[CIG-SHORT] Not able to run dynamic fault (step11) with Pylith-1.9.0 installed from source
Birendra jha
bjha7333 at yahoo.com
Tue Sep 3 13:50:33 PDT 2013
Brad
The libtests failed at SlipWeakeningTimeStable (see below). How can I fix it? The env variables look correct, friction module has SlipWeakeningTimeStable (I checked friction_wrap.cxx, friction.py), libsrc/pylith/friction/ also has the SlipWeakeningTimeStable files.
/bin/sh ../../../libtool --tag=CXX --mode=link mpicxx -g -O2 -DMPICH_IGNORE_CXX_SEEK -L/data/bjha/pylith-1.9.0/lib -o testfriction test_friction.o TestFrictionModel.o TestStaticFriction.o TestSlipWeakening.o TestSlipWeakeningTime.o TestSlipWeakeningTimeStable.o TestSlipWeakeningStress.o TestRateStateAgeing.o TestTimeWeakening.o FrictionModelData.o StaticFrictionData.o SlipWeakeningData.o SlipWeakeningTimeData.o SlipWeakeningTimeStableData.o SlipWeakeningStressData.o RateStateAgeingData.o TimeWeakeningData.o -lcppunit -ldl ../../../libsrc/pylith/libpylith.la -lspatialdata -L/data/bjha/pylith-1.9.0/lib -lpetsc -Wl,-rpath,/data/bjha/pylith-1.9.0/lib -lml -lflapack -lfblas -lpthread -lchaco -Wl,-rpath,/data/bjha/pylith-1.9.0/lib -L/data/bjha/pylith-1.9.0/lib -lhdf5 -Wl,-rpath,/mit/software/gcc/gcc-4.6.0/pkg/openmpi/openmpi-1.4.3/lib -L/mit/software/gcc/gcc-4.6.0/pkg/openmpi/openmpi-1.4.3/lib -Wl,-rpath,/usr/lib/gcc/x86_64-redhat-linux/4.6.3
-L/usr/lib/gcc/x86_64-redhat-linux/4.6.3 -Wl,-rpath,/mit/software/python/python-2.7.2/lib -L/mit/software/python/python-2.7.2/lib -lmpi_f90 -lmpi_f77 -lgfortran -lm -lgfortran -lm -lgfortran -lm -lm -lquadmath -lm -lmpi_cxx -lstdc++ -ldl -lz -lmpi -lopen-rte -lopen-pal -lnsl -lutil -lgcc_s -lpthread -ldl -lz -L/mit/software/python/python-2.7.2/lib -L/mit/software/python/python-2.7.2/lib/python2.7/config -lpython2.7 -lpthread -ldl -lutil -lm -lnetcdf_c++ -lnetcdf -lproj -lhdf5
libtool: link: mpicxx -g -O2 -DMPICH_IGNORE_CXX_SEEK -o .libs/testfriction test_friction.o TestFrictionModel.o TestStaticFriction.o TestSlipWeakening.o TestSlipWeakeningTime.o TestSlipWeakeningTimeStable.o TestSlipWeakeningStress.o TestRateStateAgeing.o TestTimeWeakening.o FrictionModelData.o StaticFrictionData.o SlipWeakeningData.o SlipWeakeningTimeData.o SlipWeakeningTimeStableData.o SlipWeakeningStressData.o RateStateAgeingData.o TimeWeakeningData.o -Wl,-rpath -Wl,/data/bjha/pylith-1.9.0/lib -Wl,-rpath -Wl,/data/bjha/pylith-1.9.0/lib -Wl,-rpath -Wl,/mit/software/gcc/gcc-4.6.0/pkg/openmpi/openmpi-1.4.3/lib -Wl,-rpath -Wl,/usr/lib/gcc/x86_64-redhat-linux/4.6.3 -Wl,-rpath -Wl,/mit/software/python/python-2.7.2/lib -L/data/bjha/pylith-1.9.0/lib /data/bjha/pylith-1.9.0/lib/libcppunit.so ../../../libsrc/pylith/.libs/libpylith.so /data/bjha/pylith-1.9.0/lib/libspatialdata.so -lpetsc -lml -lflapack -lfblas -lchaco
