
:debug:main No need to upgrade! gdbm 1.10_2 >= gdbm 1.10_2
:debug:main epoch: in tree: 0 installed: 0
:debug:main gettext 0.18.1.1_2 exists in the ports tree
:deb

Re: ghostscript problem

[Gideon Simpson]

So I VPNed into my employer's network and had no trouble getting ghostscript 
through them, but there was an issue with my home (Comcast) internet.  Very 
bizarre.

-gideon

On Jul 3, 2012, at 6:26 PM, Ryan Schmidt wrote:

> 
> On Jul 3, 2012, at 18:14, Gideon Simpson wrote:
> 
>> On Jul 3, 2012, at 6:13 PM, Ryan Schmidt wrote:
>> 
>>> cat /opt/local/var/macports/distfiles/ghostscript/ghostscript-9.05.tar.gz
>> 
>> gideon@~$ cat 
>> /opt/local/var/macports/distfiles/ghostscript/ghostscript-9.05.tar.gz
>> > "http://www.w3.org/TR/1999/REC-html401-19991224/strict.dtd";>
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> 
> That's unfortunately less helpful than I had hoped. Usually these HTML files 
> will have been generated by "that domain doesn't exist, maybe you'll like 
> these search results" servers (in which case they usually list what URL you 
> had tried to access), or "you must log in to this network" servers (in which 
> case, you must log in to the network). But in your case it tells us nothing 
> at all.
> 
> You didn't initially show us which server MacPorts was trying to reach when 
> it got this file, but it must be one of these URLs:
> 
> On Jul 3, 2012, at 09:28, Gideon Simpson wrote:
> 
>> http://downloads.ghostscript.com/public/ghostscript-9.05.tar.gz
>> http://distfiles.macports.org/ghostscript/ghostscript-9.05.tar.gz
>> http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/ghostscript/ghostscript-9.05.tar.gz
>> http://her.gr.distfiles.macports.org/mirrors/macports/mpdistfiles/ghostscript/ghostscript-9.05.tar.gz
>> http://jog.id.distfiles.macports.org/macports/mpdistfiles/ghostscript/ghostscript-9.05.tar.gz
>> http://lil.fr.distfiles.macports.org/ghostscript/ghostscript-9.05.tar.gz
>> http://sea.us.distfiles.macports.org/macports/mpdistfiles/ghostscript/ghostscript-9.05.tar.gz
>> http://ykf.ca.distfiles.macports.org/MacPorts/mpdistfiles/ghostscript/ghostscript-9.05.tar.gz
>> http://svn.macports.org/repository/macports/distfiles/ghostscript/ghostscript-9.05.tar.gz
> 
> Perhaps there was a temporary problem with the Ghostscript server or one of 
> the MacPorts servers, because I don't see a problem with any of them right 
> now. In any case, please clean and try again:
> 
> sudo port clean --all ghostscript
> sudo port install ghostscript
> 
> As part of the output, MacPorts will show you where it's downloading the 
> distfiles from. If it fails again, show us that URL. Also, try accessing that 
> URL manually in a browser and see if it works there.
> 
> 

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Re: ghostscript problem

[Gideon Simpson]

gideon@~$ sudo port install ghostscript
--->  Computing dependencies for ghostscript
--->  Fetching archive for ghostscript
--->  Attempting to fetch ghostscript-9.05_2.darwin_11.x86_64.tbz2 from 
http://packages.macports.org/ghostscript
--->  Fetching distfiles for ghostscript
--->  Attempting to fetch ghostscript-9.05.tar.gz from 
http://downloads.ghostscript.com/public/
--->  Attempting to fetch ghostscript-fonts-other-6.0.tar.gz from 
http://downloads.sourceforge.net/gs-fonts
--->  Attempting to fetch mappingresources4pdf_2unicode_20091116.tar.Z from 
http://downloads.sourceforge.net/mapping-for-pdf.adobe
--->  Attempting to fetch mappingresources4pdf_other_20091116.tar.Z from 
http://downloads.sourceforge.net/mapping-for-pdf.adobe
--->  Verifying checksum(s) for ghostscript
Error: Checksum (md5) mismatch for ghostscript-9.05.tar.gz
Error: Checksum (sha1) mismatch for ghostscript-9.05.tar.gz
Error: Checksum (rmd160) mismatch for ghostscript-9.05.tar.gz
***
The non-matching file appears to be HTML. See this page for possible reasons
for the checksum mismatch:

