Re: [Fink-users] Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

2013-11-05 Thread Dominique Dhumieres
 I just checked 3.1.3-4 into CVS.  I haven't quite built up the 
 dependencies yet on 10.9 to test it myself, but the pkgconfig logic 
 works in arpack-ng-mpi (I didn't need any extra depedencies to build 
 that).  Let me know how it works.

Thanks for the fix, but now the build fails with

...
Making all in .
/bin/sh ../libtool --tag=F77   --mode=link /sw64/bin/mpif77  -g -O2 
-no-undefined -version-info 2:0 -L/sw64/lib/openmpi -Wl,-dead_strip_dylibs 
-L/sw64/lib -o libparpack.la -rpath /sw64/lib/arpack-ng-atlas  
../SRC/libarpacksrc.la ../UTIL/libarpackutil.la 
../PARPACK/SRC/MPI/libparpacksrcmpi.la ../PARPACK/UTIL/MPI/libparpackutilmpi.la 
-ltatlas -ltatlas 
libtool: link: /sw64/bin/gfortran-fsf-4.8 -dynamiclib  -o 
.libs/libparpack.2.dylib   -Wl,-force_load ../SRC/.libs/libarpacksrc.a 
-Wl,-force_load ../UTIL/.libs/libarpackutil.a -Wl,-force_load 
../PARPACK/SRC/MPI/.libs/libparpacksrcmpi.a -Wl,-force_load 
../PARPACK/UTIL/MPI/.libs/libparpackutilmpi.a  -L/sw64/lib/openmpi -L/sw64/lib 
-ltatlas  -O2 -Wl,-dead_strip_dylibs   -install_name  
/sw64/lib/arpack-ng-atlas/libparpack.2.dylib -compatibility_version 3 
-current_version 3.0 -Wl,-single_module
Undefined symbols for architecture x86_64:
  _mpi_allreduce_, referenced from:
  _psgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psgetv0.o)
  _psnaitr_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaitr.o)
  _psnaup2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaup2.o)
  _pssaitr_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaitr.o)
  _pssaup2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaup2.o)
  _psnorm2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnorm2.o)
  _pdgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdgetv0.o)
  ...
  _mpi_comm_rank_, referenced from:
  _psnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaupd.o)
  _pssaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaupd.o)
  _pdnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdnaupd.o)
  _pdsaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdsaupd.o)
  _pcnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pcnaupd.o)
  _pcgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pcgetv0.o)
  _pznaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pznaupd.o)
  ...
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[2]: *** [libparpack.la] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1
### execution of /tmp/fink.BbgY5 failed, exit code 2
### execution of /tmp/fink.wnvHP failed, exit code 2
Removing runtime build-lock...
Removing build-lock package...
/sw64/bin/dpkg-lockwait -r fink-buildlock-arpack-ng-mpi-atlas-3.1.3-4
(Reading database ... 80270 files and directories currently installed.)
Removing fink-buildlock-arpack-ng-mpi-atlas-3.1.3-4 ...
Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-4 failed

Dominique

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Re: [Fink-users] Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

2013-11-05 Thread Alexander Hansen
On 11/5/13 12:50 AM, Dominique Dhumieres wrote:
 I just checked 3.1.3-4 into CVS.  I haven't quite built up the
 dependencies yet on 10.9 to test it myself, but the pkgconfig logic
 works in arpack-ng-mpi (I didn't need any extra depedencies to build
 that).  Let me know how it works.

