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From: Saeed S. <sa...@gn...> - 2014-05-03 22:03:04
|
Thank you. We just realized that it happened because our compiler was mpich2. By replacing it with OpenMPI everything seems to work. On 05/03/2014 12:40 AM, U.S.Bhalla wrote: > Dear Saeed, > My understanding is that the Open MPI implementation uses a > busy-loop to poll for MPI requests and as long as the process is running > it will utilize 100% cpu on all processors deployed to use MPI. > > Best, > Upi > > On Saturday 03 May 2014 03:53 AM, Saeed Shariati wrote: >> Dear Upi and Subhasis, >> >> Thank you. It was my mistake and I forgot that for using MPI, it >> should be compiled with BUILD=mpi or ompi flag. >> But, after executing "mpirun -np 1 python recurrentIntFire.py : -np >> 4 ../../../moose", all of the processors remains to work 100% busy, >> everlastingly. >> I reduced the model, but it still remains busy. >> >> Saeed >> >> On 05/02/2014 09:01 AM, U.S.Bhalla wrote: >>> Dear Saeed, >>> The following command runs a test integrate-and-fire network in >>> parallel on 6 nodes: >>> >>> mpirun -np 1 python recurrentIntFire.py : -np 5 ../../../moose >>> >>> The master node runs the version that talks to python, and the worker >>> nodes run the version without any python bindings because they receive >>> their instructions from the master node. >>> >>> This is run as Subha says, in the tests/python/mpi directory. >>> >>> The network has extensive communication between the 6 nodes. >>> >>> Do let me know if this works for you. >>> >>> Best, >>> Upi >>> >>> >>> On Friday 02 May 2014 02:34 AM, Saeed Shariati wrote: >>>> On 05/01/2014 02:14 AM, Subhasis Ray wrote: >>>>> On Wed, Apr 30, 2014 at 11:51 PM, Saeed <sa...@gn...> wrote: >>>>> >>>>>> It would be my great pleasure if you could tell me which kind of test >>>>>> cases you have used for testing the parallel execution. For example if >>>>>> one of the snippets are suitable for these test, would be great. Also, >>>>>> do you know any revision of the async13 which is working and suitable >>>>>> for parallel test? >>>>>> >>>>> Look inside tests/python/mpi. I have done this on a single host with a >>>>> multicore CPU. You may want to change the hostfile for your specific case. >>>>> Best, >>>>> Subhasis >>>>> ------------------------------------------------------------------------------ >>>>> >>>> Thank you Subhasis. Please tell me if I am wrong. These test has been >>>> made for testing functionality and performance of simultaneous >>>> independent processes and at this moment, there is no communication >>>> between these processes. Also there is no communication between python >>>> processes and the moose executable file. >>>> >>>> I am wondering what is the MPI architecture and how the GPU part can be >>>> compatible with it. If you can guide me to any documentation, I >>>> appreciate it. >>>> I have some questions about architectural compatibility that will ask >>>> them trough a different thread. >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get >>>> unparalleled scalability from the best Selenium testing platform available. >>>> Simple to use. Nothing to install. Get started now for free." >>>> http://p.sf.net/sfu/SauceLabs >>>> _______________________________________________ >>>> moose-devel mailing list >>>> moo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/moose-devel >>> ------------------------------------------------------------------------------ >>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >>> Instantly run your Selenium tests across 300+ browser/OS combos. Get >>> unparalleled scalability from the best Selenium testing platform available. >>> Simple to use. Nothing to install. Get started now for free." >>> http://p.sf.net/sfu/SauceLabs >>> _______________________________________________ >>> moose-devel mailing list >>> moo...@li... >>> https://lists.sourceforge.net/lists/listinfo/moose-devel >>> >>> >> ------------------------------------------------------------------------------ >> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >> Instantly run your Selenium tests across 300+ browser/OS combos. Get >> unparalleled scalability from the best Selenium testing platform available. >> Simple to use. Nothing to install. Get started now for free." >> http://p.sf.net/sfu/SauceLabs >> _______________________________________________ >> moose-devel mailing list >> moo...@li... >> https://lists.sourceforge.net/lists/listinfo/moose-devel > > ------------------------------------------------------------------------------ > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE > Instantly run your Selenium tests across 300+ browser/OS combos. Get > unparalleled scalability from the best Selenium testing platform available. > Simple to use. Nothing to install. Get started now for free." > http://p.sf.net/sfu/SauceLabs > _______________________________________________ > moose-devel mailing list > moo...@li... > https://lists.sourceforge.net/lists/listinfo/moose-devel > > |
|
From: Subhasis R. <ray...@gm...> - 2014-05-03 17:10:38
|
Dear Misha,
On Sat, May 3, 2014 at 9:15 PM, Misha Ahmadian <mis...@tt...>wrote:
> results, but the problem is the recurrentIntFire.py file. This file in the
> async13/tests/python/mpi could be running, but without any termination and
> real MPI working. we run this part as bellow:
>
> but still we cannot get any result from this model. Would you please let me
> know, if we can have the correct recurrentIntFire.py, to produce our
> results. It would be highly appreciated if you help us as soon as possible.
>
This seems to be system dependent issue and I am also encountering it while
others are not. From my notes I see that I had personally tested the mpi
version with recurrentIntFire.py on 24-01-2014 (that should be when
test/mpi/benchmark.py was also committed). Since something may have changed
in between, can you try checking out a revision from around that date and
see if that works? By the way, the benchmark is done when you see a
"t={some time}" message - that is the time it took to run the simulation.
If it is stuck after that, that is the command prompt of MOOSE expecting
user input - I cannot tell right away why it is acting like that, but we'll
try to address that ASAP. In the mean time also note that benchmark.py is
supposed to benchmark any pymoose script on a multicore machine and you can
imitate it to get a multi-node benchmark.
Best,
Subhasis
|
|
From: Misha A. <mis...@tt...> - 2014-05-03 15:46:09
|
Dear Sir/Madam, I'm Grad Student in Computer Science at Texas Tech University. I also working with Mr. Saeed Shariati (sa...@gn...), to profiling the the performance of the Moose on some Neuroscience models. Actually we have been working on this application about one and half month, and this Monday (May 5th) is our due date to give out the paper and presentation. We're working on this application after midnight for several days, but still we couldn't get any appropriate result. After several contact with you through the email, Saeed led us to your SVN repository to check out the project and working on async13 branch. Now we can implement some MPI profiling tool on Moose to get MPI profiling results, but the problem is the recurrentIntFire.py file. This file in the async13/tests/python/mpi could be running, but without any termination and real MPI working. we run this part as bellow: but still we cannot get any result from this model. Would you please let me know, if we can have the correct recurrentIntFire.py, to produce our results. It would be highly appreciated if you help us as soon as possible. Thanks, Best Regards, -- *Misha Ahmadian* Computer Science MS Program *Texas Tech University* http://www.ttu.edu +1 (516) 817-6335 | Lubbock, TX, US |
|
From: U.S.Bhalla <bh...@nc...> - 2014-05-03 03:40:49
|
Dear Saeed,
My understanding is that the Open MPI implementation uses a
busy-loop to poll for MPI requests and as long as the process is running
it will utilize 100% cpu on all processors deployed to use MPI.
Best,
Upi
On Saturday 03 May 2014 03:53 AM, Saeed Shariati wrote:
> Dear Upi and Subhasis,
>
> Thank you. It was my mistake and I forgot that for using MPI, it
> should be compiled with BUILD=mpi or ompi flag.
> But, after executing "mpirun -np 1 python recurrentIntFire.py : -np
> 4 ../../../moose", all of the processors remains to work 100% busy,
> everlastingly.
> I reduced the model, but it still remains busy.
>
> Saeed
>
> On 05/02/2014 09:01 AM, U.S.Bhalla wrote:
>> Dear Saeed,
>> The following command runs a test integrate-and-fire network in
>> parallel on 6 nodes:
>>
>> mpirun -np 1 python recurrentIntFire.py : -np 5 ../../../moose
>>
>> The master node runs the version that talks to python, and the worker
>> nodes run the version without any python bindings because they receive
>> their instructions from the master node.
>>
>> This is run as Subha says, in the tests/python/mpi directory.
>>
>> The network has extensive communication between the 6 nodes.
>>
>> Do let me know if this works for you.
>>
>> Best,
>> Upi
>>
>>
>> On Friday 02 May 2014 02:34 AM, Saeed Shariati wrote:
>>> On 05/01/2014 02:14 AM, Subhasis Ray wrote:
>>>> On Wed, Apr 30, 2014 at 11:51 PM, Saeed <sa...@gn...> wrote:
>>>>
>>>>> It would be my great pleasure if you could tell me which kind of test
>>>>> cases you have used for testing the parallel execution. For example if
>>>>> one of the snippets are suitable for these test, would be great. Also,
>>>>> do you know any revision of the async13 which is working and suitable
>>>>> for parallel test?
>>>>>
>>>> Look inside tests/python/mpi. I have done this on a single host with a
>>>> multicore CPU. You may want to change the hostfile for your specific case.
>>>> Best,
>>>> Subhasis
>>>> ------------------------------------------------------------------------------
>>>>
>>> Thank you Subhasis. Please tell me if I am wrong. These test has been
>>> made for testing functionality and performance of simultaneous
>>> independent processes and at this moment, there is no communication
>>> between these processes. Also there is no communication between python
>>> processes and the moose executable file.
