install woes

[mrawls]

I finally got around to trying to use this today, and wasn't able to install it. This was after I thought I'd managed to install MOOG manually but when I run it, all I get is a black box popup window with nothing plotted in it. Anyway, this is what happens with your version:

[~/Astronomy/MOOG]$ sudo pip install moog
Password:
Traceback (most recent call last):
  File "/Users/Meredith/Applications/Ureka/variants/common/lib/python2.7/site.py", line 703, in <module>
    main()
  File "/Users/Meredith/Applications/Ureka/variants/common/lib/python2.7/site.py", line 694, in main
    execsitecustomize()
  File "/Users/Meredith/Applications/Ureka/variants/common/lib/python2.7/site.py", line 548, in execsitecustomize
    import sitecustomize
  File "/Users/Meredith/Applications/Ureka/variants/common/lib/python2.7/sitecustomize.py", line 3, in <module>
    UR_DIR = os.environ['UR_DIR']
  File "/Users/Meredith/Applications/Ureka/variants/common/lib/python2.7/UserDict.py", line 23, in __getitem__
    raise KeyError(key)
KeyError: 'UR_DIR'

I realized it hated Ureka, so I disabled that with ur_forget, and tried again... it got much farther this time, but still didn't work. I'm pretty sure something terrible is happening with libraries. I know I had architecture errors like this in the past for other monstrous codes, but don't remember the specifics of how (or if) I resolved the issues. Here are (hopefully) the relevant bits:

    ld: symbol(s) not found for architecture x86_64
    collect2: error: ld returned 1 exit status
    make: *** [MOOG] Error 1
    gfortran -Wall -O4 -ffixed-line-length-72 -ff2c  -c -o Moogsilent.o Moogsilent.f
    gfortran Abfind.o Abpop.o Abunplot.o Batom.o Begin.o Binary.o Binplot.o Binplotprep.o Blends.o Bmolec.o Boxit.o Calmod.o Cdcalc.o Chabund.o Cog.o Cogplot.o Cogsyn.o Correl.o Crosscorr.o Curve.o Damping.o Defcolor.o Discov.o Doflux.o Drawcurs.o Eqlib.o Estim.o Ewfind.o Ewweighted.o Fakeline.o Findtic.o Finish.o Fluxplot.o Gammabark.o Getasci.o Getcount.o Getnum.o Gridplo.o Gridsyn.o Infile.o Inlines.o Inmodel.o Invert.o Jexpint.o Lineinfo.o Lineabund.o Linlimit.o Makeplot.o Minimax.o Molquery.o Moogsilent.o Mydriver.o Nansi.o Nearly.o Number.o Obshead.o Oneline.o Opaccouls.o OpacHelium.o OpacHydrogen.o Opacit.o Opacmetals.o Opacscat.o Params.o Partfn.o Partnew.o Plotit.o Plotremember.o Pltabun.o Pltcog.o Pltflux.o Pltspec.o Pointcurs.o Prinfo.o Putasci.o Readobs.o Rinteg.o Smooth.o Specplot.o Stats.o Sunder.o Synpop.o Synspec.o Synth.o Taukap.o Total.o Trudamp.o Ucalc.o Vargauss.o Vmacro.o Voigt.o Wavecalc.o Weedout.o Writenumber.o -o MOOGSILENT -L/usr/X11R6/lib -lX11 \
        -L/private/tmp/pip_build_root/moog/lib/smlib -lplotsub -ldevices -lutils -L/private/tmp/pip_build_root/moog/lib/aqlib -laquaterm
    ld: warning: ld: warning: ld: warning: ld: warning: ignoring file /private/tmp/pip_build_root/moog/lib/aqlib/libaquaterm.dylib, missing required architecture x86_64 in file /private/tmp/pip_build_root/moog/lib/aqlib/libaquaterm.dylib (2 slices)ignoring file /private/tmp/pip_build_root/moog/lib/smlib/libutils.a, file was built for archive which is not the architecture being linked (x86_64): /private/tmp/pip_build_root/moog/lib/smlib/libutils.aignoring file /private/tmp/pip_build_root/moog/lib/smlib/libdevices.a, file was built for archive which is not the architecture being linked (x86_64): /private/tmp/pip_build_root/moog/lib/smlib/libdevices.aignoring file /private/tmp/pip_build_root/moog/lib/smlib/libplotsub.a, file was built for archive which is not the architecture being linked (x86_64): /private/tmp/pip_build_root/moog/lib/smlib/libplotsub.a



    Undefined symbols for architecture x86_64:
      "_sm_alpha__", referenced from:
          _drawcurs_ in Drawcurs.o
          _makeplot_ in Makeplot.o
          _pointcurs_ in Pointcurs.o