 Thanks for the fix, but now the build fails with

 ...
 Making all in .
 /bin/sh ../libtool --tag=F77   --mode=link /sw64/bin/mpif77  -g -O2 
 -no-undefined -version-info 2:0 -L/sw64/lib/openmpi -Wl,-dead_strip_dylibs 
 -L/sw64/lib -o libparpack.la -rpath /sw64/lib/arpack-ng-atlas  
 ../SRC/libarpacksrc.la ../UTIL/libarpackutil.la 
 ../PARPACK/SRC/MPI/libparpacksrcmpi.la 
 ../PARPACK/UTIL/MPI/libparpackutilmpi.la -ltatlas -ltatlas
 libtool: link: /sw64/bin/gfortran-fsf-4.8 -dynamiclib  -o 
 .libs/libparpack.2.dylib   -Wl,-force_load ../SRC/.libs/libarpacksrc.a 
 -Wl,-force_load ../UTIL/.libs/libarpackutil.a -Wl,-force_load 
 ../PARPACK/SRC/MPI/.libs/libparpacksrcmpi.a -Wl,-force_load 
 ../PARPACK/UTIL/MPI/.libs/libparpackutilmpi.a  -L/sw64/lib/openmpi 
 -L/sw64/lib -ltatlas  -O2 -Wl,-dead_strip_dylibs   -install_name  
 /sw64/lib/arpack-ng-atlas/libparpack.2.dylib -compatibility_version 3 
 -current_version 3.0 -Wl,-single_module
 Undefined symbols for architecture x86_64:
_mpi_allreduce_, referenced from:
_psgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psgetv0.o)
_psnaitr_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaitr.o)
_psnaup2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaup2.o)
_pssaitr_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaitr.o)
_pssaup2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaup2.o)
_psnorm2_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnorm2.o)
_pdgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdgetv0.o)
...
_mpi_comm_rank_, referenced from:
_psnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-psnaupd.o)
_pssaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pssaupd.o)
_pdnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdnaupd.o)
_pdsaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pdsaupd.o)
_pcnaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pcnaupd.o)
_pcgetv0_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pcgetv0.o)
_pznaupd_ in libparpacksrcmpi.a(libparpacksrcmpi_la-pznaupd.o)
...
 ld: symbol(s) not found for architecture x86_64
 collect2: error: ld returned 1 exit status
 make[2]: *** [libparpack.la] Error 1
 make[1]: *** [all-recursive] Error 1
 make: *** [all-recursive] Error 1
 ### execution of /tmp/fink.BbgY5 failed, exit code 2
 ### execution of /tmp/fink.wnvHP failed, exit code 2
 Removing runtime build-lock...
 Removing build-lock package...
 /sw64/bin/dpkg-lockwait -r fink-buildlock-arpack-ng-mpi-atlas-3.1.3-4
 (Reading database ... 80270 files and directories currently installed.)
 Removing fink-buildlock-arpack-ng-mpi-atlas-3.1.3-4 ...
 Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-4 failed

 Dominique


Interesting.  I don't reproduce this on 10.9.

Try using a single build job and along with the -l option to capture a 
log.  I have a vague recollection of seeing this type of error for a a 
past build which wasn't parallel-safe.

If the build doesn't work, send me the log off list, and I'll compare 
with what I get.
-- 
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Re: [Fink-users] Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

2013-11-05 Thread Dominique Dhumieres
 Try using a single build job ...

How can I do that?

Dominique

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Re: [Fink-users] Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

2013-11-05 Thread Alexander Hansen
On 11/5/13 7:50 AM, Dominique Dhumieres wrote:
 Try using a single build job ...

 How can I do that?

 Dominique


Oops, forgot to mention that.  :-)  You can either set that via 'fink 
configure' or directly editing your fink.conf to change the MaxBuildJobs 
line.
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Re: [Fink-users] Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

2013-11-05 Thread Dominique Dhumieres
Alex,

I have found the problem: 'sw' is hardcoded in

libs=`PKG_CONFIG_PATH=/sw/lib/openmpi/pkgconfig pkg-config --libs 
ompi-f77 | cut -d\  -f2- `

If I replace 'sw' with 'sw64', everything works fine.

Dominique

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Re: [Fink-users] Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

2013-11-05 Thread Alexander Hansen
On 11/5/13 8:31 AM, Dominique Dhumieres wrote:
 Alex,

 I have found the problem: 'sw' is hardcoded in

  libs=`PKG_CONFIG_PATH=/sw/lib/openmpi/pkgconfig pkg-config --libs 
 ompi-f77 | cut -d\  -f2- `

 If I replace 'sw' with 'sw64', everything works fine.

 Dominique


Drat!  I was working late enough that I got lazy.  Thanks for finding this.

-- 
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My package updates: http://finkakh.wordpress.com/

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Re: [Fink-users] Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

2013-11-05 Thread Peter Dyballa

Am 05.11.2013 um 17:31 schrieb Dominique Dhumieres:

libs=`PKG_CONFIG_PATH=/sw/lib/openmpi/pkgconfig pkg-config --libs 
 ompi-f77 | cut -d\  -f2- `

How can that happen? When I tried hot fixes or experiments fink always 
stopped building the package… (I had to use %p, %i, etc.)

