arpack 3.1.3_0+accelerate+gcc48+universal: i386 configure cannot find BLAS

[nowornot@…]

I've tried for the last two days to update octave, and the main problem has been with arpack. I've search through previous tickets and tried many of the suggestions, but none of them work. Basic error are as follows:

mac83913:~ mp2$ sudo port clean arpack
--->  Cleaning arpack
mac83913:~ mp2$ sudo port install arpack 
--->  Computing dependencies for arpack
--->  Fetching archive for arpack
--->  Attempting to fetch arpack-3.1.3_0+accelerate+gcc48+universal.darwin_12.i386-x86_64.tbz2 from http://packages.macports.org/arpack
--->  Attempting to fetch arpack-3.1.3_0+accelerate+gcc48+universal.darwin_12.i386-x86_64.tbz2 from http://lil.fr.packages.macports.org/arpack
--->  Attempting to fetch arpack-3.1.3_0+accelerate+gcc48+universal.darwin_12.i386-x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/arpack
--->  Fetching distfiles for arpack
--->  Verifying checksums for arpack
--->  Extracting arpack
--->  Applying patches to arpack
--->  Configuring arpack
Error: Failed to configure arpack, consult /opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/work/arpack-ng-3.1.3-i386/config.log
Error: org.macports.configure for port arpack returned: configure failure: command execution failed
Please see the log file for port arpack for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port arpack failed

I've tried the +atlas option and also the -accelerate option. Here's the +atlas option:

mac83913:~ mp2$ sudo port install arpack +atlas
--->  Computing dependencies for arpack
--->  Fetching archive for arpack
--->  Attempting to fetch arpack-3.1.3_0+atlas+gcc48+universal.darwin_12.i386-x86_64.tbz2 from http://packages.macports.org/arpack
--->  Attempting to fetch arpack-3.1.3_0+atlas+gcc48+universal.darwin_12.i386-x86_64.tbz2 from http://lil.fr.packages.macports.org/arpack
--->  Attempting to fetch arpack-3.1.3_0+atlas+gcc48+universal.darwin_12.i386-x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/arpack
--->  Fetching distfiles for arpack
--->  Verifying checksums for arpack
--->  Extracting arpack
--->  Configuring arpack
Error: Failed to configure arpack, consult /opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/work/arpack-ng-3.1.3-i386/config.log
Error: org.macports.configure for port arpack returned: configure failure: command execution failed
Please see the log file for port arpack for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port arpack failed

I've updated to the lastest version of clang as recently suggested in another ticket.

mac83913:~ mp2$ clang -v
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
Target: x86_64-apple-darwin12.5.0
Thread model: posix
mac83913:~ mp2$ 

port version is 2.2.1

mac83913:~ mp2$ port version
Version: 2.2.1
mac83913:~ mp2$

I've also selfupdated port, and updated all packages, or uninstalled any problem packages.

Any ideas on how to proceed from here? Any ideas are appreciated!

[nowornot@…]

log file

[larryv (Lawrence Velázquez)]

Thanks for the ticket. In the future, please Cc relevant port maintainers (e.g., port info --maintainers arpack).

[nowornot@…]

Thank you for the quick response! It appears that I do have the BLAS libraries installed:

mac83913:~ mp2$ ls /usr/lib | grep blas
libblas.dylib
libcblas.dylib
mac83913:~ mp2$ 

[Veence (Vincent)]

Are you sure you gcc 4.8 suite was installed with the +multilib option? It seems you have no fortran compiler available for the i386 arch.

[nowornot@…]

Just to check that gcc48 has the multilib option, I reinstalled it with that option, and tried again to install arpack, and again it failed:

mac83913:~ mp2$ sudo port install gcc48 +multilib
--->  Computing dependencies for gcc48
--->  Cleaning gcc48
--->  Scanning binaries for linking errors: 100.0%
--->  No broken files found.
mac83913:~ mp2$ sudo port install arpack +atlas
--->  Computing dependencies for arpack
--->  Configuring arpack
Error: Failed to configure arpack, consult /opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/work/arpack-ng-3.1.3-i386/config.log
Error: org.macports.configure for port arpack returned: configure failure: command execution failed
Please see the log file for port arpack for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port arpack failed
mac83913:~ mp2$ 

[Veence (Vincent)]

Oops! My bad! (© Derpy)

It should be the +universal option (there is no +multilib option). gcc48 must be installed universal if you want to compile universal port with it.