-L/mit/software/gcc/gcc-4.6.0/pkg/openmpi/openmpi-1.4.3/lib -L/usr/lib/gcc/x86_64-redhat-linux/4.6.3 -L/mit/software/python/python-2.7.2/lib /mit/software/gcc/gcc-4.6.0/pkg/openmpi/openmpi-1.4.3/lib/libmpi_f90.so /mit/software/gcc/gcc-4.6.0/pkg/openmpi/openmpi-1.4.3/lib/libmpi_f77.so -lgfortran -lquadmath /mit/software/gcc/gcc-4.6.0/pkg/openmpi/openmpi-1.4.3/lib/libmpi_cxx.so -lstdc++ /mit/software/gcc/gcc-4.6.0/pkg/openmpi/openmpi-1.4.3/lib/libmpi.so /mit/software/gcc/gcc-4.6.0/pkg/openmpi/openmpi-1.4.3/lib/libopen-rte.so /mit/software/gcc/gcc-4.6.0/pkg/openmpi/openmpi-1.4.3/lib/libopen-pal.so -lnsl -lgcc_s -lz -L/mit/software/python/python-2.7.2/lib/python2.7/config -lpython2.7 -lpthread -ldl -lutil -lm /data/bjha/pylith-1.9.0/lib/libnetcdf_c++.so /data/bjha/pylith-1.9.0/lib/libnetcdf.so /data/bjha/pylith-1.9.0/lib/libproj.so /data/bjha/pylith-1.9.0/lib/libhdf5.so -pthread -Wl,-rpath -Wl,/data/bjha/pylith-1.9.0/lib -Wl,-rpath
-Wl,/mit/software/gcc/gcc-4.6.0/pkg/openmpi/openmpi-1.4.3/lib
TestSlipWeakeningTimeStable.o: In function `pylith::friction::TestSlipWeakeningTimeStable::setUp()':
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningTimeStable.cc:35: undefined reference to `pylith::friction::SlipWeakeningTimeStable::SlipWeakeningTimeStable()'
TestSlipWeakeningTimeStable.o: In function `pylith::friction::TestSlipWeakeningTimeStable::testHasPropStateVar()':
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningTimeStable.cc:83: undefined reference to `pylith::friction::SlipWeakeningTimeStable::SlipWeakeningTimeStable()'
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningTimeStable.cc:93: undefined reference to `pylith::friction::SlipWeakeningTimeStable::~SlipWeakeningTimeStable()'
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningTimeStable.cc:93: undefined reference to `pylith::friction::SlipWeakeningTimeStable::~SlipWeakeningTimeStable()'
TestSlipWeakeningTimeStable.o: In function `pylith::friction::TestSlipWeakeningTimeStable::testStateVarsMetadata()':
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningTimeStable.cc:68: undefined reference to `pylith::friction::SlipWeakeningTimeStable::SlipWeakeningTimeStable()'
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningTimeStable.cc:75: undefined reference to `pylith::friction::SlipWeakeningTimeStable::~SlipWeakeningTimeStable()'
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningTimeStable.cc:75: undefined reference to `pylith::friction::SlipWeakeningTimeStable::~SlipWeakeningTimeStable()'
TestSlipWeakeningTimeStable.o: In function `pylith::friction::TestSlipWeakeningTimeStable::testPropertiesMetadata()':
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningTimeStable.cc:45: undefined reference to `pylith::friction::SlipWeakeningTimeStable::SlipWeakeningTimeStable()'
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningTimeStable.cc:60: undefined reference to `pylith::friction::SlipWeakeningTimeStable::~SlipWeakeningTimeStable()'
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningTimeStable.cc:60: undefined reference to `pylith::friction::SlipWeakeningTimeStable::~SlipWeakeningTimeStable()'
TestSlipWeakeningStress.o: In function `pylith::friction::TestSlipWeakeningStress::setUp()':
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningStress.cc:35: undefined reference to `pylith::friction::SlipWeakeningStress::SlipWeakeningStress()'
TestSlipWeakeningStress.o: In function `pylith::friction::TestSlipWeakeningStress::testHasPropStateVar()':
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningStress.cc:75: undefined reference to `pylith::friction::SlipWeakeningStress::SlipWeakeningStress()'