>>>
>>> I am wondering what is the MPI architecture and how the GPU part can be
>>> compatible with it. If you can guide me to any documentation, I
>>> appreciate it.
>>> I have some questions about architectural compatibility that will ask
>>> them trough a different thread.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>> unparalleled scalability from the best Selenium testing platform available.
>>> Simple to use. Nothing to install. Get started now for free."
>>> http://p.sf.net/sfu/SauceLabs
>>> _______________________________________________
>>> moose-devel mailing list
>>> moo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>> unparalleled scalability from the best Selenium testing platform available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> moose-devel mailing list
>> moo...@li...
>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>>
>>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos. Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> moose-devel mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-devel
|
|
From: Saeed S. <sa...@gn...> - 2014-05-02 22:24:16
|
Dear Upi and Subhasis,
Thank you. It was my mistake and I forgot that for using MPI, it
should be compiled with BUILD=mpi or ompi flag.
But, after executing "mpirun -np 1 python recurrentIntFire.py : -np
4 ../../../moose", all of the processors remains to work 100% busy,
everlastingly.
I reduced the model, but it still remains busy.
Saeed
On 05/02/2014 09:01 AM, U.S.Bhalla wrote:
> Dear Saeed,
> The following command runs a test integrate-and-fire network in
> parallel on 6 nodes:
>
> mpirun -np 1 python recurrentIntFire.py : -np 5 ../../../moose
>
> The master node runs the version that talks to python, and the worker
> nodes run the version without any python bindings because they receive
> their instructions from the master node.
>
> This is run as Subha says, in the tests/python/mpi directory.
>
> The network has extensive communication between the 6 nodes.
>
> Do let me know if this works for you.
>
> Best,
> Upi
>
>
> On Friday 02 May 2014 02:34 AM, Saeed Shariati wrote:
>> On 05/01/2014 02:14 AM, Subhasis Ray wrote:
>>> On Wed, Apr 30, 2014 at 11:51 PM, Saeed <sa...@gn...> wrote:
>>>
>>>> It would be my great pleasure if you could tell me which kind of test
>>>> cases you have used for testing the parallel execution. For example if
>>>> one of the snippets are suitable for these test, would be great. Also,
>>>> do you know any revision of the async13 which is working and suitable
>>>> for parallel test?
>>>>
>>> Look inside tests/python/mpi. I have done this on a single host with a
>>> multicore CPU. You may want to change the hostfile for your specific case.
>>> Best,
>>> Subhasis
>>> ------------------------------------------------------------------------------
>>>
>> Thank you Subhasis. Please tell me if I am wrong. These test has been
>> made for testing functionality and performance of simultaneous
>> independent processes and at this moment, there is no communication
>> between these processes. Also there is no communication between python
>> processes and the moose executable file.
>>
>> I am wondering what is the MPI architecture and how the GPU part can be
>> compatible with it. If you can guide me to any documentation, I
>> appreciate it.
>> I have some questions about architectural compatibility that will ask
>> them trough a different thread.
>>
>>
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>> unparalleled scalability from the best Selenium testing platform available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> moose-devel mailing list
>> moo...@li...
>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos. Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> moose-devel mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-devel
>
>
|
|
From: U.S.Bhalla <bh...@nc...> - 2014-05-02 12:01:23
|
Dear Saeed,
The following command runs a test integrate-and-fire network in
parallel on 6 nodes:
mpirun -np 1 python recurrentIntFire.py : -np 5 ../../../moose
The master node runs the version that talks to python, and the worker
nodes run the version without any python bindings because they receive
their instructions from the master node.
This is run as Subha says, in the tests/python/mpi directory.
The network has extensive communication between the 6 nodes.
Do let me know if this works for you.
Best,
Upi
On Friday 02 May 2014 02:34 AM, Saeed Shariati wrote:
> On 05/01/2014 02:14 AM, Subhasis Ray wrote:
>> On Wed, Apr 30, 2014 at 11:51 PM, Saeed <sa...@gn...> wrote:
>>
>>> It would be my great pleasure if you could tell me which kind of test
>>> cases you have used for testing the parallel execution. For example if
>>> one of the snippets are suitable for these test, would be great. Also,
>>> do you know any revision of the async13 which is working and suitable
>>> for parallel test?
>>>
>> Look inside tests/python/mpi. I have done this on a single host with a
>> multicore CPU. You may want to change the hostfile for your specific case.
>> Best,
>> Subhasis
>> ------------------------------------------------------------------------------
>>
> Thank you Subhasis. Please tell me if I am wrong. These test has been
> made for testing functionality and performance of simultaneous
> independent processes and at this moment, there is no communication
> between these processes. Also there is no communication between python
> processes and the moose executable file.
>
> I am wondering what is the MPI architecture and how the GPU part can be
> compatible with it. If you can guide me to any documentation, I
> appreciate it.
> I have some questions about architectural compatibility that will ask
> them trough a different thread.
>
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos. Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> moose-devel mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-devel
|
|
From: Subhasis R. <ray...@gm...> - 2014-05-02 11:58:31
|
On Fri, May 2, 2014 at 2:34 AM, Saeed Shariati <sa...@gn...> wrote: > > On 05/01/2014 02:14 AM, Subhasis Ray wrote: > > On Wed, Apr 30, 2014 at 11:51 PM, Saeed <sa...@gn...> wrote: > > > >> It would be my great pleasure if you could tell me which kind of test > >> cases you have used for testing the parallel execution. For example if > >> one of the snippets are suitable for these test, would be great. Also, > >> do you know any revision of the async13 which is working and suitable > >> for parallel test? > >> > > Look inside tests/python/mpi. I have done this on a single host with a > > multicore CPU. You may want to change the hostfile for your specific > case. > > Best, > > Subhasis > > > ------------------------------------------------------------------------------ > > > Thank you Subhasis. Please tell me if I am wrong. These test has been > made for testing functionality and performance of simultaneous > independent processes and at this moment, there is no communication > between these processes. Also there is no communication between python > processes and the moose executable file. > There IS communication between the different processes (including Python which is on the master node) via mpi and as far as I remember, it showed decent scaling with number of processes in that test. Best, - Subhasis ( ʃʊbʱaːʃɪʃ ) |
|
From: Saeed S. <sa...@gn...> - 2014-05-01 21:05:50
|
On 05/01/2014 02:14 AM, Subhasis Ray wrote: > On Wed, Apr 30, 2014 at 11:51 PM, Saeed <sa...@gn...> wrote: > >> It would be my great pleasure if you could tell me which kind of test >> cases you have used for testing the parallel execution. For example if >> one of the snippets are suitable for these test, would be great. Also, >> do you know any revision of the async13 which is working and suitable >> for parallel test? >> > Look inside tests/python/mpi. I have done this on a single host with a > multicore CPU. You may want to change the hostfile for your specific case. > Best, > Subhasis > ------------------------------------------------------------------------------ > Thank you Subhasis. Please tell me if I am wrong. These test has been made for testing functionality and performance of simultaneous independent processes and at this moment, there is no communication between these processes. Also there is no communication between python processes and the moose executable file. I am wondering what is the MPI architecture and how the GPU part can be compatible with it. If you can guide me to any documentation, I appreciate it. I have some questions about architectural compatibility that will ask them trough a different thread. |
|
From: Saeed S. <sa...@gn...> - 2014-05-01 19:16:49
|
Hi
It's very interesting! I did not know about Travis-CI.
Thank yoy.
BTW, Cmake in the 5338 works perfectly.
Saeed
On 05/01/2014 04:04 PM, Dilawar Singh wrote:
> Hi Saeed,
>
> Removed this error also.
>
> Also, I just made an mirror of async13 branch on github and Travis-CI for
> checking the build.
>
> http://github.com/dilawar/moose
>
> The latest commit is passing the build on Travis-CI. If a commit gets
> successfully compiled, one can see a "build/passing" image on project
> README file on github. This will help you find the stable commit on the
> branch.
>
> Commit r5340 is current stable revision.
>
> Thanks again for testing the cmake based build.
>
> Dilawar
>
> On Thu, May 01, 2014 at 03:25:18PM -0300, Saeed Shariati wrote:
>> Cmake in revision 6339 produces error which is attach.
>> My system is Ubuntu 12.04
>>
>> On 05/01/2014 03:02 PM, Dilawar Singh wrote:
>>> Thanks a lot Saeed,
>>>
>>> Libxml2 turns out to be unnecessary. It has been removed now from cmake.
>>>
>>> Removed some of the compiler flags specific to gcc-4.8. This should compile
>>> now. Moose also compiles with clang++.
>>>
>>> A couple to tests might fail on default tests enabled in cmake.
>>>
>>> Dilawar
>>>
>>> On Thu, May 01, 2014 at 11:36:56AM -0300, Saeed Shariati wrote:
>>>> Thank you Dilawar.
>>>>
>>>> The CMake build system needs also libxml2-dev package to be installed
>>>> and after executing, produce the outputs which is attached to this
>>>> email.
>>>>
>>>> On 05/01/2014 01:35 AM, Dilawar Singh wrote:
>>>>> Hi Saeed,
>>>>>
>>>>> Fixed. Added missing files.