--
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Re: [Fink-users] Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

2013-11-05 Thread Alexander Hansen
On 11/5/13 10:05 AM, Peter Dyballa wrote:

 Am 05.11.2013 um 17:31 schrieb Dominique Dhumieres:

 libs=`PKG_CONFIG_PATH=/sw/lib/openmpi/pkgconfig pkg-config --libs 
 ompi-f77 | cut -d\  -f2- `

 How can that happen? When I tried hot fixes or experiments fink always 
 stopped building the package… (I had to use %p, %i, etc.)

 --
 Greetings

Pete

 Without vi there is only GNU Emacs




This can happen when not using maintainer mode.

-- 
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[Fink-users] Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

2013-11-04 Thread Dominique Dhumieres
Installing arpack-ng-mpi-atlas-3.1.3-3 on

Package manager version: 0.36.0
Distribution version: selfupdate-rsync Mon Nov  4 07:53:13 2013, 10.9, x86_64
Trees: local/main stable/main
Xcode.app: 5.0.1
Xcode command-line tools: 5.0.1.0.1.1382131676
Max. Fink build jobs:  8

failed with

configure: error: in 
`/sw64/src/fink.build/arpack-ng-mpi-atlas-3.1.3-3/arpack-ng-3.1.3':
configure: error: Fortran 77 compiler cannot create executables
See `config.log' for more details
### execution of /tmp/fink.b3OVv failed, exit code 77
### execution of /tmp/fink.VmQBZ failed, exit code 77
Removing runtime build-lock...
Removing build-lock package...
/sw64/bin/dpkg-lockwait -r fink-buildlock-arpack-ng-mpi-atlas-3.1.3-3
(Reading database ... 80018 files and directories currently installed.)
Removing fink-buildlock-arpack-ng-mpi-atlas-3.1.3-3 ...
Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

The error in config.log is

configure:2892: checking whether the Fortran 77 compiler works
configure:2914: /sw64/bin/gfortran-fsf-4.8  -Wl,-dead_strip_dylibs -L/sw64/lib 
-L/sw64/lib/openmpi conftest.f -lmpi_f77 5
ld: library not found for -lmpi_f77

TIA

Dominique

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Re: [Fink-users] Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

2013-11-04 Thread Alexander Hansen
On 11/4/13 9:19 AM, Dominique Dhumieres wrote:
 Installing arpack-ng-mpi-atlas-3.1.3-3 on

 Package manager version: 0.36.0
 Distribution version: selfupdate-rsync Mon Nov  4 07:53:13 2013, 10.9, x86_64
 Trees: local/main stable/main
 Xcode.app: 5.0.1
 Xcode command-line tools: 5.0.1.0.1.1382131676
 Max. Fink build jobs:  8

 failed with

 configure: error: in 
 `/sw64/src/fink.build/arpack-ng-mpi-atlas-3.1.3-3/arpack-ng-3.1.3':
 configure: error: Fortran 77 compiler cannot create executables
 See `config.log' for more details
 ### execution of /tmp/fink.b3OVv failed, exit code 77
 ### execution of /tmp/fink.VmQBZ failed, exit code 77
 Removing runtime build-lock...
 Removing build-lock package...
 /sw64/bin/dpkg-lockwait -r fink-buildlock-arpack-ng-mpi-atlas-3.1.3-3
 (Reading database ... 80018 files and directories currently installed.)
 Removing fink-buildlock-arpack-ng-mpi-atlas-3.1.3-3 ...
 Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

 The error in config.log is

 configure:2892: checking whether the Fortran 77 compiler works
 configure:2914: /sw64/bin/gfortran-fsf-4.8  -Wl,-dead_strip_dylibs 
 -L/sw64/lib -L/sw64/lib/openmpi conftest.f -lmpi_f77 5
 ld: library not found for -lmpi_f77

 TIA

 Dominique


It's going to take me a while to build up the dependencies for this. 
What does dpkg -L openmpi give?

-- 
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Re: [Fink-users] Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

2013-11-04 Thread Alexander Hansen
On 11/4/13 9:37 AM, Dominique d'Humières wrote:

 Le 4 nov. 2013 à 18:30, Alexander Hansen alexanderk.han...@gmail.com
 mailto:alexanderk.han...@gmail.com a écrit :

 it's going to take me a while to build up the dependencies for this.
 What does dpkg -L openmpi give?

