Frank, This is what I get for the following terminal inputs: *169-231-92-234:~ jwc137$ port installed ifeffit p5.16-ifeffit demeter-devel* The following ports are currently installed: demeter-devel @0.9.20pre10_0 demeter-devel @0.9.20-2014-06-06_0 ifeffit @1.2.11c_0+gcc48 ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @1.0.0_0 p5.16-ifeffit @2_0 (active) *169-231-92-234:~ jwc137$ ls -l /opt/local/bin/athena* ls: /opt/local/bin/athena: No such file or directory *169-231-92-234:~ jwc137$ ls -l /opt/local/bin/atoms* ls: /opt/local/bin/atoms: No such file or directory 169-231-92-234:~ jwc137$ ᐧ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter Assistant Professor Department of Materials Science and Engineering Case Western Reserve University *500B White Building* *10900 Euclid Ave.Cleveland, OH 44106-4901phone: (216) 368-4214email: jennifer.w.carter@case.edu * On Mon, Jul 14, 2014 at 2:00 PM, Schima, Frank wrote:

Jennifer,

There is nothing else to do.

What is the output of the following 3 commands?

port installed ifeffit p5.16-ifeffit demeter-devel ls -l /opt/local/bin/athena ls -l /opt/local/bin/atoms

Here is the my output (on 2 different computers):

$ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 (active) ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @2_0 (active)

$ ls -l /opt/local/bin/athena lrwxr-xr-x 1 root admin 43 Jul 14 10:53 /opt/local/bin/athena -> /opt/local/libexec/perl5.16/sitebin/dathena

$ ls -l /opt/local/bin/atoms lrwxr-xr-x 1 root admin 45 Jul 14 10:53 /opt/local/bin/atoms -> /opt/local/libexec/perl5.16/sitebin/atoms-gui

As for that perl command, make sure you are using Macports perl.

$ which perl /opt/local/bin/perl

-Frank

On Jul 14, 2014, at 2:47 PM, Jennifer Carter wrote:

Frank,

I followed the instructions for updating a current version, but now when I type "athena" or "atoms" in the terminal I get the message "command not found" am I missing a step?

running perl -e 'use Demeter; print $INC{"Demeter.pm"}, $/'

indicates that nothing was installed.

Thanks Jennifer ᐧ

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter

Assistant Professor Department of Materials Science and Engineering Case Western Reserve University

*500B White Building*

*10900 Euclid Ave. Cleveland, OH 44106-4901 phone: (216) 368-4214 email: jennifer.w.carter@case.edu *

On Mon, Jul 14, 2014 at 1:04 PM, Schima, Frank wrote:

...

Mac OS X users,

Thanks to help from Bruce Ravel and Matt Newville, I have updated ifeffit and Demeter-devel in Macports to fix a number of problems reported.

To update from your current version type the following:

sudo port selfupdate sudo port upgrade outdated

To install from scratch after installing Macports [1]:

sudo port selfupdate sudo port install demeter-devel

When done, your should see the following ports installed:

$ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 (active) ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @2_0 (active)

Please reply to the list (NOT to me directly) about how this works for you.

Cheers! Frank

[1] https://www.macports.org/install.php

_______________________________________________ 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

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

when I run *sudo port activate demeter-devel @0.9.20pre10_0* ---> Computing dependencies for demeter-devel ---> Activating demeter-devel @0.9.20pre10_0 Error: org.macports.activate for port demeter-devel returned: Image error: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/Plugins/SpecFileLongLine.pm already exists and does not belong to a registered port. Unable to activate port demeter-devel. Use 'port -f activate demeter-devel' to force the activation. Please see the log file for port demeter-devel for details: /opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_demeter-devel-0.9.20pre10_0_54f3f2fd9281aa66df973ff2918ccf4354f1f896e5b2bc57d680266a42be52f1-5435/demeter-devel/main.log Warning: Failed to execute portfile from registry for demeter-devel @0.9.20pre10_0 ---> Activating demeter-devel @0.9.20pre10_0 Error: port activate failed: Image error: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/Plugins/SpecFileLongLine.pm already exists and does not belong to a registered port. Unable to activate port demeter-devel. Use 'port -f activate demeter-devel' to force the activation. ᐧ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter Assistant Professor Department of Materials Science and Engineering Case Western Reserve University *500B White Building* *10900 Euclid Ave.Cleveland, OH 44106-4901phone: (216) 368-4214email: jennifer.w.carter@case.edu * On Mon, Jul 14, 2014 at 2:46 PM, Schima, Frank wrote:

For whatever reason, you do not have any version of demeter-devel active. You must activate the latest version as follows:

sudo port activate demeter-devel @0.9.20pre10_0

-Frank

On Jul 14, 2014, at 3:43 PM, Jennifer Carter wrote:

Frank,

This is what I get for the following terminal inputs:

*169-231-92-234:~ jwc137$ port installed ifeffit p5.16-ifeffit demeter-devel* The following ports are currently installed: demeter-devel @0.9.20pre10_0 demeter-devel @0.9.20-2014-06-06_0 ifeffit @1.2.11c_0+gcc48 ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @1.0.0_0 p5.16-ifeffit @2_0 (active) *169-231-92-234:~ jwc137$ ls -l /opt/local/bin/athena* ls: /opt/local/bin/athena: No such file or directory *169-231-92-234:~ jwc137$ ls -l /opt/local/bin/atoms* ls: /opt/local/bin/atoms: No such file or directory 169-231-92-234:~ jwc137$ ᐧ

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter

Assistant Professor Department of Materials Science and Engineering Case Western Reserve University

*500B White Building*

*10900 Euclid Ave. Cleveland, OH 44106-4901 phone: (216) 368-4214 email: jennifer.w.carter@case.edu *

On Mon, Jul 14, 2014 at 2:00 PM, Schima, Frank wrote:

...

Jennifer,

There is nothing else to do.

What is the output of the following 3 commands?

port installed ifeffit p5.16-ifeffit demeter-devel ls -l /opt/local/bin/athena ls -l /opt/local/bin/atoms

Here is the my output (on 2 different computers):

$ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 (active) ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @2_0 (active)

$ ls -l /opt/local/bin/athena lrwxr-xr-x 1 root admin 43 Jul 14 10:53 /opt/local/bin/athena -> /opt/local/libexec/perl5.16/sitebin/dathena

$ ls -l /opt/local/bin/atoms lrwxr-xr-x 1 root admin 45 Jul 14 10:53 /opt/local/bin/atoms -> /opt/local/libexec/perl5.16/sitebin/atoms-gui

As for that perl command, make sure you are using Macports perl.

$ which perl /opt/local/bin/perl

-Frank

On Jul 14, 2014, at 2:47 PM, Jennifer Carter wrote:

Frank,

I followed the instructions for updating a current version, but now when I type "athena" or "atoms" in the terminal I get the message "command not found" am I missing a step?

running perl -e 'use Demeter; print $INC{"Demeter.pm"}, $/'

indicates that nothing was installed.

Thanks Jennifer ᐧ

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter

Assistant Professor Department of Materials Science and Engineering Case Western Reserve University

*500B White Building*

*10900 Euclid Ave. Cleveland, OH 44106-4901 phone: (216) 368-4214 email: jennifer.w.carter@case.edu *

On Mon, Jul 14, 2014 at 1:04 PM, Schima, Frank wrote:

...

Mac OS X users,

Thanks to help from Bruce Ravel and Matt Newville, I have updated ifeffit and Demeter-devel in Macports to fix a number of problems reported.

To update from your current version type the following:

sudo port selfupdate sudo port upgrade outdated

To install from scratch after installing Macports [1]:

sudo port selfupdate sudo port install demeter-devel

When done, your should see the following ports installed:

$ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 (active) ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @2_0 (active)

Please reply to the list (NOT to me directly) about how this works for you.