>>>>>
>>>>> Also there is a cmake based build system. I'd be happy if you can test it on
>>>>> your system and let me know how it went. You need to install cmake and do the
>>>>> following in async branch.
>>>>>
>>>>> $ cd buildMooseUsingCmake
>>>>> $ ./build_me.sh
>>>>>
>>>>> Dilawar
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>>>> unparalleled scalability from the best Selenium testing platform available.
>>>>> Simple to use. Nothing to install. Get started now for free."
>>>>> http://p.sf.net/sfu/SauceLabs
>>>>> _______________________________________________
>>>>> moose-devel mailing list
>>>>> moo...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>>>>>
>>>>>
>>>> Removing any accidentally created cmake files.
>>>> -- The C compiler identification is GNU
>>>> -- The CXX compiler identification is GNU
>>>> -- Check for working C compiler: /usr/bin/gcc
>>>> -- Check for working C compiler: /usr/bin/gcc -- works
>>>> -- Detecting C compiler ABI info
>>>> -- Detecting C compiler ABI info - done
>>>> -- Check for working CXX compiler: /usr/bin/c++
>>>> -- Check for working CXX compiler: /usr/bin/c++ -- works
>>>> -- Detecting CXX compiler ABI info
>>>> -- Detecting CXX compiler ABI info - done
>>>> /usr
>>>> -- Using GSL from /usr
>>>> ++ Unit testing enabled.
>>>> ++ Verbosity of output is 1
>>>> -- Found: /usr/lib/libhdf5.so
>>>> -- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
>>>> --
>>>> -- Could NOT find LIBSBML (missing: LIBSBML_LIBRARY LIBSBML_INCLUDE_DIR)
>>>> -- Found Curses: /usr/lib/x86_64-linux-gnu/libcurses.so
>>>> -- Could NOT find Readline (missing: Readline_INCLUDE_DIR)
>>>> -- Found LibXML2: /usr/lib/x86_64-linux-gnu/libxml2.so
>>>> -- Found PythonInterp: /usr/bin/python (found version "2.7.3")
>>>> -- Found NumPy: version "1.6.1" /usr/lib/python2.7/dist-packages/numpy/core/include
>>>> -- Found PythonLibs: optimized;/usr/lib/libpython2.7.so.1;debug;/usr/lib/libpython2.7.so.1 (found version "2.7")
>>>> ++ PYTHONPATH is set to /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/python
>>>> -- Configuring done
>>>> -- Generating done
>>>> -- Build files have been written to: /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/buildMooseUsingCmake
>>>> Scanning dependencies of target utility
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>>>> [ 10%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHGate.cpp.o
>>>> [ 10%] Building CXX object biophysics/CMakeFiles/biophysics.dir/CaConc.cpp.o
>>>> [ 11%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Neuron.cpp.o
>>>> [ 11%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ReadCell.cpp.o
>>>> [ 12%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChanBase.cpp.o
>>>> [ 13%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChan.cpp.o
>>>> [ 13%] Building CXX object biophysics/CMakeFiles/biophysics.dir/testBiophysics.cpp.o
>>>> [ 14%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IzhikevichNrn.cpp.o
>>>> Linking CXX static library libbiophysics.a
>>>> [ 14%] Built target biophysics
>>>> Scanning dependencies of target basecode
>>>> [ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/consts.cpp.o
>>>> [ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/Element.cpp.o
>>>> [ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/DataElement.cpp.o
>>>> [ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/GlobalDataElement.cpp.o
>>>> [ 17%] Building CXX object basecode/CMakeFiles/basecode.dir/LocalDataElement.cpp.o
>>>> [ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/Eref.cpp.o
>>>> [ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/Finfo.cpp.o
>>>> [ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/DestFinfo.cpp.o
>>>> [ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o
>>>> In file included from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/header.h:17:0,
>>>> from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:10:
>>>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h: In function ???std::string mapToString(const std::map<A, B>&, bool) [with A = std::basic_string<char>, B = Cinfo*, std::string = std::basic_string<char>]???:
>>>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:208:55: instantiated from here
>>>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:110:18: error: comparison between signed and unsigned integer expressions [-Werror=sign-compare]
>>>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:112:9: error: comparison between signed and unsigned integer expressions [-Werror=sign-compare]
>>>> At global scope:
>>>> cc1plus: error: unrecognized command line option "-Wno-unused-private-field" [-Werror]
>>>> cc1plus: error: unrecognized command line option "-Wno-return-type-c-linkage" [-Werror]
>>>> cc1plus: all warnings being treated as errors
>>>> make[2]: *** [basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o] Error 1
>>>> make[1]: *** [basecode/CMakeFiles/basecode.dir/all] Error 2
>>>> make: *** [all] Error 2
>>>> ------------------------------------------------------------------------------
>>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>>> unparalleled scalability from the best Selenium testing platform available.
>>>> Simple to use. Nothing to install. Get started now for free."
>>>> http://p.sf.net/sfu/SauceLabs
>>>> _______________________________________________
>>>> moose-devel mailing list
>>>> moo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>>> ------------------------------------------------------------------------------
>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>> unparalleled scalability from the best Selenium testing platform available.
>>> Simple to use. Nothing to install. Get started now for free."
>>> http://p.sf.net/sfu/SauceLabs
>>> _______________________________________________
>>> moose-devel mailing list
>>> moo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>>>
>>>
>> Removing any accidentally created cmake files.
>> -- The C compiler identification is GNU
>> -- The CXX compiler identification is GNU
>> -- Check for working C compiler: /usr/bin/gcc
>> -- Check for working C compiler: /usr/bin/gcc -- works
>> -- Detecting C compiler ABI info
>> -- Detecting C compiler ABI info - done
>> -- Check for working CXX compiler: /usr/bin/c++
>> -- Check for working CXX compiler: /usr/bin/c++ -- works
>> -- Detecting CXX compiler ABI info
>> -- Detecting CXX compiler ABI info - done
>> /usr
>> -- Using GSL from /usr
>> ++ Unit testing enabled.
>> ++ Verbosity of output is 1
>> -- Found: /usr/lib/libhdf5.so
>> -- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
>> --
>> -- Could NOT find LIBSBML (missing: LIBSBML_LIBRARY LIBSBML_INCLUDE_DIR)
>> -- Found Curses: /usr/lib/x86_64-linux-gnu/libcurses.so
>> -- Could NOT find Readline (missing: Readline_INCLUDE_DIR)
>> -- Found PythonInterp: /usr/bin/python (found version "2.7.3")
>> -- Found NumPy: version "1.6.1" /usr/lib/python2.7/dist-packages/numpy/core/include
>> -- Found PythonLibs: optimized;/usr/lib/libpython2.7.so.1;debug;/usr/lib/libpython2.7.so.1 (found version "2.7")
>> ++ PYTHONPATH is set to /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/python
>> -- Configuring done
>> -- Generating done
>> -- Build files have been written to: /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/buildMooseUsingCmake
>> Scanning dependencies of target debug_print
>> [ 0%] Building CXX object external/debug/CMakeFiles/debug_print.dir/print_function.cc.o
>> Linking CXX static library libdebug_print.a
>> [ 0%] Built target debug_print
>> Scanning dependencies of target biophysics
>> [ 0%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeRingBuffer.cpp.o
>> [ 1%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynHandler.cpp.o
>> [ 2%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IntFire.cpp.o
>> [ 2%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Synapse.cpp.o
>> [ 3%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeGen.cpp.o
>> [ 3%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Compartment.cpp.o
>> [ 4%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SymCompartment.cpp.o
>> [ 4%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ChanBase.cpp.o
>> [ 5%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHChannel.cpp.o
>> [ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHGate.cpp.o
>> [ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/CaConc.cpp.o
>> [ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Neuron.cpp.o
>> [ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ReadCell.cpp.o
>> [ 8%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChanBase.cpp.o
>> [ 9%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChan.cpp.o
>> [ 9%] Building CXX object biophysics/CMakeFiles/biophysics.dir/testBiophysics.cpp.o
>> [ 10%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IzhikevichNrn.cpp.o
>> Linking CXX static library libbiophysics.a
>> [ 10%] Built target biophysics
>> Scanning dependencies of target basecode
>> [ 11%] Building CXX object basecode/CMakeFiles/basecode.dir/consts.cpp.o
>> [ 11%] Building CXX object basecode/CMakeFiles/basecode.dir/Element.cpp.o
>> [ 12%] Building CXX object basecode/CMakeFiles/basecode.dir/DataElement.cpp.o
>> [ 12%] Building CXX object basecode/CMakeFiles/basecode.dir/GlobalDataElement.cpp.o
>> [ 13%] Building CXX object basecode/CMakeFiles/basecode.dir/LocalDataElement.cpp.o
>> [ 14%] Building CXX object basecode/CMakeFiles/basecode.dir/Eref.cpp.o
