openbsd installation FoundationPy

Hi Patrick,

Nice to know that ESyS-Particle can be installed on BSD. I doubt the M_PI error will be a problem.

Regarding the import error, I'm not familar with BSD but on linux I would be checking that my PYTHONPATH environment variable has been set correctly e.g.

export PYTHONPATH=/path/to/esys/install/lib/python2.7/dist-packages:$PYTHONPATH

Cheers,

Dion.

Thanks for replying, Dion. Forgive me for not mentioning it, but I did try several variations on PYTHONPATHs without success (and just did it again). And the FoundationPy compiled libraries are in the same directory as the __init__.py which is trying to import them, so it's finding it to that point. I'm afraid I don't know enough about python to completely understand how it imports binary libraries as opposed to python code; could it be as simple as an incompatibility in libtool (I have 2.4.2)?

Hi Patrick:

I am not sure how BSD handle boost python, however you might need to check if libboost-python are also in PYTHONPATH, that is also necessary for the whole thing to work.

Feng

Hello Patrick:

There is not meant to be a Python file for FoundationPy, and there should be no difficulty for Python to import the FoundationPy library from the same folder that it found esys.lsm.util's __init__.py. If you are still having trouble, send me the contents of /usr/local/lib/python2.7/site-packages/esys/lsm/util/FoundationPy.la. And can you verify that the library name is in fact FoundationPy.so? I am also curious to know the names of your Boost libraries (libboost*, probably under /usr/lib/, or /usr/local/lib/). Finally, can you send me the configuration line you used before building ESyS-Particle?

Vince

Hi Vince,

I'm not sure if there's a way to attach files; if there is delete this and I'll redo it. Otherwise, the answers are below in order, and I've delineated the longer answers. I have also tried updating the openbsd packages, reinstalling, and running various variations on `libtool finish`, but I still get the same error.

Thanks!

----- esys/lsm/util/FoundationPy.la -----

# FoundationPy.la - a libtool library file
# Generated by ltmain.sh - GNU libtool 1.5.26 (1.1220.2.493 2008/02/01 16:58:18)
#
# Please DO NOT delete this file!
# It is necessary for linking the library.

# The name that we can dlopen(3).
dlname='FoundationPy.so.0.0'

# Names of this library.
library_names='FoundationPy.so.0.0 FoundationPy.so.0.0'

# The name of the static archive.
old_library='FoundationPy.a'

# Libraries that this one depends upon.
dependency_libs=' /usr/local/lib/python2.7/site-packages/esys/lsm/util/libFoundationPy.la -L/usr/lib /usr/local/lib/libFoundation.la -lboost_filesystem-mt -lboost_system-mt /usr/local/lib/libBoostPythonUtil.la -lboost_python-mt -lpython2.7'

# Version information for FoundationPy.
current=0
age=0
revision=0

# Is this an already installed library?
installed=yes

# Should we warn about portability when linking against -modules?
shouldnotlink=yes

# Files to dlopen/dlpreopen
dlopen=''
dlpreopen=''

# Directory that this library needs to be installed in:
libdir='/usr/local/lib/python2.7/site-packages/esys/lsm/util'
~
----- FoundationPy.la -----

The three FoundationPy.* files in that directory are .a, .la, and .so.0.0, which matches the contents in .la, I think.