[ long list of other undefined symbols here ]

    ld: symbol(s) not found for architecture x86_64
    collect2: error: ld returned 1 exit status
    make: *** [MOOGSILENT] Error 1
    running install
    running build
    running build_scripts
    creating build
    creating build/scripts-2.7
    error: file '/private/tmp/pip_build_root/moog/moog/MOOG' does not exist
    Complete output from command /usr/bin/python -c "import setuptools, tokenize;__file__='/private/tmp/pip_build_root/moog/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-lEz0v2-record/install-record.txt --single-version-externally-managed --compile:
    gfortran -Wall -O4 -ffixed-line-length-72 -ff2c  -c -o Abfind.o Abfind.f

... and finally ...

Cleaning up...
  Removing temporary dir /private/tmp/pip_build_root...
Command /usr/bin/python -c "import setuptools, tokenize;__file__='/private/tmp/pip_build_root/moog/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-lEz0v2-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /private/tmp/pip_build_root/moog
Exception information:
Traceback (most recent call last):
  File "/Library/Python/2.7/site-packages/pip/basecommand.py", line 122, in main
    status = self.run(options, args)
  File "/Library/Python/2.7/site-packages/pip/commands/install.py", line 283, in run
    requirement_set.install(install_options, global_options, root=options.root_path)
  File "/Library/Python/2.7/site-packages/pip/req.py", line 1435, in install
    requirement.install(install_options, global_options, *args, **kwargs)
  File "/Library/Python/2.7/site-packages/pip/req.py", line 706, in install
    cwd=self.source_dir, filter_stdout=self._filter_install, show_stdout=False)
  File "/Library/Python/2.7/site-packages/pip/util.py", line 697, in call_subprocess
    % (command_desc, proc.returncode, cwd))
InstallationError: Command /usr/bin/python -c "import setuptools, tokenize;__file__='/private/tmp/pip_build_root/moog/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-lEz0v2-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /private/tmp/pip_build_root/moog

[andycasey]

Hi Meredith,

It looks like it falls over without ureka because it is looking for supermongo. If you don't have/want supermongo, try installing the batch version (MOOGSILENT only, not MOOG) with:

pip install moogsilent

If that doesn't work please let me know what operating system you're on.

Cheers,
Andy

On 17 Dec 2014, at 9:26 am, Meredith Rawls notifications@github.com wrote:

I finally got around to trying to use this today, and wasn't able to install it. This was after I thought I'd managed to install MOOG manually but when I run it, all I get is a black box popup window with nothing plotted in it. Anyway, this is what happens with your version:

[~/Astronomy/MOOG]$ sudo pip install moog
Password:
Traceback (most recent call last):
File "/Users/Meredith/Applications/Ureka/variants/common/lib/python2.7/site.py", line 703, in
main()
File "/Users/Meredith/Applications/Ureka/variants/common/lib/python2.7/site.py", line 694, in main
execsitecustomize()
File "/Users/Meredith/Applications/Ureka/variants/common/lib/python2.7/site.py", line 548, in execsitecustomize
import sitecustomize
File "/Users/Meredith/Applications/Ureka/variants/common/lib/python2.7/sitecustomize.py", line 3, in
UR_DIR = os.environ['UR_DIR']
File "/Users/Meredith/Applications/Ureka/variants/common/lib/python2.7/UserDict.py", line 23, in getitem
raise KeyError(key)
KeyError: 'UR_DIR'
I realized it hated Ureka, so I disabled that with ur_forget, and tried again... it got much farther this time, but still didn't work. I'm pretty sure something terrible is happening with libraries. I know I had architecture errors like this in the past for other monstrous codes, but don't remember the specifics of how (or if) I resolved the issues. Here are (hopefully) the relevant bits:

ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make: *** [MOOG] Error 1
gfortran -Wall -O4 -ffixed-line-length-72 -ff2c  -c -o Moogsilent.o Moogsilent.f
gfortran Abfind.o Abpop.o Abunplot.o Batom.o Begin.o Binary.o Binplot.o Binplotprep.o Blends.o Bmolec.o Boxit.o Calmod.o Cdcalc.o Chabund.o Cog.o Cogplot.o Cogsyn.o Correl.o Crosscorr.o Curve.o Damping.o Defcolor.o Discov.o Doflux.o Drawcurs.o Eqlib.o Estim.o Ewfind.o Ewweighted.o Fakeline.o Findtic.o Finish.o Fluxplot.o Gammabark.o Getasci.o Getcount.o Getnum.o Gridplo.o Gridsyn.o Infile.o Inlines.o Inmodel.o Invert.o Jexpint.o Lineinfo.o Lineabund.o Linlimit.o Makeplot.o Minimax.o Molquery.o Moogsilent.o Mydriver.o Nansi.o Nearly.o Number.o Obshead.o Oneline.o Opaccouls.o OpacHelium.o OpacHydrogen.o Opacit.o Opacmetals.o Opacscat.o Params.o Partfn.o Partnew.o Plotit.o Plotremember.o Pltabun.o Pltcog.o Pltflux.o Pltspec.o Pointcurs.o Prinfo.o Putasci.o Readobs.o Rinteg.o Smooth.o Specplot.o Stats.o Sunder.o Synpop.o Synspec.o Synth.o Taukap.o Total.o Trudamp.o Ucalc.o Vargauss.o Vmacro.o Voigt.o Wavecalc.o Weedout.o Writenumber.o -o MOOGSILENT -L/usr/X11R6/lib -lX11 \
    -L/private/tmp/pip_build_root/moog/lib/smlib -lplotsub -ldevices -lutils -L/private/tmp/pip_build_root/moog/lib/aqlib -laquaterm
ld: warning: ld: warning: ld: warning: ld: warning: ignoring file /private/tmp/pip_build_root/moog/lib/aqlib/libaquaterm.dylib, missing required architecture x86_64 in file /private/tmp/pip_build_root/moog/lib/aqlib/libaquaterm.dylib (2 slices)ignoring file /private/tmp/pip_build_root/moog/lib/smlib/libutils.a, file was built for archive which is not the architecture being linked (x86_64): /private/tmp/pip_build_root/moog/lib/smlib/libutils.aignoring file /private/tmp/pip_build_root/moog/lib/smlib/libdevices.a, file was built for archive which is not the architecture being linked (x86_64): /private/tmp/pip_build_root/moog/lib/smlib/libdevices.aignoring file /private/tmp/pip_build_root/moog/lib/smlib/libplotsub.a, file was built for archive which is not the architecture being linked (x86_64): /private/tmp/pip_build_root/moog/lib/smlib/libplotsub.a



Undefined symbols for architecture x86_64:
  "_sm_alpha__", referenced from:
      _drawcurs_ in Drawcurs.o
      _makeplot_ in Makeplot.o
      _pointcurs_ in Pointcurs.o

[ long list of other undefined symbols here ]

ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make: *** [MOOGSILENT] Error 1
running install
running build
running build_scripts
creating build
creating build/scripts-2.7
error: file '/private/tmp/pip_build_root/moog/moog/MOOG' does not exist
Complete output from command /usr/bin/python -c "import setuptools, tokenize;__file__='/private/tmp/pip_build_root/moog/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-lEz0v2-record/install-record.txt --single-version-externally-managed --compile:
gfortran -Wall -O4 -ffixed-line-length-72 -ff2c  -c -o Abfind.o Abfind.f

... and finally ...

Cleaning up...
Removing temporary dir /private/tmp/pip_build_root...
Command /usr/bin/python -c "import setuptools, tokenize;file='/private/tmp/pip_build_root/moog/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-lEz0v2-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /private/tmp/pip_build_root/moog
Exception information:
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/pip/basecommand.py", line 122, in main
status = self.run(options, args)
File "/Library/Python/2.7/site-packages/pip/commands/install.py", line 283, in run
requirement_set.install(install_options, global_options, root=options.root_path)
File "/Library/Python/2.7/site-packages/pip/req.py", line 1435, in install
requirement.install(install_options, global_options, _args, *_kwargs)
File "/Library/Python/2.7/site-packages/pip/req.py", line 706, in install
cwd=self.source_dir, filter_stdout=self._filter_install, show_stdout=False)
File "/Library/Python/2.7/site-packages/pip/util.py", line 697, in call_subprocess
% (command_desc, proc.returncode, cwd))
InstallationError: Command /usr/bin/python -c "import setuptools, tokenize;file='/private/tmp/pip_build_root/moog/setup.py';exec(compile(getattr(tokenize, 'open', open)(file).read().replace('\r\n', '\n'), file, 'exec'))" install --record /tmp/pip-lEz0v2-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /private/tmp/pip_build_root/moog
—
Reply to this email directly or view it on GitHub.

[mrawls]

Interesting. Thanks for the speedy reply! My supermongo install is entirely independent of Ureka, though, and seems to be working fine. Installing just moogsilent doesn't work with Ureka enabled or disabled, but the errors are different now: https://gist.github.com/mrawls/bf58a5062e1f074ea520

(this try is with Ureka enabled, since that's my preference, and the errors looked basically the same either way at a glance)

I'm on OS X 10.10.1 with the latest Xcode and everything.