>> [ 14%] Building CXX object basecode/CMakeFiles/basecode.dir/Finfo.cpp.o
>> [ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/DestFinfo.cpp.o
>> [ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o
>> In file included from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/header.h:17:0,
>> from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:10:
>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h: In function ???std::string mapToString(const std::map<A, B>&, bool) [with A = std::basic_string<char>, B = Cinfo*, std::string = std::basic_string<char>]???:
>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:208:55: instantiated from here
>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:110:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
>> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:112:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
>> At global scope:
>> cc1plus: warning: unrecognized command line option "-Wno-unused-private-field" [enabled by default]
>> cc1plus: warning: unrecognized command line option "-Wno-return-type-c-linkage" [enabled by default]
>> [ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/SrcFinfo.cpp.o
>> [ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/ValueFinfo.cpp.o
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>> [ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/FieldElement.cpp.o
>> [ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/Id.cpp.o
>> [ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/PrepackedBuffer.cpp.o
>> [ 20%] Building CXX object basecode/CMakeFiles/basecode.dir/ObjId.cpp.o
>> [ 21%] Building CXX object basecode/CMakeFiles/basecode.dir/global.cpp.o
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>> [ 22%] Building CXX object basecode/CMakeFiles/basecode.dir/OpFuncBase.cpp.o
>> [ 22%] Building CXX object basecode/CMakeFiles/basecode.dir/EpFunc.cpp.o
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>> [ 24%] Building CXX object basecode/CMakeFiles/basecode.dir/doubleEq.cpp.o
>> [ 25%] Building CXX object basecode/CMakeFiles/basecode.dir/testAsync.cpp.o
>> Linking CXX static library libbasecode.a
>> [ 25%] Built target basecode
>> Scanning dependencies of target kinetics
>> [ 26%] Building CXX object kinetics/CMakeFiles/kinetics.dir/PoolBase.cpp.o
>> [ 26%] Building CXX object kinetics/CMakeFiles/kinetics.dir/Pool.cpp.o
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>> [ 28%] Building CXX object kinetics/CMakeFiles/kinetics.dir/FuncPool.cpp.o
>> [ 28%] Building CXX object kinetics/CMakeFiles/kinetics.dir/ReacBase.cpp.o
>> [ 29%] Building CXX object kinetics/CMakeFiles/kinetics.dir/Reac.cpp.o
>> [ 29%] Building CXX object kinetics/CMakeFiles/kinetics.dir/EnzBase.cpp.o
>> [ 30%] Building CXX object kinetics/CMakeFiles/kinetics.dir/CplxEnzBase.cpp.o
>> [ 30%] Building CXX object kinetics/CMakeFiles/kinetics.dir/Enz.cpp.o
>> [ 31%] Building CXX object kinetics/CMakeFiles/kinetics.dir/MMenz.cpp.o
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>> [ 32%] Building CXX object kinetics/CMakeFiles/kinetics.dir/ReadKkit.cpp.o
>> [ 33%] Building CXX object kinetics/CMakeFiles/kinetics.dir/WriteKkit.cpp.o
>> [ 33%] Building CXX object kinetics/CMakeFiles/kinetics.dir/ReadCspace.cpp.o
>> [ 34%] Building CXX object kinetics/CMakeFiles/kinetics.dir/SumTotalTerm.cpp.o
>> [ 35%] Building CXX object kinetics/CMakeFiles/kinetics.dir/MathFuncTerm.cpp.o
>> [ 35%] Building CXX object kinetics/CMakeFiles/kinetics.dir/FuncBase.cpp.o
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>> [ 36%] Building CXX object kinetics/CMakeFiles/kinetics.dir/SumFunc.cpp.o
>> [ 37%] Building CXX object kinetics/CMakeFiles/kinetics.dir/lookupVolumeFromMesh.cpp.o
>> [ 37%] Building CXX object kinetics/CMakeFiles/kinetics.dir/testKinetics.cpp.o
>> Linking CXX static library libkinetics.a
>> [ 37%] Built target kinetics
>> Scanning dependencies of target randnum
>> [ 38%] Building CXX object randnum/CMakeFiles/randnum.dir/mt19937ar.cpp.o
>> Linking CXX static library librandnum.a
>> [ 38%] Built target randnum
>> Scanning dependencies of target msg
>> [ 39%] Building CXX object msg/CMakeFiles/msg.dir/Msg.cpp.o
>> [ 39%] Building CXX object msg/CMakeFiles/msg.dir/DiagonalMsg.cpp.o
>> [ 40%] Building CXX object msg/CMakeFiles/msg.dir/OneToAllMsg.cpp.o
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>> Linking CXX static library libmsg.a
>> [ 43%] Built target msg
>> Scanning dependencies of target utility
>> [ 44%] Building CXX object utility/CMakeFiles/utility.dir/strutil.cpp.o
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>> [ 46%] Building CXX object utility/CMakeFiles/utility.dir/Annotator.cpp.o
>> [ 47%] Building CXX object utility/CMakeFiles/utility.dir/Vec.cpp.o
>> Linking CXX static library libutility.a
>> [ 47%] Built target utility
>> Scanning dependencies of target moosepython
>> [ 48%] Building CXX object pymoose/CMakeFiles/moosepython.dir/vec.cpp.o
>> [ 48%] Building CXX object pymoose/CMakeFiles/moosepython.dir/mfield.cpp.o
>> [ 49%] Building CXX object pymoose/CMakeFiles/moosepython.dir/pymooseinit.cpp.o
>> [ 50%] Building CXX object pymoose/CMakeFiles/moosepython.dir/melement.cpp.o
>> [ 50%] Building CXX object pymoose/CMakeFiles/moosepython.dir/test_moosemodule.cpp.o
>> In file included from /usr/include/python2.7/Python.h:8:0,
>> from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/pymoose/test_moosemodule.cpp:49:
>> /usr/include/python2.7/pyconfig.h:1161:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default]
>> /usr/include/features.h:164:0: note: this is the location of the previous definition
>> /usr/include/python2.7/pyconfig.h:1183:0: warning: "_XOPEN_SOURCE" redefined [enabled by default]
>> /usr/include/features.h:166:0: note: this is the location of the previous definition
>> cc1plus: warning: unrecognized command line option "-Wno-unused-private-field" [enabled by default]
>> cc1plus: warning: unrecognized command line option "-Wno-return-type-c-linkage" [enabled by default]
>> Linking CXX static library libmoosepython.a
>> [ 50%] Built target moosepython
>> Scanning dependencies of target shell
>> [ 50%] Building CXX object shell/CMakeFiles/shell.dir/Shell.cpp.o
>> [ 51%] Building CXX object shell/CMakeFiles/shell.dir/ShellCopy.cpp.o
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>> [ 52%] Building CXX object shell/CMakeFiles/shell.dir/LoadModels.cpp.o
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>> [ 54%] Building CXX object shell/CMakeFiles/shell.dir/Wildcard.cpp.o
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>> Linking CXX static library libshell.a
>> [ 54%] Built target shell
>> Scanning dependencies of target scheduling
>> [ 54%] Building CXX object scheduling/CMakeFiles/scheduling.dir/testScheduling.cpp.o
>> [ 55%] Building CXX object scheduling/CMakeFiles/scheduling.dir/Clock.cpp.o
>> Linking CXX static library libscheduling.a
>> [ 55%] Built target scheduling
>> Scanning dependencies of target moose_builtins
>> [ 55%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Arith.cpp.o
>> [ 56%] Building CXX object builtins/CMakeFiles/moose_builtins.dir/Group.cpp.o
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>> Linking CXX static library libmoose_builtins.a
>> [ 62%] Built target moose_builtins
>> Scanning dependencies of target muparser
>> [ 62%] Building CXX object external/muparser/CMakeFiles/muparser.dir/muParser.cpp.o
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>> Linking CXX static library libmuparser.a
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>> Scanning dependencies of target mesh
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>> Linking CXX static library libdiffusion.a
>> [ 94%] Built target diffusion
>> Scanning dependencies of target device
>> [ 95%] Building CXX object device/CMakeFiles/device.dir/PulseGen.cpp.o
>> [ 96%] Building CXX object device/CMakeFiles/device.dir/DiffAmp.cpp.o
>> [ 96%] Building CXX object device/CMakeFiles/device.dir/PIDController.cpp.o
>> [ 97%] Building CXX object device/CMakeFiles/device.dir/RC.cpp.o
>> Linking CXX static library libdevice.a
>> [ 97%] Built target device
>> Scanning dependencies of target benchmarks
>> [ 97%] Building CXX object benchmarks/CMakeFiles/benchmarks.dir/benchmarks.cpp.o
>> [ 98%] Building CXX object benchmarks/CMakeFiles/benchmarks.dir/kineticMarks.cpp.o
>> Linking CXX static library libbenchmarks.a
>> [ 98%] Built target benchmarks
>> Scanning dependencies of target _moose
>> [ 98%] Building CXX object CMakeFiles/_moose.dir/pymoose/moosemodule.cpp.o
>> Linking CXX shared library ../python/moose/_moose.so
>> /usr/bin/ld: pymoose/libmoosepython.a(vec.cpp.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
>> pymoose/libmoosepython.a(vec.cpp.o): could not read symbols: Bad value
>> collect2: ld returned 1 exit status
>> make[2]: *** [../python/moose/_moose.so] Error 1
>> make[1]: *** [CMakeFiles/_moose.dir/all] Error 2
>> make: *** [all] Error 2
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>> unparalleled scalability from the best Selenium testing platform available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> moose-devel mailing list
>> moo...@li...
>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos. Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> moose-devel mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-devel
>
>
|
|
From: Dilawar S. <dil...@nc...> - 2014-05-01 19:05:55
|
Hi Saeed,
Removed this error also.
