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From: Subhasis R. <ray...@gm...> - 2015-06-04 02:43:21
|
Hi, We are happy to announce that the latest release of MOOSE (3.0.1 - Gulab Jamun) is now successfully running on Neuroscience Gateway Portal (NSG, http://www.nsgportal.org/). The NSG portal provides access to High Performance Computing resources for running Neuroscience simulations. Instructions for obtaining user account available here: http://www.nsgportal.org/portal2/login!input.action. We thank the NSG team for installing and setting up MOOSE on this system. Best, - Subhasis |
|
From: Subhasis R. <ray...@gm...> - 2015-04-01 19:41:51
|
Hi, Your query had been pending moderator approval and even after approving it somehow did not come as an email, so I am copying your header and trying to answer it. Apologies for the delayed response. The way to run moose over mpi is to use Python with a script using pymoose as the setup process and run the moose executable (this gets created right inside the source directory) as compute processes. For example, if you have a multicore cpu, you could run this as: mpiexec -host localhost -np 1 /usr/bin/python test_pymoose.py : -np 1 ../../moose You can take a look at this benchmarking script for running different number of compute processes : tests/mpi/benchmark.py which will give you an idea (you can even use it for benchmarking your own script - though I have not tested it recently). Note that coexisting openmpi and mpich may cause linking issues that may show up at run time as discussed in openmpi docs (so use only openmpi). Best, - Subhasis |
|
From: Subhasis R. <ray...@gm...> - 2015-03-31 15:23:17
|
Hi,
This is more of a user issue than a development issue, hence cc to
moose-generic mailing list.
On Tue, Mar 31, 2015 at 4:38 AM, Dilawar Singh <dil...@nc...> wrote:
>
> An equation in chemical model is following:
>
> x(t) = a(t)*b(t)*c(t); (A)
>
> Variable 'x' is a proxy for three independent moose.Pool with species a,
> b, and
> c having their own kinetics. In other reactions, 'x' is treated as input;
>
What do you mean by input to a reaction?
> therefor it should be implemented as moose.Pool or moose.BufPool.
>
>
In continuation of previous query, can you tell us more about the reaction
system? A pool is a pool of molecules and I cannot imagine the number of
molecules in one pool being the product of three others in a physical
process. In another way, your equation will be dimensionally invalid.
>
> AFAIK, currently moose.Pool does not have a Dest-Finfo which I can use to
> set
> the number of molecules in Pool.
For each ValueFinfo 'x', a moose class automatically gets a 'getX' and
'setX' DestFinfos. You could see this using the builtin doc function:
>>> moose.doc('Pool')
...
*Destination message field*
setN: double
getN: PSt6vectorIdSaIdEE
setNInit: double
getNInit: PSt6vectorIdSaIdEE
setDiffConst: double
getDiffConst: PSt6vectorIdSaIdEE
...
> I can only use 'increment' or 'decrement' which
> is fine if the equation was:
>
> dx/dt = a*b*c (A1)
>
> So it boils down to having a moose.Pool where kinetics can be described
> using
> the equation (A); perhaps a combination of moose.Function and moose.Table.
> But
> in the end, I have to set the conc/n of moose.Pool using a message.
>
I am not sure if setting n externally is the right approach though. The
pools are supposed to participate in reactions and get their n updated
through that process.
>
> Another way of doing it to use the moose.Function and connect
> 'getDerivative' to
> the x (moose.Pool) 'increment'. I don't know if it would be mathematically
> wrong
> but moose.connect does not allow connecting these two Finfos. I can
> implement
> this if it is mathematically correct or does not cause numerical issues.
>
You cannot connect a DestFinfo to another DestFinfo. You can use
'derivativeOut' SrcFinfo from Function.
>
> I extended the moose.Pool class by adding a 'N' destinfo which set the n_
> to
> given value
As I mentioned above, this was unnecessary.
> but I don't know what values should A_ and B_ take. Merely changing
> n_ and setting A_ and B_ to 0 does give me correct shape of curves, but the
> values are way too high (seems like conc is replaced by number of
> molecules in
> Pool).
>
What are A_ and B_ ? conc is calculated from the number of molecules in
Pool and should be proportional.
It is not clear what you are trying to model. I would suggest you review
your model and see if chemical kinetics is really necessary.
Best,
Subhasis
|
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From: Linda J. <lin...@gm...> - 2015-03-11 06:48:04
|
Hi all,
I am trying to use Moose for some research purposes, so far, I have
successfully compiled and run for a single node, now I'm planning to run
on a multinode-cluster or using MPI, but I face a lot of difficulties
like segmentation faults and aborts.
I built using the following command first,
make BUILD=mpi
after installing, I ran the scripts like shown below
mpirun.mpich -np 4 python Demos/squid/squid.py
How to run Moose using MPI?
Below is the output, I got
__________________________________________________________________________________
on node 0, numNodes = 4, numCores = 4
++++Warning: Ignored attempt to set Cm of compartment to less than 1e-15
Traceback (most recent call last):
File "Demos/squid/squid.py", line 372, in <module>
test()
File "Demos/squid/squid.py", line 366, in test
model = SquidModel('model')
File "Demos/squid/squid.py", line 314, in __init__
self.squid_axon = SquidAxon(path+'/squid_axon')
Warning: Ignored attempt to set Cm of compartment to less than File
"Demos/squid/squid.py", line 194, in __init__
1e-15
self.specific_gl = SquidAxon.defaults['specific_gl']
File "Demos/squid/squid.py", line 257, in specific_gl
self.Rm = 1.0/(value * self.area)
ZeroDivisionError: float division by zero
+++++Warning: Ignored attempt to set Cm of compartment to less than 1e-15
Traceback (most recent call last):
File "Demos/squid/squid.py", line 372, in <module>
test()
File "Demos/squid/squid.py", line 366, in test
+ model = SquidModel('model')
File "Demos/squid/squid.py", line 314, in __init__
+ self.squid_axon = SquidAxon(path+'/squid_axon')
File "Demos/squid/squid.py", line 217, in __init__
SquidAxon.VMAX)
File "Demos/squid/squid.py", line 81, in setupAlpha
gate = moose.HHGate(self.path + '/gateX')
Traceback (most recent call last):
File "Demos/squid/squid.py", line 372, in <module>
ValueError: Parent element does not exist: /model[0]/squid_axon[0]/K[0]
Warning: Ignored attempt to set Cm of compartment to less than 1e-15
test()
File "Demos/squid/squid.py", line 366, in test
Traceback (most recent call last):
model = SquidModel('model')
File "Demos/squid/squid.py", line 372, in <module>
File "Demos/squid/squid.py", line 314, in __init__
test()
File "Demos/squid/squid.py", line 366, in test
self.squid_axon = SquidAxon(path+'/squid_axon')
File "Demos/squid/squid.py", line 205, in __init__
model = SquidModel('model')
File "Demos/squid/squid.py", line 314, in __init__
SquidAxon.VMAX)
self.squid_axon = SquidAxon(path+'/squid_axon')
File "Demos/squid/squid.py", line 194, in __init__
File "Demos/squid/squid.py", line 81, in setupAlpha
self.specific_gl = SquidAxon.defaults['specific_gl']
File "Demos/squid/squid.py", line 257, in specific_gl
self.Rm = 1.0/(value * self.area)
ZeroDivisionError: gate = moose.HHGate(self.path + '/gateX')
ValueError: float division by zero
Parent element does not exist: /model[0]/squid_axon[0]/Na[0]
*** Error in `python': free(): invalid size: 0x00007f1816bf58a0 ***
*** Error in `python': free(): invalid size: 0x00007f53f58bd8a0 ***
*** Error in `python': free(): invalid size: 0x00007f2083f898a0 ***
*** Error in `python': free(): invalid size: 0x00007fa02baa98a0 ***
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 134
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
|
|
From: Linda J <lin...@ca...> - 2015-03-11 06:38:54
|
Hi all,
I am trying to use Moose for some research purposes, so far, I have
successfully compiled and run for a single node, now I'm planning to run
on a multinode-cluster or using MPI, but I face a lot of difficulties
like segmentation faults and aborts.
I built using the following command first,
make BUILD=mpi
after installing, I ran the scripts like shown below
mpirun.mpich -np 4 python Demos/squid/squid.py
How to run Moose using MPI?
Below is the output, I got
__________________________________________________________________________________
on node 0, numNodes = 4, numCores = 4
++++Warning: Ignored attempt to set Cm of compartment to less than 1e-15
Traceback (most recent call last):
File "Demos/squid/squid.py", line 372, in <module>
test()
File "Demos/squid/squid.py", line 366, in test
model = SquidModel('model')
File "Demos/squid/squid.py", line 314, in __init__
self.squid_axon = SquidAxon(path+'/squid_axon')
Warning: Ignored attempt to set Cm of compartment to less than File
"Demos/squid/squid.py", line 194, in __init__
1e-15
self.specific_gl = SquidAxon.defaults['specific_gl']
File "Demos/squid/squid.py", line 257, in specific_gl
self.Rm = 1.0/(value * self.area)
ZeroDivisionError: float division by zero
+++++Warning: Ignored attempt to set Cm of compartment to less than 1e-15
Traceback (most recent call last):
File "Demos/squid/squid.py", line 372, in <module>
test()
File "Demos/squid/squid.py", line 366, in test
+ model = SquidModel('model')
File "Demos/squid/squid.py", line 314, in __init__
+ self.squid_axon = SquidAxon(path+'/squid_axon')
File "Demos/squid/squid.py", line 217, in __init__
SquidAxon.VMAX)
File "Demos/squid/squid.py", line 81, in setupAlpha
gate = moose.HHGate(self.path + '/gateX')
Traceback (most recent call last):
File "Demos/squid/squid.py", line 372, in <module>
ValueError: Parent element does not exist: /model[0]/squid_axon[0]/K[0]
Warning: Ignored attempt to set Cm of compartment to less than 1e-15
test()
File "Demos/squid/squid.py", line 366, in test
Traceback (most recent call last):
model = SquidModel('model')
File "Demos/squid/squid.py", line 372, in <module>
File "Demos/squid/squid.py", line 314, in __init__
test()
File "Demos/squid/squid.py", line 366, in test
self.squid_axon = SquidAxon(path+'/squid_axon')
File "Demos/squid/squid.py", line 205, in __init__
model = SquidModel('model')
File "Demos/squid/squid.py", line 314, in __init__
SquidAxon.VMAX)
self.squid_axon = SquidAxon(path+'/squid_axon')
File "Demos/squid/squid.py", line 194, in __init__
File "Demos/squid/squid.py", line 81, in setupAlpha
self.specific_gl = SquidAxon.defaults['specific_gl']
File "Demos/squid/squid.py", line 257, in specific_gl
self.Rm = 1.0/(value * self.area)
ZeroDivisionError: gate = moose.HHGate(self.path + '/gateX')
ValueError: float division by zero
Parent element does not exist: /model[0]/squid_axon[0]/Na[0]
*** Error in `python': free(): invalid size: 0x00007f1816bf58a0 ***
*** Error in `python': free(): invalid size: 0x00007f53f58bd8a0 ***
*** Error in `python': free(): invalid size: 0x00007f2083f898a0 ***
*** Error in `python': free(): invalid size: 0x00007fa02baa98a0 ***
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 134
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
--
Regards,
Linda J
|
|
From: Subhasis R. <ray...@gm...> - 2013-08-27 15:24:17
|
Dear Saeed, I do not have complete answer to your queries. The answer will also depend on the interests of your audience. You can check the features (current and planned, by release number) here: http://moose.sourceforge.net/component/option%2ccom_wrapper/Itemid%2c95/index.html A few things that came to my mind: An important aspect of MOOSE is that like GENESIS, it can handle both chemical kinetics and electrical models and mixture of both. It can even handle chemical reactions of a few molecules (Gillespie-type stochastic simulations) - as can be the case at synaptic spines. It is aimed at handling multiple scales of simulation from the beginning. The Python scripting with smooth interface to numpy is very useful from a programmer's point of view. This eliminates the steep learning curve and limitations associated with genesis scripting language. It also allows the inclusion of any third party Python library in a simulation setup script. Among new features, MOOSE reads NeuroML models, can write data in compressed HDF5 format. Again, this is only some of the features and I am sure others can point out more of them. Regarding tools, my impression is that you are talking about IDEs. Will your audience be primarily programmers? Then IDE is a matter of personal taste and experties. Personally I had little success with eclipse using Python (without MOOSE module). In my personal opinion, for programmers, a plain text editor and a terminal console should be good enough to explore moose. But if you want auto-complete, history, interaction, etc, you may want to have a look at ipython notebook. For non-programmers, the moosegui (moose/gui/mgui.py) can be a starting point for exploring some demo models. Finally, the snippets (Demos/snippets) can be a good start for exploring individual classes/features in MOOSE. Best, Subha On Mon, Aug 26, 2013 at 9:28 PM, Saeed Shariati <s.s...@uf...>wrote: > Dear all, > > In my university, UFABC, the Genesis uses as the main tool to simulate > neural networks. I want to present the Moose as a new tool and a > comprehensive replacement for Genesis. > > In this regards, do you have any suggestion or example for presenting > features of the moose? > > Furthermore, would you please guide me which kind of tools would be nice > for students to start work on the moose? For example, as I know the code > autocompletion of Moose module in the PyDev at Eclipse is not working well. > > Thank you for your consideration, > I am looking forward to hear from you. > > Best Regards, > Saeed Shariati > > Master of Computer Science > Master student of Neuroscience > Universidade Federal do ABC - UFABC > http://www.ufabc.edu.br/ > Rua Santa Adélia, 166, Santo André - SP - Brasil | CEP 09210-170 > Phone: (11) 999 233 767 > > > > > ------------------------------------------------------------------------------ > Introducing Performance Central, a new site from SourceForge and > AppDynamics. Performance Central is your source for news, insights, > analysis and resources for efficient Application Performance Management. > Visit us today! > http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk > _______________________________________________ > moose-generic mailing list > moo...@li... > https://lists.sourceforge.net/lists/listinfo/moose-generic > > |
|
From: Saeed S. <s.s...@uf...> - 2013-08-26 16:16:32
|
Dear all, In my university, UFABC, the Genesis uses as the main tool to simulate neural networks. I want to present the Moose as a new tool and a comprehensive replacement for Genesis. In this regards, do you have any suggestion or example for presenting features of the moose? Furthermore, would you please guide me which kind of tools would be nice for students to start work on the moose? For example, as I know the code autocompletion of Moose module in the PyDev at Eclipse is not working well. Thank you for your consideration, I am looking forward to hear from you. Best Regards, Saeed Shariati Master of Computer Science Master student of Neuroscience Universidade Federal do ABC - UFABC http://www.ufabc.edu.br/ Rua Santa Adélia, 166, Santo André - SP - Brasil | CEP 09210-170 Phone: (11) 999 233 767 |
