Thank you for this Zack. I have updated the text under the "Macintosh Installation" section of the Demeter home page (http://bruceravel.github.io/demeter/#mac) to try to capture some of what you said. If you (or anyone else) have any suggestions for improvements to the text on the Demeter homepage, please speak up. If you would like to provide a link to or text for a more substantial Mac installation guide, I would welcome that. Thanks, B On 11/09/2015 12:43 PM, Zack Gainsforth wrote:

I am running under El Capitan and previously under Yosemite. I didn’t really have trouble with the installation, though I do note that after you upgrade the OS, you need to reinstall ALL of macports from scratch sometimes. That means nuke the old directory, download macports from the website and install it and then install each package. And have patience, it can take hours to install all dependencies. I usually let it run overnight.

I’m also using XQuartz.

Macports has documentation about doing this:

https://trac.macports.org/wiki/Migration

and if that fails:

https://guide.macports.org/chunked/installing.macports.uninstalling.html

I would try reinstall first, and then if there is still trouble, dig deeper.

Zack

(Note, I’ve only used Hephaestus and Athena on El Capitan. But Artemis worked for me on Yosemite.)

-- 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/

Dear all, Thank you for your feedbacks. After several attempts, I was finally successful with the installation of Demeter. I attach a log file summarizing the different steps I experienced (and a screenshot of the main window). I guess step 2 and 5 would have been enough: xcode-select --install sudo port install demeter Indeed, several hours were required for the whole installation procedure (more than 9 hours, but my internet connection is quite slow at home...). I can now execute athena from the terminal, and apparently it works fine. However, I observe a strange behavior : After athena is running, I must click once on the terminal window before the main menus are active in Demeter (File, Group, Energy, etc.). But when we know that, it’s ok. And the most important, I don’t have any graphical window to display the spectra. Would you have any suggestion? (Xquartz and Aquaterm are already installed on my computer). Thank you again for your help! Manuel

Le 9 nov. 2015 à 22:58, Matt Newville a écrit :

Hi Zack,

Thanks -- I had a very bad time trying a fresh install of macports on El Capitan, with several successive errors with Xorg and various packages. I also think that macports needing to install 2 different versions of gcc from source is really quite ridiculous and we should not be relying on such a system.

Anyway, I'll try your suggestions and report back here.

--Matt

On Mon, Nov 9, 2015 at 11:43 AM, Zack Gainsforth mailto:zackg@berkeley.edu> wrote: I am running under El Capitan and previously under Yosemite. I didn’t really have trouble with the installation, though I do note that after you upgrade the OS, you need to reinstall ALL of macports from scratch sometimes. That means nuke the old directory, download macports from the website and install it and then install each package. And have patience, it can take hours to install all dependencies. I usually let it run overnight.

I’m also using XQuartz.

Macports has documentation about doing this:

https://trac.macports.org/wiki/Migration https://trac.macports.org/wiki/Migration

and if that fails:

https://guide.macports.org/chunked/installing.macports.uninstalling.html https://guide.macports.org/chunked/installing.macports.uninstalling.html

I would try reinstall first, and then if there is still trouble, dig deeper.

Zack

(Note, I’ve only used Hephaestus and Athena on El Capitan. But Artemis worked for me on Yosemite.)

...

On Nov 9, 2015, at 8:20 AM, Fowler, Joseph W. mailto:joe.fowler@nist.gov> wrote:

Bruce, Scott, Manuel:

I’m the MacPorts maintainer for demeter and ifeffit, but I’m afraid I have not been much help lately.

I’m sorry that I have not chimed in about any of the recent reports Mac / Macports problems under El Capitan. It so happens that my employer (US National Institute of Standards and Technology) does not let us upgrade to Yosemite OR El Capitan. They own the only Macs to which I have access, so I can only work under Mavericks. I’m afraid that artemis, hephaestus, and athena all start properly for me.

To Manuel from Grenoble, all I can say is that xorg-server has a lot of dependencies, and it will take a long time to install the needed ports the first time. I would not think an entire hour is out of the question, depending on your connection speed and computer performance.

To the others having trouble running (as opposed to installing), I wonder if anyone in the community is having success with the demeter suite under El Capitan? If so, we’d all be grateful if you could let us know what tricks were required. I am totally helpless on OS 10.10 and 10.11-specific problems.

Joe Fowler NIST Boulder Laboratories

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-- --Matt Newville http://cars.uchicago.edu/> 630-252-0431 _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

-- Manuel Muñoz Institut des Sciences de la Terre Université Joseph Fourier 1381 rue de la piscine – BP53 38041 Grenoble cedex 9 – France Tel.: 33 (0)4 76 51 40 54 – Fax: 33 (0)4 76 63 52 52

Hi Manuel, On Thu, Nov 12, 2015 at 3:45 AM, Muñoz Manuel wrote:

Dear all,

Thank you for your feedbacks.