Cheers! Frank

[1] https://www.macports.org/install.php

_______________________________________________ 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

_______________________________________________ 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

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

Frank, Looks like I have two versions of demeter-devel installed sudo port -f activate demeter-devel Password: ---> The following versions of demeter-devel are currently installed: ---> demeter-devel @0.9.20-2014-06-06_0 ---> demeter-devel @0.9.20pre10_0 Error: port activate failed: Registry error: Please specify the full version as recorded in the port registry. How do I specify a the full version? Thanks Jennifer ᐧ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter Assistant Professor Department of Materials Science and Engineering Case Western Reserve University *500B White Building* *10900 Euclid Ave.Cleveland, OH 44106-4901phone: (216) 368-4214email: jennifer.w.carter@case.edu * On Mon, Jul 14, 2014 at 3:00 PM, Schima, Frank wrote:

Your setup got munged somehow. You need to do what it says. Namely:

sudo port -f activate demeter-devel

-Frank

On Jul 14, 2014, at 3:55 PM, Jennifer Carter wrote:

when I run

*sudo port activate demeter-devel @0.9.20pre10_0* ---> Computing dependencies for demeter-devel ---> Activating demeter-devel @0.9.20pre10_0 Error: org.macports.activate for port demeter-devel returned: Image error: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/Plugins/SpecFileLongLine.pm already exists and does not belong to a registered port. Unable to activate port demeter-devel. Use 'port -f activate demeter-devel' to force the activation. Please see the log file for port demeter-devel for details:

/opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_demeter-devel-0.9.20pre10_0_54f3f2fd9281aa66df973ff2918ccf4354f1f896e5b2bc57d680266a42be52f1-5435/demeter-devel/main.log Warning: Failed to execute portfile from registry for demeter-devel @0.9.20pre10_0 ---> Activating demeter-devel @0.9.20pre10_0 Error: port activate failed: Image error: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/Plugins/SpecFileLongLine.pm already exists and does not belong to a registered port. Unable to activate port demeter-devel. Use 'port -f activate demeter-devel' to force the activation. ᐧ

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter

Assistant Professor Department of Materials Science and Engineering Case Western Reserve University

*500B White Building*

*10900 Euclid Ave. Cleveland, OH 44106-4901 phone: (216) 368-4214 email: jennifer.w.carter@case.edu *

On Mon, Jul 14, 2014 at 2:46 PM, Schima, Frank wrote:

...

For whatever reason, you do not have any version of demeter-devel active. You must activate the latest version as follows:

sudo port activate demeter-devel @0.9.20pre10_0

-Frank

On Jul 14, 2014, at 3:43 PM, Jennifer Carter wrote:

Frank,

This is what I get for the following terminal inputs:

*169-231-92-234:~ jwc137$ port installed ifeffit p5.16-ifeffit demeter-devel* The following ports are currently installed: demeter-devel @0.9.20pre10_0 demeter-devel @0.9.20-2014-06-06_0 ifeffit @1.2.11c_0+gcc48 ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @1.0.0_0 p5.16-ifeffit @2_0 (active) *169-231-92-234:~ jwc137$ ls -l /opt/local/bin/athena* ls: /opt/local/bin/athena: No such file or directory *169-231-92-234:~ jwc137$ ls -l /opt/local/bin/atoms* ls: /opt/local/bin/atoms: No such file or directory 169-231-92-234:~ jwc137$ ᐧ

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter

Assistant Professor Department of Materials Science and Engineering Case Western Reserve University

*500B White Building*

*10900 Euclid Ave. Cleveland, OH 44106-4901 phone: (216) 368-4214 email: jennifer.w.carter@case.edu *

On Mon, Jul 14, 2014 at 2:00 PM, Schima, Frank wrote:

...

Jennifer,

There is nothing else to do.

What is the output of the following 3 commands?

port installed ifeffit p5.16-ifeffit demeter-devel ls -l /opt/local/bin/athena ls -l /opt/local/bin/atoms

Here is the my output (on 2 different computers):

$ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 (active) ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @2_0 (active)

$ ls -l /opt/local/bin/athena lrwxr-xr-x 1 root admin 43 Jul 14 10:53 /opt/local/bin/athena -> /opt/local/libexec/perl5.16/sitebin/dathena

$ ls -l /opt/local/bin/atoms lrwxr-xr-x 1 root admin 45 Jul 14 10:53 /opt/local/bin/atoms -> /opt/local/libexec/perl5.16/sitebin/atoms-gui

As for that perl command, make sure you are using Macports perl.