|
From: Vadim A <ast...@nc...> - 2013-05-10 18:23:21
|
I see, I thought it is something like "channels" folder in NeuroML where all channels models get stored. Ok, we will concentrate on NeuroML for now and deal with GENESIS later. Best regards, Vadim. On May 7, 2013, at 9:19 PM, Subhasis Ray wrote: > Hi Vadim, > /library refers to the moose element "/library" and not some directory in the file system. You need to read the documentation about how model components are organized in GENESIS/MOOSE. The readcell documentation, which also explains the GENESIS prototype file format, is here: http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual-25.html#ss25.131. Additionally you can consult the Book of GENESIS (http://www.genesis-sim.org/GENESIS/bog/bog.html). The classes and functions may have slightly different names/format in MOOSE, but the basic concepts and functionality are very similar. > > Hope this helps, > Subha > > > On Tue, May 7, 2013 at 11:39 PM, Vadim A <ast...@nc...> wrote: > Hi Subha. > > I am exploring MOOSE with Genesis and see that in README file: > > "…..You can also load GENESIS prototype files. The same loadModel > function can be used for this (but you need to have all the channels > used in the prototype preloaded in /library): > > moose.loadModel(prototype_file_path, prototype_model_path)…." > > > > > > But I am not clear what does it mean "...you need to have all the channels > used in the prototype preloaded in /library) > > > > I do not see any folder "./library" under MOOSE installation ? > > > Could you please clarify that ? > > > Best regards > > Vadim. > > University of California San Diego. > |
|
From: Subhasis R. <ray...@gm...> - 2013-05-08 04:20:03
|
Hi Vadim, /library refers to the moose element "/library" and not some directory in the file system. You need to read the documentation about how model components are organized in GENESIS/MOOSE. The readcell documentation, which also explains the GENESIS prototype file format, is here: http://www.genesis-sim.org/GENESIS/Hyperdoc/Manual-25.html#ss25.131. Additionally you can consult the Book of GENESIS ( http://www.genesis-sim.org/GENESIS/bog/bog.html). The classes and functions may have slightly different names/format in MOOSE, but the basic concepts and functionality are very similar. Hope this helps, Subha On Tue, May 7, 2013 at 11:39 PM, Vadim A <ast...@nc...> wrote: > Hi Subha. > > I am exploring MOOSE with Genesis and see that in README file: > > "…..You can also load GENESIS prototype files. The same loadModel > function can be used for this (but you need to have all the channels > used in the prototype preloaded in /*library*): > > moose.loadModel(prototype_file_path, prototype_model_path)…." > > > > > > But I am not clear what does it mean "...you need to have all the channels > used in the prototype preloaded in /*library*) > > > > I do not see any folder "./library" under MOOSE installation ? > > > Could you please clarify that ? > > > Best regards > > Vadim. > > University of California San Diego. > |
|
From: Vadim A <ast...@nc...> - 2013-05-07 18:09:19
|
Hi Subha. I am exploring MOOSE with Genesis and see that in README file: "…..You can also load GENESIS prototype files. The same loadModel function can be used for this (but you need to have all the channels used in the prototype preloaded in /library): moose.loadModel(prototype_file_path, prototype_model_path)…." But I am not clear what does it mean "...you need to have all the channels used in the prototype preloaded in /library) I do not see any folder "./library" under MOOSE installation ? Could you please clarify that ? Best regards Vadim. University of California San Diego. |
|
From: Subhasis R. <ray...@gm...> - 2013-04-09 05:21:50
|
Hi, Given you have a local python at: /home/diag/opt/python2.7/ I assume that you also added -L/home/diag/opt/python2.7/ in front of the PYTHON_LDFLAGS. I found that libmkl_core.so provides functions for BLAS. Are you using a GSL/CBLAS built with intel compiler? Also it might be worth double checking that you run "make clean" before each new build. Beyond that I cannot see any solution to the situation. Best, Subha On Tue, Apr 9, 2013 at 12:19 AM, Vadim A <ast...@nc...> wrote: > Hi Subha. > > I try everything but still getting segmentation fault. > > > > I am pointing to new "numpy" compiled with gnu > > export > LD_LIBRARY_PATH=/home/diag/opt/python2.7/gnulib/lib/python2.7/site-packages:$LD_LIBRARY_PATH > > and modified Makefile to point to the new lib: > > PYTHON_INCLUDES := -I/home/diag/opt/python2.7/include/python2.7 > -I/home/diag/opt/python2.7/include/python2.7 > -I/home/diag/opt/python2.7/gnulib/lib/python2.7/site-packages/numpy/core/include/ > > > > > gdb shows me that new "gnulib" become used but still segmentation foult > from "libc.so" > > > Reading symbols from /opt/*intel*/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no > debugging symbols found)...done. > Loaded symbols for /opt/*intel* > /Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so > Reading symbols from > /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no > debugging symbols found)...done. > Loaded symbols for > /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so > ……… > > Reading symbols from /home/diag/opt/python2.7/*gnulib* > /lib/python2.7/site-packages/numpy/random/mtrand.so...done. > Loaded symbols for /home/diag/opt/python2.7/*gnulib* > /lib/python2.7/site-packages/numpy/random/mtrand.so > > ……. > Reading symbols from > /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_struct.so...done. > Loaded symbols for > /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_struct.so > Core was generated by `python'. > Program terminated with signal 11, Segmentation fault. > #0 0x000000344be7275e in free () from /lib64/libc.so.6 > > > > > > > I see "intel" stuff and "gnulib" > > > > > > When I run "idd" on generated _moose.so > > it shows libraries where some "gnu" some "intel" which might be a reason > for problem : > > /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so > (0x00002b1fa0b00000) > /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so > (0x00002b1fa0eb3000) > /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5 (0x00002b1fa16c8000) > /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so > (0x00002b1fa17ed000) > libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b1fa1a43000) > libdl.so.2 => /lib64/libdl.so.2 (0x00002b1fa1c5f000) > libutil.so.1 => /lib64/libutil.so.1 (0x00002b1fa1e63000) > libpython2.7.so.1.0 => /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 > (0x00002b1fa2066000) > libgsl.so.0 => /home/diag/opt/gsl/1.15/gnu/lib/libgsl.so.0 > (0x00002b1fa243e000) > libgslcblas.so.0 => /home/diag/opt/gsl/1.15/gnu/lib/libgslcblas.so.0 > (0x00002b1fa285e000) > libm.so.6 => /lib64/libm.so.6 (0x00002b1fa2a97000) > libstdc++.so.6 => /home/diag/opt/gcc/4.6.1/lib64/libstdc++.so.6 > (0x00002b1fa2d1b000) > libgcc_s.so.1 => /home/diag/opt/gcc/4.6.1/lib64/libgcc_s.so.1 > (0x00002b1fa3020000) > libc.so.6 => /lib64/libc.so.6 (0x00002b1fa3235000) > libstdc++.so.5 => /usr/lib64/libstdc++.so.5 (0x00002b1fa358d000) > libimf.so => /opt/intel/Compiler/11.1/072/lib/intel64/libimf.so > (0x00002b1fa3868000) > libsvml.so => /opt/intel/Compiler/11.1/072/lib/intel64/libsvml.so > (0x00002b1fa3bfc000) > libcxaguard.so.5 => > /opt/intel/Compiler/11.1/072/lib/intel64/libcxaguard.so.5 > (0x00002b1fa3e13000) > libintlc.so.5 => /opt/intel/Compiler/11.1/072/lib/intel64/libintlc.so.5 > (0x00002b1fa3f14000) > /lib64/ld-linux-x86-64.so.2 (0x000000344ba00000) > > > > I don't know what else we can do > > Regards, > > Vadim. > > > > On Apr 5, 2013, at 11:39 PM, Subhasis Ray wrote: > > Dear Vadim, > I am not familiar with such cluster environment. But from what I gather > on the Internet, it seems that the issue is possibly a mismatch of > compilers and libraries. If your default compiler is intel, then loading > python before gnu perhaps loads a Python compiled with intel compiler your > default. Can you see if changing the order of loading modules helps? i.e. > > module load gnu/4.6.1 > module load python > ... > > > Also, you can run `ldd` on generated _moose.so to list the linked > libraries and add the paths to the directories containing those libraries > to your LD_LIBRARY_PATH environment variable. > > hth, > Subha > > > > > On Sat, Apr 6, 2013 at 12:35 AM, Vadim A <ast...@nc...> wrote: > >> Hi, >> >> numpy has been compiled with gnu on our cluster and to access bumpy we >> do the following: >> >> module load python >> module load gnu/4.6.1 >> export >> >> PYTHONPATH=/home/diag/opt/python2.7/gnulib/lib/python2.7/site-packages:$PYT >> HONPATH >> >> >> >> Should I also adjust Makefile for MOOSE to make sure that proper >> "numpy" library will be used during compilation step ? >> >> Thanks a lot in advance for information. >> >> Vadim. >> >> >> >> >> On Mar 28, 2013, at 2:13 AM, Subhasis Ray wrote: >> >> > First please confirm that Python and numpy were also compiled with gcc. >> > >> > If so, then best option could be to allow somebody from here (niraj or >> > me) to login to your system (via some portal as Amitava mentioned >> > earlier in this thread) and run gdb as we cannot reproduce the error >> > on our system. >> > >> > On 3/28/13, Vadim A <ast...@nc...> wrote: >> >> >> >> >> >> On Mar 28, 2013, at 12:15 AM, Subhasis Ray wrote: >> >> >> >>> Hi, >> >>> On 3/28/13, Vadim A <ast...@nc...> wrote: >> >>>> When I compile, I always see lines with g++ >> >>>> >> >>>> >> >>>> g++ -g -pthread -fpermissive -fno-strict-aliasing -fPIC >> >>>> -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS >> >>>> -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I >> >>>> /home/diag/opt/gsl/1.15/gnu/include/ basecode/_basecode.o >> msg/_msg.o >> >>>> shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o >> >>>> randnum/_randnum.o >> >>>> scheduling/_scheduling.o builtins/_builtins.o device/_device.o >> >>>> kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o >> >>>> utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o >> >>>> signeur/_signeur.o -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 >> >>>> -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl >> >>>> -lgslcblas >> >>>> -lm -o moose >> >>>> >> >>>> >> >>>> >> >>>> That tells me that I am using g++ (which is gcc) but not Intel >> compiler, >> >>>> right ? >> >>> >> >>> Yes, moose is being compiled by g++ >> >>> >> >>>> >> >>>> So, I kind of confused what should I do here. >> >>>> >> >>> >> >>> But what about Python libs? In your previous mail >> >>> >> >>> ----8<----------------->8--- >> >>> gdb -c core.8851 /home/diag/opt/python2.7/bin/python >> >>> >> >>> Reading symbols from >> >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no >> >>> debugging symbols found)...done. >> >>> Loaded symbols for >> >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so >> >>> Reading symbols from >> >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no >> >>> debugging symbols found)...done. >> >>> Loaded symbols for >> >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so >> >>> Reading symbols from >> >>> /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5...(no debugging >> >>> symbols found)...done. >> >>> Loaded symbols for >> /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5 >> >>> Reading symbols from >> >>> >> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so...(no >> >>> debugging symbols found)...done. >> >>> Loaded symbols for >> >>> >> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so >> >>> Reading symbols from >> >>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0...done. >> >>> Loaded symbols for /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 >> >>> >> >>> ----8<----------------->8--- >> >>> >> >>> shows that several libraries from intel compiler are being loaded >> >>> before scipy/sparse/sparsetools/_coo.so and libpython2.7.so. >> >>> >> >>> Did you compile Python in >> >>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 and/or numpy/scipy >> >>> from source? In that case, did you use intel compiler to compile them? >> >>> >> >>> Though this could be red herring, I do not see any reason for the >> >>> control to reach basecode/SetGet.h:289. May be a debugging session >> >>> could help. >> >>> >> >>> Best, >> >>> Subha >> >>> >> >> >> >> >> > >> >> > > |
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From: Vadim A <ast...@nc...> - 2013-04-08 18:50:06
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Hi Subha. I try everything but still getting segmentation fault. I am pointing to new "numpy" compiled with gnu export LD_LIBRARY_PATH=/home/diag/opt/python2.7/gnulib/lib/python2.7/site-packages:$LD_LIBRARY_PATH and modified Makefile to point to the new lib: PYTHON_INCLUDES := -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/gnulib/lib/python2.7/site-packages/numpy/core/include/ gdb shows me that new "gnulib" become used but still segmentation foult from "libc.so" Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so ……… Reading symbols from /home/diag/opt/python2.7/gnulib/lib/python2.7/site-packages/numpy/random/mtrand.so...done. Loaded symbols for /home/diag/opt/python2.7/gnulib/lib/python2.7/site-packages/numpy/random/mtrand.so ……. Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_struct.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_struct.so Core was generated by `python'. Program terminated with signal 11, Segmentation fault. #0 0x000000344be7275e in free () from /lib64/libc.so.6 I see "intel" stuff and "gnulib" When I run "idd" on generated _moose.so it shows libraries where some "gnu" some "intel" which might be a reason for problem : /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so (0x00002b1fa0b00000) /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so (0x00002b1fa0eb3000) /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5 (0x00002b1fa16c8000) /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so (0x00002b1fa17ed000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b1fa1a43000) libdl.so.2 => /lib64/libdl.so.2 (0x00002b1fa1c5f000) libutil.so.1 => /lib64/libutil.so.1 (0x00002b1fa1e63000) libpython2.7.so.1.0 => /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 (0x00002b1fa2066000) libgsl.so.0 => /home/diag/opt/gsl/1.15/gnu/lib/libgsl.so.0 (0x00002b1fa243e000) libgslcblas.so.0 => /home/diag/opt/gsl/1.15/gnu/lib/libgslcblas.so.0 (0x00002b1fa285e000) libm.so.6 => /lib64/libm.so.6 (0x00002b1fa2a97000) libstdc++.so.6 => /home/diag/opt/gcc/4.6.1/lib64/libstdc++.so.6 (0x00002b1fa2d1b000) libgcc_s.so.1 => /home/diag/opt/gcc/4.6.1/lib64/libgcc_s.so.1 (0x00002b1fa3020000) libc.so.6 => /lib64/libc.so.6 (0x00002b1fa3235000) libstdc++.so.5 => /usr/lib64/libstdc++.so.5 (0x00002b1fa358d000) libimf.so => /opt/intel/Compiler/11.1/072/lib/intel64/libimf.so (0x00002b1fa3868000) libsvml.so => /opt/intel/Compiler/11.1/072/lib/intel64/libsvml.so (0x00002b1fa3bfc000) libcxaguard.so.5 => /opt/intel/Compiler/11.1/072/lib/intel64/libcxaguard.so.5 (0x00002b1fa3e13000) libintlc.so.5 => /opt/intel/Compiler/11.1/072/lib/intel64/libintlc.so.5 (0x00002b1fa3f14000) /lib64/ld-linux-x86-64.so.2 (0x000000344ba00000) I don't know what else we can do Regards, Vadim. On Apr 5, 2013, at 11:39 PM, Subhasis Ray wrote: > Dear Vadim, > I am not familiar with such cluster environment. But from what I gather on the Internet, it seems that the issue is possibly a mismatch of compilers and libraries. If your default compiler is intel, then loading python before gnu perhaps loads a Python compiled with intel compiler your default. Can you see if changing the order of loading modules helps? i.e. > > module load gnu/4.6.1 > module load python > ... > > > Also, you can run `ldd` on generated _moose.so to list the linked libraries and add the paths to the directories containing those libraries to your LD_LIBRARY_PATH environment variable. > > hth, > Subha > > > > > On Sat, Apr 6, 2013 at 12:35 AM, Vadim A <ast...