----- boost files -----

galena 20:44:43 $ ls /usr/local/lib/*boost*
/usr/local/lib/libboost_date_time-mt.a
/usr/local/lib/libboost_date_time-mt.so.2.0
/usr/local/lib/libboost_date_time-mt.so.4.0
/usr/local/lib/libboost_date_time.a
/usr/local/lib/libboost_date_time.so.2.0
/usr/local/lib/libboost_date_time.so.4.0
/usr/local/lib/libboost_filesystem-mt.a
/usr/local/lib/libboost_filesystem-mt.so.2.0
/usr/local/lib/libboost_filesystem-mt.so.4.0
/usr/local/lib/libboost_filesystem.a
/usr/local/lib/libboost_filesystem.so.2.0
/usr/local/lib/libboost_filesystem.so.4.0
/usr/local/lib/libboost_graph-mt.a
/usr/local/lib/libboost_graph-mt.so.2.0
/usr/local/lib/libboost_graph-mt.so.4.0
/usr/local/lib/libboost_graph.a
/usr/local/lib/libboost_graph.so.2.0
/usr/local/lib/libboost_graph.so.4.0
/usr/local/lib/libboost_iostreams-mt.a
/usr/local/lib/libboost_iostreams-mt.so.2.0
/usr/local/lib/libboost_iostreams-mt.so.4.0
/usr/local/lib/libboost_iostreams.a
/usr/local/lib/libboost_iostreams.so.2.0
/usr/local/lib/libboost_iostreams.so.4.0
/usr/local/lib/libboost_math_c99-mt.a
/usr/local/lib/libboost_math_c99-mt.so.2.0
/usr/local/lib/libboost_math_c99-mt.so.4.0
/usr/local/lib/libboost_math_c99.a
/usr/local/lib/libboost_math_c99.so.2.0
/usr/local/lib/libboost_math_c99.so.4.0
/usr/local/lib/libboost_math_c99f-mt.a
/usr/local/lib/libboost_math_c99f-mt.so.2.0
/usr/local/lib/libboost_math_c99f-mt.so.4.0
/usr/local/lib/libboost_math_c99f.a
/usr/local/lib/libboost_math_c99f.so.2.0
/usr/local/lib/libboost_math_c99f.so.4.0
/usr/local/lib/libboost_math_c99l-mt.a
/usr/local/lib/libboost_math_c99l-mt.so.2.0
/usr/local/lib/libboost_math_c99l-mt.so.4.0
/usr/local/lib/libboost_math_c99l.a
/usr/local/lib/libboost_math_c99l.so.2.0
/usr/local/lib/libboost_math_c99l.so.4.0
/usr/local/lib/libboost_math_tr1-mt.a
/usr/local/lib/libboost_math_tr1-mt.so.2.0
/usr/local/lib/libboost_math_tr1-mt.so.4.0
/usr/local/lib/libboost_math_tr1.a
/usr/local/lib/libboost_math_tr1.so.2.0
/usr/local/lib/libboost_math_tr1.so.4.0
/usr/local/lib/libboost_math_tr1f-mt.a
/usr/local/lib/libboost_math_tr1f-mt.so.2.0
/usr/local/lib/libboost_math_tr1f-mt.so.4.0
/usr/local/lib/libboost_math_tr1f.a
/usr/local/lib/libboost_math_tr1f.so.2.0
/usr/local/lib/libboost_math_tr1f.so.4.0
/usr/local/lib/libboost_math_tr1l-mt.a
/usr/local/lib/libboost_math_tr1l-mt.so.2.0
/usr/local/lib/libboost_math_tr1l-mt.so.4.0
/usr/local/lib/libboost_math_tr1l.a
/usr/local/lib/libboost_math_tr1l.so.2.0
/usr/local/lib/libboost_math_tr1l.so.4.0
/usr/local/lib/libboost_prg_exec_monitor-mt.a
/usr/local/lib/libboost_prg_exec_monitor-mt.so.2.0
/usr/local/lib/libboost_prg_exec_monitor-mt.so.4.0
/usr/local/lib/libboost_prg_exec_monitor.a
/usr/local/lib/libboost_prg_exec_monitor.so.2.0
/usr/local/lib/libboost_prg_exec_monitor.so.4.0
/usr/local/lib/libboost_program_options-mt.a
/usr/local/lib/libboost_program_options-mt.so.2.0
/usr/local/lib/libboost_program_options-mt.so.4.0
/usr/local/lib/libboost_program_options.a
/usr/local/lib/libboost_program_options.so.2.0
/usr/local/lib/libboost_program_options.so.4.0
/usr/local/lib/libboost_python-mt.a
/usr/local/lib/libboost_python-mt.so.2.0
/usr/local/lib/libboost_python-mt.so.4.0
/usr/local/lib/libboost_python.a
/usr/local/lib/libboost_python.so.2.0
