Hi Frank, Let me start out thanking you for writing and maintaining the OSX build of Demeter. Up until the latest release the different elements Athena, Artemis, and Hephaestus have been running more or less fine. In the latest update, I encountered a build error upon giving the command "port upgrade outdated". Here is the content of the log file. Do you have any advise as to how to proceed? Best wishes, Paul FOns ~ $cat /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/main.log version:1 :msg:clean ---> Computing dependencies for p5.16-ifeffit:info:clean .:debug:clean p5.16-ifeffit has no conflicts :debug:clean Searching for dependency: perl5.16 :debug:clean Found Dependency: receipt exists for perl5.16 :debug:clean Searching for dependency: ifeffit :debug:clean Found Dependency: receipt exists for ifeffit :msg:clean :debug:main Executing org.macports.main (p5.16-ifeffit) :debug:main changing euid/egid - current euid: 0 - current egid: 0 :debug:main egid changed to: 502 :debug:main euid changed to: 503 :debug:main Skipping completed org.macports.archivefetch (p5.16-ifeffit) :debug:main Privilege de-escalation not attempted as not running as root. :debug:main Skipping completed org.macports.fetch (p5.16-ifeffit) :debug:main Privilege de-escalation not attempted as not running as root. :debug:main Skipping completed org.macports.checksum (p5.16-ifeffit) :debug:main Privilege de-escalation not attempted as not running as root. :debug:main Skipping completed org.macports.extract (p5.16-ifeffit) :debug:main Privilege de-escalation not attempted as not running as root. :debug:main Skipping completed org.macports.patch (p5.16-ifeffit) :debug:main Privilege de-escalation not attempted as not running as root. :debug:main Skipping completed org.macports.configure (p5.16-ifeffit) :debug:main Privilege de-escalation not attempted as not running as root. :debug:build build phase started at Mon Aug 25 11:25:07 JST 2014 :notice:build ---> Building p5.16-ifeffit :debug:build Executing org.macports.build (p5.16-ifeffit) :debug:build Environment: CC_PRINT_OPTIONS='YES' CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/work/.CC_PRINT_OPTIONS' CPATH='/opt/local/include' LIBRARY_PATH='/opt/local/lib' MACOSX_DEPLOYMENT_TARGET='10.9' :debug:build Assembled command: 'cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/work/ifeffit-1.2.final/wrappers/perl" && /usr/bin/make -j8 -w all' :debug:build Executing command line: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/work/ifeffit-1.2.final/wrappers/perl" && /usr/bin/make -j8 -w all :info:build make: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/work/ifeffit-1.2.final/wrappers/perl' :info:build rm -f blib/arch/auto/Ifeffit/Ifeffit.bundle :info:build LD_RUN_PATH="/usr/lib" /usr/bin/clang -shared ifeffit_wrap.o -arch x86_64 -o blib/arch/auto/Ifeffit/Ifeffit.bundle \ :info:build /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level/CORE/libperl.dylib -L/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/work/ifeffit-1.2.final/wrappers/perl/../../src/lib -L/opt/local/lib -lifeffit -lnopgplot -L/opt/local/lib -lSystem -lm \ :info:build :info:build Undefined symbols for architecture x86_64: :info:build "__gfortran_compare_string", referenced from: :info:build _iffcmd_exec_ in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _settxt_ in libifeffit.a(misc_vars.o) :info:build _setsca_ in libifeffit.a(misc_vars.o) :info:build ... :info:build "__gfortran_concat_string", referenced from: :info:build _iffcmd_exec_ in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _set_array_index_ in libifeffit.a(misc_arr.o) :info:build _getsca_ in libifeffit.a(misc_vars.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build ... :info:build "__gfortran_getenv", referenced from: :info:build _iff_config_ in libifeffit.a(iff_config.o) :info:build "__gfortran_st_close", referenced from: :info:build _close_echofile_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _iff_history_ in libifeffit.a(iff_history.o) :info:build _iff_load_ in libifeffit.a(iff_load.o) :info:build _iff_log_ in libifeffit.a(iff_log.o) :info:build _iff_rddata_ in libifeffit.a(iff_rddata.o) :info:build _iff_save_ in libifeffit.a(iff_save.o) :info:build ... :info:build "__gfortran_st_inquire", referenced from: :info:build _iff_config_ in libifeffit.a(iff_config.o) :info:build _fefinp_ in libifeffit.a(fefinp.o) :info:build _openfl_ in libifeffit.a(misc_io.o) :info:build _newfil_ in libifeffit.a(misc_io.o) :info:build "__gfortran_st_open", referenced from: :info:build _rcldat_ in libifeffit.a(clcalc.o) :info:build _openfl_ in libifeffit.a(misc_io.o) :info:build "__gfortran_st_read", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _str2dp_ in libifeffit.a(str.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_st_read_done", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _str2dp_ in libifeffit.a(str.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_st_write", referenced from: :info:build _iffcmd_exec_ in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _echo_.part.0 in libifeffit.a(echo.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build ... :info:build "__gfortran_st_write_done", referenced from: :info:build _iffcmd_exec_ in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _echo_.part.0 in libifeffit.a(echo.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build ... :info:build "__gfortran_stop_string", referenced from: :info:build _fstop_ in libifeffit.a(echo.o) :info:build "__gfortran_string_index", referenced from: :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _isvnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _hexcol_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_string_len_trim", referenced from: :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _fixarr_ in libifeffit.a(misc_arr.o) :info:build _iofarr_ in libifeffit.a(misc_arr.o) :info:build ... :info:build "__gfortran_transfer_character", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_transfer_character_write", referenced from: :info:build _iffcmd_exec_ in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_transfer_integer_write", referenced from: :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_getpath_ in libifeffit.a(iff_getpath.o) :info:build _iff_load_ in libifeffit.a(iff_load.o) :info:build _iff_macro_do_ in libifeffit.a(iff_macro.o) :info:build ... :info:build "__gfortran_transfer_real", referenced from: :info:build _str2dp_ in libifeffit.a(str.o) :info:build "__gfortran_transfer_real_write", referenced from: :info:build _iff_correl_s_.part.0 in libifeffit.a(iff_correl.o) :info:build _iff_cursor_ in libifeffit.a(iff_cursor.o) :info:build _iff_zoom_ in libifeffit.a(iff_cursor.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_print_ in libifeffit.a(iff_print.o) :info:build _iff_save_ in libifeffit.a(iff_save.o) :info:build _ishsca_ in libifeffit.a(iff_show.o) :info:build ... :info:build ld: symbol(s) not found for architecture x86_64 :info:build clang: error: linker command failed with exit code 1 (use -v to see invocation) :info:build make: *** [blib/arch/auto/Ifeffit/Ifeffit.bundle] Error 1 :info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/work/ifeffit-1.2.final/wrappers/perl' :info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/work/ifeffit-1.2.final/wrappers/perl" && /usr/bin/make -j8 -w all :info:build Exit code: 2 :error:build org.macports.build for port p5.16-ifeffit returned: command execution failed :debug:build Error code: CHILDSTATUS 48139 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 p5.16-ifeffit: org.macports.install org.macports.build org.macports.destroot :notice:build Please see the log file for port p5.16-ifeffit for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.16-ifeffit/main.log