@nc...> wrote: > Hi, > > numpy has been compiled with gnu on our cluster and to access bumpy we do the following: > > module load python > module load gnu/4.6.1 > export > PYTHONPATH=/home/diag/opt/python2.7/gnulib/lib/python2.7/site-packages:$PYT > HONPATH > > > > Should I also adjust Makefile for MOOSE to make sure that proper "numpy" library will be used during compilation step ? > > Thanks a lot in advance for information. > > Vadim. > > > > > On Mar 28, 2013, at 2:13 AM, Subhasis Ray wrote: > > > First please confirm that Python and numpy were also compiled with gcc. > > > > If so, then best option could be to allow somebody from here (niraj or > > me) to login to your system (via some portal as Amitava mentioned > > earlier in this thread) and run gdb as we cannot reproduce the error > > on our system. > > > > On 3/28/13, Vadim A <ast...@nc...> wrote: > >> > >> > >> On Mar 28, 2013, at 12:15 AM, Subhasis Ray wrote: > >> > >>> Hi, > >>> On 3/28/13, Vadim A <ast...@nc...> wrote: > >>>> When I compile, I always see lines with g++ > >>>> > >>>> > >>>> g++ -g -pthread -fpermissive -fno-strict-aliasing -fPIC > >>>> -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS > >>>> -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I > >>>> /home/diag/opt/gsl/1.15/gnu/include/ basecode/_basecode.o msg/_msg.o > >>>> shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o > >>>> randnum/_randnum.o > >>>> scheduling/_scheduling.o builtins/_builtins.o device/_device.o > >>>> kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o > >>>> utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o > >>>> signeur/_signeur.o -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 > >>>> -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl > >>>> -lgslcblas > >>>> -lm -o moose > >>>> > >>>> > >>>> > >>>> That tells me that I am using g++ (which is gcc) but not Intel compiler, > >>>> right ? > >>> > >>> Yes, moose is being compiled by g++ > >>> > >>>> > >>>> So, I kind of confused what should I do here. > >>>> > >>> > >>> But what about Python libs? In your previous mail > >>> > >>> ----8<----------------->8--- > >>> gdb -c core.8851 /home/diag/opt/python2.7/bin/python > >>> > >>> Reading symbols from > >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no > >>> debugging symbols found)...done. > >>> Loaded symbols for > >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so > >>> Reading symbols from > >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no > >>> debugging symbols found)...done. > >>> Loaded symbols for > >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so > >>> Reading symbols from > >>> /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5...(no debugging > >>> symbols found)...done. > >>> Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5 > >>> Reading symbols from > >>> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so...(no > >>> debugging symbols found)...done. > >>> Loaded symbols for > >>> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so > >>> Reading symbols from > >>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0...done. > >>> Loaded symbols for /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 > >>> > >>> ----8<----------------->8--- > >>> > >>> shows that several libraries from intel compiler are being loaded > >>> before scipy/sparse/sparsetools/_coo.so and libpython2.7.so. > >>> > >>> Did you compile Python in > >>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 and/or numpy/scipy > >>> from source? In that case, did you use intel compiler to compile them? > >>> > >>> Though this could be red herring, I do not see any reason for the > >>> control to reach basecode/SetGet.h:289. May be a debugging session > >>> could help. > >>> > >>> Best, > >>> Subha > >>> > >> > >> > > > > |
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From: Subhasis R. <ray...@gm...> - 2013-04-06 21:35:06
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Yes, the GCC compiled numpy should be in LD_LIBRARY_PATH and in the makefile. On Sat, Apr 6, 2013 at 11:22 PM, Vadim Astakhov <ast...@nc...>wrote: > Hi. > Our python is GCC not intell > Only numpy was intell but we now install new numpy compiled by gnu. My > question is should I add path to this new compiled numpy to your Make file ? > Thanks a lot in advance for clarification. > > Vadim. > > > Subhasis Ray <ray...@gm...> wrote: > > Dear Vadim, > I am not familiar with such cluster environment. But from what I gather > on the Internet, it seems that the issue is possibly a mismatch of > compilers and libraries. If your default compiler is intel, then loading > python before gnu perhaps loads a Python compiled with intel compiler your > default. Can you see if changing the order of loading modules helps? i.e. > > module load gnu/4.6.1 > module load python > ... > > > Also, you can run `ldd` on generated _moose.so to list the linked > libraries and add the paths to the directories containing those libraries > to your LD_LIBRARY_PATH environment variable. > > hth, > Subha > > > > > On Sat, Apr 6, 2013 at 12:35 AM, Vadim A <ast...@nc...> wrote: > >> Hi, >> >> numpy has been compiled with gnu on our cluster and to access bumpy we >> do the following: >> >> module load python >> module load gnu/4.6.1 >> export >> >> PYTHONPATH=/home/diag/opt/python2.7/gnulib/lib/python2.7/site-packages:$PYT >> HONPATH >> >> >> >> Should I also adjust Makefile for MOOSE to make sure that proper >> "numpy" library will be used during compilation step ? >> >> Thanks a lot in advance for information. >> >> Vadim. >> >> >> >> >> On Mar 28, 2013, at 2:13 AM, Subhasis Ray wrote: >> >> > First please confirm that Python and numpy were also compiled with gcc. >> > >> > If so, then best option could be to allow somebody from here (niraj or >> > me) to login to your system (via some portal as Amitava mentioned >> > earlier in this thread) and run gdb as we cannot reproduce the error >> > on our system. >> > >> > On 3/28/13, Vadim A <ast...@nc...> wrote: >> >> >> >> >> >> On Mar 28, 2013, at 12:15 AM, Subhasis Ray wrote: >> >> >> >>> Hi, >> >>> On 3/28/13, Vadim A <ast...@nc...> wrote: >> >>>> When I compile, I always see lines with g++ >> >>>> >> >>>> >> >>>> g++ -g -pthread -fpermissive -fno-strict-aliasing -fPIC >> >>>> -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS >> >>>> -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I >> >>>> /home/diag/opt/gsl/1.15/gnu/include/ basecode/_basecode.o >> msg/_msg.o >> >>>> shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o >> >>>> randnum/_randnum.o >> >>>> scheduling/_scheduling.o builtins/_builtins.o device/_device.o >> >>>> kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o >> >>>> utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o >> >>>> signeur/_signeur.o -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 >> >>>> -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl >> >>>> -lgslcblas >> >>>> -lm -o moose >> >>>> >> >>>> >> >>>> >> >>>> That tells me that I am using g++ (which is gcc) but not Intel >> compiler, >> >>>> right ? >> >>> >> >>> Yes, moose is being compiled by g++ >> >>> >> >>>> >> >>>> So, I kind of confused what should I do here. >> >>>> >> >>> >> >>> But what about Python libs? In your previous mail >> >>> >> >>> ----8<----------------->8--- >> >>> gdb -c core.8851 /home/diag/opt/python2.7/bin/python >> >>> >> >>> Reading symbols from >> >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no >> >>> debugging symbols found)...done. >> >>> Loaded symbols for >> >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so >> >>> Reading symbols from >> >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no >> >>> debugging symbols found)...done. >> >>> Loaded symbols for >> >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so >> >>> Reading symbols from >> >>> /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5...(no debugging >> >>> symbols found)...done. >> >>> Loaded symbols for >> /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5 >> >>> Reading symbols from >> >>> >> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so...(no >> >>> debugging symbols found)...done. >> >>> Loaded symbols for >> >>> >> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so >> >>> Reading symbols from >> >>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0...done. >> >>> Loaded symbols for /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 >> >>> >> >>> ----8<----------------->8--- >> >>> >> >>> shows that several libraries from intel compiler are being loaded >> >>> before scipy/sparse/sparsetools/_coo.so and libpython2.7.so. >> >>> >> >>> Did you compile Python in >> >>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 and/or numpy/scipy >> >>> from source? In that case, did you use intel compiler to compile them? >> >>> >> >>> Though this could be red herring, I do not see any reason for the >> >>> control to reach basecode/SetGet.h:289. May be a debugging session >> >>> could help. >> >>> >> >>> Best, >> >>> Subha >> >>> >> >> >> >> >> > >> >> > |
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From: Vadim A. <ast...@nc...> - 2013-04-06 17:53:17
|
Hi. Our python is GCC not intell Only numpy was intell but we now install new numpy compiled by gnu. My question is should I add path to this new compiled numpy to your Make file ? Thanks a lot in advance for clarification. Vadim. Subhasis Ray <ray...@gm...> wrote: >Dear Vadim, > > I am not familiar with such cluster environment. But from what I gather on the Internet, it seems that the issue is possibly a mismatch of compilers and libraries. If your default compiler is intel, then loading python before gnu perhaps loads a Python compiled with intel compiler your default. Can you see if changing the order of loading modules helps? i.e. > >module load gnu/4.6.1 >module load python >... > > >Also, you can run `ldd` on generated _moose.so to list the linked libraries and add the paths to the directories containing those libraries to your LD_LIBRARY_PATH environment variable. > >hth, > > Subha > > > > > >On Sat, Apr 6, 2013 at 12:35 AM, Vadim A <ast...@nc...> wrote: > >Hi, > >numpy has been compiled with gnu on our cluster and to access bumpy we do the following: > >module load python >module load gnu/4.6.1 >export >PYTHONPATH=/home/diag/opt/python2.7/gnulib/lib/python2.7/site-packages:$PYT >HONPATH > > > >Should I also adjust Makefile for MOOSE to make sure that proper "numpy" library will be used during compilation step ? > >Thanks a lot in advance for information. > >Vadim. > > > > > >On Mar 28, 2013, at 2:13 AM, Subhasis Ray wrote: > >> First please confirm that Python and numpy were also compiled with gcc. >> >> If so, then best option could be to allow somebody from here (niraj or >> me) to login to your system (via some portal as Amitava mentioned >> earlier in this thread) and run gdb as we cannot reproduce the error >> on our system. >> >> On 3/28/13, Vadim A <ast...@nc...> wrote: >>> >>> > >>> On Mar 28, 2013, at 12:15 AM, Subhasis Ray wrote: >>> >>>> Hi, >>>> On 3/28/13, Vadim A <ast...@nc...> wrote: >>>>> When I compile, I always see lines with g++ >>>>> >>>>> >>>>> g++ -g -pthread -fpermissive -fno-strict-aliasing -fPIC >>>>> -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS >>>>> -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I >>>>> /home/diag/opt/gsl/1.15/gnu/include/ basecode/_basecode.o msg/_msg.o >>>>> shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o >>>>> randnum/_randnum.o >>>>> scheduling/_scheduling.o builtins/_builtins.o device/_device.o >>>>> kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o >>>>> utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o >>>>> signeur/_signeur.o -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 >>>>> -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl >>>>> -lgslcblas >>>>> -lm -o moose >>>>> >>>>> >>>>> >>>>> That tells me that I am using g++ (which is gcc) but not Intel compiler, >>>>> right ? >>>> >>>> Yes, moose is being compiled by g++ >>>> >>>>> >>>>> So, I kind of confused what should I do here. >>>>> >>>> >>>> But what about Python libs? In your previous mail >>>> >>>> ----8<----------------->8--- >>>> gdb -c core.8851 /home/diag/opt/python2.7/bin/python >>>> >>>> Reading symbols from >>>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no >>>> debugging symbols found)...done. >>>> Loaded symbols for >>>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so >>>> Reading symbols from >>>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no >>>> debugging symbols found)...done. >>>> Loaded symbols for >>>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so >>>> Reading symbols from >>>> /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5...(no debugging >>>> symbols found)...done. >>>> Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5 >>>> Reading symbols from >>>> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so...(no >>>> debugging symbols found)...done. >>>> Loaded symbols for >>>> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so >>>> Reading symbols from >>>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0...done. >>>> Loaded symbols for /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 >>>> >>>> ----8<----------------->8--- >>>> >>>> shows that several libraries from intel compiler are being loaded >>>> before scipy/sparse/sparsetools/_coo.so and libpython2.7.so. >>>> >>>> Did you compile Python in >>>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 and/or numpy/scipy >>>> from source? In that case, did you use intel compiler to compile them? >>>> >>>> Though this could be red herring, I do not see any reason for the >>>> control to reach basecode/SetGet.h:289. May be a debugging session >>>> could help. >>>> >>>> Best, >>>> Subha >>>> >>> >>> >> > > |
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From: Subhasis R. <ray...@gm...> - 2013-04-06 06:39:56
|