 [Book15] /Users/dominiq% dpkg -L openmpi
 /.

snip

 /sw64/lib
 /sw64/lib/openmpi
 /sw64/lib/openmpi/libmpi.a
 /sw64/lib/openmpi/libmpi.la
 /sw64/lib/openmpi/libmpi_cxx.a
 /sw64/lib/openmpi/libmpi_cxx.la
 /sw64/lib/openmpi/libmpi_mpifh.a
 /sw64/lib/openmpi/libmpi_mpifh.la
 /sw64/lib/openmpi/libmpi_usempi.a
 /sw64/lib/openmpi/libmpi_usempi.la
 /sw64/lib/openmpi/libompitrace.a
 /sw64/lib/openmpi/libompitrace.la
 /sw64/lib/openmpi/libopen-pal.a
 /sw64/lib/openmpi/libopen-pal.la
 /sw64/lib/openmpi/libopen-rte.a
 /sw64/lib/openmpi/libopen-rte.la
 /sw64/lib/openmpi/libopen-trace-format.a
 /sw64/lib/openmpi/libopen-trace-format.la
 /sw64/lib/openmpi/libotfaux.a
 /sw64/lib/openmpi/libotfaux.la
 /sw64/lib/openmpi/libvt-hyb.a
 /sw64/lib/openmpi/libvt-hyb.la
 /sw64/lib/openmpi/libvt-mpi-unify.a
 /sw64/lib/openmpi/libvt-mpi-unify.la
 /sw64/lib/openmpi/libvt-mpi.a
 /sw64/lib/openmpi/libvt-mpi.la
 /sw64/lib/openmpi/libvt-mt.a
 /sw64/lib/openmpi/libvt-mt.la
 /sw64/lib/openmpi/libvt.a
 /sw64/lib/openmpi/libvt.la
 /sw64/lib/openmpi/mpi.mod
 /sw64/lib/openmpi/openmpi
 /sw64/lib/openmpi/openmpi/libompi_dbg_msgq.a
 /sw64/lib/openmpi/openmpi/libompi_dbg_msgq.la
 /sw64/lib/openmpi/openmpi/libompi_dbg_msgq.so
 /sw64/lib/openmpi/pkgconfig
 /sw64/lib/openmpi/pkgconfig/ompi-c.pc
 /sw64/lib/openmpi/pkgconfig/ompi-cxx.pc
 /sw64/lib/openmpi/pkgconfig/ompi-fort.pc
 /sw64/lib/openmpi/pkgconfig/ompi.pc
 /sw64/lib/openmpi/pkgconfig/opal.pc
 /sw64/lib/openmpi/pkgconfig/orte.pc

snip

 /sw64/lib/openmpi/libmpi.dylib
 /sw64/lib/openmpi/libmpi_cxx.dylib
 /sw64/lib/openmpi/libmpi_mpifh.dylib
 /sw64/lib/openmpi/libmpi_usempi.dylib
 /sw64/lib/openmpi/libompitrace.dylib
 /sw64/lib/openmpi/libopal.dylib
 /sw64/lib/openmpi/libopen-pal.dylib
 /sw64/lib/openmpi/libopen-rte.dylib
 /sw64/lib/openmpi/libopen-trace-format.dylib
 /sw64/lib/openmpi/liborte.dylib
 /sw64/lib/openmpi/libotfaux.dylib
 /sw64/lib/openmpi/libvt-hyb.dylib
 /sw64/lib/openmpi/libvt-mpi-unify.dylib
 /sw64/lib/openmpi/libvt-mpi.dylib
 /sw64/lib/openmpi/libvt-mt.dylib
 /sw64/lib/openmpi/libvt.dylib
 /sw64/lib/openmpi/pkgconfig/ompi-f77.pc
 /sw64/lib/openmpi/pkgconfig/ompi-f90.pc

snip

Aha.  I hardcoded the library name in the arpack-mpi* build procedure. 
I'll update it to use pkgconfig and hopefully that will be portable 
across 10.7 - 10.9.
-- 
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Re: [Fink-users] Failed: phase compiling: arpack-ng-mpi-atlas-3.1.3-3 failed

2013-11-04 Thread Alexander Hansen
On 11/4/13 10:32 AM, Alexander Hansen wrote:
 On 11/4/13 9:37 AM, Dominique d'Humières wrote:

 Le 4 nov. 2013 à 18:30, Alexander Hansen alexanderk.han...@gmail.com
 mailto:alexanderk.han...@gmail.com a écrit :

 it's going to take me a while to build up the dependencies for this.
 What does dpkg -L openmpi give?

