Re: [Ifeffit] port for demeter failure

[Ping, Yuan]

Hi Justin,

I had a similar problem. Wayne Lukens’s idea of installing each package 
individually by ”sudo port install libcxx” worked for me. But I am stuck with 
perl5.24:

sudo port install perl5.24

--->  Computing dependencies for perl5.24

--->  Installing perl5.24 @5.24.0_0

Error: org.macports.install for port perl5.24 returned: no destroot found at: 
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_perl5/perl5.24/work/destroot

Please see the log file for port perl5.24 for details:


/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_perl5/perl5.24/main.log

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

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

Error: Processing of port perl5.24 failed


How did you pass that?


Thanks,

Yuan




On 11/3/16, 10:08 AM, "Ifeffit on behalf of justin park" 

 on behalf of justin.pc...@gmail.com> wrote:

Hello Matt,

Thanks for the help.  I seem to have gotten it to work by cleaning and then 
trying the command below multiple times. I had installed macports and then used 
this command.

sudo port install xorg-server demeter


and it gave the error
Error: org.macports.archivefetch for port libcxx returned: archivefetch failed 
for libcxx @3.7.1_0+universal

 then a bunch more lines of code which I assummed were the files it didn't get 
to in the port. Then it just said

Error: port of Demeter failed.



I ended up getting past all that. and had another error too many files opened  
but jean has answered that for me now as well.


Thanks for all the help


-Justin



On Thu, Nov 3, 2016 at 11:27 AM, Matthew Newville 
> wrote:

Hi Jason,

On Nov 2, 2016 6:28 PM, "justin park" 
> wrote:
Hello,

I have followed the steps to install macports on my mac and it seems to be 
working. However when I went to port in demeter it start and fails rather 
quickly giving this error message.

Error: org.macports.archivefetch for port libcxx returned: archivefetch failed 
for libcxx @3.7.1_0+universal

What do I need to do in macports to get it to properly fetch libcxx?


Several of people (including me) have observed that they sometimes need to do 
"sudo port install" of many of the dependencies (say, libgcc or perl packages), 
and that sometimes they need to try multiple times.

But also: can you give a more complete report of exactly what commands you 
typed and exactly what the error messages were?  "I followed the steps" is 
actually ambiguous, as you're assuming that we know which steps you followed.   
We might be able to guess correctly what you actually did, but if you tell us 
explicitly then we wouldn't have to guess.

--Matt

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Re: [Ifeffit] demeter installation in OSX El Capitan

[Ping, Yuan]

Hi Joe,

Thanks for your reply. In my first email I forgot to mention that I did install 
MacPorts-2.3.4-10.11-ElCapitan.

Yuan



On 7/21/16, 11:27 AM, "Ifeffit on behalf of Fowler, Joseph W. (Assoc)" 

 on behalf of joe.fow...@nist.gov> wrote:

Dear Yuan,

Thanks for the log file, but I’m afraid I don’t know what your Mac Ports 
problem is. The log file indicates a failure to fetch the archive at all. After 
waiting a day, did the problem go away?

My workplace has lots of rules about how and when to upgrade to El Cap. As a 
result, I have not done it myself yet. Have you visited the Mac Ports team’s 
page on OS X 10.11? https://trac.macports.org/wiki/ElCapitanProblems  There are 
no specific problems mentioning libcxx, I notice. Did you remember to 
re-install Mac Ports itself? If not, then problems are inevitable. Also, are 
Xcode and its command-line tools both updated to match the OS?

If you’ve followed all the upgrade instructions and cannot install libcxx, then 
I think you have a Mac Ports problem and should look to that project’s issue 
tracker (possibly filing an issue yourself).

Best wishes,
Joe Fowler
NIST Boulder Labs

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[Ifeffit] demeter installation in OSX El Capitan

[Ping, Yuan]

Dear all,

I recently upgraded my mac to OSX El Capitan, and tried to install demeter 
following the steps at http://bruceravel.github.io/demeter/


XQuartz 2.7.9 (xorg-server 1.17.4), Xcode 7.3.1, command line tools, “sudo port 
-v self update”, “port upgrade outdated” were all OK. When I tried “sudo port 
install xorg-server demeter”, it showed:


--->  Computing dependencies for xorg-server

--->  Cleaning xorg-server

--->  Computing dependencies for demeter

--->  Dependencies to be installed: ifeffit libgcc cctools llvm-3.8 libcxx 
libffi llvm_select gmp isl ld64 ld64-latest libmpc mpfr pgplot gcc5 ... (a long 
list)


Then after many attempts to fetch libcxx-3.7.1_0.darwin_15.x86_64.tbz2 from 
various websites, it showed:


Error: org.macports.archivefetch for port libcxx returned: archivefetch failed 
for libcxx @3.7.1_0

Error: Failed to install libcxx

Please see the log file for port libcxx for details:

   
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_libcxx/libcxx/main.log

The log file is attached. What should I do to fix it? Any suggestion will be 
appreciated.

Thanks.
Yuan






main.log
Description: main.log
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Re: [Ifeffit] Third cumulant in DWF

[Ping, Yuan]

Thanks, Bruce.

Does the math expression in IFEFFIT include the term -4k*sigma2*(1/labmda
+1/R) in the phase? If yes, the 1st cumulant is sigma1= R+dR. If no, sigma1=
R+dR+2*sigma2*(1/labmda +1/R). It this correct?

Yuan


On 4/1/11 2:18 PM, Bruce Ravel bra...@bnl.gov wrote:

 On Friday, April 01, 2011 05:03:17 pm Ping, Yuan wrote:
 Dear IFEFFIT experts:
 
 Is it possible to add a k^3 term in the phase for fitting to take into
 account anharmonic effect? The fitted coefficient will be proportional to
 the 3rd cumulant of Debye-Waller factor. I work with high-temperature
 high-pressure systems where anharmonic effect is not negligible.
 
 Thanks.
 Yuan Ping
 
 
 Hi Yuan,
 
 Here is the relevant page from the Ifeffit reference manual:
 
http://cars9.uchicago.edu/~ifeffit/refman/node51.html
 
 You want to use the 3rd path parameter, which adds a term
 proportional to C3*k^3 to the sine function in the exafs equation.
 
 See the attached figure for the place in Artemis where this parameter
 is introduced.
 
 HTH,
 B


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[Ifeffit] Third cumulant in DWF

[Ping, Yuan]

Dear IFEFFIT experts:

Is it possible to add a k^3 term in the phase for fitting to take into account 
anharmonic effect? The fitted coefficient will be proportional to the 3rd 
cumulant of Debye-Waller factor. I work with high-temperature high-pressure 
systems where anharmonic effect is not negligible.

Thanks.
Yuan Ping
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