Dear Vadim, I am not familiar with such cluster environment. But from what I gather on the Internet, it seems that the issue is possibly a mismatch of compilers and libraries. If your default compiler is intel, then loading python before gnu perhaps loads a Python compiled with intel compiler your default. Can you see if changing the order of loading modules helps? i.e. module load gnu/4.6.1 module load python ... Also, you can run `ldd` on generated _moose.so to list the linked libraries and add the paths to the directories containing those libraries to your LD_LIBRARY_PATH environment variable. hth, Subha On Sat, Apr 6, 2013 at 12:35 AM, Vadim A <ast...@nc...> wrote: > Hi, > > numpy has been compiled with gnu on our cluster and to access bumpy we do > the following: > > module load python > module load gnu/4.6.1 > export > PYTHONPATH=/home/diag/opt/python2.7/gnulib/lib/python2.7/site-packages:$PYT > HONPATH > > > > Should I also adjust Makefile for MOOSE to make sure that proper > "numpy" library will be used during compilation step ? > > Thanks a lot in advance for information. > > Vadim. > > > > > On Mar 28, 2013, at 2:13 AM, Subhasis Ray wrote: > > > First please confirm that Python and numpy were also compiled with gcc. > > > > If so, then best option could be to allow somebody from here (niraj or > > me) to login to your system (via some portal as Amitava mentioned > > earlier in this thread) and run gdb as we cannot reproduce the error > > on our system. > > > > On 3/28/13, Vadim A <ast...@nc...> wrote: > >> > >> > >> On Mar 28, 2013, at 12:15 AM, Subhasis Ray wrote: > >> > >>> Hi, > >>> On 3/28/13, Vadim A <ast...@nc...> wrote: > >>>> When I compile, I always see lines with g++ > >>>> > >>>> > >>>> g++ -g -pthread -fpermissive -fno-strict-aliasing -fPIC > >>>> -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS > >>>> -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I > >>>> /home/diag/opt/gsl/1.15/gnu/include/ basecode/_basecode.o > msg/_msg.o > >>>> shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o > >>>> randnum/_randnum.o > >>>> scheduling/_scheduling.o builtins/_builtins.o device/_device.o > >>>> kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o > >>>> utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o > >>>> signeur/_signeur.o -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 > >>>> -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl > >>>> -lgslcblas > >>>> -lm -o moose > >>>> > >>>> > >>>> > >>>> That tells me that I am using g++ (which is gcc) but not Intel > compiler, > >>>> right ? > >>> > >>> Yes, moose is being compiled by g++ > >>> > >>>> > >>>> So, I kind of confused what should I do here. > >>>> > >>> > >>> But what about Python libs? In your previous mail > >>> > >>> ----8<----------------->8--- > >>> gdb -c core.8851 /home/diag/opt/python2.7/bin/python > >>> > >>> Reading symbols from > >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no > >>> debugging symbols found)...done. > >>> Loaded symbols for > >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so > >>> Reading symbols from > >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no > >>> debugging symbols found)...done. > >>> Loaded symbols for > >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so > >>> Reading symbols from > >>> /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5...(no debugging > >>> symbols found)...done. > >>> Loaded symbols for > /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5 > >>> Reading symbols from > >>> > /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so...(no > >>> debugging symbols found)...done. > >>> Loaded symbols for > >>> > /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so > >>> Reading symbols from > >>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0...done. > >>> Loaded symbols for /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 > >>> > >>> ----8<----------------->8--- > >>> > >>> shows that several libraries from intel compiler are being loaded > >>> before scipy/sparse/sparsetools/_coo.so and libpython2.7.so. > >>> > >>> Did you compile Python in > >>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 and/or numpy/scipy > >>> from source? In that case, did you use intel compiler to compile them? > >>> > >>> Though this could be red herring, I do not see any reason for the > >>> control to reach basecode/SetGet.h:289. May be a debugging session > >>> could help. > >>> > >>> Best, > >>> Subha > >>> > >> > >> > > > > |
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From: Vadim A <ast...@nc...> - 2013-04-05 19:05:38
|
Hi, numpy has been compiled with gnu on our cluster and to access bumpy we do the following: module load python module load gnu/4.6.1 export PYTHONPATH=/home/diag/opt/python2.7/gnulib/lib/python2.7/site-packages:$PYT HONPATH Should I also adjust Makefile for MOOSE to make sure that proper "numpy" library will be used during compilation step ? Thanks a lot in advance for information. Vadim. On Mar 28, 2013, at 2:13 AM, Subhasis Ray wrote: > First please confirm that Python and numpy were also compiled with gcc. > > If so, then best option could be to allow somebody from here (niraj or > me) to login to your system (via some portal as Amitava mentioned > earlier in this thread) and run gdb as we cannot reproduce the error > on our system. > > On 3/28/13, Vadim A <ast...@nc...> wrote: >> >> >> On Mar 28, 2013, at 12:15 AM, Subhasis Ray wrote: >> >>> Hi, >>> On 3/28/13, Vadim A <ast...@nc...> wrote: >>>> When I compile, I always see lines with g++ >>>> >>>> >>>> g++ -g -pthread -fpermissive -fno-strict-aliasing -fPIC >>>> -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS >>>> -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I >>>> /home/diag/opt/gsl/1.15/gnu/include/ basecode/_basecode.o msg/_msg.o >>>> shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o >>>> randnum/_randnum.o >>>> scheduling/_scheduling.o builtins/_builtins.o device/_device.o >>>> kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o >>>> utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o >>>> signeur/_signeur.o -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 >>>> -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl >>>> -lgslcblas >>>> -lm -o moose >>>> >>>> >>>> >>>> That tells me that I am using g++ (which is gcc) but not Intel compiler, >>>> right ? >>> >>> Yes, moose is being compiled by g++ >>> >>>> >>>> So, I kind of confused what should I do here. >>>> >>> >>> But what about Python libs? In your previous mail >>> >>> ----8<----------------->8--- >>> gdb -c core.8851 /home/diag/opt/python2.7/bin/python >>> >>> Reading symbols from >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no >>> debugging symbols found)...done. >>> Loaded symbols for >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so >>> Reading symbols from >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no >>> debugging symbols found)...done. >>> Loaded symbols for >>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so >>> Reading symbols from >>> /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5...(no debugging >>> symbols found)...done. >>> Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5 >>> Reading symbols from >>> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so...(no >>> debugging symbols found)...done. >>> Loaded symbols for >>> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so >>> Reading symbols from >>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0...done. >>> Loaded symbols for /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 >>> >>> ----8<----------------->8--- >>> >>> shows that several libraries from intel compiler are being loaded >>> before scipy/sparse/sparsetools/_coo.so and libpython2.7.so. >>> >>> Did you compile Python in >>> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 and/or numpy/scipy >>> from source? In that case, did you use intel compiler to compile them? >>> >>> Though this could be red herring, I do not see any reason for the >>> control to reach basecode/SetGet.h:289. May be a debugging session >>> could help. >>> >>> Best, >>> Subha >>> >> >> > |
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From: Subhasis R. <ray...@gm...> - 2013-03-28 07:15:41
|
Hi, On 3/28/13, Vadim A <ast...@nc...> wrote: > When I compile, I always see lines with g++ > > > g++ -g -pthread -fpermissive -fno-strict-aliasing -fPIC > -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS > -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I > /home/diag/opt/gsl/1.15/gnu/include/ basecode/_basecode.o msg/_msg.o > shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o > scheduling/_scheduling.o builtins/_builtins.o device/_device.o > kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o > utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o > signeur/_signeur.o -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 > -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas > -lm -o moose > > > > That tells me that I am using g++ (which is gcc) but not Intel compiler, > right ? Yes, moose is being compiled by g++ > > So, I kind of confused what should I do here. > But what about Python libs? In your previous mail ----8<----------------->8--- gdb -c core.8851 /home/diag/opt/python2.7/bin/python Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5 Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so Reading symbols from /home/diag/opt/python2.7/lib/libpython2.7.so.1.0...done. Loaded symbols for /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 ----8<----------------->8--- shows that several libraries from intel compiler are being loaded before scipy/sparse/sparsetools/_coo.so and libpython2.7.so. Did you compile Python in /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 and/or numpy/scipy from source? In that case, did you use intel compiler to compile them? Though this could be red herring, I do not see any reason for the control to reach basecode/SetGet.h:289. May be a debugging session could help. Best, Subha |
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From: Vadim A <ast...@nc...> - 2013-03-28 06:54:12
|
When I compile, I always see lines with g++
g++ -g -pthread -fpermissive -fno-strict-aliasing -fPIC -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/ basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -o moose
That tells me that I am using g++ (which is gcc) but not Intel compiler, right ?
So, I kind of confused what should I do here.
V.
On Mar 27, 2013, at 11:34 PM, Subhasis Ray wrote:
> Dear Vadim,
>
> On 3/28/13, Vadim A <ast...@nc...> wrote:
>> 1. I modified the code
>>
>> /// Go through all elements under /classes and ask for defining a
>> /// Python class for it.
>> static int defineAllClasses(PyObject * module_dict)
>> {
>> ///static vector <Id> classes(Field< vector<Id>
>>> ::get(ObjId("/classes"),"children"));
>> static const string children("children");
>> static const string path("/classes");
>> static const ObjId cle(path);
>> assert(!(cle == ObjId::bad()));
>> static vector <Id> classes = Field<vector<Id> >::get(cle,children);
>> //static vector <Id> classes = Field<vector<Id>
>>> ::get(ObjId(path),children);
>>
>>
>>
>> What should I expect to see with that assert ? I did not noticed any
>> differences when I did compile and import.
>>
>>
>
> I was suspecting a static initialization order issue. Had the
> "/classes" element not been created by the time defineAllClasses tries
> to access it, the program would have exited with an assertion failure
> in stead of segmentation fault. But from your results it does not
> seem to be the problem.
>
>>
>> Also, when I do inspect core , I do see some references to Intel compiler,
>> can it be indication of some problem ?
>>
>
> Since gdb is loading libraries related to intel compiler before
> python, is it possible that you built Python with intel compiler? In
> that case can you see if rebuilding it with gcc and then building
> moose helps?
>
> Best,
> Subha
>
|
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From: Subhasis R. <ray...@gm...> - 2013-03-28 06:34:39
|
Dear Vadim,
On 3/28/13, Vadim A <ast...@nc...> wrote:
> 1. I modified the code
>
> /// Go through all elements under /classes and ask for defining a
> /// Python class for it.
> static int defineAllClasses(PyObject * module_dict)
> {
> ///static vector <Id> classes(Field< vector<Id>
>>::get(ObjId("/classes"),"children"));
> static const string children("children");
> static const string path("/classes");
> static const ObjId cle(path);
> assert(!(cle == ObjId::bad()));
> static vector <Id> classes = Field<vector<Id> >::get(cle,children);
> //static vector <Id> classes = Field<vector<Id>
>>::get(ObjId(path),children);
>
>
>
> What should I expect to see with that assert ? I did not noticed any
> differences when I did compile and import.
>
>
I was suspecting a static initialization order issue. Had the
"/classes" element not been created by the time defineAllClasses tries
to access it, the program would have exited with an assertion failure
in stead of segmentation fault. But from your results it does not
seem to be the problem.
>
> Also, when I do inspect core , I do see some references to Intel compiler,
> can it be indication of some problem ?
>
Since gdb is loading libraries related to intel compiler before
python, is it possible that you built Python with intel compiler? In
that case can you see if rebuilding it with gcc and then building
moose helps?
Best,
Subha
|
|
From: Vadim A <ast...@nc...> - 2013-03-27 20:27:01
|
Hi Subha.
Thank you for suggestion. Here what I did:
1. I modified the code
/// Go through all elements under /classes and ask for defining a
/// Python class for it.
static int defineAllClasses(PyObject * module_dict)
{
///static vector <Id> classes(Field< vector<Id> >::get(ObjId("/classes"),"children"));
static const string children("children");
static const string path("/classes");
static const ObjId cle(path);
assert(!(cle == ObjId::bad()));
static vector <Id> classes = Field<vector<Id> >::get(cle,children);
//static vector <Id> classes = Field<vector<Id> >::get(ObjId(path),children);
What should I expect to see with that assert ? I did not noticed any differences when I did compile and import.
2. make BUILD=debug USE_HDF5=0
I see that g++ get used
-->
All Libs compiled
g++ -g -pthread -fpermissive -fno-strict-aliasing -fPIC -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/ basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -o moose
/usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/libpthread.a when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm
/usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/libpthread.a when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc
Moose compilation finished
make -C basecode pymoose
make[1]: Entering directory `/home/astakhov/moose/moose/moose/basecode'
g++ -c -o main_pymoose.o -g -pthread -fpermissive -fno-strict-aliasing -fPIC -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/ -DPYMOOSE -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/include/ -DPYMOOSE -I../msg main.cpp
PrepackedBuffer.h: In member function 'unsigned int PrepackedBuffer::dataSize() const':
PrepackedBuffer.h:66: warning: converting to 'unsigned int' from 'double'
moosemodule.cpp:1595: warning: ISO C++ forbids casting between pointer-to-function and pointer-to-object
moosemodule.cpp: In function 'PyObject* moose_ObjId_getattro(_ObjId*, PyObject*)':
moosemodule.cpp:2317: warning: ISO C++ forbids casting between pointer-to-function and pointer-to-object
……………..