***
Error: org.macports.checksum for port ghostscript returned: Unable to verify 
file checksums
Please see the log file for port ghostscript for details:

/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_print_ghostscript/ghostscript/main.log
To report a bug, follow the instructions in the guide:
http://guide.macports.org/#project.tickets
Error: Processing of port ghostscript failed

-gideon

On Jul 3, 2012, at 6:26 PM, Ryan Schmidt wrote:

> sudo port install ghostscript

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Re: ghostscript problem

[Gideon Simpson]

gideon@~$ cat 
/opt/local/var/macports/distfiles/ghostscript/ghostscript-9.05.tar.gz
http://www.w3.org/TR/1999/REC-html401-19991224/strict.dtd";>











-gideon

On Jul 3, 2012, at 6:13 PM, Ryan Schmidt wrote:

> cat /opt/local/var/macports/distfiles/ghostscript/ghostscript-9.05.tar.gz

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Re: ghostscript problem

[Gideon Simpson]

r.Z
  
http://iweb.dl.sourceforge.net/mapping-for-pdf.adobe/mappingresources4pdf_other_20091116.tar.Z
  
http://jaist.dl.sourceforge.net/mapping-for-pdf.adobe/mappingresources4pdf_other_20091116.tar.Z
  
http://kent.dl.sourceforge.net/mapping-for-pdf.adobe/mappingresources4pdf_other_20091116.tar.Z
  
http://nchc.dl.sourceforge.net/mapping-for-pdf.adobe/mappingresources4pdf_other_20091116.tar.Z
  
http://ncu.dl.sourceforge.net/mapping-for-pdf.adobe/mappingresources4pdf_other_20091116.tar.Z
  
http://netcologne.dl.sourceforge.net/mapping-for-pdf.adobe/mappingresources4pdf_other_20091116.tar.Z
  
http://space.dl.sourceforge.net/mapping-for-pdf.adobe/mappingresources4pdf_other_20091116.tar.Z
  
http://sunet.dl.sourceforge.net/mapping-for-pdf.adobe/mappingresources4pdf_other_20091116.tar.Z
  
http://surfnet.dl.sourceforge.net/mapping-for-pdf.adobe/mappingresources4pdf_other_20091116.tar.Z
  
http://switch.dl.sourceforge.net/mapping-for-pdf.adobe/mappingresources4pdf_other_20091116.tar.Z
  
http://ufpr.dl.sourceforge.net/mapping-for-pdf.adobe/mappingresources4pdf_other_20091116.tar.Z
  
http://voxel.dl.sourceforge.net/mapping-for-pdf.adobe/mappingresources4pdf_other_20091116.tar.Z
  
http://waix.dl.sourceforge.net/mapping-for-pdf.adobe/mappingresources4pdf_other_20091116.tar.Z
  
http://distfiles.macports.org/ghostscript/mappingresources4pdf_other_20091116.tar.Z
  
http://aarnet.au.distfiles.macports.org/pub/macports/mpdistfiles/ghostscript/mappingresources4pdf_other_20091116.tar.Z
  
http://her.gr.distfiles.macports.org/mirrors/macports/mpdistfiles/ghostscript/mappingresources4pdf_other_20091116.tar.Z
  
http://jog.id.distfiles.macports.org/macports/mpdistfiles/ghostscript/mappingresources4pdf_other_20091116.tar.Z
  
http://lil.fr.distfiles.macports.org/ghostscript/mappingresources4pdf_other_20091116.tar.Z
  
http://sea.us.distfiles.macports.org/macports/mpdistfiles/ghostscript/mappingresources4pdf_other_20091116.tar.Z
  
http://ykf.ca.distfiles.macports.org/MacPorts/mpdistfiles/ghostscript/mappingresources4pdf_other_20091116.tar.Z
  
http://svn.macports.org/repository/macports/distfiles/ghostscript/mappingresources4pdf_other_20091116.tar.Z
 

-gideon

On Jul 3, 2012, at 12:20 AM, Lawrence Velázquez wrote:

> On Jul 2, 2012, at 11:45 p.m., Gideon Simpson wrote:
> 
>> How do I determine that?
> 
> Use "port distfiles ghostscript" to get the absolute path of the distfile, 
> then open it in a text editor or feed it to cat or less or something.
> 
> 
> vq
> 

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Re: ghostscript problem

[Gideon Simpson]

How do I determine that?