 [Book15] /Users/dominiq% dpkg -L openmpi
 /.

 snip

 /sw64/lib
 /sw64/lib/openmpi
 /sw64/lib/openmpi/libmpi.a
 /sw64/lib/openmpi/libmpi.la
 /sw64/lib/openmpi/libmpi_cxx.a
 /sw64/lib/openmpi/libmpi_cxx.la
 /sw64/lib/openmpi/libmpi_mpifh.a
 /sw64/lib/openmpi/libmpi_mpifh.la
 /sw64/lib/openmpi/libmpi_usempi.a
 /sw64/lib/openmpi/libmpi_usempi.la
 /sw64/lib/openmpi/libompitrace.a
 /sw64/lib/openmpi/libompitrace.la
 /sw64/lib/openmpi/libopen-pal.a
 /sw64/lib/openmpi/libopen-pal.la
 /sw64/lib/openmpi/libopen-rte.a
 /sw64/lib/openmpi/libopen-rte.la
 /sw64/lib/openmpi/libopen-trace-format.a
 /sw64/lib/openmpi/libopen-trace-format.la
 /sw64/lib/openmpi/libotfaux.a
 /sw64/lib/openmpi/libotfaux.la
 /sw64/lib/openmpi/libvt-hyb.a
 /sw64/lib/openmpi/libvt-hyb.la
 /sw64/lib/openmpi/libvt-mpi-unify.a
 /sw64/lib/openmpi/libvt-mpi-unify.la
 /sw64/lib/openmpi/libvt-mpi.a
 /sw64/lib/openmpi/libvt-mpi.la
 /sw64/lib/openmpi/libvt-mt.a
 /sw64/lib/openmpi/libvt-mt.la
 /sw64/lib/openmpi/libvt.a
 /sw64/lib/openmpi/libvt.la
 /sw64/lib/openmpi/mpi.mod
 /sw64/lib/openmpi/openmpi
 /sw64/lib/openmpi/openmpi/libompi_dbg_msgq.a
 /sw64/lib/openmpi/openmpi/libompi_dbg_msgq.la
 /sw64/lib/openmpi/openmpi/libompi_dbg_msgq.so
 /sw64/lib/openmpi/pkgconfig
 /sw64/lib/openmpi/pkgconfig/ompi-c.pc
 /sw64/lib/openmpi/pkgconfig/ompi-cxx.pc
 /sw64/lib/openmpi/pkgconfig/ompi-fort.pc
 /sw64/lib/openmpi/pkgconfig/ompi.pc
 /sw64/lib/openmpi/pkgconfig/opal.pc
 /sw64/lib/openmpi/pkgconfig/orte.pc

 snip

 /sw64/lib/openmpi/libmpi.dylib
 /sw64/lib/openmpi/libmpi_cxx.dylib
 /sw64/lib/openmpi/libmpi_mpifh.dylib
 /sw64/lib/openmpi/libmpi_usempi.dylib
 /sw64/lib/openmpi/libompitrace.dylib
 /sw64/lib/openmpi/libopal.dylib
 /sw64/lib/openmpi/libopen-pal.dylib
 /sw64/lib/openmpi/libopen-rte.dylib
 /sw64/lib/openmpi/libopen-trace-format.dylib
 /sw64/lib/openmpi/liborte.dylib
 /sw64/lib/openmpi/libotfaux.dylib
 /sw64/lib/openmpi/libvt-hyb.dylib
 /sw64/lib/openmpi/libvt-mpi-unify.dylib
 /sw64/lib/openmpi/libvt-mpi.dylib
 /sw64/lib/openmpi/libvt-mt.dylib
 /sw64/lib/openmpi/libvt.dylib
 /sw64/lib/openmpi/pkgconfig/ompi-f77.pc
 /sw64/lib/openmpi/pkgconfig/ompi-f90.pc

 snip

 Aha.  I hardcoded the library name in the arpack-mpi* build procedure.
 I'll update it to use pkgconfig and hopefully that will be portable
 across 10.7 - 10.9.

I just checked 3.1.3-4 into CVS.  I haven't quite built up the 
dependencies yet on 10.9 to test it myself, but the pkgconfig logic 
works in arpack-ng-mpi (I didn't need any extra depedencies to build 
that).  Let me know how it works.

-- 
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/

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