atlas @3.10.1 (math) octave @3.2.4 install fails by hanging indefinitely

[sathyanarayana-a]

Been trying to install octave via command: sudo port install octave.

The package atlas hangs indefinitely while installing. Have tried multiple times and left it to go for over 10 hours but no progress.

Terminal output:

New-MacBook-Pro:~$ sudo port install octave
--->  Computing dependencies for octave
--->  Dependencies to be installed: atlas fftw-3 fftw-3-single ftgl gawk readline gnuplot aquaterm lua pango Xft2 harfbuzz graphite2 pdflib gsed hdf5-18 metis pcre qhull qrupdate texinfo
--->  Fetching distfiles for atlas
--->  Verifying checksum(s) for atlas
--->  Extracting atlas
--->  Applying patches to atlas
--->  Configuring atlas
Selected C compiler: /opt/local/bin/clang-mp-3.3
Selected F77 compiler: gfortran47
--->  Building atlas

Using MacPorts Version Version: 2.1.3, Xcode Version 4.6.3 (4H1503), OS X 10.8.4 (12E55)

[Veence (Vincent)]

Which machine are you running on? Do you try to build a universal version? Do you have a log to post? Thanks!

[ryandesign (Ryan Carsten Schmidt)]

atlas can take a long time to build, depending on how fast your machine is.

You can enable debug output with sudo port -d install octave to see if it's still thinking about things or whether it's truly stuck somewhere.

[sathyanarayana-a]

Don't have any log. Not sure how to get one.

Have tried a new way. Tried forcing a non atlas version by trying:

sudo port install octave +accelerate +gcc47

This seems to have worked (not sure if the atlas or accelerate version is now installed in my machine. how to check?), even though atlas was added on as a dependancy, but was installed last in the list of dependencies. Not sure what has happened to make it work this time. Is there a way to get the log file for this install?

I am running a 2.9 GHz Intel Core i7 8GB 1600 MHz DDR3 MacBook Pro.

[Veence (Vincent)]

If you use the +accelerate option, you disable the use of Atlas in favor of the use of the internal Apple-provided Accelerate framework which is bundled with OS X. It should work okay, but I’m still unsure that you’ll get the same level of performance. I should carry out tests based on Python scipy but I didn’t have time up to now. I think I’ll be able to do it during summer.

The log you should find at the standard location /opt/local/var/macports/logs

Oh. You use a core i7. I think the clang3.3 version that is still in macports (and which is not the final release) has a bug in core-i7 code handling. Try again once the clang3.3 is updated to the final release (soon I hope).

[sathyanarayana-a]

the log file for the latest octave installation attempt

[sathyanarayana-a]

Is it possible to remove the current octave installation and reinstall the universal version without the accelerate or atlas options? (sorry a little newbie with this stuff) So I can send to you a logfile where the atlas fails for your reference once you get time to work on debugging this problem.

I have attached the log file for the current octave installation (the +accelerate +docs version which worked).

[Veence (Vincent)]

Your log seems to be truncated but that’s not a problem. Keep your octave installed. Instead try rebuild atlas: port -v build atlas +universal

You’ll get a lot of message printed out, and be able to see how the compilation unfolds.

V.

[larryv (Lawrence Velázquez)]

Replying to vince@…:

I think the clang3.3 version that is still in macports (and which is not the final release) has a bug in core-i7 code handling. Try again once the clang3.3 is updated to the final release (soon I hope).

I’ve opened #39520 for this.

[Veence (Vincent)]

Nice move Larry. Thanks!

[sathyanarayana-a]

debug output of build atlas +universal

[sathyanarayana-a]

Have attached the screen output of sudo port -v build atlas +universal. The build did fail after a good 6 hours of marathon session.

[Veence (Vincent)]

Oh. I see what’s wrong: you try to build a universal Atlas, but your gcc compiler seems to have been built for x86_64 only. Can you confirm this by giving me the result of:

port installed gcc47

Thanks!

[sathyanarayana-a]

Response is:

New-MacBook-Pro:~$ sudo port installed gcc47 Password: The following ports are currently installed:

gcc47 @4.7.3_0 (active)

New-MacBook-Pro:~$

Regards,

[Veence (Vincent)]

Yup, that’s it. You should rebuild gcc47 (or gcc48) with the +universal flag and try again.

[sathyanarayana-a]

sudo port build gcc47 +universal

or

sudo port install gcc47 +universal

Btw what's the difference for an already installed port to execute the build command versus using it for an uninstalled port.

Thanks & Regards,

[larryv (Lawrence Velázquez)]

Replying to sathyanarayana.a@…:

Btw what's the difference for an already installed port to execute the build command versus using it for an uninstalled port.

No difference. Assuming a clean start state, port build will always perform a compile, regardless of whether the port is already installed or not.

[sathyanarayana-a]

Have built & installed gcc47 +universal. Trying out to rebuild atlas universal variant again. Will post the results and log soon.

Regards,

[sathyanarayana-a]

gcc47 +universal and atlas +universal log

[sathyanarayana-a]

Atlas failed again. Have attached the log for gcc47 +universal and atlas +universal.

[talksense101@…]

Atlas is still a problem with Port version 2.3.1 and Octave 3.8.1. I cancelled the build after 7 hours on a Macbook Pro (2.3GHz i7 with 8GB memory). The build log was stuck on step 2.4.5. I rebuilt with +accelerate so that I can get Octave, but the warning messages aren't very inspiring.

---

WARNING: Dependency 'arpack' is installed with the +accelerate variant, using Apple's Vector Libraries which have some known bugs that can cause Octave to crash if using certain functions in arpack. The +atlas variant does not have these issues with Octave, but does take many hours to compile even on modern hardware.

WARNING: The +accelerate variant has been selected, using Apple's Vector Libraries which have some known bugs that can cause Octave to crash. The +atlas variant does not have these issues with Octave, but does take many hours to compile even on modern hardware.

---

[Veence (Vincent)]

Please have a look at #44290. I put there a new Portfile and a patchfile to upgrade to a new, but unstable version. Could you please try compiling with these files, following the instructions given in the aforementioned ticket, and let me know if it solves the problem. In which case I will commit the Patchfile to trunk to let anybody upgrade.

[Veence (Vincent)]

No response → closing