On Aug 25, 2014, at 6:17 AM, Bruce Ravel mailto:bravel@bnl.gov> wrote: On 08/24/2014 10:33 PM, Paul Fons wrote: Let me start out thanking you for writing and maintaining the OSX build of Demeter. Up until the latest release the different elements Athena, Artemis, and Hephaestus have been running more or less fine. In the latest update, I encountered a build error upon giving the command "port upgrade outdated". Here is the content of the log file. Do you have any advise as to how to proceed? Paul, Errors like this: :info:build Undefined symbols for architecture x86_64: :info:build "__gfortran_compare_string", referenced from: suggest a missing library that is being referenced but which cannot be linked to. Perhaps you are missing some package associated with gfortran...? I'd likely know how to solve this problem on Ubuntu, but on macports….. Thanks for responding Bruce. You are correct and this is a new bug I have seen recently. While I don’t know why this is happening exactly, fortunately the workaround is easy. sudo port install ifeffit +gcc49 sudo port clean p5.16-ifeffit sudo port upgrade outdated Cheers! Frank

Hi (again) Frank, The problem with the black windows in artemis was solved last time by installing the demeter-devel package, however, you suggested installing the ifeffit package. I had assumed that this version would have solved the black window problem. I then tried installing demeter-devel and all programs ran without error. I am a little confused as to what is the most recent version -- am I now running an older version of demeter than before? Is this black window problem something wrong on my end (with the version installed by port install ifeffit +gcc49)? In any case, thank you very much for your efforts. Best wishes, Paul On Aug 26, 2014, at 0:50, Schima, Frank wrote:

On Aug 25, 2014, at 6:17 AM, Bruce Ravel wrote:

...