After several attempts, I was finally successful with the installation of Demeter. I attach a log file summarizing the different steps I experienced (and a screenshot of the main window). I guess step 2 and 5 would have been enough: xcode-select --install sudo port install demeter

Indeed, several hours were required for the whole installation procedure (more than 9 hours, but my internet connection is quite slow at home...).

I can now execute athena from the terminal, and apparently it works fine. However, I observe a strange behavior : After athena is running, I must click once on the terminal window before the main menus are active in Demeter (File, Group, Energy, etc.). But when we know that, it’s ok.

And the most important, I don’t have any graphical window to display the spectra. Would you have any suggestion? (Xquartz and Aquaterm are already installed on my computer).

Thank you again for your help! Manuel

That's great that it worked for you. I tried again with a completely fresh install of MacPorts, starting a few days ago, and again, it did not work for me. To be clear, I have Xcode and command-line tools (as from xcode-select --install ) installed, and can compile and build many programs. Starting with installing the latest MacPorts package, the initial ~> sudo port -v selfupdate works fine. Similar to what you saw, ~> sudo port install xorg-server also works, but takes at least 8 hours. Really. For me ~> sudo port install demeter took about two days of running close to full time, And it failed. As I mentioned earlier, the demeter package depends on llvm, libgcc, gcc4.9 and gcc5.2 all of which must be built FROM SOURCE, which is completely, utterly stupid. Really, this alone pretty much convinces me that MacPorts is not a good solution for distributing Athena for Mac OS X. More later. Anyway building all these compilers and effectively building an isolated BSD user-space from source did work, and most of the dependencies and perl modules correctly installed. What failed to install was perl-5.22-pdl. This gave a compilation error using some GSL component. I uninstalled the gsl port, successfully installed the rest of the perl modules, and got the point where ~> sudo port -v install demeter reports ---> Computing dependencies for demeter.... ---> Dependencies to be installed: p5.22-pdl gsl p5.22-pdl-stats That is, all other required components (including the wxPerl package) were installed. GSL (2.0) does install, but p5.22-pdl fails with with ========================== ... /usr/bin/clang -c "-I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-pdl/p5.22-pdl/work/PDL-2.013/Basic/Core" -I/opt/local/include -pipe -Os -fno-common -DPERL_DARWIN -I/opt/local/include -fno-strict-aliasing -fstack-protector-strong -I/opt/local/include -arch x86_64 -O3 -DVERSION=\"2.013\" -DXS_VERSION=\"2.013\" "-I/opt/local/lib/perl5/5.22/darwin-thread-multi-2level/CORE" ELLINT.c ELLINT.xs:1736:159: error: too many arguments to function call, expected 4, have 5 GSLERR(gsl_sf_ellint_D_e,((phi_datap)[0] PDL_COMMENT("ACCESS()") ,(k_datap)[0] PDL_COMMENT("ACCESS()") ,(n_datap)[0] PDL_COMMENT("ACCESS()") ,GSL_PREC_DOUBLE,&r)) ~~~~~~~~~~~~~~~~~ ^~ ./../gslerr.h:5:37: note: expanded from macro 'GSLERR' #define GSLERR(x,y) if ((status = x y)) {snprintf(buf,200,"Error in %s: %s", #x, gsl_strerror(status));barf("%s", buf);} ^ /opt/local/include/gsl/gsl_sf_ellint.h:84:1: note: 'gsl_sf_ellint_D_e' declared here int gsl_sf_ellint_D_e(double phi, double k, gsl_mode_t mode, gsl_sf_result * result); ^ 1 error generated. ========================== I could not find anything about this with simple searches on the MacPorts or PDL sites, but haven't looked in great detail. I haven't looked in great detail at what might workaround or solve this issue. As I've said before, I find the "install from source" nature of MacPorts to be very problematic, and believe we cannot use this approach. Telling users to set aside 3 days to install Athena and Artemis just doesn't seem reasonable, and that assumes that it works. A main feature of Mac OS X is that it is highly controlled. Binary compatibility should be (and usually is) no problem for a known version of OS X. Thus, the fact that MacPorts EVER installs from source is really hard for me to understand -- this is exactly the case where it is least necessary. That demeter requires 3 separate C compilers to be installed (in addition to the predictable vendor-supplied compiler already available with the system) is very weird. I don't understand why this is necessary. I've looked into using Brew or CitrusPerl, but getting modern versions of these to work with wxPerl seems challenging. I've tried to figure out what MacPorts does to install wxPerl that the others don't, but have had a difficult time figuring out where the MacPorts Portfiles actually are. Like I said, I haven't looked into this in great detail, but MacPorts is not very transparent. I'm also trying to assess using Brew (which, conveniently installs binaries, but inconveniently uses /usr/local instead of its own folder) or other options for Larch. Suggestions on the best way to do these things would be greatly appreciated. --Matt Newville