-gideon

On Jul 2, 2012, at 8:52 PM, Ryan Schmidt wrote:

> 
> On Jul 2, 2012, at 20:43, Gideon Simpson wrote:
> 
>> gideon@~$ sudo port install ghostscript
>> --->  Computing dependencies for ghostscript
>> --->  Verifying checksum(s) for ghostscript
>> Error: Checksum (md5) mismatch for ghostscript-9.05.tar.gz
>> Error: Checksum (sha1) mismatch for ghostscript-9.05.tar.gz
>> Error: Checksum (rmd160) mismatch for ghostscript-9.05.tar.gz
>> ***
>> The non-matching file appears to be HTML. See this page for possible reasons
>> for the checksum mismatch:
>> <https://trac.macports.org/wiki/MisbehavingServers>
>> ***
> 
> And what does the HTML file contain?
> 
> 

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ghostscript problem

[Gideon Simpson]

gideon@~$ sudo port install ghostscript
--->  Computing dependencies for ghostscript
--->  Verifying checksum(s) for ghostscript
Error: Checksum (md5) mismatch for ghostscript-9.05.tar.gz
Error: Checksum (sha1) mismatch for ghostscript-9.05.tar.gz
Error: Checksum (rmd160) mismatch for ghostscript-9.05.tar.gz
***
The non-matching file appears to be HTML. See this page for possible reasons
for the checksum mismatch:

***
Error: org.macports.checksum for port ghostscript returned: Unable to verify 
file checksums
Please see the log file for port ghostscript for details:
   
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_print_ghostscript/ghostscript/main.log
To report a bug, follow the instructions in the guide:
   http://guide.macports.org/#project.tickets
Error: Processing of port ghostscript failed
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Re: port problem upon update

[Gideon Simpson]

da... no
:info:configure checking how to compare bootstrapped objects... cmp 
--ignore-initial=16 $$f1 $$f2
:info:configure checking for objdir... .libs
:info:configure checking for the correct version of gmp.h... yes
:info:configure checking for the correct version of mpfr.h... yes
:info:configure checking for the correct version of mpc.h... yes
:info:configure checking for the correct version of the gmp/mpfr/mpc 
libraries... yes
:info:configure checking for PWL_handle_timeout in -lpwl... no
:info:configure checking for version 0.11 (revision 0 or later) of PPL... no
:info:configure configure: error: Unable to find a usable PPL.  See config.log 
for details.
:info:configure Command failed:  cd 
"/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc46/gcc46/work/build"
 && ../gcc-4.6.3/configure --prefix=/opt/local --build=x86_64-apple-darwin11 
--enable-languages=c,c++,objc,obj-c++,lto,fortran --libdir=/opt/local/lib/gcc46 
--includedir=/opt/local/include/gcc46 --infodir=/opt/local/share/info 
--mandir=/opt/local/share/man --datarootdir=/opt/local/share/gcc-4.6 
--with-local-prefix=/opt/local --with-libiconv-prefix=/opt/local 
--with-system-zlib --disable-nls --program-suffix=-mp-4.6 
--with-gxx-include-dir=/opt/local/include/gcc46/c++/ --with-gmp=/opt/local 
--with-mpfr=/opt/local --with-mpc=/opt/local --with-ppl=/opt/local 
--with-cloog=/opt/local --enable-cloog-backend=isl --enable-stage1-checking 
--disable-multilib --enable-lto --with-as=/opt/local/bin/as 
--with-ld=/opt/local/bin/ld --with-ar=/opt/local/bin/ar 
--with-bugurl=https://trac.macports.org/newticket --with-pkgversion="MacPorts 
gcc46 4.6.3_2" 
:info:configure Exit code: 1
:error:configure org.macports.configure for port gcc46 returned: configure 
failure: command execution failed
:debug:configure Error code: NONE
:debug:configure Backtrace: configure failure: command execution failed
   while executing
"$procedure $targetname"
:info:configure Warning: targets not executed for gcc46: org.macports.activate 
org.macports.configure org.macports.build org.macports.destroot 
org.macports.install
:notice:configure Please see the log file for port gcc46 for details:
   