On 08/24/2014 10:33 PM, Paul Fons wrote:

...

Let me start out thanking you for writing and maintaining the OSX build of Demeter. Up until the latest release the different elements Athena, Artemis, and Hephaestus have been running more or less fine. In the latest update, I encountered a build error upon giving the command "port upgrade outdated". Here is the content of the log file. Do you have any advise as to how to proceed?

Paul,

Errors like this:

:info:build Undefined symbols for architecture x86_64: :info:build "__gfortran_compare_string", referenced from:

suggest a missing library that is being referenced but which cannot be linked to. Perhaps you are missing some package associated with gfortran...?

I'd likely know how to solve this problem on Ubuntu, but on macports…..

Thanks for responding Bruce. You are correct and this is a new bug I have seen recently. While I don’t know why this is happening exactly, fortunately the workaround is easy.

sudo port install ifeffit +gcc49 sudo port clean p5.16-ifeffit sudo port upgrade outdated

Cheers! Frank

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

Dr. Paul Fons Senior Research Scientist Functional Nano-phase-change Research Team Nanoelectronics Research Institute National Institute for Advanced Industrial Science & Technology METI AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons@aist.go.jp The following lines are in a Japanese font 〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所 ナノエレクトロニクス研究部門 相変化新規機能デバイス研究チーム 上級主究員 ポール・フォンス

Hi Paul, demeter-devel is the most current version of Demeter available via Macports--you can always check by checking the port documentation itself. Since Demeter is a front-end to ifeffit, the black windows have to do with how Demeter renders on Macs and nothing to do with how up-to-date ifeffit is (as far as I know). Ifeffit was the dependency (of demeter) with the problem when called automatically by Macports, but updating that manually won't also update your demeter front-end. If you have the most recent ifeffit (now that you've updated it manually) and demeter-devel you should have the most updated version of everything. Best, Alison On Tue, Aug 26, 2014 at 11:28 PM, Paul Fons wrote:

Hi Bruce, Thank you for the suggestion. I would have tried addressing this directly, but the macports is supposed to handle dependencies automatically (like yum or yast in linux). The suggestion by Frank apparently solved the installation problem, but there is a potential "black window" problem in artemis. I can avoid this by using the package demeter-devel, but it was my impression that the package ifeffit was the most recent version. Hope I figure this out soon.

Cheers, Paul

On Aug 25, 2014, at 21:17, Bruce Ravel wrote:

On 08/24/2014 10:33 PM, Paul Fons wrote:

Let me start out thanking you for writing and maintaining the OSX build of Demeter. Up until the latest release the different elements Athena, Artemis, and Hephaestus have been running more or less fine. In the latest update, I encountered a build error upon giving the command "port upgrade outdated". Here is the content of the log file. Do you have any advise as to how to proceed?

Paul,

Errors like this:

:info:build Undefined symbols for architecture x86_64: :info:build "__gfortran_compare_string", referenced from:

suggest a missing library that is being referenced but which cannot be linked to. Perhaps you are missing some package associated with gfortran...?

I'd likely know how to solve this problem on Ubuntu, but on macports.....

B

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

National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 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

Dr. Paul Fons Senior Research Scientist Functional Nano-phase-change Research Team Nanoelectronics Research Institute National Institute for Advanced Industrial Science & Technology METI

AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568

tel. +81-298-61-5636 fax. +81-298-61-2939

email: *paul-fons@aist.go.jp *

The following lines are in a Japanese font

〒305-8562 茨城県つくば市つくば中央東 1-1-1 産業技術総合研究所 ナノエレクトロニクス研究部門 相変化新規機能デバイス研究チーム 上級主究員 ポール・フォンス

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