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningStress.cc:83: undefined reference to `pylith::friction::SlipWeakeningStress::~SlipWeakeningStress()'
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningStress.cc:83: undefined reference to `pylith::friction::SlipWeakeningStress::~SlipWeakeningStress()'
TestSlipWeakeningStress.o: In function `pylith::friction::TestSlipWeakeningStress::testStateVarsMetadata()':
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningStress.cc:60: undefined reference to `pylith::friction::SlipWeakeningStress::SlipWeakeningStress()'
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningStress.cc:67: undefined reference to `pylith::friction::SlipWeakeningStress::~SlipWeakeningStress()'
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningStress.cc:67: undefined reference to `pylith::friction::SlipWeakeningStress::~SlipWeakeningStress()'
TestSlipWeakeningStress.o: In function `pylith::friction::TestSlipWeakeningStress::testPropertiesMetadata()':
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningStress.cc:45: undefined reference to `pylith::friction::SlipWeakeningStress::SlipWeakeningStress()'
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningStress.cc:52: undefined reference to `pylith::friction::SlipWeakeningStress::~SlipWeakeningStress()'
/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction/../../../../pylith-1.9.0/unittests/libtests/friction/TestSlipWeakeningStress.cc:52: undefined reference to `pylith::friction::SlipWeakeningStress::~SlipWeakeningStress()'
collect2: ld returned 1 exit status
make[3]: *** [testfriction] Error 1
make[3]: Leaving directory `/net/eaps-80-11/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction'
make[2]: *** [check-am] Error 2
make[2]: Leaving directory `/net/eaps-80-11/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction'
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory `/net/eaps-80-11/data/bjha/build/pylith-1.9.0/pylith-build/unittests/libtests/friction'
make: *** [check-recursive] Error 1
Thanks and regards
Birendra
--------------------------------------------
On Tue, 9/3/13, Brad Aagaard <baagaard at usgs.gov> wrote:
Subject: Re: [CIG-SHORT] Not able to run dynamic fault (step11) with Pylith-1.9.0 installed from source
To: cig-short at geodynamics.org
Date: Tuesday, September 3, 2013, 8:40 AM
On 9/2/13 7:32 PM, Birendra jha
wrote:
> Brad
>
> Running ldd lists the correct pylith version:
> libpylith.so.0 =>
/data/bjha/pylith-1.9.0/lib/libpylith.so.0
(0x00007f5460452000)
>
> How should I check python unit tests?
Start by not cleaning, just run the tests.
To be safe, start with the libtests
cd pylith-build/unittests/libtests
make check
and if they pass, do the python unit tests (note that these
often don't
stop even if there is an error, so you need to actually
check the
output). Pay particular attention to the friction and fault
unit tests.
cd pylith-build/unittests/pytests
make check
If these pass, then look at all of the environment variables
in
config.log and compare them against the output of "env". If
the tests
pass then something must be different between the
environment when you
built and now.