-->
3. I did import and getting segmentation fault:
Python 2.7.1 (r271:86832, May 17 2012, 20:01:20)
[GCC 4.6.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import moose
on node 0, numNodes = 1, numCores = 16, numComputeThreads = 16
Segmentation fault (core dumped)
4. Here the trace, but I do not see any indication on what might be the problem:
(gdb) where
#0 0x000000344be7275e in free () from /lib64/libc.so.6
#1 0x00000035f8a9db6a in std::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string() ()
from /usr/lib64/libstdc++.so.6
#2 0x00002afaefd95075 in Field<std::vector<Id, std::allocator<Id> > >::get (dest=..., field=...) at ../basecode/SetGet.h:289
#3 0x00002afaf018066d in defineAllClasses (module_dict=0x1116d9a0) at moosemodule.cpp:4290
#4 0x00002afaf018ceb6 in init_moose () at moosemodule.cpp:4956
#5 0x00002afaea25f705 in _PyImport_LoadDynamicModule (name=0x7fff8e7143e0 "moose._moose",
pathname=0x7fff8e7132f0 "/home/astakhov/moose/moose/moose/python/moose/_moose.so", fp=<value optimized out>)
at ./Python/importdl.c:53
#6 0x00002afaea25d7d8 in import_submodule (mod=0x10e8f398, subname=0x10e8ee04 "_moose",
fullname=0x7fff8e7143e0 "moose._moose") at Python/import.c:2596
#7 0x00002afaea25dd40 in ensure_fromlist (mod=0x10e8f398, fromlist=0x10e85cd0, buf=0x7fff8e7143e0 "moose._moose", buflen=5,
recursive=0) at Python/import.c:2507
#8 0x00002afaea25e1b7 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0x10e85cd0, level=1,
locals=<value optimized out>) at Python/import.c:2175
#9 0x00002afaea25e66a in PyImport_ImportModuleLevel (name=0x2afaeb00e644 "", globals=0x10ee5190,
locals=<value optimized out>, fromlist=0x10e85cd0, level=1) at Python/import.c:2189
#10 0x00002afaea23c13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>,
kwds=<value optimized out>) at Python/bltinmodule.c:49
#11 0x00002afaea1a07e3 in PyObject_Call (func=0x2afaeb031dd0, arg=<value optimized out>, kw=<value optimized out>)
at Objects/abstract.c:2529
#12 0x00002afaea23de97 in PyEval_CallObjectWithKeywords (func=0x2afaeb031dd0, arg=0x10f5b3b0, kw=<value optimized out>)
at Python/ceval.c:3881
#13 0x00002afaea240c81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2332
#14 0x00002afaea245515 in PyEval_EvalCodeEx (co=<value optimized out>, globals=<value optimized out>,
locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0,
closure=0x0) at Python/ceval.c:3252
#15 0x00002afaea245652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>,
locals=<value optimized out>) at Python/ceval.c:666
#16 0x00002afaea25c342 in PyImport_ExecCodeModuleEx (name=0x7fff8e7179d0 "moose.moose", co=0x10e84430,
pathname=0x7fff8e7168f0 "/home/astakhov/moose/moose/moose/python/moose/moose.py") at Python/import.c:681
#17 0x00002afaea25c68e in load_source_module (name=0x7fff8e7179d0 "moose.moose",
pathname=0x7fff8e7168f0 "/home/astakhov/moose/moose/moose/python/moose/moose.py", fp=<value optimized out>)
at Python/import.c:1021
#18 0x00002afaea25d7d8 in import_submodule (mod=0x10e8f398, subname=0x7fff8e7179d6 "moose",
fullname=0x7fff8e7179d0 "moose.moose") at Python/import.c:2596
#19 0x00002afaea25da52 in load_next (mod=0x10e8f398, altmod=0x10e8f398, p_name=<value optimized out>,
buf=0x7fff8e7179d0 "moose.moose", p_buflen=0x7fff8e7189e0) at Python/import.c:2416
#20 0x00002afaea25e062 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0x10e6e290, level=1,
locals=<value optimized out>) at Python/import.c:2137
#21 0x00002afaea25e66a in PyImport_ImportModuleLevel (name=0x10e8ec54 "moose", globals=0x10ec3200,
locals=<value optimized out>, fromlist=0x10e6e290, level=1) at Python/import.c:2189
#22 0x00002afaea23c13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>,
kwds=<value optimized out>) at Python/bltinmodule.c:49
#23 0x00002afaea1a07e3 in PyObject_Call (func=0x2afaeb031dd0, arg=<value optimized out>, kw=<value optimized out>)
at Objects/abstract.c:2529
#24 0x00002afaea23de97 in PyEval_CallObjectWithKeywords (func=0x2afaeb031dd0, arg=0x2afaeb0ca590, kw=<value optimized out>)
#25 0x00002afaea240c81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2332
#26 0x00002afaea245515 in PyEval_EvalCodeEx (co=<value optimized out>, globals=<value optimized out>,
locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0,
closure=0x0) at Python/ceval.c:3252
#27 0x00002afaea245652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>,
locals=<value optimized out>) at Python/ceval.c:666
#28 0x00002afaea25c342 in PyImport_ExecCodeModuleEx (name=0x7fff8e71c010 "moose", co=0x2afaeb0f2f30,
pathname=0x7fff8e719ed0 "/home/astakhov/moose/moose/moose/python/moose/__init__.py") at Python/import.c:681
#29 0x00002afaea25c68e in load_source_module (name=0x7fff8e71c010 "moose",
pathname=0x7fff8e719ed0 "/home/astakhov/moose/moose/moose/python/moose/__init__.py", fp=<value optimized out>)
at Python/import.c:1021
#30 0x00002afaea25d444 in load_package (name=0x7fff8e71c010 "moose", pathname=<value optimized out>) at Python/import.c:1077
#31 0x00002afaea25d7d8 in import_submodule (mod=0x2afaea4f68c0, subname=0x7fff8e71c010 "moose",
fullname=0x7fff8e71c010 "moose") at Python/import.c:2596
#32 0x00002afaea25da52 in load_next (mod=0x2afaea4f68c0, altmod=0x2afaea4f68c0, p_name=<value optimized out>,
buf=0x7fff8e71c010 "moose", p_buflen=0x7fff8e71d020) at Python/import.c:2416
#33 0x00002afaea25e062 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0x2afaea4f68c0, level=-1,
locals=<value optimized out>) at Python/import.c:2137
#34 0x00002afaea25e66a in PyImport_ImportModuleLevel (name=0x10e8ec54 "moose", globals=0x10dfda00,
locals=<value optimized out>, fromlist=0x2afaea4f68c0, level=-1) at Python/import.c:2189
#35 0x00002afaea23c13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>,
kwds=<value optimized out>) at Python/bltinmodule.c:49
#36 0x00002afaea1a07e3 in PyObject_Call (func=0x2afaeb031dd0, arg=<value optimized out>, kw=<value optimized out>)
at Objects/abstract.c:2529
#37 0x00002afaea23de97 in PyEval_CallObjectWithKeywords (func=0x2afaeb031dd0, arg=0x2afaeb0dae68, kw=<value optimized out>)
at Python/ceval.c:3881
#38 0x00002afaea240c81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2332
#39 0x00002afaea245515 in PyEval_EvalCodeEx (co=<value optimized out>, globals=<value optimized out>,
locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0,
closure=0x0) at Python/ceval.c:3252
#40 0x00002afaea245652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>,
locals=<value optimized out>) at Python/ceval.c:666
#41 0x00002afaea268b02 in run_mod (fp=<value optimized out>, filename=0x2afaea2affff "<stdin>", flags=0x7fff8e71d560)
at Python/pythonrun.c:1346
#42 PyRun_InteractiveOneFlags (fp=<value optimized out>, filename=0x2afaea2affff "<stdin>", flags=0x7fff8e71d560)
at Python/pythonrun.c:845
#43 0x00002afaea268d3e in PyRun_InteractiveLoopFlags (fp=0x344c1516a0, filename=0x2afaea2affff "<stdin>",
flags=0x7fff8e71d560) at Python/pythonrun.c:765
#44 0x00002afaea2692ec in PyRun_AnyFileExFlags (fp=0x344c1516a0, filename=0x2afaea2affff "<stdin>", closeit=0,
flags=0x7fff8e71d560) at Python/pythonrun.c:734
#45 0x00002afaea27b44b in Py_Main (argc=<value optimized out>, argv=<value optimized out>) at Modules/main.c:599
#46 0x000000344be1d994 in __libc_start_main () from /lib64/libc.so.6
#47 0x0000000000400619 in _start ()
Also, when I do inspect core , I do see some references to Intel compiler, can it be indication of some problem ?
gdb -c core.8851 /home/diag/opt/python2.7/bin/python
Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so
Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so
Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so...(no debugging symbols found)...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so
Reading symbols from /home/diag/opt/python2.7/lib/libpython2.7.so.1.0...done.
Loaded symbols for /home/diag/opt/python2.7/lib/libpython2.7.so.1.0
Reading symbols from /lib64/libpthread.so.0...(no debugging symbols found)...done.
Loaded symbols for /lib64/libpthread.so.0
Reading symbols from /lib64/libdl.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/libdl.so.2
Reading symbols from /lib64/libutil.so.1...(no debugging symbols found)...done.
Loaded symbols for /lib64/libutil.so.1
Reading symbols from /lib64/libm.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/libm.so.6
Reading symbols from /lib64/libc.so.6...(no debugging symbols found)...done.
Loaded symbols for /lib64/libc.so.6
Reading symbols from /usr/lib64/libstdc++.so.5...(no debugging symbols found)...done.
Loaded symbols for /usr/lib64/libstdc++.so.5
Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libimf.so...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libimf.so
Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libsvml.so...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libsvml.so
Reading symbols from /lib64/libgcc_s.so.1...(no debugging symbols found)...done.
Loaded symbols for /lib64/libgcc_s.so.1
Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libcxaguard.so.5...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libcxaguard.so.5
Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libintlc.so.5...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libintlc.so.5
Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols found)...done.
Loaded symbols for /lib64/ld-linux-x86-64.so.2
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/readline.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/readline.so
Reading symbols from /usr/lib64/libreadline.so.5...(no debugging symbols found)...done.
Loaded symbols for /usr/lib64/libreadline.so.5
Reading symbols from /usr/lib64/libncursesw.so.5...(no debugging symbols found)...done.
Loaded symbols for /usr/lib64/libncursesw.so.5
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cStringIO.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cStringIO.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/strop.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/strop.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/operator.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/operator.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_collections.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_collections.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/itertools.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/itertools.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_bisect.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_bisect.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_heapq.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_heapq.so
Reading symbols from /home/astakhov/moose/moose/moose/python/moose/_moose.so...done.
Loaded symbols for /home/astakhov/moose/moose/moose/python/moose/_moose.so
Reading symbols from /home/diag/opt/gsl/1.15/pgi/lib/libgsl.so.0...(no debugging symbols found)...done.
Loaded symbols for /home/diag/opt/gsl/1.15/pgi/lib/libgsl.so.0
Reading symbols from /home/diag/opt/gsl/1.15/pgi/lib/libgslcblas.so.0...(no debugging symbols found)...done.
Loaded symbols for /home/diag/opt/gsl/1.15/pgi/lib/libgslcblas.so.0
Reading symbols from /usr/lib64/libstdc++.so.6...(no debugging symbols found)...done.
Loaded symbols for /usr/lib64/libstdc++.so.6
Reading symbols from /opt/pgi/linux86-64/10.5/libso/libpgc.so...(no debugging symbols found)...done.
Loaded symbols for /opt/pgi/linux86-64/10.5/libso/libpgc.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/multiarray.so...(no debugging symbols found)...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/multiarray.so
Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libiomp5.so...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libiomp5.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/umath.so...(no debugging symbols found)...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/umath.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_sort.so...(no debugging symbols found)...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_sort.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_dotblas.so...(no debugging symbols found)...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_dotblas.so
Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_def.so...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_def.so
Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so
Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.so...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.so
Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_avx.so...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_avx.so
Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_mc.so...(no debugging symbols found)...done.
Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_mc.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cPickle.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cPickle.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/scalarmath.so...(no debugging symbols found)...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/scalarmath.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_functools.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_functools.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/time.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/time.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/math.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/math.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/lib/_compiled_base.so...(no debugging symbols found)...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/lib/_compiled_base.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so...(no debugging symbols found)...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/grp.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/grp.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so...(no debugging symbols found)...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/random/mtrand.so...(no debugging symbols found)...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/random/mtrand.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_ctypes.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_ctypes.so
Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_struct.so...done.
Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_struct.so
Core was generated by `python'.
Program terminated with signal 11, Segmentation fault.
#0 0x000000344be7275e in free () from /lib64/libc.so.6
On Mar 25, 2013, at 9:46 PM, Subhasis Ray wrote:
> Dear Vadim,
> I suspect that the problem now might be deeper than just compiler/library issues: possibly this an unusual case of the so called "static initialization fiasco". Can you please try this modification in moosemodule.cpp (same range of lines as before)?
>
>
> static int defineAllClasses(PyObject * module_dict)
> {
> static const string children("children");
> static const string path("/classes");
> static const ObjId cle(path);
> assert(!(cle == ObjId::bad()));
> static vector <Id> classes = Field< vector<Id> >::get(cle,
> children);
>
>
>
> and make a debug build and try importing moose. An assertion failure should indicate an initialization issue. Otherwise we can discuss if a debugging session is possible on your system.
>
> Best,
> Subha
>
|
|
From: Subhasis R. <ray...@gm...> - 2013-03-26 04:46:32
|
Dear Vadim,
I suspect that the problem now might be deeper than just
compiler/library issues: possibly this an unusual case of the so called
"static initialization fiasco". Can you please try this modification in
moosemodule.cpp (same range of lines as before)?
static int defineAllClasses(PyObject * module_dict)
{
static const string children("children");
static const string path("/classes");
static const ObjId cle(path);
assert(!(cle == ObjId::bad()));
static vector <Id> classes = Field< vector<Id> >::get(cle,
children);
and make a debug build and try importing moose. An assertion failure should
indicate an initialization issue. Otherwise we can discuss if a debugging
session is possible on your system.
Best,
Subha
|
|
From: Vadim A <ast...@nc...> - 2013-03-25 20:42:23
|
Hi Subha.
Thanks for your comments. I did try what you've suggested:
1. Modifications was performed in "moosemodule.cpp"
2. I double check that we use g++ :
[astakhov@trestles-login1 moose]$ make BUILD=debug USE_HDF5=0
make[1]: Entering directory `/home/astakhov/moose/moose/moose/basecode'
g++ -g -pthread -fpermissive -fno-strict-aliasing -fPIC -fno-inline-functions -Wall -Wno-long-long -pedantic -DDO_UNIT_TESTS -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/ -I../msg consts.cpp -c
3. And I did "make BUILD=debug"
but we still getting segmentation fault:
>>> import moose
on node 0, numNodes = 1, numCores = 16, numComputeThreads = 1
Segmentation fault (core dumped)
I wonder, is it possible to make a teleconference session where we can call you and share our screen to demonstrate all steps.
May be this way we could find the problem and have MOOSE finally installed for us.
Please let me know how do you feel about that.
Also, I attached trace to the end of this e-mail, may be you can advice us what we are still missing.
#0 0x000000344be7275e in free () from /lib64/libc.so.6
#1 0x00000035f8a9db6a in std::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string() ()
from /usr/lib64/libstdc++.so.6
#2 0x00002b0af62f6075 in Field<std::vector<Id, std::allocator<Id> > >::get (dest=..., field=...)