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc46/gcc46/main.log

-gideon

On Jul 2, 2012, at 10:51 AM, Lawrence Velázquez wrote:

> On Jul 2, 2012, at 11:48 a.m., Gideon Simpson wrote:
> 
>> Error: org.macports.configure for port gcc46 returned: configure failure: 
>> command execution failed
>> Error: Failed to install gcc46
>> Please see the log file for port gcc46 for details:
>>  
>> /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc46/gcc46/main.log
> 
> Can you show us this file?
> 
> vq
> 

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port problem upon update

[Gideon Simpson]

I did an "update outdated", and the following happened:

gideon@~$ sudo port upgrade outdated
--->  liblzma is replaced by xz
--->  Computing dependencies for xz
--->  Fetching archive for xz
--->  Attempting to fetch xz-5.0.4_0.darwin_11.x86_64.tbz2 from 
http://packages.macports.org/xz
--->  Attempting to fetch xz-5.0.4_0.darwin_11.x86_64.tbz2.rmd160 from 
http://packages.macports.org/xz
--->  Installing xz @5.0.4_0
--->  Cleaning xz
--->  Deactivating liblzma @5.0.3_0
--->  Unable to deactivate liblzma @5.0.3_0, the following ports depend on it:
--->ImageMagick @6.7.7-2_0+q16
Warning: Deactivate forced.  Proceeding despite dependencies.
--->  Cleaning liblzma
--->  Computing dependencies for xz
--->  Deactivating xz @5.0.3_0
--->  Cleaning xz
--->  Activating xz @5.0.4_0
--->  Cleaning xz
--->  Fetching archive for libpixman
--->  Attempting to fetch libpixman-0.26.2_0.darwin_11.x86_64.tbz2 from 
http://packages.macports.org/libpixman
--->  Attempting to fetch libpixman-0.26.2_0.darwin_11.x86_64.tbz2.rmd160 from 
http://packages.macports.org/libpixman
--->  Installing libpixman @0.26.2_0
--->  Cleaning libpixman
--->  Deactivating libpixman @0.26.0_0
--->  Cleaning libpixman
--->  Activating libpixman @0.26.2_0
--->  Cleaning libpixman
--->  Computing dependencies for metis
--->  Fetching archive for metis
--->  Attempting to fetch metis-5.0.2_1.darwin_11.x86_64.tbz2 from 
http://packages.macports.org/metis
--->  Fetching distfiles for metis
--->  Attempting to fetch metis-5.0.2.tar.gz from 
http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/
--->  Verifying checksum(s) for metis
--->  Extracting metis
--->  Applying patches to metis
--->  Configuring metis
--->  Building metis
--->  Staging metis into destroot
--->  Installing metis @5.0.2_1
--->  Cleaning metis
--->  Deactivating metis @4.0.3_1
--->  Cleaning metis
--->  Activating metis @5.0.2_1
--->  Cleaning metis
--->  Computing dependencies for netcdf
--->  Fetching archive for netcdf
--->  Attempting to fetch netcdf-4.2.0_4+dap+netcdf4.darwin_11.x86_64.tbz2 from 
http://packages.macports.org/netcdf
--->  Attempting to fetch 
netcdf-4.2.0_4+dap+netcdf4.darwin_11.x86_64.tbz2.rmd160 from 
http://packages.macports.org/netcdf
--->  Installing netcdf @4.2.0_4+dap+netcdf4
--->  Cleaning netcdf
--->  Computing dependencies for netcdf
--->  Deactivating netcdf @4.2.0_3+dap+netcdf4
--->  Cleaning netcdf
--->  Activating netcdf @4.2.0_4+dap+netcdf4

As of version 4.2 c++ and fortran interfaces are separate ports, netcdf-cxx and
netcdf-fortran, respectively.