[nowornot@…]

I think it was installed with the +universal option, based on this output:

mac83913:~ mp2$ port installed | grep gcc
  gcc48 @4.8.2_0+universal (active)
  gcc_select @0.1_7
  gcc_select @0.1_8 (active)
  gccmakedep @1.0.2_3 (active)
  libgcc @4.8.2_0+universal (active)
mac83913:~ mp2$ 

Please correct me if I am wrong.

[Veence (Vincent)]

IT should. What gives you the output of:

ls -l /opt/local/lib/gcc48/i386

[nowornot@…]

Here you go!

mac83913:~ mp2$ ls -l /opt/local/lib/gcc48/i386
total 153728
drwxr-xr-x  7 root  admin       238 Jan 11 10:01 gcj-4.8.2-14
lrwxr-xr-x  1 root  admin        37 Jan 11 10:00 libasan.0.dylib -> /opt/local/lib/libgcc/libasan.0.dylib
lrwxr-xr-x  1 root  admin        15 Jan 11 09:59 libasan.dylib -> libasan.0.dylib
-rwxr-xr-x  1 root  admin       931 Jan 11 10:00 libasan.la
-rw-r--r--  1 root  admin      3644 Jan 11 09:59 libasan_preinit.o
lrwxr-xr-x  1 root  admin        39 Jan 11 10:00 libatomic.1.dylib -> /opt/local/lib/libgcc/libatomic.1.dylib
-rw-r--r--  1 root  admin    192896 Jan 11 10:00 libatomic.a
lrwxr-xr-x  1 root  admin        17 Jan 11 10:00 libatomic.dylib -> libatomic.1.dylib
-rwxr-xr-x  1 root  admin       961 Jan 11 10:00 libatomic.la
-rwxr-xr-x  1 root  admin   6240904 Jan 11 10:00 libgcj-tools.14.dylib
lrwxr-xr-x  1 root  admin        21 Jan 11 10:00 libgcj-tools.dylib -> libgcj-tools.14.dylib
-rwxr-xr-x  1 root  admin       959 Jan 11 10:00 libgcj-tools.la
-rwxr-xr-x  1 root  admin  56848284 Jan 11 10:00 libgcj.14.dylib
lrwxr-xr-x  1 root  admin        15 Jan 11 10:00 libgcj.dylib -> libgcj.14.dylib
-rwxr-xr-x  1 root  admin       929 Jan 11 10:00 libgcj.la
lrwxr-xr-x  1 root  admin        41 Jan 11 10:00 libgfortran.3.dylib -> /opt/local/lib/libgcc/libgfortran.3.dylib
-rw-r--r--  1 root  admin   5742456 Jan 11 09:59 libgfortran.a
lrwxr-xr-x  1 root  admin        19 Jan 11 09:59 libgfortran.dylib -> libgfortran.3.dylib
-rwxr-xr-x  1 root  admin       964 Jan 11 10:00 libgfortran.la
-rw-r--r--  1 root  admin       198 Jan 11 09:59 libgfortran.spec
-rwxr-xr-x  1 root  admin     14220 Jan 11 10:00 libgij.14.dylib
lrwxr-xr-x  1 root  admin        15 Jan 11 10:00 libgij.dylib -> libgij.14.dylib
-rwxr-xr-x  1 root  admin       929 Jan 11 10:00 libgij.la
lrwxr-xr-x  1 root  admin        37 Jan 11 10:00 libgomp.1.dylib -> /opt/local/lib/libgcc/libgomp.1.dylib