at ../basecode/SetGet.h:289
#3 0x00002b0af66e1525 in defineAllClasses (module_dict=0xc826f10) at moosemodule.cpp:4288
#4 0x00002b0af66edd7e in init_moose () at moosemodule.cpp:4953
#5 0x00002b0af07c0705 in _PyImport_LoadDynamicModule (name=0x7fffaa57dda0 "moose._moose",
pathname=0x7fffaa57ccb0 "/home/astakhov/moose/moose/moose/python/moose/_moose.so", fp=<value optimized out>)
at ./Python/importdl.c:53
#6 0x00002b0af07be7d8 in import_submodule (mod=0xc54a398, subname=0xc549e34 "_moose",
fullname=0x7fffaa57dda0 "moose._moose") at Python/import.c:2596
#7 0x00002b0af07bed40 in ensure_fromlist (mod=0xc54a398, fromlist=0xc540cd0, buf=0x7fffaa57dda0 "moose._moose",
buflen=5, recursive=0) at Python/import.c:2507
#8 0x00002b0af07bf1b7 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0xc540cd0,
level=1, locals=<value optimized out>) at Python/import.c:2175
#9 0x00002b0af07bf66a in PyImport_ImportModuleLevel (name=0x2b0af156f644 "", globals=0xc591030,
locals=<value optimized out>, fromlist=0xc540cd0, level=1) at Python/import.c:2189
#10 0x00002b0af079d13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>,
kwds=<value optimized out>) at Python/bltinmodule.c:49
#11 0x00002b0af07017e3 in PyObject_Call (func=0x2b0af1592dd0, arg=<value optimized out>, kw=<value optimized out>)
at Objects/abstract.c:2529
#12 0x00002b0af079ee97 in PyEval_CallObjectWithKeywords (func=0x2b0af1592dd0, arg=0xc6153b0,
kw=<value optimized out>) at Python/ceval.c:3881
#13 0x00002b0af07a1c81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>)
at Python/ceval.c:2332
#14 0x00002b0af07a6515 in PyEval_EvalCodeEx (co=<value optimized out>, globals=<value optimized out>,
locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0,
closure=0x0) at Python/ceval.c:3252
#15 0x00002b0af07a6652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>,
---Type <return> to continue, or q <return> to quit---
locals=<value optimized out>) at Python/ceval.c:666
#16 0x00002b0af07bd342 in PyImport_ExecCodeModuleEx (name=0x7fffaa581390 "moose.moose", co=0xc53f430,
pathname=0x7fffaa5802b0 "/home/astakhov/moose/moose/moose/python/moose/moose.py") at Python/import.c:681
#17 0x00002b0af07bd68e in load_source_module (name=0x7fffaa581390 "moose.moose",
pathname=0x7fffaa5802b0 "/home/astakhov/moose/moose/moose/python/moose/moose.py", fp=<value optimized out>)
at Python/import.c:1021
#18 0x00002b0af07be7d8 in import_submodule (mod=0xc54a398, subname=0x7fffaa581396 "moose",
fullname=0x7fffaa581390 "moose.moose") at Python/import.c:2596
#19 0x00002b0af07bea52 in load_next (mod=0xc54a398, altmod=0xc54a398, p_name=<value optimized out>,
buf=0x7fffaa581390 "moose.moose", p_buflen=0x7fffaa5823a0) at Python/import.c:2416
#20 0x00002b0af07bf062 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0xc529290,
level=1, locals=<value optimized out>) at Python/import.c:2137
#21 0x00002b0af07bf66a in PyImport_ImportModuleLevel (name=0xc549cb4 "moose", globals=0xc57e200,
locals=<value optimized out>, fromlist=0xc529290, level=1) at Python/import.c:2189
#22 0x00002b0af079d13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>,
kwds=<value optimized out>) at Python/bltinmodule.c:49
#23 0x00002b0af07017e3 in PyObject_Call (func=0x2b0af1592dd0, arg=<value optimized out>, kw=<value optimized out>)
at Objects/abstract.c:2529
#24 0x00002b0af079ee97 in PyEval_CallObjectWithKeywords (func=0x2b0af1592dd0, arg=0x2b0af162b590,
kw=<value optimized out>) at Python/ceval.c:3881
#25 0x00002b0af07a1c81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>)
at Python/ceval.c:2332
#26 0x00002b0af07a6515 in PyEval_EvalCodeEx (co=<value optimized out>, globals=<value optimized out>,
locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0,
closure=0x0) at Python/ceval.c:3252
#27 0x00002b0af07a6652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>,
locals=<value optimized out>) at Python/ceval.c:666
#28 0x00002b0af07bd342 in PyImport_ExecCodeModuleEx (name=0x7fffaa5859d0 "moose", co=0x2b0af1653f30,
pathname=0x7fffaa583890 "/home/astakhov/moose/moose/moose/python/moose/__init__.py") at Python/import.c:681
#29 0x00002b0af07bd68e in load_source_module (name=0x7fffaa5859d0 "moose",
---Type <return> to continue, or q <return> to quit---
pathname=0x7fffaa583890 "/home/astakhov/moose/moose/moose/python/moose/__init__.py", fp=<value optimized out>)
at Python/import.c:1021
#30 0x00002b0af07be444 in load_package (name=0x7fffaa5859d0 "moose", pathname=<value optimized out>)
at Python/import.c:1077
#31 0x00002b0af07be7d8 in import_submodule (mod=0x2b0af0a578c0, subname=0x7fffaa5859d0 "moose",
fullname=0x7fffaa5859d0 "moose") at Python/import.c:2596
#32 0x00002b0af07bea52 in load_next (mod=0x2b0af0a578c0, altmod=0x2b0af0a578c0, p_name=<value optimized out>,
buf=0x7fffaa5859d0 "moose", p_buflen=0x7fffaa5869e0) at Python/import.c:2416
#33 0x00002b0af07bf062 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0x2b0af0a578c0,
level=-1, locals=<value optimized out>) at Python/import.c:2137
#34 0x00002b0af07bf66a in PyImport_ImportModuleLevel (name=0xc549cb4 "moose", globals=0xc4b8a00,
locals=<value optimized out>, fromlist=0x2b0af0a578c0, level=-1) at Python/import.c:2189
#35 0x00002b0af079d13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>,
kwds=<value optimized out>) at Python/bltinmodule.c:49
#36 0x00002b0af07017e3 in PyObject_Call (func=0x2b0af1592dd0, arg=<value optimized out>, kw=<value optimized out>)
at Objects/abstract.c:2529
#37 0x00002b0af079ee97 in PyEval_CallObjectWithKeywords (func=0x2b0af1592dd0, arg=0x2b0af163be68,
kw=<value optimized out>) at Python/ceval.c:3881
#38 0x00002b0af07a1c81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>)
at Python/ceval.c:2332
#39 0x00002b0af07a6515 in PyEval_EvalCodeEx (co=<value optimized out>, globals=<value optimized out>,
locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0,
closure=0x0) at Python/ceval.c:3252
#40 0x00002b0af07a6652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>,
locals=<value optimized out>) at Python/ceval.c:666
#41 0x00002b0af07c9b02 in run_mod (fp=<value optimized out>, filename=0x2b0af0810fff "<stdin>",
flags=0x7fffaa586f20) at Python/pythonrun.c:1346
#42 PyRun_InteractiveOneFlags (fp=<value optimized out>, filename=0x2b0af0810fff "<stdin>", flags=0x7fffaa586f20)
at Python/pythonrun.c:845
#43 0x00002b0af07c9d3e in PyRun_InteractiveLoopFlags (fp=0x344c1516a0, filename=0x2b0af0810fff "<stdin>",
---Type <return> to continue, or q <return> to quit---
flags=0x7fffaa586f20) at Python/pythonrun.c:765
#44 0x00002b0af07ca2ec in PyRun_AnyFileExFlags (fp=0x344c1516a0, filename=0x2b0af0810fff "<stdin>", closeit=0,
flags=0x7fffaa586f20) at Python/pythonrun.c:734
#45 0x00002b0af07dc44b in Py_Main (argc=<value optimized out>, argv=<value optimized out>) at Modules/main.c:599
#46 0x000000344be1d994 in __libc_start_main () from /lib64/libc.so.6
#47 0x0000000000400619 in _start ()
GNU gdb (GDB) Red Hat Enterprise Linux (7.0.1-23.el5_5.1)
Copyright (C) 2009 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /home/diag/opt/python2.7/bin/python...done.
[New Thread 15492]
Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no debugging symbols found)...done.
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Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_heapq.so...done.
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Reading symbols from /home/astakhov/moose/moose/moose/python/moose/_moose.so...done.
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Core was generated by `python'.
Program terminated with signal 11, Segmentation fault.
#0 0x000000344be7275e in free () from /lib64/libc.so.6
(gdb)
On Mar 20, 2013, at 10:18 PM, Subhasis Ray wrote:
> Dear Vadim,
> I could not reproduce this. Are you using g++? In the trace
>
> "Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no debugging symbols found)...done."
>
> seems to indicate that you have Intel C++ compiler and related libraries installed (and possibly linked to in moose).
>
> Can you please try out the following in moose/pymoose/moosemodule.cpp: Go to line 4277 and modify:
>
> ------8<------------------------------->8-------
>
> static int defineAllClasses(PyObject * module_dict)
> {
> static vector <Id> classes(Field< vector<Id> >::get(ObjId("/classes"),
> "children"));
>
> ------8<------------------------------->8-------
>
> into ...
>
> ------8<------------------------------->8-------
>
> static int defineAllClasses(PyObject * module_dict)
> {
> static const string children("children");
> static const string path("/classes");
> static vector <Id> classes = Field< vector<Id> >::get(ObjId(path),
> children);
>
> ------8<------------------------------->8-------
> and rebuild.
>
> You can also try reducing the number of threads by setting the NUMPTHREADS environment variable:
>
> export NUMPTHREADS=1
>
> in the shell before starting the Python interpreter. But I doubt if that will help.
>
> Beyond that, you can do a "make clean" and the "make BUILD=debug" to create a debug build, which may avoid some issues caused by compiler optimizations and give more elaborate backtrace.
>
> Best,
> Subha
>
>
|
|
From: Subhasis R. <ray...@gm...> - 2013-03-21 05:18:49
|
Dear Vadim,
I could not reproduce this. Are you using g++? In the trace
"Reading symbols from
/opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no debugging
symbols found)...done."
seems to indicate that you have Intel C++ compiler and related libraries
installed (and possibly linked to in moose).
Can you please try out the following in moose/pymoose/moosemodule.cpp: Go
to line 4277 and modify:
------8<------------------------------->8-------
static int defineAllClasses(PyObject * module_dict)
{
static vector <Id> classes(Field< vector<Id>
>::get(ObjId("/classes"),
"children"));
------8<------------------------------->8-------
into ...
------8<------------------------------->8-------
static int defineAllClasses(PyObject * module_dict)
{
static const string children("children");
static const string path("/classes");
static vector <Id> classes = Field< vector<Id> >::get(ObjId(path),
children);
------8<------------------------------->8-------
and rebuild.
You can also try reducing the number of threads by setting the NUMPTHREADS
environment variable:
export NUMPTHREADS=1
in the shell before starting the Python interpreter. But I doubt if that
will help.
Beyond that, you can do a "make clean" and the "make BUILD=debug" to create
a debug build, which may avoid some issues caused by compiler optimizations
and give more elaborate backtrace.
Best,
Subha
On Thu, Mar 21, 2013 at 12:03 AM, Vadim A <ast...@nc...> wrote:
> Hi Subha,
>
> We are trying import MOOSE and having problem. I provide some trace
> information at the end of this e-mail. And very appreciate any comments.
>
> May be we should turn threading off? What would be your suggestions?
>
>
>
> >>> import moose
> on node 0, numNodes = 1, numCores = 16, numComputeThreads = 16
> Segmentation fault (core dumped)
>
>
>
>
> [astakhov@trestles-login1 moose]$ gdb -c core.24245
> /home/diag/opt/python2.7/bin/python
> GNU gdb (GDB) Red Hat Enterprise Linux (7.0.1-23.el5_5.1)
> Copyright (C) 2009 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later <
> http://gnu.org/licenses/gpl.html>
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law. Type "show copying"
> and "show warranty" for details.
> This GDB was configured as "x86_64-redhat-linux-gnu".
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>...
> Reading symbols from /home/diag/opt/python2.7/bin/python...done.
> [New Thread 24275]
> [New Thread 24274]
> [New Thread 24273]
> [New Thread 24272]
> [New Thread 24271]
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> [New Thread 24260]
> Reading symbols from
> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no debugging
> symbols found)...done.
> Loaded symbols for
> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so
> Reading symbols from
> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no
> debugging symbols found)...done.
> Loaded symbols for
> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so
> Reading symbols from
> /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5...(no debugging
> symbols found)...done.
> Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so...(no
> debugging symbols found)...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/libpython2.7.so.1.0...done.
> Loaded symbols for /home/diag/opt/python2.7/lib/libpython2.7.so.1.0
> Reading symbols from /lib64/libpthread.so.0...(no debugging symbols
> found)...done.
> Loaded symbols for /lib64/libpthread.so.0
> Reading symbols from /lib64/libdl.so.2...(no debugging symbols
> found)...done.
> Loaded symbols for /lib64/libdl.so.2
> Reading symbols from /lib64/libutil.so.1...(no debugging symbols
> found)...done.
> Loaded symbols for /lib64/libutil.so.1
> Reading symbols from /lib64/libm.so.6...(no debugging symbols
> found)...done.
> Loaded symbols for /lib64/libm.so.6
> Reading symbols from /lib64/libc.so.6...(no debugging symbols
> found)...done.
> Loaded symbols for /lib64/libc.so.6
> Reading symbols from /usr/lib64/libstdc++.so.5...(no debugging symbols
> found)...done.
> Loaded symbols for /usr/lib64/libstdc++.so.5
> Reading symbols from
> /opt/intel/Compiler/11.1/072/lib/intel64/libimf.so...(no debugging symbols
> found)...done.
> Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libimf.so
> Reading symbols from
> /opt/intel/Compiler/11.1/072/lib/intel64/libsvml.so...(no debugging symbols
> found)...done.
> Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libsvml.so
> Reading symbols from /lib64/libgcc_s.so.1...(no debugging symbols
> found)...done.
> Loaded symbols for /lib64/libgcc_s.so.1
> Reading symbols from
> /opt/intel/Compiler/11.1/072/lib/intel64/libcxaguard.so.5...(no debugging
> symbols found)...done.
> Loaded symbols for
> /opt/intel/Compiler/11.1/072/lib/intel64/libcxaguard.so.5
> Reading symbols from
> /opt/intel/Compiler/11.1/072/lib/intel64/libintlc.so.5...(no debugging
> symbols found)...done.
> Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libintlc.so.5
> Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols
> found)...done.
> Loaded symbols for /lib64/ld-linux-x86-64.so.2
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/readline.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/readline.so
> Reading symbols from /usr/lib64/libreadline.so.5...(no debugging symbols
> found)...done.
> Loaded symbols for /usr/lib64/libreadline.so.5
> Reading symbols from /usr/lib64/libncursesw.so.5...(no debugging symbols
> found)...done.
> Loaded symbols for /usr/lib64/libncursesw.so.5
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cStringIO.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cStringIO.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/strop.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/strop.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/operator.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/operator.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_collections.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_collections.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/itertools.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/itertools.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_bisect.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_bisect.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_heapq.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_heapq.so
> Reading symbols from
> /home/astakhov/moose/moose/moose/python/moose/_moose.so...(no debugging
> symbols found)...done.
> Loaded symbols for /home/astakhov/moose/moose/moose/python/moose/_moose.so
> Reading symbols from /home/diag/opt/gsl/1.15/pgi/lib/libgsl.so.0...(no
> debugging symbols found)...done.
> Loaded symbols for /home/diag/opt/gsl/1.15/pgi/lib/libgsl.so.0
> Reading symbols from
> /home/diag/opt/gsl/1.15/pgi/lib/libgslcblas.so.0...(no debugging symbols
> found)...done.
> Loaded symbols for /home/diag/opt/gsl/1.15/pgi/lib/libgslcblas.so.0
> Reading symbols from /usr/lib64/libstdc++.so.6...(no debugging symbols
> found)...done.
> Loaded symbols for /usr/lib64/libstdc++.so.6
> Reading symbols from /opt/pgi/linux86-64/10.5/libso/libpgc.so...(no
> debugging symbols found)...done.
> Loaded symbols for /opt/pgi/linux86-64/10.5/libso/libpgc.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/multiarray.so...(no
> debugging symbols found)...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/multiarray.so
> Reading symbols from
> /opt/intel/Compiler/11.1/072/lib/intel64/libiomp5.so...(no debugging
> symbols found)...done.
> Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libiomp5.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/umath.so...(no
> debugging symbols found)...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/umath.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_sort.so...(no
> debugging symbols found)...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_sort.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_dotblas.so...(no
> debugging symbols found)...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_dotblas.so
> Reading symbols from
> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_def.so...(no debugging
> symbols found)...done.
> Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_def.so
> Reading symbols from
> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so...(no
> debugging symbols found)...done.
> Loaded symbols for
> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so
> Reading symbols from
> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.so...(no
> debugging symbols found)...done.
> Loaded symbols for
> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.so
> Reading symbols from
> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_avx.so...(no debugging
> symbols found)...done.
> Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_avx.so
> Reading symbols from
> /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_mc.so...(no debugging
> symbols found)...done.
> Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_mc.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cPickle.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cPickle.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/scalarmath.so...(no
> debugging symbols found)...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/scalarmath.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_functools.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_functools.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/time.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/time.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/math.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/math.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/lib/_compiled_base.so...(no
> debugging symbols found)...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/lib/_compiled_base.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so...(no
> debugging symbols found)...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/grp.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/grp.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so...(no
> debugging symbols found)...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/random/mtrand.so...(no
> debugging symbols found)...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/random/mtrand.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_ctypes.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_ctypes.so
> Reading symbols from
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_struct.so...done.
> Loaded symbols for
> /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_struct.so
> Core was generated by `python'.
> Program terminated with signal 11, Segmentation fault.
> #0 0x000000344be7275e in free () from /lib64/libc.so.6
> (gdb) where
> #0 0x000000344be7275e in free () from /lib64/libc.so.6
> #1 0x00002b3b34bcc2db in Field<std::vector<Id, std::allocator<Id> >
> >::get(ObjId const&, std::basic_string<char, std::char_traits<char>,
> std::allocator<char> > const&) () from
> /home/astakhov/moose/moose/moose/python/moose/_moose.so
> #2 0x00002b3b34f238e0 in defineAllClasses () from
> /home/astakhov/moose/moose/moose/python/moose/_moose.so
> #3 0x00002b3b34f24108 in init_moose () from
> /home/astakhov/moose/moose/moose/python/moose/_moose.so
> #4 0x00002b3b2f25d705 in _PyImport_LoadDynamicModule (name=0x7fff9742c950
> "moose._moose",
> pathname=0x7fff9742b860
> "/home/astakhov/moose/moose/moose/python/moose/_moose.so", fp=<value
> optimized out>) at ./Python/importdl.c:53
> #5 0x00002b3b2f25b7d8 in import_submodule (mod=0x189c03d0,
> subname=0x189bfd14 "_moose", fullname=0x7fff9742c950 "moose._moose")
> at Python/import.c:2596
> #6 0x00002b3b2f25bd40 in ensure_fromlist (mod=0x189c03d0,
> fromlist=0x189b6cd0, buf=0x7fff9742c950 "moose._moose", buflen=5,
> recursive=0)
> at Python/import.c:2507
> #7 0x00002b3b2f25c1b7 in import_module_level (name=0x0, globals=<value
> optimized out>, fromlist=0x189b6cd0, level=1,
> locals=<value optimized out>) at Python/import.c:2175
> #8 0x00002b3b2f25c66a in PyImport_ImportModuleLevel (name=0x2b3b3000c644
> "", globals=0x18a16350, locals=<value optimized out>,
> fromlist=0x189b6cd0, level=1) at Python/import.c:2189
> #9 0x00002b3b2f23a13f in builtin___import__ (self=<value optimized out>,
> args=<value optimized out>, kwds=<value optimized out>)
> at Python/bltinmodule.c:49
> #10 0x00002b3b2f19e7e3 in PyObject_Call (func=0x2b3b3002fdd0, arg=<value
> optimized out>, kw=<value optimized out>)
> at Objects/abstract.c:2529
> #11 0x00002b3b2f23be97 in PyEval_CallObjectWithKeywords
> (func=0x2b3b3002fdd0, arg=0x18a483b0, kw=<value optimized out>)
> at Python/ceval.c:3881
> #12 0x00002b3b2f23ec81 in PyEval_EvalFrameEx (f=<value optimized out>,
> throwflag=<value optimized out>) at Python/ceval.c:2332
> #13 0x00002b3b2f243515 in PyEval_EvalCodeEx (co=<value optimized out>,
> globals=<value optimized out>, locals=<value optimized out>,
> args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0,
> defcount=0, closure=0x0) at Python/ceval.c:3252
> #14 0x00002b3b2f243652 in PyEval_EvalCode (co=<value optimized out>,
> globals=<value optimized out>, locals=<value optimized out>)
> at Python/ceval.c:666
> #15 0x00002b3b2f25a342 in PyImport_ExecCodeModuleEx (name=0x7fff9742ff40
> "moose.moose", co=0x189b53b0,
> pathname=0x7fff9742dd50
> "/home/astakhov/moose/moose/moose/python/moose/moose.pyc") at
> Python/import.c:681
> #16 0x00002b3b2f25a68e in load_source_module (name=0x7fff9742ff40
> "moose.moose",
> pathname=0x7fff9742dd50
> "/home/astakhov/moose/moose/moose/python/moose/moose.pyc", fp=<value
> optimized out>) at Python/import.c:1021
> #17 0x00002b3b2f25b7d8 in import_submodule (mod=0x189c03d0,
> subname=0x7fff9742ff46 "moose", fullname=0x7fff9742ff40 "moose.moose")
> at Python/import.c:2596
> #18 0x00002b3b2f25ba52 in load_next (mod=0x189c03d0, altmod=0x189c03d0,
> p_name=<value optimized out>, buf=0x7fff9742ff40 "moose.moose",
> p_buflen=0x7fff97430f50) at Python/import.c:2416
> #19 0x00002b3b2f25c062 in import_module_level (name=0x0, globals=<value
> optimized out>, fromlist=0x1899f290, level=1,
> locals=<value optimized out>) at Python/import.c:2137
> #20 0x00002b3b2f25c66a in PyImport_ImportModuleLevel (name=0x189bfc54
> "moose", globals=0x189f43c0, locals=<value optimized out>,
> fromlist=0x1899f290, level=1) at Python/import.c:2189
> #21 0x00002b3b2f23a13f in builtin___import__ (self=<value optimized out>,
> args=<value optimized out>, kwds=<value optimized out>)
> at Python/bltinmodule.c:49
> #22 0x00002b3b2f19e7e3 in PyObject_Call (func=0x2b3b3002fdd0, arg=<value
> optimized out>, kw=<value optimized out>)
> at Objects/abstract.c:2529
> #23 0x00002b3b2f23be97 in PyEval_CallObjectWithKeywords
> (func=0x2b3b3002fdd0, arg=0x2b3b300c8590, kw=<value optimized out>)
> at Python/ceval.c:3881
> #24 0x00002b3b2f23ec81 in PyEval_EvalFrameEx (f=<value optimized out>,
> throwflag=<value optimized out>) at Python/ceval.c:2332
> #25 0x00002b3b2f243515 in PyEval_EvalCodeEx (co=<value optimized out>,
> globals=<value optimized out>, locals=<value optimized out>,
> args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0,
> defcount=0, closure=0x0) at Python/ceval.c:3252
> #26 0x00002b3b2f243652 in PyEval_EvalCode (co=<value optimized out>,
> globals=<value optimized out>, locals=<value optimized out>)
> at Python/ceval.c:666
> ---Type <return> to continue, or q <return> to quit---
> #27 0x00002b3b2f25a342 in PyImport_ExecCodeModuleEx (name=0x7fff97434580
> "moose", co=0x2b3b300f0eb0,
> pathname=0x7fff97431340
> "/home/astakhov/moose/moose/moose/python/moose/__init__.pyc") at
> Python/import.c:681
> #28 0x00002b3b2f25a68e in load_source_module (name=0x7fff97434580 "moose",
> pathname=0x7fff97431340
> "/home/astakhov/moose/moose/moose/python/moose/__init__.pyc", fp=<value
> optimized out>) at Python/import.c:1021
> #29 0x00002b3b2f25b444 in load_package (name=0x7fff97434580 "moose",
> pathname=<value optimized out>) at Python/import.c:1077
> #30 0x00002b3b2f25b7d8 in import_submodule (mod=0x2b3b2f4f48c0,
> subname=0x7fff97434580 "moose", fullname=0x7fff97434580 "moose")
> at Python/import.c:2596
> #31 0x00002b3b2f25ba52 in load_next (mod=0x2b3b2f4f48c0,
> altmod=0x2b3b2f4f48c0, p_name=<value optimized out>, buf=0x7fff97434580
> "moose",
> p_buflen=0x7fff97435590) at Python/import.c:2416
> #32 0x00002b3b2f25c062 in import_module_level (name=0x0, globals=<value
> optimized out>, fromlist=0x2b3b2f4f48c0, level=-1,
> locals=<value optimized out>) at Python/import.c:2137
> #33 0x00002b3b2f25c66a in PyImport_ImportModuleLevel (name=0x189bfc54
> "moose", globals=0x1892ea00, locals=<value optimized out>,
> fromlist=0x2b3b2f4f48c0, level=-1) at Python/import.c:2189
> #34 0x00002b3b2f23a13f in builtin___import__ (self=<value optimized out>,
> args=<value optimized out>, kwds=<value optimized out>)
> at Python/bltinmodule.c:49
> #35 0x00002b3b2f19e7e3 in PyObject_Call (func=0x2b3b3002fdd0, arg=<value
> optimized out>, kw=<value optimized out>)
> at Objects/abstract.c:2529
> #36 0x00002b3b2f23be97 in PyEval_CallObjectWithKeywords
> (func=0x2b3b3002fdd0, arg=0x2b3b300d8e68, kw=<value optimized out>)
> at Python/ceval.c:3881
> #37 0x00002b3b2f23ec81 in PyEval_EvalFrameEx (f=<value optimized out>,
> throwflag=<value optimized out>) at Python/ceval.c:2332
> #38 0x00002b3b2f243515 in PyEval_EvalCodeEx (co=<value optimized out>,
> globals=<value optimized out>, locals=<value optimized out>,
> args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0,
> defcount=0, closure=0x0) at Python/ceval.c:3252
> #39 0x00002b3b2f243652 in PyEval_EvalCode (co=<value optimized out>,
> globals=<value optimized out>, locals=<value optimized out>)
> at Python/ceval.c:666
> #40 0x00002b3b2f266b02 in run_mod (fp=<value optimized out>,
> filename=0x2b3b2f2adfff "<stdin>", flags=0x7fff97435ad0)
> at Python/pythonrun.c:1346
> #41 PyRun_InteractiveOneFlags (fp=<value optimized out>,
> filename=0x2b3b2f2adfff "<stdin>", flags=0x7fff97435ad0) at
> Python/pythonrun.c:845
> #42 0x00002b3b2f266d3e in PyRun_InteractiveLoopFlags (fp=0x344c1516a0,
> filename=0x2b3b2f2adfff "<stdin>", flags=0x7fff97435ad0)
> at Python/pythonrun.c:765
> #43 0x00002b3b2f2672ec in PyRun_AnyFileExFlags (fp=0x344c1516a0,
> filename=0x2b3b2f2adfff "<stdin>", closeit=0, flags=0x7fff97435ad0)
> at Python/pythonrun.c:734
> #44 0x00002b3b2f27944b in Py_Main (argc=<value optimized out>, argv=<value
> optimized out>) at Modules/main.c:599
> #45 0x000000344be1d994 in __libc_start_main () from /lib64/libc.so.6
> #46 0x0000000000400619 in _start ()
> (gdb)
>
>
|
|
From: Vadim A <ast...@nc...> - 2013-03-20 18:34:07
|
Hi Subha, We are trying import MOOSE and having problem. I provide some trace information at the end of this e-mail. And very appreciate any comments. May be we should turn threading off? What would be your suggestions? >>> import moose on node 0, numNodes = 1, numCores = 16, numComputeThreads = 16 Segmentation fault (core dumped) [astakhov@trestles-login1 moose]$ gdb -c core.24245 /home/diag/opt/python2.7/bin/python GNU gdb (GDB) Red Hat Enterprise Linux (7.0.1-23.el5_5.1) Copyright (C) 2009 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-redhat-linux-gnu". For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>... Reading symbols from /home/diag/opt/python2.7/bin/python...done. [New Thread 24275] [New Thread 24274] [New Thread 24273] [New Thread 24272] [New Thread 24271] [New Thread 24270] [New Thread 24269] [New Thread 24268] [New Thread 24267] [New Thread 24266] [New Thread 24265] [New Thread 24264] [New Thread 24263] [New Thread 24262] [New Thread 24261] [New Thread 24260] Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_core.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_sequential.so Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libpdbx.so.5 Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/scipy/sparse/sparsetools/_coo.so Reading symbols from /home/diag/opt/python2.7/lib/libpython2.7.so.1.0...done. Loaded symbols for /home/diag/opt/python2.7/lib/libpython2.7.so.1.0 Reading symbols from /lib64/libpthread.so.0...(no debugging symbols found)...done. Loaded symbols for /lib64/libpthread.so.0 Reading symbols from /lib64/libdl.so.2...(no debugging symbols found)...done. Loaded symbols for /lib64/libdl.so.2 Reading symbols from /lib64/libutil.so.1...(no debugging symbols found)...done. Loaded symbols for /lib64/libutil.so.1 Reading symbols from /lib64/libm.so.6...(no debugging symbols found)...done. Loaded symbols for /lib64/libm.so.6 Reading symbols from /lib64/libc.so.6...(no debugging symbols found)...done. Loaded symbols for /lib64/libc.so.6 Reading symbols from /usr/lib64/libstdc++.so.5...(no debugging symbols found)...done. Loaded symbols for /usr/lib64/libstdc++.so.5 Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libimf.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libimf.so Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libsvml.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libsvml.so Reading symbols from /lib64/libgcc_s.so.1...(no debugging symbols found)...done. Loaded symbols for /lib64/libgcc_s.so.1 Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libcxaguard.so.5...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libcxaguard.so.5 Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libintlc.so.5...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libintlc.so.5 Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols found)...done. Loaded symbols for /lib64/ld-linux-x86-64.so.2 Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/readline.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/readline.so Reading symbols from /usr/lib64/libreadline.so.5...(no debugging symbols found)...done. Loaded symbols for /usr/lib64/libreadline.so.5 Reading symbols from /usr/lib64/libncursesw.so.5...(no debugging symbols found)...done. Loaded symbols for /usr/lib64/libncursesw.so.5 Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cStringIO.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cStringIO.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/strop.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/strop.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/operator.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/operator.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_collections.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_collections.