$ which perl /opt/local/bin/perl

-Frank

On Jul 14, 2014, at 2:47 PM, Jennifer Carter wrote:

Frank,

I followed the instructions for updating a current version, but now when I type "athena" or "atoms" in the terminal I get the message "command not found" am I missing a step?

running perl -e 'use Demeter; print $INC{"Demeter.pm"}, $/'

indicates that nothing was installed.

Thanks Jennifer ᐧ

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter

Assistant Professor Department of Materials Science and Engineering Case Western Reserve University

*500B White Building*

*10900 Euclid Ave. Cleveland, OH 44106-4901 phone: (216) 368-4214 email: jennifer.w.carter@case.edu *

On Mon, Jul 14, 2014 at 1:04 PM, Schima, Frank wrote:

...

Mac OS X users,

Thanks to help from Bruce Ravel and Matt Newville, I have updated ifeffit and Demeter-devel in Macports to fix a number of problems reported.

To update from your current version type the following:

sudo port selfupdate sudo port upgrade outdated

To install from scratch after installing Macports [1]:

sudo port selfupdate sudo port install demeter-devel

When done, your should see the following ports installed:

$ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 (active) ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @2_0 (active)

Please reply to the list (NOT to me directly) about how this works for you.

Cheers! Frank

[1] https://www.macports.org/install.php

_______________________________________________ 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

_______________________________________________ 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

_______________________________________________ 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

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

You simply type the complete name. I should have wrote that initially. sudo port -f activate demeter-devel @0.9.20pre10_0 -Frank On Jul 14, 2014, at 4:13 PM, Jennifer Carter mailto:jwc137@case.edu> wrote: Frank, Looks like I have two versions of demeter-devel installed sudo port -f activate demeter-devel Password: ---> The following versions of demeter-devel are currently installed: ---> demeter-devel @0.9.20-2014-06-06_0 ---> demeter-devel @0.9.20pre10_0 Error: port activate failed: Registry error: Please specify the full version as recorded in the port registry. How do I specify a the full version? Thanks Jennifer [https://mailfoogae.appspot.com/t?sender=aandjMTM3QGNhc2UuZWR1&type=zerocontent&guid=ea034fd1-0125-4a6f-9531-0a82c40c5238]ᐧ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter Assistant Professor Department of Materials Science and Engineering Case Western Reserve University 500B White Building 10900 Euclid Ave. Cleveland, OH 44106-4901 phone: (216) 368-4214 email: jennifer.w.carter@case.edumailto:jennifer.w.carter@case.edu On Mon, Jul 14, 2014 at 3:00 PM, Schima, Frank mailto:frank.schima@nist.gov> wrote: Your setup got munged somehow. You need to do what it says. Namely: sudo port -f activate demeter-devel -Frank On Jul 14, 2014, at 3:55 PM, Jennifer Carter mailto:jwc137@case.edu> wrote: when I run sudo port activate demeter-devel @0.9.20pre10_0 ---> Computing dependencies for demeter-devel ---> Activating demeter-devel @0.9.20pre10_0 Error: org.macports.activate for port demeter-devel returned: Image error: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/Plugins/SpecFileLongLine.pm already exists and does not belong to a registered port. Unable to activate port demeter-devel. Use 'port -f activate demeter-devel' to force the activation. Please see the log file for port demeter-devel for details: /opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_demeter-devel-0.9.20pre10_0_54f3f2fd9281aa66df973ff2918ccf4354f1f896e5b2bc57d680266a42be52f1-5435/demeter-devel/main.log Warning: Failed to execute portfile from registry for demeter-devel @0.9.20pre10_0 ---> Activating demeter-devel @0.9.20pre10_0 Error: port activate failed: Image error: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/Plugins/SpecFileLongLine.pm already exists and does not belong to a registered port. Unable to activate port demeter-devel. Use 'port -f activate demeter-devel' to force the