SATIVA installation with AVX instructions

[Carolina Gandini]

Hi, I'm trying to install SATIVA in my mac OSX El Capitan v 10.11.6. I already installed gcc version 4.7.4 but when I run the script install.sh I keep having the same error:

Carolinas-MacBook-Pro:~ carolinagandini$ gcc --version

gcc (MacPorts gcc47 4.7.4_5) 4.7.4

Copyright (C) 2012 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Carolinas-MacBook-Pro:~ carolinagandini$ /Users/carolinagandini/SATIVA/install.sh 

Your CPU provides AVX instuctions, but you default compiler () is too old to support them.

Please consider using a more recent compiler (GCC 4.6+ or clang 3.3+) for optimal performance.

If you want to use a (slower) SSE3 RAxML version instead, please run this script with --no-avx option.

Can you tell me if I'm doing something wrong?

Thanks

[lucas...@h-its.org]

Hi Carolina,

OSX is a bit tricky, it always wants you to do things "the Apple way"... By default, it uses clang as compiler. Installing gcc will make gcc available, but not use it as default right away. This might help: http://apple.stackexchange.com/a/99078

Alternatively, you could install a newer version of clang instead.

So long
Lucas

[Carolina Gandini]

I tried this but it does not work. I also checked clang version, and I think it is ok:

Carolinas-MacBook-Pro:~ carolinagandini$ clang --version

Apple LLVM version 7.3.0 (clang-703.0.31)

Target: x86_64-apple-darwin15.6.0

Thread model: posix

InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

I do not understand why it's not recognising any of each... :(

[lucas...@h-its.org]

Hm okay. Can you please post the full output of the install script? There should be something like

Your compiler: ...

Building AVX: ...

Building AVX2: ...

after the warning about AVX.

Also, what is the output if you call `uname` from a terminal?

Thanks
Lucas

[Carolina Gandini]

Last login: Tue Aug 30 12:08:51 on ttys000

Carolinas-MacBook-Pro:~ carolinagandini$ /Users/carolinagandini/SATIVA/install.sh 

Your CPU provides AVX instuctions, but you default compiler () is too old to support them.

Please consider using a more recent compiler (GCC 4.6+ or clang 3.3+) for optimal performance.

If you want to use a (slower) SSE3 RAxML version instead, please run this script with --no-avx option.

Carolinas-MacBook-Pro:~ carolinagandini$ 

Carolinas-MacBook-Pro:~ carolinagandini$ uname

Darwin

That's all the output, nothing of your compiler or building AVX... Thanks!

[lucas...@h-its.org]

Ah, my bad. Try running it with the --no-avx flag, then it should report those lines.

[Carolina Gandini]

It's ok :)

Carolinas-MacBook-Pro:~ carolinagandini$ /Users/carolinagandini/SATIVA/install.sh --no-avx

Your compiler: 

Building AVX: no

Building AVX2: no

/Users/carolinagandini/SATIVA/install.sh: line 60: cd: raxml: No such file or directory

make: *** No targets specified and no makefile found.  Stop.

mkdir: tmp: Permission denied

Done!

[Alexey Kozlov]

Dear Carolina,

many thanks for reporting this!

It seems like "clang --version" output has changed in the recent OSX releases, that's why the installation script was
unable to recognize it. So you're right, your clang version has support for AVX/AVX2 and you don't need to install gcc.

I fixed the script now, could you please try the new version (attached)? (just save it to /Users/carolinagandini/SATIVA,
overwriting the old file).

Best,
Alexey

> might help: http://apple.stackexchange.com/a/99078 <http://apple.stackexchange.com/a/99078>

>
> Alternatively, you could install a newer version of clang instead.
>
> So long
> Lucas
>

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[Carolina Gandini]

Dear Alexey,

Thank you very much for your help and the script update. I think there was a spelling error in the new script because it wasn't working:

Carolinas-MacBook-Pro:sativa-master carolinagandini$ ./install.sh 

-bash: ./install.sh: /bin/bash^M: bad interpreter: No such file or directory

I copied the new elsif you add into the old install.sh script and now works perfectly! I leave it here.

file:///Users/carolinagandini/sativa-master/install.sh

Again, thanks for all!

Carolina Gandini

[Alexey Kozlov]

Great, thanks again for testing!

I committed the corrected installation script to the github.

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