Hi Matt, I am just guessing here, but Zack and Manuel both mention installing XQuartz, whereas you mention installing xorg-server. While Demeter should work with either, perhaps on the new OS there is a problem installing Demeter with xorg-server and one has to go with xQuartz. Have you tried installing xQuartz or following Zack's instructions exactly? That is installing xQuartz and not installing xorg-server at all? George On Thu, Nov 12, 2015 at 2:00 PM, Zack Gainsforth wrote:

Hi Matt,

I have to agree it is a real annoyance to have to rebuild from scratch — and no there isn’t any great reason why that is better. I’ve always chimed to myself “a macports version is better than no version” whenever I get an arcane fail message from macports.

In the worst case, mac users can always run demeter from within a virtual machine (VMware, Parallels or VirtualBox).

On the other hand, there is a method of using macports to produce a dmg (mac install file). I have never used it, but the command goes like:

sudo port mdmg demeter

https://guide.macports.org/chunked/using.binaries.html

My guess is that there would be a bit of development to make that work, but it is worth looking into. Then, we build it once for each new version and release a dmg.

Zack

On Nov 12, 2015, at 10:53 AM, Matt Newville wrote:

Hi Manuel,

On Thu, Nov 12, 2015 at 3:45 AM, Muñoz Manuel < manuel.munoz@ujf-grenoble.fr> wrote:

...

Dear all,

Thank you for your feedbacks.

After several attempts, I was finally successful with the installation of Demeter. I attach a log file summarizing the different steps I experienced (and a screenshot of the main window). I guess step 2 and 5 would have been enough: xcode-select --install sudo port install demeter

Indeed, several hours were required for the whole installation procedure (more than 9 hours, but my internet connection is quite slow at home...).

I can now execute athena from the terminal, and apparently it works fine. However, I observe a strange behavior : After athena is running, I must click once on the terminal window before the main menus are active in Demeter (File, Group, Energy, etc.). But when we know that, it’s ok.

And the most important, I don’t have any graphical window to display the spectra. Would you have any suggestion? (Xquartz and Aquaterm are already installed on my computer).

Thank you again for your help! Manuel

That's great that it worked for you.

I tried again with a completely fresh install of MacPorts, starting a few days ago, and again, it did not work for me. To be clear, I have Xcode and command-line tools (as from xcode-select --install ) installed, and can compile and build many programs.

Starting with installing the latest MacPorts package, the initial

~> sudo port -v selfupdate

works fine. Similar to what you saw,

~> sudo port install xorg-server

also works, but takes at least 8 hours. Really. For me

~> sudo port install demeter

took about two days of running close to full time, And it failed. As I mentioned earlier, the demeter package depends on llvm, libgcc, gcc4.9 and gcc5.2 all of which must be built FROM SOURCE, which is completely, utterly stupid. Really, this alone pretty much convinces me that MacPorts is not a good solution for distributing Athena for Mac OS X. More later. Anyway building all these compilers and effectively building an isolated BSD user-space from source did work, and most of the dependencies and perl modules correctly installed.

What failed to install was perl-5.22-pdl. This gave a compilation error using some GSL component. I uninstalled the gsl port, successfully installed the rest of the perl modules, and got the point where

~> sudo port -v install demeter

reports ---> Computing dependencies for demeter.... ---> Dependencies to be installed: p5.22-pdl gsl p5.22-pdl-stats

That is, all other required components (including the wxPerl package) were installed. GSL (2.0) does install, but p5.22-pdl fails with with