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/itertools.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/itertools.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_bisect.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_bisect.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_heapq.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_heapq.so Reading symbols from /home/astakhov/moose/moose/moose/python/moose/_moose.so...(no debugging symbols found)...done. Loaded symbols for /home/astakhov/moose/moose/moose/python/moose/_moose.so Reading symbols from /home/diag/opt/gsl/1.15/pgi/lib/libgsl.so.0...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/gsl/1.15/pgi/lib/libgsl.so.0 Reading symbols from /home/diag/opt/gsl/1.15/pgi/lib/libgslcblas.so.0...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/gsl/1.15/pgi/lib/libgslcblas.so.0 Reading symbols from /usr/lib64/libstdc++.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib64/libstdc++.so.6 Reading symbols from /opt/pgi/linux86-64/10.5/libso/libpgc.so...(no debugging symbols found)...done. Loaded symbols for /opt/pgi/linux86-64/10.5/libso/libpgc.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/multiarray.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/multiarray.so Reading symbols from /opt/intel/Compiler/11.1/072/lib/intel64/libiomp5.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/lib/intel64/libiomp5.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/umath.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/umath.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_sort.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_sort.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_dotblas.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/_dotblas.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_def.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_def.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_lp64.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_intel_thread.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_avx.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_avx.so Reading symbols from /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_mc.so...(no debugging symbols found)...done. Loaded symbols for /opt/intel/Compiler/11.1/072/mkl/lib/em64t/libmkl_mc.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cPickle.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/cPickle.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/scalarmath.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/scalarmath.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_functools.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_functools.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/time.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/time.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/math.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/math.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/lib/_compiled_base.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/lib/_compiled_base.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/linalg/lapack_lite.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/grp.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/grp.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/fft/fftpack_lite.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/random/mtrand.so...(no debugging symbols found)...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/random/mtrand.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_ctypes.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_ctypes.so Reading symbols from /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_struct.so...done. Loaded symbols for /home/diag/opt/python2.7/lib/python2.7/lib-dynload/_struct.so Core was generated by `python'. Program terminated with signal 11, Segmentation fault. #0 0x000000344be7275e in free () from /lib64/libc.so.6 (gdb) where #0 0x000000344be7275e in free () from /lib64/libc.so.6 #1 0x00002b3b34bcc2db in Field<std::vector<Id, std::allocator<Id> > >::get(ObjId const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) () from /home/astakhov/moose/moose/moose/python/moose/_moose.so #2 0x00002b3b34f238e0 in defineAllClasses () from /home/astakhov/moose/moose/moose/python/moose/_moose.so #3 0x00002b3b34f24108 in init_moose () from /home/astakhov/moose/moose/moose/python/moose/_moose.so #4 0x00002b3b2f25d705 in _PyImport_LoadDynamicModule (name=0x7fff9742c950 "moose._moose", pathname=0x7fff9742b860 "/home/astakhov/moose/moose/moose/python/moose/_moose.so", fp=<value optimized out>) at ./Python/importdl.c:53 #5 0x00002b3b2f25b7d8 in import_submodule (mod=0x189c03d0, subname=0x189bfd14 "_moose", fullname=0x7fff9742c950 "moose._moose") at Python/import.c:2596 #6 0x00002b3b2f25bd40 in ensure_fromlist (mod=0x189c03d0, fromlist=0x189b6cd0, buf=0x7fff9742c950 "moose._moose", buflen=5, recursive=0) at Python/import.c:2507 #7 0x00002b3b2f25c1b7 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0x189b6cd0, level=1, locals=<value optimized out>) at Python/import.c:2175 #8 0x00002b3b2f25c66a in PyImport_ImportModuleLevel (name=0x2b3b3000c644 "", globals=0x18a16350, locals=<value optimized out>, fromlist=0x189b6cd0, level=1) at Python/import.c:2189 #9 0x00002b3b2f23a13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>, kwds=<value optimized out>) at Python/bltinmodule.c:49 #10 0x00002b3b2f19e7e3 in PyObject_Call (func=0x2b3b3002fdd0, arg=<value optimized out>, kw=<value optimized out>) at Objects/abstract.c:2529 #11 0x00002b3b2f23be97 in PyEval_CallObjectWithKeywords (func=0x2b3b3002fdd0, arg=0x18a483b0, kw=<value optimized out>) at Python/ceval.c:3881 #12 0x00002b3b2f23ec81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2332 #13 0x00002b3b2f243515 in PyEval_EvalCodeEx (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3252 #14 0x00002b3b2f243652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>) at Python/ceval.c:666 #15 0x00002b3b2f25a342 in PyImport_ExecCodeModuleEx (name=0x7fff9742ff40 "moose.moose", co=0x189b53b0, pathname=0x7fff9742dd50 "/home/astakhov/moose/moose/moose/python/moose/moose.pyc") at Python/import.c:681 #16 0x00002b3b2f25a68e in load_source_module (name=0x7fff9742ff40 "moose.moose", pathname=0x7fff9742dd50 "/home/astakhov/moose/moose/moose/python/moose/moose.pyc", fp=<value optimized out>) at Python/import.c:1021 #17 0x00002b3b2f25b7d8 in import_submodule (mod=0x189c03d0, subname=0x7fff9742ff46 "moose", fullname=0x7fff9742ff40 "moose.moose") at Python/import.c:2596 #18 0x00002b3b2f25ba52 in load_next (mod=0x189c03d0, altmod=0x189c03d0, p_name=<value optimized out>, buf=0x7fff9742ff40 "moose.moose", p_buflen=0x7fff97430f50) at Python/import.c:2416 #19 0x00002b3b2f25c062 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0x1899f290, level=1, locals=<value optimized out>) at Python/import.c:2137 #20 0x00002b3b2f25c66a in PyImport_ImportModuleLevel (name=0x189bfc54 "moose", globals=0x189f43c0, locals=<value optimized out>, fromlist=0x1899f290, level=1) at Python/import.c:2189 #21 0x00002b3b2f23a13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>, kwds=<value optimized out>) at Python/bltinmodule.c:49 #22 0x00002b3b2f19e7e3 in PyObject_Call (func=0x2b3b3002fdd0, arg=<value optimized out>, kw=<value optimized out>) at Objects/abstract.c:2529 #23 0x00002b3b2f23be97 in PyEval_CallObjectWithKeywords (func=0x2b3b3002fdd0, arg=0x2b3b300c8590, kw=<value optimized out>) at Python/ceval.c:3881 #24 0x00002b3b2f23ec81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2332 #25 0x00002b3b2f243515 in PyEval_EvalCodeEx (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3252 #26 0x00002b3b2f243652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>) at Python/ceval.c:666 ---Type <return> to continue, or q <return> to quit--- #27 0x00002b3b2f25a342 in PyImport_ExecCodeModuleEx (name=0x7fff97434580 "moose", co=0x2b3b300f0eb0, pathname=0x7fff97431340 "/home/astakhov/moose/moose/moose/python/moose/__init__.pyc") at Python/import.c:681 #28 0x00002b3b2f25a68e in load_source_module (name=0x7fff97434580 "moose", pathname=0x7fff97431340 "/home/astakhov/moose/moose/moose/python/moose/__init__.pyc", fp=<value optimized out>) at Python/import.c:1021 #29 0x00002b3b2f25b444 in load_package (name=0x7fff97434580 "moose", pathname=<value optimized out>) at Python/import.c:1077 #30 0x00002b3b2f25b7d8 in import_submodule (mod=0x2b3b2f4f48c0, subname=0x7fff97434580 "moose", fullname=0x7fff97434580 "moose") at Python/import.c:2596 #31 0x00002b3b2f25ba52 in load_next (mod=0x2b3b2f4f48c0, altmod=0x2b3b2f4f48c0, p_name=<value optimized out>, buf=0x7fff97434580 "moose", p_buflen=0x7fff97435590) at Python/import.c:2416 #32 0x00002b3b2f25c062 in import_module_level (name=0x0, globals=<value optimized out>, fromlist=0x2b3b2f4f48c0, level=-1, locals=<value optimized out>) at Python/import.c:2137 #33 0x00002b3b2f25c66a in PyImport_ImportModuleLevel (name=0x189bfc54 "moose", globals=0x1892ea00, locals=<value optimized out>, fromlist=0x2b3b2f4f48c0, level=-1) at Python/import.c:2189 #34 0x00002b3b2f23a13f in builtin___import__ (self=<value optimized out>, args=<value optimized out>, kwds=<value optimized out>) at Python/bltinmodule.c:49 #35 0x00002b3b2f19e7e3 in PyObject_Call (func=0x2b3b3002fdd0, arg=<value optimized out>, kw=<value optimized out>) at Objects/abstract.c:2529 #36 0x00002b3b2f23be97 in PyEval_CallObjectWithKeywords (func=0x2b3b3002fdd0, arg=0x2b3b300d8e68, kw=<value optimized out>) at Python/ceval.c:3881 #37 0x00002b3b2f23ec81 in PyEval_EvalFrameEx (f=<value optimized out>, throwflag=<value optimized out>) at Python/ceval.c:2332 #38 0x00002b3b2f243515 in PyEval_EvalCodeEx (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>, args=<value optimized out>, argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3252 #39 0x00002b3b2f243652 in PyEval_EvalCode (co=<value optimized out>, globals=<value optimized out>, locals=<value optimized out>) at Python/ceval.c:666 #40 0x00002b3b2f266b02 in run_mod (fp=<value optimized out>, filename=0x2b3b2f2adfff "<stdin>", flags=0x7fff97435ad0) at Python/pythonrun.c:1346 #41 PyRun_InteractiveOneFlags (fp=<value optimized out>, filename=0x2b3b2f2adfff "<stdin>", flags=0x7fff97435ad0) at Python/pythonrun.c:845 #42 0x00002b3b2f266d3e in PyRun_InteractiveLoopFlags (fp=0x344c1516a0, filename=0x2b3b2f2adfff "<stdin>", flags=0x7fff97435ad0) at Python/pythonrun.c:765 #43 0x00002b3b2f2672ec in PyRun_AnyFileExFlags (fp=0x344c1516a0, filename=0x2b3b2f2adfff "<stdin>", closeit=0, flags=0x7fff97435ad0) at Python/pythonrun.c:734 #44 0x00002b3b2f27944b in Py_Main (argc=<value optimized out>, argv=<value optimized out>) at Modules/main.c:599 #45 0x000000344be1d994 in __libc_start_main () from /lib64/libc.so.6 #46 0x0000000000400619 in _start () (gdb) |
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From: Subhasis R. <ray...@gm...> - 2013-03-16 03:59:52
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Most likely you have multiple installations of Python and the Python interpreter you are using is different from the version of python your modules are linked to. Searching the Internet shows this: http://mail.scipy.org/pipermail/scipy-dev/2008-January/008205.html and/or this: http://timhatch.com/ark/2008/08/07/py_initmodule4_64 might have solution to your problem. - Subha On Sat, Mar 16, 2013 at 3:23 AM, Vadim Astakhov <ast...@nc...>wrote: > I did that before import and it does not work. > Vadim > > > Kenneth Yoshimoto <ke...@sd...> wrote: > > > > >I think there is a bunch of extra python stuff available > >through > >module load python > > > >Give that a try. > > > >Kenneth > > > >On Fri, 15 Mar 2013, Vadim A wrote: > > > >> Date: Fri, 15 Mar 2013 13:24:45 -0700 > >> From: Vadim A <ast...@nc...> > >> To: Subhasis Ray <ray...@gm...> > >> Cc: Kenneth Yoshimoto <ke...@sd...>, > >> Subhashini Sivagnanam <siv...@sd...>, > >> Amitava Majumdar <maj...@sd...>, > >> "moo...@li..." > >> <moo...@li...> > >> Subject: Re: [moose-generic] MOOSE_installation_problem > >> > >> Also, I am getting error when I just importing MOOSE : > >> import moose > >> on node 0, numNodes = 1, numCores = 16, numComputeThreads = 16 > >> ImportError: numpy.core.multiarray failed to import > >> Traceback (most recent call last): > >> File "<stdin>", line 1, in <module> > >> File "/home/astakhov/moose/moose/moose/python/moose/__init__.py", line > >> 201, in <module> > >> from .moose import * > >> File "/home/astakhov/moose/moose/moose/python/moose/moose.py", line > 40, in > >> <module> > >> from . import _moose > >> ImportError: numpy.core.multiarray failed to import > >> > >> > >> > >> . Sorry for bothering but it seems that we are still missing > >> something. > >> > >> I exported PYTHONPATH and trying to run examples from Demo/snippets > >> > >> but none of them work for me and I am getting errors like this > >> > >> > >> Traceback (most recent call last): > >> > >> > >> File "./Demos/snippets/compartment_net.py", line 53, in <module> > >> from pylab import * > >> …... > >> import numpy as np > >> File "/home/diag/opt/python/lib64/python/numpy/__init__.py", line > >> 130, in <module> > >> import add_newdocs > >> File "/home/diag/opt/python/lib64/python/numpy/add_newdocs.py", line > >> 9, in <module> > >> from lib import add_newdoc > >> File "/home/diag/opt/python/lib64/python/numpy/lib/__init__.py", > >> line 4, in <module> > >> from type_check import * > >> File "/home/diag/opt/python/lib64/python/numpy/lib/type_check.py", > >> line 8, in <module> > >> import numpy.core.numeric as _nx > >> File "/home/diag/opt/python/lib64/python/numpy/core/__init__.py", > >> line 5, in <module> > >> import multiarray > >> > >> > >> ImportError: > >> /home/diag/opt/python/lib64/python/numpy/core/multiarray.so: undefined > >> symbol: Py_InitModule4 > >> > >> > >> > >> Do you know what we might need to adjust ? > >> > >> > >> Is there any other test examples which we can try ? > >> > >> Thanks a lot in advance for any advice. > >> > >> Vadim. > >> > >> > >> On Mar 12, 2013, at 8:22 PM, Subhasis Ray wrote: > >> > >> > >> > >> > >> On Wed, Mar 13, 2013 at 2:53 AM, Vadim A > >> <ast...@nc...> wrote: > >> You saying that I don't really need to do > >> "make install" ? > >> after " make BUILD=release USE_HDF5=0" > >> > >> return -> pymoose module built. > >> > >> > >> All I need to do just export PYTHONPATH, correct ? > >> > >> > >> Yes, that is all :) > >> > >> > >> > --------------------------------------------------------------------------- > >> --- > >> Everyone hates slow websites. So do we. > >> Make your web apps faster with AppDynamics > >> Download AppDynamics Lite for free today: > >> > http://p.sf.net/sfu/appdyn_d2d_mar_________________________________________ > >> ______ > >> moose-generic mailing list > >> moo...@li... > >> https://lists.sourceforge.net/lists/listinfo/moose-generic > >> > >> > >> > >> > |
