Altas build fails during Octave install

[andy@…]

Hello,

Please forgive me if I've missed something obvious.

When I tried to install Octave (sudo port install octave), it chugged away for a while, then froze building atlas. I looked for similar errors, saw that maybe spotlight was a problem, so I disabled it. That didn't unhang things, so I did a control-C and said "sudo port install octave" again. This time I got an error, I'm attaching the log file.

Interestingly, when I do a "sudo port clean octave", and then "sudo port install octave", the build tries to pick up where it left off, building atlas. I didn't expect that - I thought it would start at the beginning of the octave install.

I'm running Xcode 5 and OS X 10.8.5

Thanks!

• Andy Voelkel

[Veence (Vincent)]

What computer are you using? From your log, I can infer something like a 13" MacBookPro or MacBookAir or MacMini ?

[andy@…]

Replying to vince@…:

What computer are you using? From your log, I can infer something like a 13" MacBookPro or MacBookAir or MacMini ?

Macbook Air 13 inch

[Veence (Vincent)]

Do me a favor, try to build atlas separately with the gcc48 option (port -v install atlas +gcc48) and tell me if it fails, too. Thanks!

[andy@…]

Here is what happened when I tried that:

$ sudo port -v install atlas +gcc48 Error: Requested variants "+gcc48" do not match original selection "+mpclang33". Please use the same variants again, perform 'port clean atlas' or specify the force option (-f). To report a bug, follow the instructions in the guide:

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

Error: Processing of port atlas failed

So I did "sudo port clean atlas" and then tried "sudo port -v install atlas +gcc48" again. After a seemingly interminable period of time, it completed successfully. I then continued with the octave install. I was convinced that it was hung for quite some time, but it eventually finished, and seems to be working. Thanks for the help. Do you know what was wrong?

And why is it that the install/build takes so agonizingly long? It feels like 1980 all over again. Is it waiting on network access? That would make sense, since much of the time the terminal process seems to consume only 1.5% of CPU.

• Andy

[Veence (Vincent)]

Andy, there seems to be a lurking bug with ‘mpclang33’ during Atlas compilation on the machine you’re using. Can you give me more informations, e.g. the processor of your computer? Atlas takes a long time, because it is all about optimization. For each elementary matrix operation that builds up the library, Atlas tries a bunch of different values (cache size, number of registers used, preloading, etc.) and picks up the one that gives the best performance. Since sometimes there are more than a thousand possible combinations, it takes a moderately long time to test the whole set and pick up the most efficient. Multiply this by every operation, knowing that each operation can be carried out in four precisions: single (s), double (d), single complex (c), double complex (z), each one optimized with its own values. Moreover, to avoid thread interference, Atlas carries out its measures using a single threaded model, meaning that even with 32,768 cores, for example, it would not compile faster. Now, I will try to dig further to see what’s happening.

[andy@…]

Processor 1.8 GHz Intel Core i5 Memory 4 GB 1600 MHz DDR3 Graphics Intel HD Graphics 4000 512 MB

[jwbwater@…]

I was happy to hear this worked for you Andy since I have been trying to install Octave using MacPorts for several days. I've tried each variant with no success, most of the time I just end up killing the process after several hours.

So I tried:

$sudo port clean atlas
$sudo port -v install atlas +gcc48

and after more than 12 hours it failed complaining of a missing libf77blas.a

I didn't start a new ticket because it seems like the same issue, not sure why it works for Andy but not me.

I'm using a new 11" Macbook Air running OS X 10.8.5 (12F37) on a 1.3 GHz Core i5 (Haswell) with 4GB of 1600 MHz DDR3 ram.

I am a linux user and this is my first go with OS X, but I did get MacPorts to install TeX Live and that works fine.

[jwbwater@…]

Cc Me!

[Veence (Vincent)]

Sorry, I’m a bit late on this. Should be fixed in r111734 But please try to install atlas using clang instead (sudo port -v install altas +clang)

[Veence (Vincent)]

Sorry, should be r111736. r111734 included a bump to an unstable version which was not intended.

[jwbwater@…]

Hi Vince,

Thanks for looking at this. I updated my port tree and now it says port atlas not found.

I can see the new port file /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/ports/math/atlas/Portfile

but atlas does not seem to be in the port index /opt/local/var/macports/sources/rsync.macports.org/release/tarballs/PortIndex

[Veence (Vincent)]

Drat. There was a non-breakable space in the Portfile. With the French keyboard layout, I have to type ALT-( to get a {. If my finger straggles on the ALT, the next space turns out to be an ALT-SPACE, which is a non-breakable space, and gets rejected by TCL. Sorry for the delay.

[jwbwater@…]

Didn't get too far with clang. I tried:

sudo port -v install atlas +clang

and got an error about how clang is temporarily disabled.

[Veence (Vincent)]

Oh yes, I left this. I will commit a patch today to re-enable the clang version bundled with Xcode 5. Sorry for botching all this.

[jwbwater@…]

Hi Vince,

I decided to try the command below since gcc47 was recommended by the macports error message I got when I tried clang (and it seems to be the compiler used to test the latest version of atlas according to the website) :

sudo port -v install atlas +gcc47

and it appeared to work, but so fast that it makes me wonder. Building Octave now.

[jwbwater@…]

Octave installed and appears to work. Yay!

Not sure what you did, but I know I tried installing the gcc47 variant of atlas before and it didn't work so thanks Vince!

[Veence (Vincent)]

I think you installed atlas from the precompiled binaries. This is suboptimal (you won’t get the best performance out of your CPU), but it works. Great to know it worked. Have fun.