atlas @3.10.2_1+Failed to install atlas

[weiken1991@…]

the problem is, i am trying to install SuiteSparse, which depends on atlas, but the atlas cannot be installed.

compilers: C:clang Fortan:gfortran49

model: macbook air 2014 + OS X Mavericks

By the way, the installation takes sooo long at the "building atlas" procedure. Any tips will be highly appreciated. Thank you!

wf211-029:~ shiweili$ sudo port clean Atlas
--->  Cleaning atlas
wf211-029:~ shiweili$ sudo port install SuiteSparse +atlas+metis+universal
--->  Computing dependencies for SuiteSparse
--->  Dependencies to be installed: atlas
--->  Fetching archive for atlas
--->  Attempting to fetch atlas-3.10.2_1+clang+universal.darwin_13.i386-x86_64.tbz2 from http://jog.id.packages.macports.org/macports/packages/atlas
--->  Attempting to fetch atlas-3.10.2_1+clang+universal.darwin_13.i386-x86_64.tbz2 from http://packages.macports.org/atlas
--->  Attempting to fetch atlas-3.10.2_1+clang+universal.darwin_13.i386-x86_64.tbz2 from http://lil.fr.packages.macports.org/atlas
--->  Fetching distfiles for atlas
--->  Verifying checksums for atlas
--->  Extracting atlas
--->  Applying patches to atlas
--->  Configuring atlas
Selected C compiler: /usr/bin/clang
Selected F77 compiler: gfortran49
--->  Building atlas
Error: org.macports.build for port atlas returned: command execution failed
Error: Failed to install atlas
Please see the log file for port atlas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log
Error: The following dependencies were not installed: atlas
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port SuiteSparse failed

[weiken1991@…]

log file

[weiken1991@…]

wf211-029:~ shiweili$ sudo port clean Atlas
--->  Cleaning atlas
wf211-029:~ shiweili$ sudo port install SuiteSparse +atlas+metis+universal
--->  Computing dependencies for SuiteSparse
--->  Dependencies to be installed: atlas
--->  Fetching archive for atlas
--->  Attempting to fetch atlas-3.10.2_1+clang+universal.darwin_13.i386-x86_64.tbz2 from http://jog.id.packages.macports.org/macports/packages/atlas
--->  Attempting to fetch atlas-3.10.2_1+clang+universal.darwin_13.i386-x86_64.tbz2 from http://packages.macports.org/atlas
--->  Attempting to fetch atlas-3.10.2_1+clang+universal.darwin_13.i386-x86_64.tbz2 from http://lil.fr.packages.macports.org/atlas
--->  Fetching distfiles for atlas
--->  Verifying checksums for atlas
--->  Extracting atlas
--->  Applying patches to atlas
--->  Configuring atlas
Selected C compiler: /usr/bin/clang
Selected F77 compiler: gfortran49
--->  Building atlas
Error: org.macports.build for port atlas returned: command execution failed
Error: Failed to install atlas
Please see the log file for port atlas for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_atlas/atlas/main.log
Error: The following dependencies were not installed: atlas
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port SuiteSparse failed

[mf2k (Frank Schima)]

The Priority field is for use by Macports team members only. In the future, please fill in the Port field and Cc the port maintainers (port info --maintainers atlas). As reporter, you do not need to Cc yourself.

[Veence (Vincent)]

There is obviously something wrong with libtool, I'm going to have a look.

[weiken1991@…]

Replying to vince@…:

There is obviously something wrong with libtool, I'm going to have a look.

Thanks vince! My libtool version is libtool @2.4.2_3

[petrrr]

By the way, the installation takes sooo long at the "building atlas" procedure. Any tips will be highly appreciated. Thank you!

The fact that installation of atlas (Automatically Tuned Linear Algebra Software) takes very long is pretty normal. It uses an auto-tuning procedure to optimize of the individual machine, which implies several cycles of compiling and benchmarking of the library.

[weiken1991@…]

Replying to petr@…:

The fact that installation of atlas (Automatically Tuned Linear Algebra Software) takes very long is pretty normal. It uses an auto-tuning procedure to optimize of the individual machine, which implies several cycles of compiling and benchmarking of the library.