--->  Cleaning netcdf
--->  Computing dependencies for openjpeg
--->  Fetching archive for openjpeg
--->  Attempting to fetch openjpeg-1.5.0_2.darwin_11.x86_64.tbz2 from 
http://packages.macports.org/openjpeg
--->  Attempting to fetch openjpeg-1.5.0_2.darwin_11.x86_64.tbz2.rmd160 from 
http://packages.macports.org/openjpeg
--->  Installing openjpeg @1.5.0_2
--->  Cleaning openjpeg
--->  Computing dependencies for openjpeg
--->  Deactivating openjpeg @1.5.0_1
--->  Cleaning openjpeg
--->  Activating openjpeg @1.5.0_2
--->  Cleaning openjpeg
--->  Computing dependencies for ppl
--->  Fetching archive for ppl
--->  Attempting to fetch ppl-1.0_0.darwin_11.x86_64.tbz2 from 
http://packages.macports.org/ppl
--->  Attempting to fetch ppl-1.0_0.darwin_11.x86_64.tbz2.rmd160 from 
http://packages.macports.org/ppl
--->  Installing ppl @1.0_0
--->  Cleaning ppl
--->  Computing dependencies for ppl
--->  Deactivating ppl @0.12.1_2
--->  Cleaning ppl
--->  Activating ppl @1.0_0
--->  Cleaning ppl
--->  Updating database of binaries: 100.0%
--->  Scanning binaries for linking errors: 100.0%
--->  Found 6 broken file(s), matching files to ports
--->  Found 1 broken port(s), determining rebuild order
--->  Rebuilding in order
 gcc46 @4.6.3 
--->  Computing dependencies for gcc46
--->  Cleaning gcc46
--->  Scanning binaries for linking errors: 100.0%
--->  Found 6 broken file(s), matching files to ports
--->  Found 1 broken port(s), determining rebuild order
--->  Rebuilding in order
 gcc46 @4.6.3 
--->  Computing dependencies for gcc46
--->  Cleaning gcc46
--->  Unable to uninstall gcc46 @4.6.3_2, the following ports depend on it:
--->fftw-3 @3.3.2_0+gcc46
--->py27-scipy @0.10.1_1+gcc46
--->qrupdate @1.1.2_1+atlas+gcc46
--->openmpi @1.5.5_0+gcc46
Warning: Uninstall forced.  Proceeding despite dependencies.
--->  Deactivating gcc46 @4.6.3_2
--->  Unable to deactivate gcc46 @4.6.3_2, the following ports depend on it:
--->fftw-3 @3.3.2_0+gcc46
--->py27-scipy @0.10.1_1+gcc46
--->qrupdate @1.1.2_1+atlas+gcc46
--->openmpi @1.5.5_0+gcc46
Warning: Deactivate forced.  Proceeding despite dependencies.
--->  Cleaning gcc46
--->  Uninstalling gcc46 @4.6.3_2
--->  Cleaning gcc46
--->  Computing dependencies for gcc46
--->  Fetching distfiles for gcc46
--->  Verifying checksum(s) for gcc46
--->  Extracting gcc46
--->  Configuring gcc46
Error: org.macports.configure for port gcc46 returned: co

Re: error with package

[Gideon Simpson]

Ok, but what about this?  Do I want to force that  uninstall?

--->  Unable to uninstall cloog @0.16.3_1, the following ports depend on it:
--->gcc46 @4.6.3_2
Error: org.macports.uninstall for port cloog returned: Please uninstall the 
ports that depend on cloog first.
Please see the log file for port cloog for details:

/opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_cloog_0.16.3_1/cloog/main.log
Warning: Failed to execute portfile from registry for cloog @0.16.3_1
--->  Unable to uninstall cloog @0.16.3_1, the following ports depend on it:
--->gcc46 @4.6.3_2
Error: port uninstall failed: Please uninstall the ports that depend on cloog 
first.

-gideon

On May 18, 2012, at 6:28 PM, Lawrence Velázquez wrote:

> On May 18, 2012, at 7:17 p.m., Gideon Simpson wrote:
> 
>> --->  Computing dependencies for cloog
>> --->  Dependencies to be installed: isl
>> --->  Activating isl @0.07_0
>> Error: org.macports.activate for port isl returned: Image error: 
>> /opt/local/include/isl/aff.h is being used by the active cloog port.  Please 
>> deactivate this port first, or use 'port -f activate isl' to force the 
>> activation.
>> Error: Failed to install isl
> 
> cloog was recently updated to use an external isl port rather than installing 
> its own internal isl. Oddly, trying to activate isl while the old cloog is 
> still installed results in the conflict you ran into.
> 
> I did a "sudo port -f uninstall cloog" followed by "sudo port install cloog", 
> and it worked itself out.
> 
> vq
> 

