Dear Alison/ and All,
        As you suggested I tried to install the demeter and xorg separately. As you expected the xorg installation went very well and was complete. However, when i tried to install demeter-devel it did not go well and I had following error.
 Attempting to fetch 1.2.final.tar.gz from http://cjj.kr.distfiles.macports.org/ifeffit
--->  Verifying checksums for p5.16-ifeffit                                    
--->  Extracting p5.16-ifeffit
--->  Configuring p5.16-ifeffit
--->  Building p5.16-ifeffit
Error: org.macports.build for port p5.16-ifeffit returned: command execution failed
Error: Failed to install p5.16-ifeffit

Then there was log file which is attached to this email including other steps i did. and then following error again.

To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port demeter-devel failed

So as you expected there was a problem installing demeter-devel.
any help in this aspect will be highly appreciated. I am not sure if this is a bug and can be fixed easily? shoudl I just try once more? I am afraid that i would mess up again by multiple installation.
Thank you very much for help and pursuing this prooblem to be solved.

Sincerely
Pushkar


On Tue, Sep 2, 2014 at 2:16 AM, Alison Tebo <agtebo@umich.edu> wrote:
Hi Pushkar,
I messed up and said athena is its own port--it's not, Athena, Artemis, and Hephaestus all go with demeter-devel. Sorry about that! xorg-server and demeter-devel are two separate ports. Since you're having trouble installing them, I would highly recommend that you do them separately so you know which one is broken.  I'm not sure if libgcc is a dependency of X11 or Demeter, probably Demeter though. Either way, if you get a truncation of the installation like that, then Athena, Artemis, and Hephaestus won't work.  

Best,
Alison


On Mon, Sep 1, 2014 at 11:33 AM, pushkar shejwalkar <pshejwalkar2004@gmail.com> wrote:
Dear Alison,
    Thank you very much for the response. Sorry for the earlier email not being detailed. I will try to explain everything in detail this time.
As you suggested, I uninstalled macports and then  XQuartz (Essentially I googled how to do it and followed the steps they said)
sudo rm -rf \
    /opt/local \
    /Applications/DarwinPorts \
    /Applications/MacPorts \
    /Library/LaunchDaemons/org.macports.* \
    /Library/Receipts/DarwinPorts*.pkg \
    /Library/Receipts/MacPorts*.pkg \
    /Library/StartupItems/DarwinPortsStartup \
    /Library/Tcl/darwinports1.0 \
    /Library/Tcl/macports1.0 \
    ~/.macports
after this I reinstalled macports by double clicking my earlier downloaded file. After that I 
reinstalled xorg by typing the sudo port install xorg-server demeter-devel command. this time it took too 





long to install. Essentially I could see individual things getting checked downloaded and cleaned
etc. but the error message occured towards the end




-->  Attempting to fetch
libmpc-1.0.2_0.darwin_13.x86_64.tbz2.rmd160 from
http://packages.macports.org/libmpc

--->  Installing libmpc @1.0.2_0

--->  Activating libmpc @1.0.2_0

--->  Cleaning libmpc

--->  Fetching archive for libgcc

--->  Attempting to fetch libgcc-4.9.1_0.darwin_13.x86_64.tbz2 from http://packages.macports.org/libgcc

--->  Attempting to fetch libgcc-4.9.1_0.darwin_13.x86_64.tbz2.rmd160 from http://packages.macports.org/libgcc

Error: org.macports.archivefetch for port libgcc returned: Failed to fetch signature for archive: Connection timed out after 30023 milliseconds

Error: Failed to install libgcc

Please see the log file for port libgcc for details:

The log file is attached to this email. neverthless I still logged out by typing logout in terminal 
(if thats what it means) and clicked terminal again. this time I checked the $DISPLAY command and it





showed the following message.

Last login: Mon Sep  1 23:18:41 on ttys000

Pushkar-Shejwalkars-MacBook:~ Pushkar$ echo $DISPLAY

/tmp/launch-WZNfFS/org.macosforge.xquartz:0

after this I typed 

sudo port install athena
and error read as 

Error: Port athena not found

Pushkar-Shejwalkars-MacBook:~ Pushkar$ athena

-bash: athena: command not found

Pushkar-Shejwalkars-MacBook:~ Pushkar$ sudo port install athena

Error: Port athena not found

Pushkar-Shejwalkars-MacBook:~ Pushkar$

Please tell me what did I do wrong? I am sure I am missing something here very important step.
Thanks a lot for your help. Hope to hear back with some possible suggestions.
Best




Pushkar


On Mon, Sep 1, 2014 at 11:49 AM, Alison Tebo <agtebo@umich.edu> wrote:
Hi Pushkar,

It's a little hard to tell what you did and in what order. When you activated Macports and then installed athena did you type something like 'sudo port install xorg-server athena'? Is that when you first came across the library duplicate? When you tried to run athena, what error did you get? You didn't report this. It sounds like you might have installed xorg-server (which is the same thing you downloaded from the XQuartz site) and didn't logout and then back in to reset your DISPLAY variable and then downloaded it again manually, messing up your ports. I can't really tell from the information you gave. What is the output of typing echo $DISPLAY? 