[andycasey]

OK. I won't be able to resolve this now, so I will have to look into this in more detail later.

Thanks for filing the issue!

Andy

On 17 Dec 2014, at 9:38 am, Meredith Rawls notifications@github.com wrote:

Interesting. Thanks for the speedy reply! My supermongo install is entirely independent of Ureka, though, and seems to be working fine. Installing just moogsilent doesn't work with Ureka enabled or disabled, but the errors are different now: https://gist.github.com/mrawls/bf58a5062e1f074ea520

(this try is with Ureka enabled, since that's my preference, and the errors looked basically the same either way at a glance)

I'm on OS X 10.10.1 with the latest Xcode and everything.

—
Reply to this email directly or view it on GitHub.

[andycasey]

Hi @mrawls, sorry about the late reply on this.

Ureka is continuing to cause problems. In your gist I can see at https://gist.github.com/mrawls/bf58a5062e1f074ea520#file-moogsilent-take-1-L2834 that the folder for moogsilent is being truncated, causing the Fortran build to fail.

Try downloading the moogsilent code directly from GH (on the 'batch' branch of this repo) using this link:

https://github.com/andycasey/moog/archive/batch.zip

And put it in a folder name that's not unreasonably long. Then run python setup.py install --user (or sudo if you need it) to install MOOGSILENT. That should work.

[mrawls]

Thanks for tracking down the issue. Smells like Fortran all right! This seems to have worked... I have an executable called MOOGSILENT now, and it even seems to work. Do you think I could install "full" MOOG in a similar way? I do have supermongo etc... right now I tend to manually iterate a lot when running MOOG, so the real-time plots are rather important.

Regardless, thank you!

[andycasey]

If Ureka is no longer playing up, you might be able to get the full MOOG in a similar way.

Try downloading this repository and installing it with:

git clone git@github.com:andycasey/moog.git moog
cd moog
sudo python setup.py install

[mrawls]

Hmm. Close... it is whining about 32-bit vs. 64-bit things. I see you are explicitly handling the SMLIB and AQLIB business in setup.py, and that you default to 32-bit, which is probably because 64-bit things aren't available. But my machine isn't happy about it... I get several 'ld: symbol(s) not found for architecture x86_64' errors for supermongo-related stuff. Similar errors happened when I tried to install "real" MOOG and wasn't pointing to the proper libraries in the Makefile, I believe. The full output is in the gist. FWIW, my supermongo lives in /usr/local/bin.

[andycasey]

Ah, actually I think SuperMongo might be a real problem on 10.10. I have never installed it on 10.10 myself, and I know a few people who have tried without success. Ben Thompson did get it to work successfully, but it wasn't pretty: http://bathompso.com/blog/moog/

Sorry Meredith, I think this is at the limit where I am helpful.

[mrawls]

Good heavens, that's a pile of fun right there... thanks much for the pointer and your patience :) I'll go ahead and close this since the issue seems to mostly be Yosemite (sigh). Thank you again for your time!

[mrawls]

Update for any future souls with similarly poor life choices:

My issue was ACTUALLY RESOLVED thanks to @bathompso. There are binaries of the June 2014 version of MOOG in his fork of @andycasey's moog repo, and I literally just copied them over and they seem to work. Miracles exist.

Get the binaries here
https://github.com/bathompso/moog/tree/master/bin

And be sure to also read the notes here
http://bathompso.com/blog/moog/

[jtmyles]

Thanks for this info -- but unfortunately the binaries aren't working for me right now on Yosemite 10.10.4. I have sm working (on it's own -- I don't have scisoft). The error I get when I use $MOOG is:

open: No such file or directory apparent state: unit 35 named /.moog/Barklem.dat lately writing sequential formatted external IO Abort trap: 6

But I do have .moog in my home folder, and it has the Barklem files inside, and both the directory and files have been made readable/writable with:

$sudo chmod +rw .moog and $sudo chmod +rw Bark*

Were there any other details you worked through to get the binaries working? Any advice would be appreciated. Thank you. I've also posted on astronomy stack exchange

[bathompso]

The difference between Andy's version of the installer and mine is that I place the Barklem datafiles into a "globally-accessible" folder: /.moog (the root of your hard drive, not your user folder). The problem may be just moving that .moog folder to / instead of ~/

[jtmyles]

Solved -- thank you, Ben!

[bathompso]

My README documentation is quite lacking, and it something on my to-do list, so that it's a bit easier to understand what my forked changes are. Glad it's all sorted out.