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error with package

[Gideon Simpson]

Got this recently when upgrading outdated packages:

--->  Computing dependencies for glib2
--->  Fetching archive for glib2
--->  Attempting to fetch glib2-2.32.3_0.darwin_11.x86_64.tbz2 from 
http://packages.macports.org/glib2
--->  Attempting to fetch glib2-2.32.3_0.darwin_11.x86_64.tbz2.rmd160 from 
http://packages.macports.org/glib2
--->  Installing glib2 @2.32.3_0
--->  Cleaning glib2
--->  Computing dependencies for glib2
--->  Deactivating glib2 @2.32.2_0
--->  Cleaning glib2
--->  Activating glib2 @2.32.3_0
--->  Cleaning glib2
--->  Computing dependencies for cloog
--->  Dependencies to be installed: isl
--->  Activating isl @0.07_0
Error: org.macports.activate for port isl returned: Image error: 
/opt/local/include/isl/aff.h is being used by the active cloog port.  Please 
deactivate this port first, or use 'port -f activate isl' to force the 
activation.
Error: Failed to install isl
Please see the log file for port isl for details:

/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_devel_isl/isl/main.log
Error: The following dependencies were not installed: isl
Error: Unable to upgrade port: 1
To report a bug, follow the instructions in the guide:
http://guide.macports.org/#project.tickets

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Re: building SPRNG with macports gcc45 & mpich2

[Gideon Simpson]

Even sorting out the flags, I'm still getting the error:

Undefined symbols for architecture x86_64:
  "_main", referenced from:
  start in crt1.10.5.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status


-gideon

On Dec 23, 2011, at 4:57 AM, Ryan Schmidt wrote:

> 
> On Dec 22, 2011, at 22:45, Gideon Simpson wrote:
> 
>> Slightly off topic, but I was wondering if anyone had successfully built 
>> SPRNG (http://sprng.cs.fsu.edu/) with a macports based gcc and mpich2.
>> 
>> I have gcc45 and mpich+gcc45 installed, and I receive the error:
>> 
>> Undefined symbols for architecture x86_64:
>> "_main", referenced from:
>> start in crt1.10.5.o
>> ld: symbol(s) not found for architecture x86_64
>> collect2: ld returned 1 exit status
>> if g++ -DHAVE_CONFIG_H -I../SRC -I../include   -DAdd_  -DSPRNG_MPI-g -O2 
>> -Wno-deprecated -DLONG64=long -MT libsprng_a-sprng.o -MD -MP -MF 
>> ".deps/libsprng_a-sprng.Tpo" -c -o libsprng_a-sprng.o `test -f 'sprng.cpp' 
>> || echo './'`sprng.cpp; \
>>  then mv -f ".deps/libsprng_a-sprng.Tpo" ".deps/libsprng_a-sprng.Po"; 
>> else rm -f ".deps/libsprng_a-sprng.Tpo"; exit 1; fi
>> In file included from sprng.cpp:6:0:
>> communicate.cpp:2:17: fatal error: mpi.h: No such file or directory
> 
> Where is the mpi.h header? (I can't seem to build mpich myself.) You probably 
> need to add that directory to CPPFLAGS with an -I argument. For example if it 
> is in /opt/local/include, you need...
> 
> export CPPFLAGS=-I/opt/local/include
> 
> ...before you begin. Similarly, you probably need to say where the libraries 
> are, e.g. with:
> 
> export LDFLAGS=-L/opt/local/lib
> 
> 

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building SPRNG with macports gcc45 & mpich2

[Gideon Simpson]

Slightly off topic, but I was wondering if anyone had successfully built SPRNG 
(http://sprng.cs.fsu.edu/) with a macports based gcc and mpich2.