Brad
> --------------------------------------------
> On Tue, 9/3/13, Brad Aagaard <baagaard at usgs.gov>
wrote:
>
> Subject: Re: [CIG-SHORT] Not able to
run dynamic fault (step11) with Pylith-1.9.0 installed from
source
> To: cig-short at geodynamics.org
> Date: Tuesday, September 3, 2013, 7:23
AM
>
> Birendra,
>
> The error you are getting with
"import
> pylith.faults.FaultCohesiveDyn"
> indicates that the friction module is
missing a symbol for
> pylith::friction::SlipWeakeningTimeStable.
This was added in
> v1.9, so
> either the module or pylith library
didn't build properly or
> your
> environment when you run the examples
is finding the pylith
> library from
> v1.8.
>
> Run "ldd
> /data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/friction/_frictionmodule.so".
>
> If it lists libpylith.so from v1.8,
then you need to fix
> your
> environment (check it against the
variables from setup.sh).
> If it shows
> libpylith.so from v1.9, then your
pylith build has a
> problem. Check the
> python unit tests again.
>
> Brad
>
> On 9/2/13 6:27 PM, Birendra jha
wrote:
> > Brad
> >
> > I agree something is wrong with
my installation.
> However, all the tests passed when I
built pylith using the
> installer.
> > Here is the result of running
nemesis:
> >
> > [bjha at login refined]$ nemesis
> > Python 2.7.2 (default, Jul 12
2011, 10:24:30)
> > [GCC 4.6.0 20110530 (Red Hat
4.6.0-9)] on linux2
> > Type "help", "copyright",
"credits" or "license" for
> more information.
> >>>> import
pylith.faults.FaultCohesiveDyn
> > Traceback (most recent call
last):
> > File
"<stdin>", line 1, in
> <module>
> > File
> "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/faults/FaultCohesiveDyn.py",
> line 34, in <module>
> > class
> FaultCohesiveDyn(FaultCohesive,
Integrator,
> ModuleFaultCohesiveDyn):
> > File
> "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/faults/FaultCohesiveDyn.py",
> line 75, in FaultCohesiveDyn
> > from
pylith.friction.StaticFriction
> import StaticFriction
> > File
> "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/friction/StaticFriction.py",
> line 26, in <module>
> > from friction
import StaticFriction
> as ModuleStaticFriction
> > File
> "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/friction/friction.py",
> line 26, in <module>
> > _friction =
swig_import_helper()
> > File
> "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/friction/friction.py",
> line 22, in swig_import_helper
> > _mod =
imp.load_module('_friction',
> fp, pathname, description)
> > ImportError:
> /data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pylith/friction/_frictionmodule.so:
> undefined symbol:
> _ZN6pylith8friction23SlipWeakeningTimeStableC1Ev
> >>>>
pylith.faults.FaultCohesiveDyn.__file__
> > Traceback (most recent call
last):
> > File
"<stdin>", line 1, in
> <module>
> > NameError: name 'pylith' is not
defined
> >>>>
> >
> > I checked PATH, PYTHONPATH and
they are exclusively
> pointing to Pylith-1.9.0, not
Pylith-1.8.0.
> >
> > What do you suggest?
> > Birendra
> >
--------------------------------------------
> > On Tue, 9/3/13, Brad Aagaard
<baagaard at usgs.gov>
> wrote:
> >
> > Subject: Re:
[CIG-SHORT] Not able to
> run dynamic fault (step11) with
Pylith-1.9.0 installed from
> source
> > To: cig-short at geodynamics.org
> > Date: Tuesday,
September 3, 2013, 2:29
> AM
> >
> > Birendra,
> >
> > I don't find any
problems with
> examples/3d/hex8/step11. It
> > runs fine for
> > me using the
binary and building from
> source. My guess is
> > that something
> > is wrong with
your installation. Did
> you wipe out all of the
> > old PyLith
> > stuff in your
PATH, PYTHONPATH, etc or
> at least adjust your
> > PATH,
> > PYTHONPATH, etc
so that they only see
> v1.9.0? Did all of the
> > tests pass
> > when you built
pylith using the
> installer?
> >
> > What happens
when you do the
> following?