What I would do: start over. Uninstall all of your X11s. For the XQuartz one start here: http://xquartz.macosforge.org/trac/wiki/X11-UsersFAQ. For the Macports one, uninstall and clean both the 'athena' and 'xorg-server' ports. Then, reinstall xorg-server by itself. Log out and then back in. Then type echo $DISPLAY. Your DISPLAY variable should be something like /tmp/launch-XXXXXX/org.macports:0.  Then install athena (sudo port install athena). Are there any errors? If so, what are they?

I'm not very knowledgable about this stuff but this seems like a pretty reasonable first step to me. Since I'm on an older Mac OS, if there's 10.9-specific issues I won't be much help. Hopefully this resolves your issues.

Best,
Alison


On Sun, Aug 31, 2014 at 1:50 AM, pushkar shejwalkar <pshejwalkar2004@gmail.com> wrote:
Dear All,
            I am new to the mac and mac apps as well as not a techie either. I am trying to install the latest version of demeter (artemis, athena and heph) on my macbook using Mavericks OS. For this I followed the steps given on the site with Macports installation, then its activation step. and then I used terminal to connect and download the athena. However there was error which I thought might because of not having the windowing environment ( I am using all the words from site and dont know anything what it means). So I clicked to download X11 from XQuartz site. After that I logged out from terminal and logged in again. to check if anything changes but the following message was observed (the complete message is attached as word document but some part essentially the last portion talking about the error is pasted below.

--->  Activating xorg-libXau @1.0.8_0

Error: org.macports.activate for port xorg-libXau returned: Image error: /opt/local/lib/libXau.6.dylib already exists and does not belong to a registered port.  Unable to activate port xorg-libXau. Use 'port -f activate xorg-libXau' to force the activation.

Error: Failed to install xorg-libXau

Please see the log file for port xorg-libXau for details:

    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_x11_xorg-libXau/xorg-libXau/main.log

Error: The following dependencies were not installed: quartz-wm xorg-libAppleWM xorg-libXext xorg-libX11 xorg-libXau xorg-libXdmcp xorg-libxcb python27 bzip2 db46 db_select gettext expat libiconv ncurses libedit openssl zlib python_select sqlite3 xorg-libpthread-stubs xorg-xcb-proto libxml2 xz xorg-xextproto xorg-libXinerama xorg-xineramaproto xorg-libXrandr xorg-randrproto xrender xorg-renderproto xinit mkfontdir mkfontscale freetype libpng xorg-libfontenc xauth xorg-libXmu xorg-libXt xorg-libsm xorg-libice xrdb xset xorg-libXfontcache xorg-fontcacheproto xorg-libXp xorg-printproto xorg-libXxf86misc xorg-xf86miscproto xkeyboard-config xkbcomp xorg-libxkbfile xorg-fonts font-adobe-100dpi fontconfig font-adobe-75dpi font-adobe-utopia-100dpi font-adobe-utopia-75dpi font-adobe-utopia-type1 font-alias font-arabic-misc font-bh-100dpi font-bh-75dpi font-bh-lucidatypewriter-100dpi font-bh-lucidatypewriter-75dpi font-bh-ttf font-bh-type1 font-bitstream-100dpi font-bitstream-75dpi font-bitstream-speedo font-bitstream-type1 font-cronyx-cyrillic font-cursor-misc font-daewoo-misc font-dec-misc font-ibm-type1 font-isas-misc font-jis-misc font-micro-misc font-misc-cyrillic font-misc-ethiopic font-misc-meltho font-misc-misc font-mutt-misc font-schumacher-misc font-screen-cyrillic font-sony-misc font-sun-misc font-winitzki-cyrillic font-xfree86-type1 xorg-encodings xorg-libXfixes xorg-fixesproto xorg-libXfont xorg-fontsproto

To report a bug, follow the instructions in the guide:

    http://guide.macports.org/#project.tickets

Error: Processing of port xorg-server failed

Pushkar-Shejwalkars-MacBook:~ Pushkar$

 

Please help me installing it properly. Really very sorry for the long email but I thought it will be more helpful this way.
Waiting for the replies.
Thank you very much

--
Best Regards,
Pushkar Shejwalkar.
Post-doctoral -Researcher,JSPS Fellow
Hokkaido University,
Sapporo,
Japan


_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit



_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit




--
Best Regards,
Pushkar Shejwalkar.
Post-doctoral -Researcher,JSPS Fellow
Hokkaido University,
Sapporo,
Japan


_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit



_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit




--
Best Regards,
Pushkar Shejwalkar.
Post-doctoral -Researcher,JSPS Fellow
Hokkaido University,
Sapporo,
Japan