I have gcc45 and mpich+gcc45 installed, and I receive the error:

Undefined symbols for architecture x86_64:
  "_main", referenced from:
  start in crt1.10.5.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
if g++ -DHAVE_CONFIG_H -I../SRC -I../include   -DAdd_  -DSPRNG_MPI-g -O2 
-Wno-deprecated -DLONG64=long -MT libsprng_a-sprng.o -MD -MP -MF 
".deps/libsprng_a-sprng.Tpo" -c -o libsprng_a-sprng.o `test -f 'sprng.cpp' || 
echo './'`sprng.cpp; \
then mv -f ".deps/libsprng_a-sprng.Tpo" ".deps/libsprng_a-sprng.Po"; 
else rm -f ".deps/libsprng_a-sprng.Tpo"; exit 1; fi
In file included from sprng.cpp:6:0:
communicate.cpp:2:17: fatal error: mpi.h: No such file or directory
compilation terminated.

Thanks,

-gideon

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mpich2 and mpif77

[Gideon Simpson]

When I install mpich2, the port doesn't provide mpif77 (or mpif90, etc.)  Is 
this deliberate?

-gideon

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openmpi port and wrappers

[Gideon Simpson]

Is there a way to automatically get the openmpi compilers to be linked as 
mpicc, mpic++, etc.?

-gideon

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matplotlib on lion

[Gideon Simpson]

I recently moved to a new machine running lion, and I am trying to get
matplotlib up and running.  I am receiving the following error:

Error: Target org.macports.build returned: shell command failed (see log
for details)
Log for py27-matplotlib is at:
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_python_py-matplotlib/py27-matplotlib/main.log
Error: Status 1 encountered during processing.

The tail of the log file, where the error appears, is:

:info:build /Developer/usr/bin/clang -DNDEBUG -g -O3 -Wall -arch x86_64
-DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include
-I/opt/local/include -I/opt/local/include/python/opt/local -I.
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include
-Isrc -Iagg24/include -I.
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include
-I/opt/local/include/freetype2 -I/opt/local/include
-I/opt/local/include/python/opt/local -I.
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
-c CXX/IndirectPythonInterface.cxx -o
build/temp.macosx-10.7-x86_64-2.7/CXX/IndirectPythonInterface.o
:info:build /Developer/usr/bin/clang -DNDEBUG -g -O3 -Wall -arch x86_64
-DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include
-I/opt/local/include -I/opt/local/include/python/opt/local -I.
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include
-Isrc -Iagg24/include -I.
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include
-I/opt/local/include/freetype2 -I/opt/local/include
-I/opt/local/include/python/opt/local -I.
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
-c CXX/cxxextensions.c -o
build/temp.macosx-10.7-x86_64-2.7/CXX/cxxextensions.o
:info:build /Developer/usr/bin/clang -DNDEBUG -g -O3 -Wall -arch x86_64
-DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -DPYCXX_ISO_CPP_LIB=1
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include
-I/opt/local/include -I/opt/local/include/python/opt/local -I.
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include
-Isrc -Iagg24/include -I.
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/include
-I/opt/local/include/freetype2 -I/opt/local/include
-I/opt/local/include/python/opt/local -I.
-I/opt/local/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
-c src/backend_agg.cpp -o
build/temp.macosx-10.7-x86_64-2.7/src/backend_agg.o
:info:build In file included from src/backend_agg.cpp:11:
:info:build In file included from src/_backend_agg.h:34:
:info:build agg24/include/agg_renderer_outline_aa.h:1368:45: error: binding
of reference to type 'agg::line_profile_aa' to a value of type 'const
agg::line_profile_aa' drops qualifiers
:info:build line_profile_aa& profile() { return *m_profile; }
:info:build ^~
:info:build 1 error generated.
:info:build error: command '/Developer/usr/bin/clang' failed with exit
status 1
:info:build shell command " cd
"/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_python_py-matplotlib/py27-matplotlib/work/matplotlib-1.1.0"
&&
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7
setup.py --no-user-cfg build " returned error 1
:error:build Target org.macports.build returned: shell command failed (see
log for details)
:debug:build Backtrace: shell command failed (see log for details)
while executing
"command_exec build"
(procedure "portbuild::build_main" line 8)
invoked from within
"$procedure $targetname"
:info:build Warning: the following items did not execute (for
py27-matplotlib): org.macports.activate org.macports.build
org.macports.destroot org.macports.install
:notice:build Log for py27-matplotlib is at:
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_python_py-matplotlib/py27-matplotlib/main.log


-- 
gideon
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