> > nemesis
> > import
pylith.faults.FaultCohesiveDyn
> > pylith.faults.FaultCohesiveDyn.__file__
> >
> > You can also try
running
> > pylithinfo
--verbose step11.cfg
> >
> > The output will
be written to
> pylith_parameters.txt. It will
> > show you
> > where every
parameter is set. You
> would first need to fix
> > any validation
> > errors to get
this far, because those
> are tripped before the
> > parameters
> > can be written.
> >
> > Regards,
> > Brad
> >
> >
> > On 9/1/13 10:26
PM, Birendra jha
> wrote:
> > > Hi Pylith
developers
> > >
> > > I installed
Pylith-1.9.0 using
> the installer on the
> > pylith website.
Installation was
> successful with no error
> > messages except
in the beginning when
> I ran configure I got
> > a message about
existing software:
> > >
> > > WARNING:
Existing version of HDF5
> installed. Found
> > /usr/bin/h5dump
> > > WARNING:
Existing version of
> NetCDF installed. Found
> > /usr/bin/ncdump
> > >
> > > configure:
error: "Configure
> failed due to conflict
> > with existing
software. Existing
> software may interfere with
> > proper
installation of PyLith, may be
> configured incorrectly
> > for use with
PyLith, or may have been
> built with
> > incompatible
compilers. Remove
> existing software
> > (RECOMMENDED) or
reconfigure with
> --enable-force-install to
> > override error
message. "
> > >
> > > As per
suggestion, I reran
> configure with
> > --enable-force-install
option, and it
> finished successfully
> > along with
'make'.
> > >
> > > I am able
to run successfully all
> examples e.g. step01,
> > step06 except
examples with dynamic
> fault e.g. step11:
> > >
> > > [bjha at login
hex8]$ pylith
> step11.cfg
> > > Traceback
(most recent call
> last):
> > >
File
> "/data/bjha/pylith-1.9.0/bin/pylith",
> > line 39, in
<module>
> > >
> start(applicationClass=PyLithApp)
> > >
File
> > "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applications/__init__.py",
> > line 41, in
start
> > >
> shell.run(**kwds)
> > >
File
> > "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/applications/Shell.py",
> > line 125, in
run
> > >
> app.applyConfiguration(context)
> > >
File
> > "/data/bjha/pylith-1.9.0/lib/python2.7/site-packages/pythia-0.8.1.15-py2.7.egg/pyre/inventory/Configurable.py",
> > line 84, in
applyConfiguration
> > >
raise
> ValueError("%s\nBacktrace -
> > Component %s" %
(err.message,
> aliases))
> > > ValueError:
Error while
> configuring spatial database
> > reader
(simpleioascii, iohandler):
> > > Filename
for spatial database not
> specified.
> > > Backtrace -
Component
> simpleioascii, iohandler
> > > Backtrace -
Component simpledb,
> slip
> > > Backtrace -
Component stepslipfn,
> slip_function
> > > Backtrace -
Component eqkinsrc,
> rupture
> > > Backtrace -
Component
> singlerupture, eq_srcs
> > > Backtrace -
Component
> faultcohesivekin, fault
> > > Backtrace -
Component interfaces
> > > Backtrace -
Component
> timedependent, problem
> > > Backtrace -
Component pylithapp
> > >
> > > Why is it
saying faultcohesivekin
> when it is
> > FaultCohesiveDyn
in the step11.cfg? I
> am able to run this in
> > my Pylith-1.8.0
copy.
> > > Please
help.
> > >
> > > Thanks and
regards
> > > Birendra
> > >
> > >
> _______________________________________________
> > > CIG-SHORT
mailing list
> > > CIG-SHORT at geodynamics.org
> > > http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> > >
> >
> > _______________________________________________
> > CIG-SHORT
mailing list
> > CIG-SHORT at geodynamics.org
> > http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >
> >
_______________________________________________
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> > http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> >
>
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