Thanks. I understand now. Costing much time is not a very big deal...but many libraries depend on atlas. Another strange problem is, i had once successfully installed the atlas(sudo port install atlas), but when i try to install the SuitSparse, it failed to detect my atlas library installed in my machine, and automatically download the atlas source files again and builded it. But it turned out fail (as I reported).

[Veence (Vincent)]

Sorry I was away from my computer (in vacation) and could not tackle your problem before.

What do your last comment mean? That Atlas has been installed? Did you try port installed | grep atlas?

[weiken1991@…]

Replying to vince@…:

Sorry I was away from my computer (in vacation) and could not tackle your problem before.

What do your last comment mean? That Atlas has been installed? Did you try port installed | grep atlas?

I mean, if I install the atlas independently (sudo port install atlas), the atlas would be installed successfully without error. But if I try to install SuiteSparse (sudo port install SuiteSparse +atlas+metis+universal), the installation couldn't detect I have atlas (one of the dependencies of SuiteSparse) installed, and it will download the atlas again and build it but finally failed... Now I have uninstalled the atlas...

[Veence (Vincent)]

Rats! I was going to ask you to search for libraries in your Atlas installation. can you reinstall it as a standalone port? Thanks!

[weiken1991@…]

Replying to vince@…:

Rats! I was going to ask you to search for libraries in your Atlas installation. can you reinstall it as a standalone port? Thanks!

Yes. Now I have atlas installed... And the SuiteSparse still fails to be installed...

wf215-016:~ shiweili$ sudo port clean atlas
Password:
--->  Cleaning atlas
wf215-016:~ shiweili$ sudo port install atlas
--->  Fetching archive for atlas
--->  Attempting to fetch atlas-3.10.2_1+clang.darwin_13.x86_64.tbz2 from http://jog.id.packages.macports.org/macports/packages/atlas
--->  Attempting to fetch atlas-3.10.2_1+clang.darwin_13.x86_64.tbz2 from http://packages.macports.org/atlas
--->  Attempting to fetch atlas-3.10.2_1+clang.darwin_13.x86_64.tbz2 from http://nue.de.packages.macports.org/macports/packages/atlas
--->  Fetching distfiles for atlas
--->  Verifying checksums for atlas
--->  Extracting atlas
--->  Applying patches to atlas
--->  Configuring atlas
Selected C compiler: /usr/bin/clang
Selected F77 compiler: gfortran49
--->  Building atlas
--->  Staging atlas into destroot
--->  Installing atlas @3.10.2_1+clang
--->  Activating atlas @3.10.2_1+clang
--->  Cleaning atlas
--->  Updating database of binaries
--->  Scanning binaries for linking errors
--->  No broken files found.                             
wf215-016:~ shiweili$ port installed | grep atlas
  atlas @3.10.2_1+clang (active)
wf215-016:~ shiweili$ 

[Veence (Vincent)]

Okay. What is the output of

ls /opt/local/lib/lib*atlas*

Thanks!

[weiken1991@…]

Replying to vince@…:

wf104-139:~ shiweili$ ls /opt/local/lib/lib*atlas*
/opt/local/lib/libatlas.a	/opt/local/lib/libtatlas.dylib
/opt/local/lib/libsatlas.dylib
wf104-139:~ shiweili$ 

[Veence (Vincent)]

Can you repeat it with "ls -l" instead of "ls"? Thanks again!

[weiken1991@…]

wf104-139:~ shiweili$ ls -l /opt/local/lib/lib*atlas*
-rw-r--r--  1 root  admin   8323664  8 11 12:18 /opt/local/lib/libatlas.a
-rwxr-xr-x  1 root  admin  13172720  8 11 12:18 /opt/local/lib/libsatlas.dylib
-rwxr-xr-x  1 root  admin  13282904  8 11 12:18 /opt/local/lib/libtatlas.dylib
wf104-139:~ shiweili$ 

[Veence (Vincent)]

Did you manage to cope with this bug?

[Veence (Vincent)]

• Not relevant anymore -