-rw-r--r--  1 root  admin    382832 Jan 11 10:00 libgomp.a
lrwxr-xr-x  1 root  admin        15 Jan 11 10:00 libgomp.dylib -> libgomp.1.dylib
-rwxr-xr-x  1 root  admin       940 Jan 11 10:00 libgomp.la
-rw-r--r--  1 root  admin       165 Jan 11 10:00 libgomp.spec
lrwxr-xr-x  1 root  admin        36 Jan 11 10:00 libitm.1.dylib -> /opt/local/lib/libgcc/libitm.1.dylib
-rw-r--r--  1 root  admin   1255600 Jan 11 10:00 libitm.a
lrwxr-xr-x  1 root  admin        14 Jan 11 10:00 libitm.dylib -> libitm.1.dylib
-rwxr-xr-x  1 root  admin       934 Jan 11 10:00 libitm.la
-rw-r--r--  1 root  admin       162 Jan 11 10:00 libitm.spec
lrwxr-xr-x  1 root  admin        41 Jan 11 10:00 libobjc-gnu.4.dylib -> /opt/local/lib/libgcc/libobjc-gnu.4.dylib
-rw-r--r--  1 root  admin    394264 Jan 11 09:59 libobjc-gnu.a
lrwxr-xr-x  1 root  admin        19 Jan 11 09:59 libobjc-gnu.dylib -> libobjc-gnu.4.dylib
-rwxr-xr-x  1 root  admin       964 Jan 11 10:00 libobjc-gnu.la
lrwxr-xr-x  1 root  admin        41 Jan 11 10:00 libquadmath.0.dylib -> /opt/local/lib/libgcc/libquadmath.0.dylib
-rw-r--r--  1 root  admin    957048 Jan 11 09:59 libquadmath.a
lrwxr-xr-x  1 root  admin        19 Jan 11 09:59 libquadmath.dylib -> libquadmath.0.dylib
-rwxr-xr-x  1 root  admin       964 Jan 11 10:00 libquadmath.la
lrwxr-xr-x  1 root  admin        36 Jan 11 10:00 libssp.0.dylib -> /opt/local/lib/libgcc/libssp.0.dylib
-rw-r--r--  1 root  admin     57672 Jan 11 09:59 libssp.a
lrwxr-xr-x  1 root  admin        14 Jan 11 09:59 libssp.dylib -> libssp.0.dylib
-rwxr-xr-x  1 root  admin       934 Jan 11 10:00 libssp.la
-rw-r--r--  1 root  admin      2400 Jan 11 09:59 libssp_nonshared.a
-rwxr-xr-x  1 root  admin       923 Jan 11 10:00 libssp_nonshared.la
lrwxr-xr-x  1 root  admin        39 Jan 11 10:00 libstdc++.6.dylib -> /opt/local/lib/libgcc/libstdc++.6.dylib
-rw-r--r--  1 root  admin   5880616 Jan 11 09:59 libstdc++.a
-rw-r--r--  1 root  admin      2323 Jan 11 09:59 libstdc++.a-gdb.py
lrwxr-xr-x  1 root  admin        17 Jan 11 09:59 libstdc++.dylib -> libstdc++.6.dylib
-rwxr-xr-x  1 root  admin       953 Jan 11 10:00 libstdc++.la
-rw-r--r--  1 root  admin    547784 Jan 11 09:59 libsupc++.a
-rwxr-xr-x  1 root  admin       902 Jan 11 10:00 libsupc++.la
-rw-r--r--  1 root  admin      1437 Jan 11 10:00 logging.properties
drwxr-xr-x  3 root  admin       102 Jan 11 10:01 security
mac83913:~ mp2$ 