activation. [https://mailfoogae.appspot.com/t?sender=aandjMTM3QGNhc2UuZWR1&type=zerocontent&guid=469920f1-a525-4ea3-96e5-780c6c639ac4]ᐧ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter Assistant Professor Department of Materials Science and Engineering Case Western Reserve University 500B White Building 10900 Euclid Ave. Cleveland, OH 44106-4901 phone: (216) 368-4214 email: jennifer.w.carter@case.edumailto:jennifer.w.carter@case.edu On Mon, Jul 14, 2014 at 2:46 PM, Schima, Frank mailto:frank.schima@nist.gov> wrote: For whatever reason, you do not have any version of demeter-devel active. You must activate the latest version as follows: sudo port activate demeter-devel @0.9.20pre10_0 -Frank On Jul 14, 2014, at 3:43 PM, Jennifer Carter mailto:jwc137@case.edu> wrote: Frank, This is what I get for the following terminal inputs: 169-231-92-234:~ jwc137$ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 demeter-devel @0.9.20-2014-06-06_0 ifeffit @1.2.11c_0+gcc48 ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @1.0.0_0 p5.16-ifeffit @2_0 (active) 169-231-92-234:~ jwc137$ ls -l /opt/local/bin/athena ls: /opt/local/bin/athena: No such file or directory 169-231-92-234:~ jwc137$ ls -l /opt/local/bin/atoms ls: /opt/local/bin/atoms: No such file or directory 169-231-92-234:~ jwc137$ [https://mailfoogae.appspot.com/t?sender=aandjMTM3QGNhc2UuZWR1&type=zerocontent&guid=65036228-9c54-447b-993a-c4ada3d12ec4]ᐧ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter Assistant Professor Department of Materials Science and Engineering Case Western Reserve University 500B White Building 10900 Euclid Ave. Cleveland, OH 44106-4901 phone: (216) 368-4214 email: jennifer.w.carter@case.edumailto:jennifer.w.carter@case.edu On Mon, Jul 14, 2014 at 2:00 PM, Schima, Frank mailto:frank.schima@nist.gov> wrote: Jennifer, There is nothing else to do. What is the output of the following 3 commands? port installed ifeffit p5.16-ifeffit demeter-devel ls -l /opt/local/bin/athena ls -l /opt/local/bin/atoms Here is the my output (on 2 different computers): $ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 (active) ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @2_0 (active) $ ls -l /opt/local/bin/athena lrwxr-xr-x 1 root admin 43 Jul 14 10:53 /opt/local/bin/athena -> /opt/local/libexec/perl5.16/sitebin/dathena $ ls -l /opt/local/bin/atoms lrwxr-xr-x 1 root admin 45 Jul 14 10:53 /opt/local/bin/atoms -> /opt/local/libexec/perl5.16/sitebin/atoms-gui As for that perl command, make sure you are using Macports perl. $ which perl /opt/local/bin/perl -Frank On Jul 14, 2014, at 2:47 PM, Jennifer Carter mailto:jwc137@case.edu> wrote: Frank, I followed the instructions for updating a current version, but now when I type "athena" or "atoms" in the terminal I get the message "command not found" am I missing a step? running perl -e 'use Demeter; print $INC{"Demeter.pm"}, $/' indicates that nothing was installed. Thanks Jennifer [https://mailfoogae.appspot.com/t?sender=aandjMTM3QGNhc2UuZWR1&type=zerocontent&guid=da579cbd-6543-4821-bd89-17fb33a6662e]ᐧ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Jennifer L.W. Carter Assistant Professor Department of Materials Science and Engineering Case Western Reserve University 500B White Building 10900 Euclid Ave. Cleveland, OH 44106-4901 phone: (216) 368-4214 email: jennifer.w.carter@case.edumailto:jennifer.w.carter@case.edu On Mon, Jul 14, 2014 at 1:04 PM, Schima, Frank mailto:frank.schima@nist.gov> wrote: Mac OS X users, Thanks to help from Bruce Ravel and Matt Newville, I have updated ifeffit and Demeter-devel in Macports to fix a number of problems reported. To update from your current version type the following: sudo port selfupdate sudo port upgrade outdated To install from scratch after installing Macports [1]: sudo port selfupdate sudo port install demeter-devel When done, your should see the following ports installed: $ port installed ifeffit p5.16-ifeffit demeter-devel The following ports are currently installed: demeter-devel @0.9.20pre10_0 (active) ifeffit @1.2.13_0+gcc48 (active) p5.16-ifeffit @2_0 (active) Please reply to the list (NOT to me directly) about how this works for you. Cheers! Frank [1] https://www.macports.org/install.php _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.govmailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit