Athena and Artemis installation problem

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Wuhib Tamrat

26 Oct 2015 26 Oct '15

9:42 a.m.

Hi all, This is with regard to an installation problem that I am facing at the moment on my Mac. Sorry, if this is too basic a problem and the email is spamming your mail box. Below are specifics of three fold problems that I would be happy if I could find a solution for at least one. Problem1: I am working on El Capitan (the latest Mac Operating System) and what I guess the problem to be is compatibility issues with the different required components (X11, XQuartz and Aqua term). And may be with the required macports as well. I installed using the disk image provided on http://cars9.uchicago.edu/ifeffit/Downloads http://cars9.uchicago.edu/ifeffit/Downloads and had followed all the instructions given. I see that the latest OS available is for ‘Snow Leopard’ but the package works well on colleagues’ computers with latter versions of mac OS. The problem is that all get installed but when I open the software suit, the initial small window that has the three individual programs opens but what ever I do to it afterwards it does not open into anything else. There is also the option to choose a file. So I navigate and choose a file thinking it will help pushing the program to open but that leads to nowhere as well. So, I am wondering if anybody had faced similar problem installing on the latest versions of mac OS and has a solution. Problem 2: Initially I tried installing the “demeter” suit via ‘Terminal’ as specified in the site [http://bruceravel.github.io/demeter/ http://bruceravel.github.io/demeter/]. By writing a command on Terminal as opposed to with a disc image as in the case of Problem 1). My operating system at that time was Yosemite. All worked as explained on the website, even writing “athena” on a terminal window calls the program Athena. But that is just it, no explanation as how to call Artemis or Hephaestus exist on the site. So I am wondering if the installation procedure given on the site works also with the other two programs and if so, is there a way to open them or call them via ’Terminal'. Problem 3: My last problem was when Athena closed unexpectedly. As most programs, Athena had an auto recover option which opens when it is restarted. But this time the auto recover option always comes up and this option renders the whole program inactive; “Application Not Responding”. Every time I open Athena, “Auto recover” option comes up and Athena become unresponsive. I tried updating the software in hope of changing something but that did not change anything. Uninstalling it is also a problem because there were no files that I could find to uninstall from or delete. I could not find the location where terminal installed the “Demeter” suit. There is a way to delete on terminal by writing “Sudo rm-rf/file name” but that is not removing “demeter” either. And yes, I have consulted the IT/informatics people at my institution and they were no help. I thank you in advance for any suggestion or similar experience sharing. And also for baring with me reading this long mail. Regards Wuhib

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Bruce Ravel

26 Oct 26 Oct

1:35 p.m.

I am going to preface this comment, as I do with many about the Mac package, by reminding you that I do not own a Mac and do not have any personal experience running my own software on a Mac. The Mac package is graciously maintained by Joe Fowler, not because it is in his job description to do so, but because he is a good and helpful guy.

...

_Problem 2:_ Initially I tried installing the “demeter” suit via ‘Terminal’ as specified in the site [http://bruceravel.github.io/demeter/]. By writing a command on Terminal as opposed to with a disc image as in the case of Problem 1). My operating system at that time was Yosemite. All worked as explained on the website, even writing “athena” on a terminal window calls the program Athena. But that is just it, no explanation as how to call Artemis or Hephaestus exist on the site. So I am wondering if the installation procedure given on the site works also with the other two programs and if so, is there a way to open them or call them via ’Terminal'.

So .... do I understand this correctly? The program "Athena" is executed by typing "athena" at the command line and your question is about how to start "Artemis" or "Hephaestus"? I would think that the answer was obvious, but perhaps one of the Mac users on the list could weight in.

...

_Problem 3:_ My last problem was when Athena closed unexpectedly. As most programs, Athena had an auto recover option which opens when it is restarted. But this time the auto recover option always comes up and this option renders the whole program inactive; “Application Not Responding”. Every time I open Athena, “Auto recover” option comes up and Athena become unresponsive. I tried updating the software in hope of changing something but that did not change anything. Uninstalling it is also a problem because there were no files that I could find to uninstall from or delete. I could not find the location where terminal installed the “Demeter” suit. There is a way to delete on terminal by writing “Sudo rm-rf/file name” but that is not removing “demeter” either.

If you start Athena from the terminal, it should write error messages to the terminal when it runs into problems. This is explained in some detail here: http://bruceravel.github.io/demeter/pods/bugs.pod.html and here: http://bruceravel.github.com/demeter/pods/help.pod.html A useful, actionable bug report would include those error messages, which tend to be a lot more helpful for me than this sort of narrative, which is hard for me to understand. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

Wuhib Tamrat

3:33 p.m.

I am assuming the obvious way to execute “Artemis” and “Hephaestus” you were talking about would be to do the same thing as “Athena”; that is to type the name of the software and execute. But, I have tried that for both and it did not work. So I will wait for a response from a Mac expert on that. And when the program becomes unresponsive you guessed error messages might be displayed on the terminal window which I neglected to include in my previous mail. But no error messages exist. Thank you Wuhib

...

On 26 Oct 2015, at 14:35, Bruce Ravel wrote:

I am going to preface this comment, as I do with many about the Mac package, by reminding you that I do not own a Mac and do not have any personal experience running my own software on a Mac. The Mac package is graciously maintained by Joe Fowler, not because it is in his job description to do so, but because he is a good and helpful guy.

...
_Problem 2:_ Initially I tried installing the “demeter” suit via ‘Terminal’ as specified in the site [http://bruceravel.github.io/demeter/]. By writing a command on Terminal as opposed to with a disc image as in the case of Problem 1). My operating system at that time was Yosemite. All worked as explained on the website, even writing “athena” on a terminal window calls the program Athena. But that is just it, no explanation as how to call Artemis or Hephaestus exist on the site. So I am wondering if the installation procedure given on the site works also with the other two programs and if so, is there a way to open them or call them via ’Terminal'.

So .... do I understand this correctly? The program "Athena" is executed by typing "athena" at the command line and your question is about how to start "Artemis" or "Hephaestus"?

I would think that the answer was obvious, but perhaps one of the Mac users on the list could weight in.

...
_Problem 3:_ My last problem was when Athena closed unexpectedly. As most programs, Athena had an auto recover option which opens when it is restarted. But this time the auto recover option always comes up and this option renders the whole program inactive; “Application Not Responding”. Every time I open Athena, “Auto recover” option comes up and Athena become unresponsive. I tried updating the software in hope of changing something but that did not change anything. Uninstalling it is also a problem because there were no files that I could find to uninstall from or delete. I could not find the location where terminal installed the “Demeter” suit. There is a way to delete on terminal by writing “Sudo rm-rf/file name” but that is not removing “demeter” either.

If you start Athena from the terminal, it should write error messages to the terminal when it runs into problems. This is explained in some detail here: http://bruceravel.github.io/demeter/pods/bugs.pod.html and here: http://bruceravel.github.com/demeter/pods/help.pod.html

A useful, actionable bug report would include those error messages, which tend to be a lot more helpful for me than this sort of narrative, which is hard for me to understand.

B

-- Bruce Ravel ------------------------------------ bravel@bnl.gov

National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973

Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Chris Patridge

3:48 p.m.

Hi Wuhib, If these problems persist, instead of relying on Bruce or others, perhaps consider running a free virtual machine of windows to install Demeter. I have a Mac as a main computer and run the software through virtual Windows machine without much of problem. Just a thought, Chris Sent from my iPhone

...

On Oct 26, 2015, at 11:33 AM, Wuhib Tamrat wrote:

I am assuming the obvious way to execute “Artemis” and “Hephaestus” you were talking about would be to do the same thing as “Athena”; that is to type the name of the software and execute. But, I have tried that for both and it did not work. So I will wait for a response from a Mac expert on that.

And when the program becomes unresponsive you guessed error messages might be displayed on the terminal window which I neglected to include in my previous mail. But no error messages exist.

Thank you

Wuhib

...
On 26 Oct 2015, at 14:35, Bruce Ravel wrote:

I am going to preface this comment, as I do with many about the Mac package, by reminding you that I do not own a Mac and do not have any personal experience running my own software on a Mac. The Mac package is graciously maintained by Joe Fowler, not because it is in his job description to do so, but because he is a good and helpful guy.

...
_Problem 2:_ Initially I tried installing the “demeter” suit via ‘Terminal’ as specified in the site [http://bruceravel.github.io/demeter/]. By writing a command on Terminal as opposed to with a disc image as in the case of Problem 1). My operating system at that time was Yosemite. All worked as explained on the website, even writing “athena” on a terminal window calls the program Athena. But that is just it, no explanation as how to call Artemis or Hephaestus exist on the site. So I am wondering if the installation procedure given on the site works also with the other two programs and if so, is there a way to open them or call them via ’Terminal'.

So .... do I understand this correctly? The program "Athena" is executed by typing "athena" at the command line and your question is about how to start "Artemis" or "Hephaestus"?

I would think that the answer was obvious, but perhaps one of the Mac users on the list could weight in.

