Opened 6 years ago

Last modified 5 years ago

#44553 new defect

atlas @3.10.2_1+Failed to install atlas

Reported by: weiken1991@… Owned by: Veence (Vincent)
Priority: Normal Milestone:
Component: ports Version: 2.3.1
Keywords: Cc:
Port: atlas

Description (last modified by mf2k (Frank Schima))

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

Attachments (1)

main.log (12.1 MB) - added by weiken1991@… 6 years ago.
log file

Change History (16)

Changed 6 years ago by weiken1991@…

Attachment: main.log added

log file

comment:1 Changed 6 years ago by weiken1991@…

Cc: weiken1991@… added
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
Last edited 6 years ago by weiken1991@… (previous) (diff)

comment:2 Changed 6 years ago by mf2k (Frank Schima)

Cc: weiken1991@… removed
Description: modified (diff)
Owner: changed from macports-tickets@… to vince@…
Port: atlas added
Priority: HighNormal

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.

comment:3 Changed 6 years ago by Veence (Vincent)

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

comment:4 in reply to:  3 Changed 6 years ago by 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

comment:5 in reply to:  description ; Changed 6 years ago by 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.

comment:6 in reply to:  5 Changed 6 years ago by 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).

comment:7 Changed 6 years ago by 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?

comment:8 in reply to:  7 Changed 6 years ago by 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...

comment:9 Changed 6 years ago by 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!

comment:10 in reply to:  9 Changed 6 years ago by 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$ 
Last edited 6 years ago by weiken1991@… (previous) (diff)

comment:11 Changed 6 years ago by Veence (Vincent)

Okay. What is the output of

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

Thanks!

comment:12 in reply to:  11 Changed 6 years ago by 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$ 

comment:13 Changed 6 years ago by Veence (Vincent)

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

comment:14 Changed 6 years ago by 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$ 

comment:15 Changed 5 years ago by Veence (Vincent)

Did you manage to cope with this bug?

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