========================== ... /usr/bin/clang -c "-I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-pdl/p5.22-pdl/work/PDL-2.013/Basic/Core" -I/opt/local/include -pipe -Os -fno-common -DPERL_DARWIN -I/opt/local/include -fno-strict-aliasing -fstack-protector-strong -I/opt/local/include -arch x86_64 -O3 -DVERSION=\"2.013\" -DXS_VERSION=\"2.013\" "-I/opt/local/lib/perl5/5.22/darwin-thread-multi-2level/CORE" ELLINT.c ELLINT.xs:1736:159: error: too many arguments to function call, expected 4, have 5 GSLERR(gsl_sf_ellint_D_e,((phi_datap)[0] PDL_COMMENT("ACCESS()") ,(k_datap)[0] PDL_COMMENT("ACCESS()") ,(n_datap)[0] PDL_COMMENT("ACCESS()") ,GSL_PREC_DOUBLE,&r))

~~~~~~~~~~~~~~~~~ ^~ ./../gslerr.h:5:37: note: expanded from macro 'GSLERR' #define GSLERR(x,y) if ((status = x y)) {snprintf(buf,200,"Error in %s: %s", #x, gsl_strerror(status));barf("%s", buf);} ^ /opt/local/include/gsl/gsl_sf_ellint.h:84:1: note: 'gsl_sf_ellint_D_e' declared here int gsl_sf_ellint_D_e(double phi, double k, gsl_mode_t mode, gsl_sf_result * result); ^ 1 error generated. ==========================

I could not find anything about this with simple searches on the MacPorts or PDL sites, but haven't looked in great detail. I haven't looked in great detail at what might workaround or solve this issue.

As I've said before, I find the "install from source" nature of MacPorts to be very problematic, and believe we cannot use this approach. Telling users to set aside 3 days to install Athena and Artemis just doesn't seem reasonable, and that assumes that it works.

A main feature of Mac OS X is that it is highly controlled. Binary compatibility should be (and usually is) no problem for a known version of OS X. Thus, the fact that MacPorts EVER installs from source is really hard for me to understand -- this is exactly the case where it is least necessary. That demeter requires 3 separate C compilers to be installed (in addition to the predictable vendor-supplied compiler already available with the system) is very weird. I don't understand why this is necessary.

I've looked into using Brew or CitrusPerl, but getting modern versions of these to work with wxPerl seems challenging. I've tried to figure out what MacPorts does to install wxPerl that the others don't, but have had a difficult time figuring out where the MacPorts Portfiles actually are. Like I said, I haven't looked into this in great detail, but MacPorts is not very transparent. I'm also trying to assess using Brew (which, conveniently installs binaries, but inconveniently uses /usr/local instead of its own folder) or other options for Larch.

Suggestions on the best way to do these things would be greatly appreciated.

--Matt Newville _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

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Hi Matt, Thanks for explaining. I didn't realize all of the differences between what you and Zack had done. You mention that the instructions say to install xorg-server. Even so, it is not necessary if you have xQuartz installed. Hopefully this can at least save some people 8 hours! George On Thu, Nov 12, 2015 at 8:37 PM, Matt Newville wrote:

Hi George,

On Thu, Nov 12, 2015 at 7:59 PM, George Sterbinsky < GeorgeSterbinsky@u.northwestern.edu> wrote:

...

Hi Matt,

I am just guessing here, but Zack and Manuel both mention installing XQuartz, whereas you mention installing xorg-server. While Demeter should work with either, perhaps on the new OS there is a problem installing Demeter with xorg-server and one has to go with xQuartz.

I do have XQuartz installed, from before starting to build MacPorts. The installation instructions for demeter say to install xorg-server.

Have you tried installing xQuartz or following Zack's instructions

...

exactly?

Depends on what "exactly" means. ;). I did not "migrate", I built MacPorts from scratch, after completely erasing any trace of MacPorts as described in their own uninstalling description. This was my second attempt at a completely fresh install on El Capitan, and I've installed Demeter with MacPorts on several machines using previous OS / MacPorts / Demeter versions. Something is definitely broken.

...

That is installing xQuartz and not installing xorg-server at all?

The problem I see is not related to X. It's that Perl's PDL does not compile with GSL. I submitted a ticket about this to the MacPorts site.

--Matt

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On 11/13/2015 11:34 AM, Matt Newville wrote:

With that, Demeter then installs, though there are some warnings about missing dependencies (Heap, XMLRPC::Lite, File::Slurp::Tiny, Encoding::FixLatin::XS)

Thanks, Matt. This is helpful. Heap and XMLRPC::Lite are long-time dependencies and are in the Build script. That they are not a dependency of the MacPorts package seems like a MacPorts mistake. File::Slurp::Tiny is obsolete in the sense that between 0.22 and 0.23 I switched from using that module to using one called File::Slurper. Since the current MacPorts package uses Demeter 0.22, F::S::T should have been a dependency, but in the future, it will not be. The dependency on Encoding::FixLatin::XS is a mistake made by me. I made it a recommendation to quiet a spurious warning that happens on Windows but not on linux. (No clue about the Mac.) It's not actually used for anything and I just edited the build script to remove it as a dependency except on Windows. So, if the portfile gets updated, it should be checked to be sure that Heap, XMLRPC::Lite, and (File::Slurp::Tiny | File::Slurper) are properly listed as dependencies and get installed. Thanks, 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/