/usr/local/lib/libboost_python.so.4.0
/usr/local/lib/libboost_regex-mt.a
/usr/local/lib/libboost_regex-mt.so.2.0
/usr/local/lib/libboost_regex-mt.so.4.0
/usr/local/lib/libboost_regex.a
/usr/local/lib/libboost_regex.so.2.0
/usr/local/lib/libboost_regex.so.4.0
/usr/local/lib/libboost_serialization-mt.a
/usr/local/lib/libboost_serialization-mt.so.2.0
/usr/local/lib/libboost_serialization-mt.so.4.0
/usr/local/lib/libboost_serialization.a
/usr/local/lib/libboost_serialization.so.2.0
/usr/local/lib/libboost_serialization.so.4.0
/usr/local/lib/libboost_signals-mt.a
/usr/local/lib/libboost_signals-mt.so.2.0
/usr/local/lib/libboost_signals-mt.so.4.0
/usr/local/lib/libboost_signals.a
/usr/local/lib/libboost_signals.so.2.0
/usr/local/lib/libboost_signals.so.4.0
/usr/local/lib/libboost_system-mt.a
/usr/local/lib/libboost_system-mt.so.2.0
/usr/local/lib/libboost_system-mt.so.4.0
/usr/local/lib/libboost_system.a
/usr/local/lib/libboost_system.so.2.0
/usr/local/lib/libboost_system.so.4.0
/usr/local/lib/libboost_test_exec_monitor-mt.a
/usr/local/lib/libboost_test_exec_monitor.a
/usr/local/lib/libboost_thread-mt.a
/usr/local/lib/libboost_thread-mt.so.2.0
/usr/local/lib/libboost_thread-mt.so.4.0
/usr/local/lib/libboost_unit_test_framework-mt.a
/usr/local/lib/libboost_unit_test_framework-mt.so.2.0
/usr/local/lib/libboost_unit_test_framework-mt.so.4.0
/usr/local/lib/libboost_unit_test_framework.a
/usr/local/lib/libboost_unit_test_framework.so.2.0
/usr/local/lib/libboost_unit_test_framework.so.4.0
/usr/local/lib/libboost_wave-mt.a
/usr/local/lib/libboost_wave-mt.so.2.0
/usr/local/lib/libboost_wave-mt.so.4.0
/usr/local/lib/libboost_wave.a
/usr/local/lib/libboost_wave.so.2.0
/usr/local/lib/libboost_wave.so.4.0
/usr/local/lib/libboost_wserialization-mt.a
/usr/local/lib/libboost_wserialization-mt.so.2.0
/usr/local/lib/libboost_wserialization-mt.so.4.0
/usr/local/lib/libboost_wserialization.a
/usr/local/lib/libboost_wserialization.so.2.0
/usr/local/lib/libboost_wserialization.so.4.0

----- boost files -----

It was created by ESyS-Particle configure 2.2, which was
generated by GNU Autoconf 2.68. Invocation command line was

  $ ./configure CC=mpicc CXX=mpic++ CXXFLAGS=-DM_PIl=M_PI

Hi Patrick,

This is proving to be a tricky problem!

I just now noticed that the command you are using to run the test script is slightly incorrect. It should be:
mpirun -np 2 esysparticle test.py

ESyS-Particle always requires N+1 MPI processes where N is the number of workers/subdomains and the extra 1 is the master process.

Unfortunately I doubt that fixing this is going to solve your problem though...over to Vince again.

Cheers,

Dion

Dion,

Correct; I had initially tried to run it on two nodes and the '-np 1' was just an attempt at simplification. I don't have anything better to add.

Thanks!

Hi Vince,

That did the trick! Thanks!

Pat

Thanks Vince Boros, that solved my question.

Hi Pat:

Good. But there are more ESyS-Particle libraries that need .so links in order to exploit the full potential of the code. Of course you can create the links manually, but much better to work out how to get the Autotools on BSD Unix to generate them. They should be generated automatically as on our Linux systems, but currently I don't know why they are not.

Vince