...
_Problem 3:_ My last problem was when Athena closed unexpectedly. As most programs, Athena had an auto recover option which opens when it is restarted. But this time the auto recover option always comes up and this option renders the whole program inactive; “Application Not Responding”. Every time I open Athena, “Auto recover” option comes up and Athena become unresponsive. I tried updating the software in hope of changing something but that did not change anything. Uninstalling it is also a problem because there were no files that I could find to uninstall from or delete. I could not find the location where terminal installed the “Demeter” suit. There is a way to delete on terminal by writing “Sudo rm-rf/file name” but that is not removing “demeter” either.

If you start Athena from the terminal, it should write error messages to the terminal when it runs into problems. This is explained in some detail here: http://bruceravel.github.io/demeter/pods/bugs.pod.html and here: http://bruceravel.github.com/demeter/pods/help.pod.html

A useful, actionable bug report would include those error messages, which tend to be a lot more helpful for me than this sort of narrative, which is hard for me to understand.

B

-- Bruce Ravel ------------------------------------ bravel@bnl.gov

National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973

Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ 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

Matt Newville

28 Oct 28 Oct

1:59 a.m.

New subject: *****SPAM*****Re: Athena and Artemis installation problem

Hi Wuhib, Sorry to jump in a little late. On Mon, Oct 26, 2015 at 4:42 AM, Wuhib Tamrat wrote:

...

Hi all, This is with regard to an installation problem that I am facing at the moment on my Mac. Sorry, if this is too basic a problem and the email is spamming your mail box. Below are specifics of three fold problems that I would be happy if I could find a solution for at least one.

*Problem1:* I am working on El Capitan (the latest Mac Operating System) and what I guess the problem to be is compatibility issues with the different required components (X11, XQuartz and Aqua term). And may be with the required macports as well. I installed using the disk image provided on http://cars9.uchicago.edu/ifeffit/Downloads and had followed all the instructions given. I see that the latest OS available is for ‘Snow Leopard’ but the package works well on colleagues’ computers with latter versions of mac OS. The problem is that all get installed but when I open the software suit, the initial small window that has the three individual programs opens but what ever I do to it afterwards it does not open into anything else. There is also the option to choose a file. So I navigate and choose a file thinking it will help pushing the program to open but that leads to nowhere as well. So, I am wondering if anybody had faced similar problem installing on the latest versions of mac OS and has a solution.

This will absolutely not work. No chance, don't even bother trying. This is a very, very outdated version of Athena/Artemis. As you no doubt read at the top of that Downloads page, this is no longer supported. The link should probably be removed.

...

*Problem 2:* Initially I tried installing the “demeter” suit via ‘Terminal’ as specified in the site [http://bruceravel.github.io/demeter/]. By writing a command on Terminal as opposed to with a disc image as in the case of Problem 1). My operating system at that time was Yosemite. All worked as explained on the website, even writing “athena” on a terminal window calls the program Athena. But that is just it, no explanation as how to call Artemis or Hephaestus exist on the site. So I am wondering if the installation procedure given on the site works also with the other two programs and if so, is there a way to open them or call them via ’Terminal'.

I can't tell from this what you did at the command line. For El Capitan you will absolutely have to upgrade Xcode, and it's command-line tools, as instructed in the MacPorts page referenced. I upgraded to El Capitan this past weekend. I upgraded Xcode and blew away the Macports install, and tried to do a clean install of demeter with "sudo port install demeter". Unfortunately, the default macports install would install from source and needs to build libgcc, gcc4.9 and gcc 5.2 all from source. This takes many hours. The best word available in the English language to describe this is "idiotic". Macports *does* allow binary installs (port install -b). This is faster. Unfortunately, I've hit snags with that too (expat, for example, fails to build this way). I'll keep trying. I am not convinced that Macports is a good way to be distributing Demeter. Has any tried building Demeter with Homebrew? I haven't yet, but installed several homebrew packages, including gfortran, python, many python packages with no trouble at all. I haven't tried building wx Perl. But it seems like there is no chance it can be worse than MacPorts. I'll try that too.

...

*Problem 3:* My last problem was when Athena closed unexpectedly. As most programs, Athena had an auto recover option which opens when it is restarted. But this time the auto recover option always comes up and this option renders the whole program inactive; “Application Not Responding”. Every time I open Athena, “Auto recover” option comes up and Athena become unresponsive. I tried updating the software in hope of changing something but that did not change anything. Uninstalling it is also a problem because there were no files that I could find to uninstall from or delete. I could not find the location where terminal installed the “Demeter” suit. There

is a way to delete on terminal by writing “Sudo rm-rf/file name” but that

...

is not removing “demeter” either.

Wait, did Demeter get installed or not? I cannot tell. If you're trying to run an older version that will absolutely not work. Anyway, sorry for the trouble, and I wish I had a working Demeter too. I'll keep trying.... --Matt

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Bruce Ravel
Chris Patridge
Matt Newville
Wuhib Tamrat