[Veence (Vincent)]

And what is the output of

file /opt/local/lib/libgcc/libgfortran.3.dylib

?

[nowornot@…]

mac83913:~ mp2$ file /opt/local/lib/libgcc/libgfortran.3.dylib
/opt/local/lib/libgcc/libgfortran.3.dylib: Mach-O universal binary with 2 architectures
/opt/local/lib/libgcc/libgfortran.3.dylib (for architecture x86_64):	Mach-O 64-bit dynamically linked shared library x86_64
/opt/local/lib/libgcc/libgfortran.3.dylib (for architecture i386):	Mach-O dynamically linked shared library i386
mac83913:~ mp2$ 

Thanks!

[Veence (Vincent)]

You're welcome! If you try

arch -32 gfortran-mp-4.8

what message do you get?

[nowornot@…]

I think you're zeroing in on it!

mac83913:~ mp2$ arch -32 gfortran-mp-4.8
arch: posix_spawnp: gfortran-mp-4.8: Bad CPU type in executable
mac83913:~ mp2$ 

[Veence (Vincent)]

Well, on this side everything looks ok. Can you upload this file:

/opt/local/var/macports/build/_Macports_dports_math_arpack/arpack/work/arpack-ng-3.1.3/config.log

Thanks!

[nowornot@…]

/opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/work/arpack-ng-3.1.3-i386/

[nowornot@…]

/opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/work/arpack-ng-3.1.3-x86_64/

[nowornot@…]

I found two config.log files in similar directories, and I've uploaded both of them. Here is my directory structure:

ls /opt/local/var/macports/build/
_opt_local_var_macports_sources_www.macports.org_files_ports_lang_gcc45
_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack
_opt_local_var_macports_sources_www.macports.org_files_ports_math_metis
_opt_local_var_macports_sources_www.macports.org_files_ports_math_octave
_opt_local_var_macports_sources_www.macports.org_files_ports_math_octave-devel
_opt_local_var_macports_sources_www.macports.org_files_ports_www_webkit-gtk
mac83913:~ mp2$ ls /opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/
arpack
mac83913:~ mp2$ ls /opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/
arpack
mac83913:~ mp2$ ls /opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/
work
mac83913:~ mp2$ ls /opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/work/
arpack-ng-3.1.3		arpack-ng-3.1.3-i386	arpack-ng-3.1.3-x86_64
mac83913:~ mp2$ ls /opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/work/arpack-ng-3.1.3-i386/
CHANGES			Makefile.in		TESTS			arpack.pc.in		configure.ac		m4
COPYING			PARPACK			TODO			config.guess		depcomp			missing
DOCUMENTS		PARPACK_CHANGES		UTIL			config.log		detect_arpack_bug.m4
EXAMPLES		README			VISUAL_STUDIO		config.sub		install-sh
Makefile.am		SRC			aclocal.m4		configure		ltmain.sh
mac83913:~ mp2$ ls /opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/work/arpack-ng-3.1.3-
arpack-ng-3.1.3-i386/   arpack-ng-3.1.3-x86_64/ 
mac83913:~ mp2$ ls /opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/work/arpack-ng-3.1.3-x86_64/
CHANGES			Makefile.in		TODO			config.guess		depcomp			missing
COPYING			PARPACK			UTIL			config.log		detect_arpack_bug.m4
DOCUMENTS		PARPACK_CHANGES		VISUAL_STUDIO		config.status		install-sh
EXAMPLES		README			aclocal.m4		config.sub		libtool
Makefile		SRC			arpack.pc		configure		ltmain.sh
Makefile.am		TESTS			arpack.pc.in		configure.ac		m4
mac83913:~ mp2$ 

[nowornot@…]

P.S. There was no config.log file in /opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/work/arpack-ng-3.1.3

 ls /opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_math_arpack/arpack/work/arpack-ng-3.1.3
CHANGES			Makefile.in		TESTS			arpack.pc.in		depcomp			missing
COPYING			PARPACK			TODO			config.guess		detect_arpack_bug.m4
DOCUMENTS		PARPACK_CHANGES		UTIL			config.sub		install-sh
EXAMPLES		README			VISUAL_STUDIO		configure		ltmain.sh
Makefile.am		SRC			aclocal.m4		configure.ac		m4
mac83913:~ mp2$ 

[Veence (Vincent)]

The culprit is here:

configure:15014: /opt/local/bin/gcc-mp-4.8 -o conftest -pipe -Os -m32 -I/opt/local/include  conftest.c cfortran_test.o   -L/opt/local/lib -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin12/4.8.2 -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin12/4.8.2/../../.. -lgfortran -lquadmath -lm >&5
ld: warning: ignoring file cfortran_test.o, file was built for unsupported file format ( 0xcf 0xfa 0xed 0xfe 0x 7 0x 0 0x 0 0x 1 0x 3 0x 0 0x 0 0x 0 0x 1 0x 0 0x 0 0x 0 ) which is not the architecture being linked (i386): cfortran_test.o
ld: warning: ignoring file /opt/local/lib/gcc48/gcc/x86_64-apple-darwin12/4.8.2/libgcc.a, file was built for archive which is not the architecture being linked (i386): /opt/local/lib/gcc48/gcc/x86_64-apple-darwin12/4.8.2/libgcc.a
Undefined symbols for architecture i386:
             "_foobar", referenced from:
	      _main in cc7dY1NU.o
ld: symbol(s) not found for architecture i386
collect2: error: ld returned 1 exit status
configure:15014: $? = 1

The 32-bit compiler tries to use the 64-bit library, causing the failure. But why it does, I have no clue (as yet).

[nowornot@…]

Excellent progress! Thank you! I'd be happy to temporarily rename a directory or something like that to make progress on this...

[Veence (Vincent)]

I quit for tonight. I'll be back tomorrow maybe with a better clue. Sorry for the trudge.

[nowornot@…]

No problem! I greatly appreciate your help.

[nowornot@…]

I tried installing the previous two versions of arpack by downloading the appropriate files from here: log:trunk/dports/math/arpack?rev=110855 but had no luck with various errors. What is the path forward on this? Thanks!

[jabrouwer82@…]

Cc Me!

[MarcusCalhoun-Lopez (Marcus Calhoun-Lopez)]

Should be fixed in r140910.