Also, I just made an mirror of async13 branch on github and Travis-CI for
checking the build.
http://github.com/dilawar/moose
The latest commit is passing the build on Travis-CI. If a commit gets
successfully compiled, one can see a "build/passing" image on project
README file on github. This will help you find the stable commit on the
branch.
Commit r5340 is current stable revision.
Thanks again for testing the cmake based build.
Dilawar
On Thu, May 01, 2014 at 03:25:18PM -0300, Saeed Shariati wrote:
>Cmake in revision 6339 produces error which is attach.
>My system is Ubuntu 12.04
>
>On 05/01/2014 03:02 PM, Dilawar Singh wrote:
>>Thanks a lot Saeed,
>>
>> Libxml2 turns out to be unnecessary. It has been removed now from cmake.
>>
>> Removed some of the compiler flags specific to gcc-4.8. This should compile
>> now. Moose also compiles with clang++.
>>
>> A couple to tests might fail on default tests enabled in cmake.
>>
>>Dilawar
>>
>>On Thu, May 01, 2014 at 11:36:56AM -0300, Saeed Shariati wrote:
>>>Thank you Dilawar.
>>>
>>>The CMake build system needs also libxml2-dev package to be installed
>>>and after executing, produce the outputs which is attached to this
>>>email.
>>>
>>>On 05/01/2014 01:35 AM, Dilawar Singh wrote:
>>>>Hi Saeed,
>>>>
>>>>Fixed. Added missing files.
>>>>
>>>>Also there is a cmake based build system. I'd be happy if you can test it on
>>>>your system and let me know how it went. You need to install cmake and do the
>>>>following in async branch.
>>>>
>>>> $ cd buildMooseUsingCmake
>>>> $ ./build_me.sh
>>>>
>>>>Dilawar
>>>>
>>>>
>>>>------------------------------------------------------------------------------
>>>>"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>>>Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>>>unparalleled scalability from the best Selenium testing platform available.
>>>>Simple to use. Nothing to install. Get started now for free."
>>>>http://p.sf.net/sfu/SauceLabs
>>>>_______________________________________________
>>>>moose-devel mailing list
>>>>moo...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/moose-devel
>>>>
>>>>
>>>Removing any accidentally created cmake files.
>>>-- The C compiler identification is GNU
>>>-- The CXX compiler identification is GNU
>>>-- Check for working C compiler: /usr/bin/gcc
>>>-- Check for working C compiler: /usr/bin/gcc -- works
>>>-- Detecting C compiler ABI info
>>>-- Detecting C compiler ABI info - done
>>>-- Check for working CXX compiler: /usr/bin/c++
>>>-- Check for working CXX compiler: /usr/bin/c++ -- works
>>>-- Detecting CXX compiler ABI info
>>>-- Detecting CXX compiler ABI info - done
>>>/usr
>>>-- Using GSL from /usr
>>>++ Unit testing enabled.
>>>++ Verbosity of output is 1
>>>-- Found: /usr/lib/libhdf5.so
>>>-- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
>>>--
>>>-- Could NOT find LIBSBML (missing: LIBSBML_LIBRARY LIBSBML_INCLUDE_DIR)
>>>-- Found Curses: /usr/lib/x86_64-linux-gnu/libcurses.so
>>>-- Could NOT find Readline (missing: Readline_INCLUDE_DIR)
>>>-- Found LibXML2: /usr/lib/x86_64-linux-gnu/libxml2.so
>>>-- Found PythonInterp: /usr/bin/python (found version "2.7.3")
>>>-- Found NumPy: version "1.6.1" /usr/lib/python2.7/dist-packages/numpy/core/include
>>>-- Found PythonLibs: optimized;/usr/lib/libpython2.7.so.1;debug;/usr/lib/libpython2.7.so.1 (found version "2.7")
>>>++ PYTHONPATH is set to /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/python
>>>-- Configuring done
>>>-- Generating done
>>>-- Build files have been written to: /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/buildMooseUsingCmake
>>>Scanning dependencies of target utility
>>>[ 1%] Building CXX object utility/CMakeFiles/utility.dir/strutil.cpp.o
>>>[ 1%] Building CXX object utility/CMakeFiles/utility.dir/types.cpp.o
>>>[ 2%] Building CXX object utility/CMakeFiles/utility.dir/setupenv.cpp.o
>>>[ 2%] Building CXX object utility/CMakeFiles/utility.dir/numutil.cpp.o
>>>[ 3%] Building CXX object utility/CMakeFiles/utility.dir/Annotator.cpp.o
>>>[ 4%] Building CXX object utility/CMakeFiles/utility.dir/Vec.cpp.o
>>>Linking CXX static library libutility.a
>>>[ 4%] Built target utility
>>>Scanning dependencies of target debug_print
>>>[ 4%] Building CXX object external/debug/CMakeFiles/debug_print.dir/print_function.cc.o
>>>Linking CXX static library libdebug_print.a
>>>[ 4%] Built target debug_print
>>>Scanning dependencies of target biophysics
>>>[ 4%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeRingBuffer.cpp.o
>>>[ 5%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynHandler.cpp.o
>>>[ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IntFire.cpp.o
>>>[ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Synapse.cpp.o
>>>[ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeGen.cpp.o
>>>[ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Compartment.cpp.o
>>>[ 8%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SymCompartment.cpp.o
>>>[ 8%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ChanBase.cpp.o
>>>[ 9%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHChannel.cpp.o
>>>[ 10%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHGate.cpp.o
>>>[ 10%] Building CXX object biophysics/CMakeFiles/biophysics.dir/CaConc.cpp.o
>>>[ 11%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Neuron.cpp.o
>>>[ 11%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ReadCell.cpp.o
>>>[ 12%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChanBase.cpp.o
>>>[ 13%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChan.cpp.o
>>>[ 13%] Building CXX object biophysics/CMakeFiles/biophysics.dir/testBiophysics.cpp.o
>>>[ 14%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IzhikevichNrn.cpp.o
>>>Linking CXX static library libbiophysics.a
>>>[ 14%] Built target biophysics
>>>Scanning dependencies of target basecode
>>>[ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/consts.cpp.o
>>>[ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/Element.cpp.o
>>>[ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/DataElement.cpp.o
>>>[ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/GlobalDataElement.cpp.o
>>>[ 17%] Building CXX object basecode/CMakeFiles/basecode.dir/LocalDataElement.cpp.o
>>>[ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/Eref.cpp.o
>>>[ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/Finfo.cpp.o
>>>[ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/DestFinfo.cpp.o
>>>[ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o
>>>In file included from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/header.h:17:0,
>>> from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:10:
>>>/home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h: In function ???std::string mapToString(const std::map<A, B>&, bool) [with A = std::basic_string<char>, B = Cinfo*, std::string = std::basic_string<char>]???:
>>>/home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:208:55: instantiated from here
>>>/home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:110:18: error: comparison between signed and unsigned integer expressions [-Werror=sign-compare]
>>>/home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:112:9: error: comparison between signed and unsigned integer expressions [-Werror=sign-compare]
>>>At global scope:
>>>cc1plus: error: unrecognized command line option "-Wno-unused-private-field" [-Werror]
>>>cc1plus: error: unrecognized command line option "-Wno-return-type-c-linkage" [-Werror]
>>>cc1plus: all warnings being treated as errors
>>>make[2]: *** [basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o] Error 1
>>>make[1]: *** [basecode/CMakeFiles/basecode.dir/all] Error 2
>>>make: *** [all] Error 2
>>>------------------------------------------------------------------------------
>>>"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>>Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>>unparalleled scalability from the best Selenium testing platform available.
>>>Simple to use. Nothing to install. Get started now for free."
>>>http://p.sf.net/sfu/SauceLabs
>>>_______________________________________________
>>>moose-devel mailing list
>>>moo...@li...
>>>https://lists.sourceforge.net/lists/listinfo/moose-devel
>>
>>------------------------------------------------------------------------------
>>"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>unparalleled scalability from the best Selenium testing platform available.
>>Simple to use. Nothing to install. Get started now for free."
>>http://p.sf.net/sfu/SauceLabs
>>_______________________________________________
>>moose-devel mailing list
>>moo...@li...
>>https://lists.sourceforge.net/lists/listinfo/moose-devel
>>
>>
>
>Removing any accidentally created cmake files.
>-- The C compiler identification is GNU
>-- The CXX compiler identification is GNU
>-- Check for working C compiler: /usr/bin/gcc
>-- Check for working C compiler: /usr/bin/gcc -- works
>-- Detecting C compiler ABI info
>-- Detecting C compiler ABI info - done
>-- Check for working CXX compiler: /usr/bin/c++
>-- Check for working CXX compiler: /usr/bin/c++ -- works
>-- Detecting CXX compiler ABI info
>-- Detecting CXX compiler ABI info - done
>/usr
>-- Using GSL from /usr
>++ Unit testing enabled.
>++ Verbosity of output is 1
>-- Found: /usr/lib/libhdf5.so
>-- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
>--
>-- Could NOT find LIBSBML (missing: LIBSBML_LIBRARY LIBSBML_INCLUDE_DIR)
>-- Found Curses: /usr/lib/x86_64-linux-gnu/libcurses.so
>-- Could NOT find Readline (missing: Readline_INCLUDE_DIR)
>-- Found PythonInterp: /usr/bin/python (found version "2.7.3")
>-- Found NumPy: version "1.6.1" /usr/lib/python2.7/dist-packages/numpy/core/include
>-- Found PythonLibs: optimized;/usr/lib/libpython2.7.so.1;debug;/usr/lib/libpython2.7.so.1 (found version "2.7")
>++ PYTHONPATH is set to /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/python
>-- Configuring done
>-- Generating done
>-- Build files have been written to: /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/buildMooseUsingCmake
>Scanning dependencies of target debug_print
>[ 0%] Building CXX object external/debug/CMakeFiles/debug_print.dir/print_function.cc.o
>Linking CXX static library libdebug_print.a
>[ 0%] Built target debug_print
>Scanning dependencies of target biophysics
>[ 0%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeRingBuffer.cpp.o
>[ 1%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynHandler.cpp.o
>[ 2%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IntFire.cpp.o
>[ 2%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Synapse.cpp.o
>[ 3%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeGen.cpp.o
>[ 3%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Compartment.cpp.o
>[ 4%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SymCompartment.cpp.o
>[ 4%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ChanBase.cpp.o
>[ 5%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHChannel.cpp.o
>[ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHGate.cpp.o
>[ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/CaConc.cpp.o
>[ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Neuron.cpp.o
>[ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ReadCell.cpp.o
>[ 8%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChanBase.cpp.o
>[ 9%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChan.cpp.o
>[ 9%] Building CXX object biophysics/CMakeFiles/biophysics.dir/testBiophysics.cpp.o
>[ 10%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IzhikevichNrn.cpp.o
>Linking CXX static library libbiophysics.a
>[ 10%] Built target biophysics
>Scanning dependencies of target basecode
>[ 11%] Building CXX object basecode/CMakeFiles/basecode.dir/consts.cpp.o
>[ 11%] Building CXX object basecode/CMakeFiles/basecode.dir/Element.cpp.o
>[ 12%] Building CXX object basecode/CMakeFiles/basecode.dir/DataElement.cpp.o
>[ 12%] Building CXX object basecode/CMakeFiles/basecode.dir/GlobalDataElement.cpp.o
>[ 13%] Building CXX object basecode/CMakeFiles/basecode.dir/LocalDataElement.cpp.o
>[ 14%] Building CXX object basecode/CMakeFiles/basecode.dir/Eref.cpp.o
>[ 14%] Building CXX object basecode/CMakeFiles/basecode.dir/Finfo.cpp.o
>[ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/DestFinfo.cpp.o
>[ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o
>In file included from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/header.h:17:0,
> from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:10:
>/home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h: In function ???std::string mapToString(const std::map<A, B>&, bool) [with A = std::basic_string<char>, B = Cinfo*, std::string = std::basic_string<char>]???:
>/home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:208:55: instantiated from here
>/home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:110:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
>/home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:112:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
>At global scope:
>cc1plus: warning: unrecognized command line option "-Wno-unused-private-field" [enabled by default]
>cc1plus: warning: unrecognized command line option "-Wno-return-type-c-linkage" [enabled by default]
>[ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/SrcFinfo.cpp.o
>[ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/ValueFinfo.cpp.o
>[ 17%] Building CXX object basecode/CMakeFiles/basecode.dir/SharedFinfo.cpp.o
>[ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/FieldElementFinfo.cpp.o
>[ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/FieldElement.cpp.o
>[ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/Id.cpp.o
>[ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/PrepackedBuffer.cpp.o
>[ 20%] Building CXX object basecode/CMakeFiles/basecode.dir/ObjId.cpp.o
>[ 21%] Building CXX object basecode/CMakeFiles/basecode.dir/global.cpp.o
>[ 21%] Building CXX object basecode/CMakeFiles/basecode.dir/SetGet.cpp.o
>[ 22%] Building CXX object basecode/CMakeFiles/basecode.dir/OpFuncBase.cpp.o
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>[ 23%] Building CXX object basecode/CMakeFiles/basecode.dir/HopFunc.cpp.o
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>[ 24%] Building CXX object basecode/CMakeFiles/basecode.dir/doubleEq.cpp.o
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>Linking CXX static library libbasecode.a
>[ 25%] Built target basecode
>Scanning dependencies of target kinetics
>[ 26%] Building CXX object kinetics/CMakeFiles/kinetics.dir/PoolBase.cpp.o
>[ 26%] Building CXX object kinetics/CMakeFiles/kinetics.dir/Pool.cpp.o
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>[ 28%] Building CXX object kinetics/CMakeFiles/kinetics.dir/FuncPool.cpp.o
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>[ 32%] Building CXX object kinetics/CMakeFiles/kinetics.dir/Species.cpp.o
>[ 32%] Building CXX object kinetics/CMakeFiles/kinetics.dir/ReadKkit.cpp.o
>[ 33%] Building CXX object kinetics/CMakeFiles/kinetics.dir/WriteKkit.cpp.o
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>[ 34%] Building CXX object kinetics/CMakeFiles/kinetics.dir/SumTotalTerm.cpp.o
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>Linking CXX static library libkinetics.a
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>[ 46%] Building CXX object utility/CMakeFiles/utility.dir/Annotator.cpp.o
>[ 47%] Building CXX object utility/CMakeFiles/utility.dir/Vec.cpp.o
>Linking CXX static library libutility.a
>[ 47%] Built target utility
>Scanning dependencies of target moosepython
>[ 48%] Building CXX object pymoose/CMakeFiles/moosepython.dir/vec.cpp.o
>[ 48%] Building CXX object pymoose/CMakeFiles/moosepython.dir/mfield.cpp.o
>[ 49%] Building CXX object pymoose/CMakeFiles/moosepython.dir/pymooseinit.cpp.o
>[ 50%] Building CXX object pymoose/CMakeFiles/moosepython.dir/melement.cpp.o
>[ 50%] Building CXX object pymoose/CMakeFiles/moosepython.dir/test_moosemodule.cpp.o
>In file included from /usr/include/python2.7/Python.h:8:0,
> from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/pymoose/test_moosemodule.cpp:49:
>/usr/include/python2.7/pyconfig.h:1161:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default]
>/usr/include/features.h:164:0: note: this is the location of the previous definition
>/usr/include/python2.7/pyconfig.h:1183:0: warning: "_XOPEN_SOURCE" redefined [enabled by default]
>/usr/include/features.h:166:0: note: this is the location of the previous definition
>cc1plus: warning: unrecognized command line option "-Wno-unused-private-field" [enabled by default]
>cc1plus: warning: unrecognized command line option "-Wno-return-type-c-linkage" [enabled by default]
>Linking CXX static library libmoosepython.a
>[ 50%] Built target moosepython
>Scanning dependencies of target shell
>[ 50%] Building CXX object shell/CMakeFiles/shell.dir/Shell.cpp.o
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>------------------------------------------------------------------------------
>"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>Instantly run your Selenium tests across 300+ browser/OS combos. Get
>unparalleled scalability from the best Selenium testing platform available.
>Simple to use. Nothing to install. Get started now for free."
>http://p.sf.net/sfu/SauceLabs
>_______________________________________________
>moose-devel mailing list
>moo...@li...
>https://lists.sourceforge.net/lists/listinfo/moose-devel
|
|
From: Saeed S. <sa...@gn...> - 2014-05-01 18:26:14
|
Cmake in revision 6339 produces error which is attach. My system is Ubuntu 12.04 On 05/01/2014 03:02 PM, Dilawar Singh wrote: > Thanks a lot Saeed, > > Libxml2 turns out to be unnecessary. It has been removed now from cmake. > > Removed some of the compiler flags specific to gcc-4.8. This should compile > now. Moose also compiles with clang++. > > A couple to tests might fail on default tests enabled in cmake. > > Dilawar > > On Thu, May 01, 2014 at 11:36:56AM -0300, Saeed Shariati wrote: >> Thank you Dilawar. >> >> The CMake build system needs also libxml2-dev package to be installed >> and after executing, produce the outputs which is attached to this >> email. >> >> On 05/01/2014 01:35 AM, Dilawar Singh wrote: >>> Hi Saeed, >>> >>> Fixed. Added missing files. >>> >>> Also there is a cmake based build system. I'd be happy if you can test it on >>> your system and let me know how it went. You need to install cmake and do the >>> following in async branch. >>> >>> $ cd buildMooseUsingCmake >>> $ ./build_me.sh >>> >>> Dilawar >>> >>> >>> ------------------------------------------------------------------------------ >>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >>> Instantly run your Selenium tests across 300+ browser/OS combos. Get >>> unparalleled scalability from the best Selenium testing platform available. >>> Simple to use. Nothing to install. Get started now for free." >>> http://p.sf.net/sfu/SauceLabs >>> _______________________________________________ >>> moose-devel mailing list >>> moo...@li... >>> https://lists.sourceforge.net/lists/listinfo/moose-devel >>> >>> >> Removing any accidentally created cmake files. >> -- The C compiler identification is GNU >> -- The CXX compiler identification is GNU >> -- Check for working C compiler: /usr/bin/gcc >> -- Check for working C compiler: /usr/bin/gcc -- works >> -- Detecting C compiler ABI info >> -- Detecting C compiler ABI info - done >> -- Check for working CXX compiler: /usr/bin/c++ >> -- Check for working CXX compiler: /usr/bin/c++ -- works >> -- Detecting CXX compiler ABI info >> -- Detecting CXX compiler ABI info - done >> /usr >> -- Using GSL from /usr >> ++ Unit testing enabled. >> ++ Verbosity of output is 1 >> -- Found: /usr/lib/libhdf5.so >> -- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR) >> -- >> -- Could NOT find LIBSBML (missing: LIBSBML_LIBRARY LIBSBML_INCLUDE_DIR) >> -- Found Curses: /usr/lib/x86_64-linux-gnu/libcurses.so >> -- Could NOT find Readline (missing: Readline_INCLUDE_DIR) >> -- Found LibXML2: /usr/lib/x86_64-linux-gnu/libxml2.so >> -- Found PythonInterp: /usr/bin/python (found version "2.7.3") >> -- Found NumPy: version "1.6.1" /usr/lib/python2.7/dist-packages/numpy/core/include >> -- Found PythonLibs: optimized;/usr/lib/libpython2.7.so.1;debug;/usr/lib/libpython2.7.so.1 (found version "2.7") >> ++ PYTHONPATH is set to /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/python >> -- Configuring done >> -- Generating done >> -- Build files have been written to: /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/buildMooseUsingCmake >> Scanning dependencies of target utility >> [ 1%] Building CXX object utility/CMakeFiles/utility.dir/strutil.cpp.o >> [ 1%] Building CXX object utility/CMakeFiles/utility.dir/types.cpp.o >> [ 2%] Building CXX object utility/CMakeFiles/utility.dir/setupenv.cpp.o >> [ 2%] Building CXX object utility/CMakeFiles/utility.dir/numutil.cpp.o >> [ 3%] Building CXX object utility/CMakeFiles/utility.dir/Annotator.cpp.o >> [ 4%] Building CXX object utility/CMakeFiles/utility.dir/Vec.cpp.o >> Linking CXX static library libutility.a >> [ 4%] Built target utility >> Scanning dependencies of target debug_print >> [ 4%] Building CXX object external/debug/CMakeFiles/debug_print.dir/print_function.cc.o >> Linking CXX static library libdebug_print.a >> [ 4%] Built target debug_print >> Scanning dependencies of target biophysics >> [ 4%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeRingBuffer.cpp.o >> [ 5%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynHandler.cpp.o >> [ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IntFire.cpp.o >> [ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Synapse.cpp.o >> [ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeGen.cpp.o >> [ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Compartment.cpp.o >> [ 8%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SymCompartment.cpp.o >> [ 8%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ChanBase.cpp.o >> [ 9%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHChannel.cpp.o >> [ 10%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHGate.cpp.o >> [ 10%] Building CXX object biophysics/CMakeFiles/biophysics.dir/CaConc.cpp.o >> [ 11%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Neuron.cpp.o >> [ 11%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ReadCell.cpp.o >> [ 12%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChanBase.cpp.o >> [ 13%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChan.cpp.o >> [ 13%] Building CXX object biophysics/CMakeFiles/biophysics.dir/testBiophysics.cpp.o >> [ 14%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IzhikevichNrn.cpp.o >> Linking CXX static library libbiophysics.a >> [ 14%] Built target biophysics >> Scanning dependencies of target basecode >> [ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/consts.cpp.o >> [ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/Element.cpp.o >> [ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/DataElement.cpp.o >> [ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/GlobalDataElement.cpp.o >> [ 17%] Building CXX object basecode/CMakeFiles/basecode.dir/LocalDataElement.cpp.o >> [ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/Eref.cpp.o >> [ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/Finfo.cpp.o >> [ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/DestFinfo.cpp.o >> [ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o >> In file included from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/header.h:17:0, >> from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:10: >> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h: In function ???std::string mapToString(const std::map<A, B>&, bool) [with A = std::basic_string<char>, B = Cinfo*, std::string = std::basic_string<char>]???: >> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:208:55: instantiated from here >> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:110:18: error: comparison between signed and unsigned integer expressions [-Werror=sign-compare] >> /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:112:9: error: comparison between signed and unsigned integer expressions [-Werror=sign-compare] >> At global scope: >> cc1plus: error: unrecognized command line option "-Wno-unused-private-field" [-Werror] >> cc1plus: error: unrecognized command line option "-Wno-return-type-c-linkage" [-Werror] >> cc1plus: all warnings being treated as errors >> make[2]: *** [basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o] Error 1 >> make[1]: *** [basecode/CMakeFiles/basecode.dir/all] Error 2 >> make: *** [all] Error 2 >> ------------------------------------------------------------------------------ >> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >> Instantly run your Selenium tests across 300+ browser/OS combos. Get >> unparalleled scalability from the best Selenium testing platform available. >> Simple to use. Nothing to install. Get started now for free." >> http://p.sf.net/sfu/SauceLabs >> _______________________________________________ >> moose-devel mailing list >> moo...@li... >> https://lists.sourceforge.net/lists/listinfo/moose-devel > > ------------------------------------------------------------------------------ > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE > Instantly run your Selenium tests across 300+ browser/OS combos. Get > unparalleled scalability from the best Selenium testing platform available. > Simple to use. Nothing to install. Get started now for free." > http://p.sf.net/sfu/SauceLabs > _______________________________________________ > moose-devel mailing list > moo...@li... > https://lists.sourceforge.net/lists/listinfo/moose-devel > > |
|
From: Dilawar S. <dil...@gm...> - 2014-05-01 18:03:42
|
Thanks a lot Saeed,
Libxml2 turns out to be unnecessary. It has been removed now from cmake.
Removed some of the compiler flags specific to gcc-4.8. This should compile
now. Moose also compiles with clang++.
A couple to tests might fail on default tests enabled in cmake.
Dilawar
On Thu, May 01, 2014 at 11:36:56AM -0300, Saeed Shariati wrote:
>Thank you Dilawar.
>
>The CMake build system needs also libxml2-dev package to be installed
>and after executing, produce the outputs which is attached to this
>email.
>
>On 05/01/2014 01:35 AM, Dilawar Singh wrote:
>>Hi Saeed,
>>
>>Fixed. Added missing files.
>>
>>Also there is a cmake based build system. I'd be happy if you can test it on
>>your system and let me know how it went. You need to install cmake and do the
>>following in async branch.
>>
>> $ cd buildMooseUsingCmake
>> $ ./build_me.sh
>>
>>Dilawar
>>
>>
>>------------------------------------------------------------------------------
>>"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>unparalleled scalability from the best Selenium testing platform available.
>>Simple to use. Nothing to install. Get started now for free."
>>http://p.sf.net/sfu/SauceLabs
>>_______________________________________________
>>moose-devel mailing list
>>moo...@li...
>>https://lists.sourceforge.net/lists/listinfo/moose-devel
>>
>>
>
>Removing any accidentally created cmake files.
>-- The C compiler identification is GNU
>-- The CXX compiler identification is GNU
>-- Check for working C compiler: /usr/bin/gcc
>-- Check for working C compiler: /usr/bin/gcc -- works
>-- Detecting C compiler ABI info
>-- Detecting C compiler ABI info - done
>-- Check for working CXX compiler: /usr/bin/c++
>-- Check for working CXX compiler: /usr/bin/c++ -- works
>-- Detecting CXX compiler ABI info
>-- Detecting CXX compiler ABI info - done
>/usr
>-- Using GSL from /usr
>++ Unit testing enabled.
>++ Verbosity of output is 1
>-- Found: /usr/lib/libhdf5.so
>-- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
>--
>-- Could NOT find LIBSBML (missing: LIBSBML_LIBRARY LIBSBML_INCLUDE_DIR)
>-- Found Curses: /usr/lib/x86_64-linux-gnu/libcurses.so
>-- Could NOT find Readline (missing: Readline_INCLUDE_DIR)
>-- Found LibXML2: /usr/lib/x86_64-linux-gnu/libxml2.so
>-- Found PythonInterp: /usr/bin/python (found version "2.7.3")
>-- Found NumPy: version "1.6.1" /usr/lib/python2.7/dist-packages/numpy/core/include
>-- Found PythonLibs: optimized;/usr/lib/libpython2.7.so.1;debug;/usr/lib/libpython2.7.so.1 (found version "2.7")
>++ PYTHONPATH is set to /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/python
>-- Configuring done
>-- Generating done
>-- Build files have been written to: /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/buildMooseUsingCmake
>Scanning dependencies of target utility
>[ 1%] Building CXX object utility/CMakeFiles/utility.dir/strutil.cpp.o
>[ 1%] Building CXX object utility/CMakeFiles/utility.dir/types.cpp.o
>[ 2%] Building CXX object utility/CMakeFiles/utility.dir/setupenv.cpp.o
>[ 2%] Building CXX object utility/CMakeFiles/utility.dir/numutil.cpp.o
>[ 3%] Building CXX object utility/CMakeFiles/utility.dir/Annotator.cpp.o
>[ 4%] Building CXX object utility/CMakeFiles/utility.dir/Vec.cpp.o
>Linking CXX static library libutility.a
>[ 4%] Built target utility
>Scanning dependencies of target debug_print
>[ 4%] Building CXX object external/debug/CMakeFiles/debug_print.dir/print_function.cc.o
>Linking CXX static library libdebug_print.a
>[ 4%] Built target debug_print
>Scanning dependencies of target biophysics
>[ 4%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeRingBuffer.cpp.o
>[ 5%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynHandler.cpp.o
>[ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IntFire.cpp.o
>[ 6%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Synapse.cpp.o
>[ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SpikeGen.cpp.o
>[ 7%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Compartment.cpp.o
>[ 8%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SymCompartment.cpp.o
>[ 8%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ChanBase.cpp.o
>[ 9%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHChannel.cpp.o
>[ 10%] Building CXX object biophysics/CMakeFiles/biophysics.dir/HHGate.cpp.o
>[ 10%] Building CXX object biophysics/CMakeFiles/biophysics.dir/CaConc.cpp.o
>[ 11%] Building CXX object biophysics/CMakeFiles/biophysics.dir/Neuron.cpp.o
>[ 11%] Building CXX object biophysics/CMakeFiles/biophysics.dir/ReadCell.cpp.o
>[ 12%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChanBase.cpp.o
>[ 13%] Building CXX object biophysics/CMakeFiles/biophysics.dir/SynChan.cpp.o
>[ 13%] Building CXX object biophysics/CMakeFiles/biophysics.dir/testBiophysics.cpp.o
>[ 14%] Building CXX object biophysics/CMakeFiles/biophysics.dir/IzhikevichNrn.cpp.o
>Linking CXX static library libbiophysics.a
>[ 14%] Built target biophysics
>Scanning dependencies of target basecode
>[ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/consts.cpp.o
>[ 15%] Building CXX object basecode/CMakeFiles/basecode.dir/Element.cpp.o
>[ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/DataElement.cpp.o
>[ 16%] Building CXX object basecode/CMakeFiles/basecode.dir/GlobalDataElement.cpp.o
>[ 17%] Building CXX object basecode/CMakeFiles/basecode.dir/LocalDataElement.cpp.o
>[ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/Eref.cpp.o
>[ 18%] Building CXX object basecode/CMakeFiles/basecode.dir/Finfo.cpp.o
>[ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/DestFinfo.cpp.o
>[ 19%] Building CXX object basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o
>In file included from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/header.h:17:0,
> from /home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:10:
>/home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h: In function ???std::string mapToString(const std::map<A, B>&, bool) [with A = std::basic_string<char>, B = Cinfo*, std::string = std::basic_string<char>]???:
>/home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/Cinfo.cpp:208:55: instantiated from here
>/home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:110:18: error: comparison between signed and unsigned integer expressions [-Werror=sign-compare]
>/home/saeed/src/cuda-workspace/moose-code/moose/branches/async13/basecode/../external/debug/print_function.h:112:9: error: comparison between signed and unsigned integer expressions [-Werror=sign-compare]
>At global scope:
>cc1plus: error: unrecognized command line option "-Wno-unused-private-field" [-Werror]
>cc1plus: error: unrecognized command line option "-Wno-return-type-c-linkage" [-Werror]
>cc1plus: all warnings being treated as errors
>make[2]: *** [basecode/CMakeFiles/basecode.dir/Cinfo.cpp.o] Error 1
>make[1]: *** [basecode/CMakeFiles/basecode.dir/all] Error 2
>make: *** [all] Error 2
>------------------------------------------------------------------------------
>"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>Instantly run your Selenium tests across 300+ browser/OS combos. Get
>unparalleled scalability from the best Selenium testing platform available.
>Simple to use. Nothing to install. Get started now for free."
>http://p.sf.net/sfu/SauceLabs
>_______________________________________________
>moose-devel mailing list
>moo...@li...
>https://lists.sourceforge.net/lists/listinfo/moose-devel
|
|
From: Saeed S. <sa...@gn...> - 2014-05-01 14:37:54
|
Thank you Dilawar. The CMake build system needs also libxml2-dev package to be installed and after executing, produce the outputs which is attached to this email. On 05/01/2014 01:35 AM, Dilawar Singh wrote: > Hi Saeed, > > Fixed. Added missing files. > > Also there is a cmake based build system. I'd be happy if you can test it on > your system and let me know how it went. You need to install cmake and do the > following in async branch. > > $ cd buildMooseUsingCmake > $ ./build_me.sh > > Dilawar > > > ------------------------------------------------------------------------------ > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE > Instantly run your Selenium tests across 300+ browser/OS combos. Get > unparalleled scalability from the best Selenium testing platform available. > Simple to use. Nothing to install. Get started now for free." > http://p.sf.net/sfu/SauceLabs > _______________________________________________ > moose-devel mailing list > moo...@li... > https://lists.sourceforge.net/lists/listinfo/moose-devel > > |
|
From: Dilawar S. <dil...@gm...> - 2014-05-01 09:28:14
|
Hi Saeed,
Script testHsolve.py runs now. Checkout #5330.
Numpy vector will be printed on console. I am not sure about the correctness
of results. This revision (#5330) should be stable for building moose.
Dilawar
On Tue, Apr 29, 2014 at 03:16:52PM -0300, Saeed wrote:
>Hi Dilawar,
>
> Thank you for importing hsolve. I thought it might be not related
>to HSolve because it happened before defining HSovle and for example at
>Hopfield I got the same error.
> Thank you again. Therefore, I wont change anything now and will
>wait for the code to be stable.
>
>Saeed
>
>
>On 29-04-2014 15:02, Dilawar Singh wrote:
>> Hi Saeed,
>>
>> We are in process of integrating 'hsolve' into async13 branch. Only today, I
>> got some sanity check of hsolve working. I am not sure how long it will take
>> to get hsolve properly integrated with python.
>>
>> For time being -- if you want to use async13 branch -- you can change the
>> solver to 'ee' from 'hsolve'.
>>
>> I'll let you know as soon as hsolve is ready.
>>
>> Dilawar
>>
>> On Tue, Apr 29, 2014 at 02:58:28PM -0300, Saeed wrote:
>>> Sure, Sorry for the lack of information.
>>> As I found it happens in many of Demo files, for example at "async13/Demos/snippets/testHsolve.py" the below error produces:
>>>
>>> =====================================
>>> on node 0, numNodes = 1, numCores = 12
>>> Info: Time to define moose classes:0
>>> Info: Time to initialize module:0.05
>>> Created 306 path=/n numData=1 isGlobal=0 baseType=Neutral
>>> Created 307 path=/n/compt numData=1 isGlobal=0 baseType=SymCompartment
>>> Created 308 path=/n/compt/Na numData=1 isGlobal=0 baseType=HHChannel
>>> Created 312 path=/n/compt/K numData=1 isGlobal=0 baseType=HHChannel
>>> Created 316 path=/n/compt/synInput numData=1 isGlobal=0 baseType=SpikeGen
>>> Created 317 path=/n[0]/shaft0 numData=1 isGlobal=0 baseType=SymCompartment
>>> Created 318 path=/n[0]/head0 numData=1 isGlobal=0 baseType=SymCompartment
>>> Created 319 path=/n[0]/head0[0]/gluR numData=1 isGlobal=0 baseType=SynChan
>>> Created 321 path=/n[0]/head0[0]/ca numData=1 isGlobal=0 baseType=CaConc
>>> 0: Shell::doAddMsg: Error: Failed to find field event on src: synInput
>>> Traceback (most recent call last):
>>> File "testHsolve.py", line 297, in <module>
>>> main()
>>> File "testHsolve.py", line 294, in main
>>> test_elec_alone()
>>> File "testHsolve.py", line 265, in test_elec_alone
>>> make_spiny_compt()
>>> File "testHsolve.py", line 243, in make_spiny_compt
>>> moose.connect( synInput, 'event', syn, 'addSpike', 'Single' )
>>> NameError: check field names and type compatibility.
>>>
>>> ======================================
>>>
>>> It seems that the finfoMap_ array at Cinfo.cpp:214 does not contains all object names.
>>>
>>>
>>>
>>>> Upi
>>>> Dear Saeed,
>>>> Please give script snippet where this happens. Also you might wish
>>>> to look in Demos/snippets for examples of the correct use of the function.
>>>> Best,
>>>> Upi
>>>> On Tuesday 29 April 2014 09:04 PM, Saeed Shariati wrote:
>>>>> Hi,
>>>>>
>>>>> At async13 branch, when it tries to use connect method, the below error
>>>>> throws away:
>>>>>
>>>>> 0: Shell::doAddMsg: Error: Failed to find field spike on src: cell_0
>>>>>
>>>>> It would be my please if you have a look at this.
>>>>>
>>>>> Bests,
>>>>> Saeed
>>>>> ------------------------------------------------------------------------------
>>>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>>>> unparalleled scalability from the best Selenium testing platform available.
>>>>> Simple to use. Nothing to install. Get started now for free."
>>>>> http://p.sf.net/sfu/SauceLabs
>>>>> _______________________________________________
>>>>> moose-devel mailing list
>>>>> moose-devel@...
>>>>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>>>
>>> ------------------------------------------------------------------------------
>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>> unparalleled scalability from the best Selenium testing platform available.
>>> Simple to use. Nothing to install. Get started now for free."
>>> http://p.sf.net/sfu/SauceLabs
>>> _______________________________________________
>>> moose-devel mailing list
>>> moo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>> ------------------------------------------------------------------------------
>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>> unparalleled scalability from the best Selenium testing platform available.
>> Simple to use. Nothing to install. Get started now for free."
>> http://p.sf.net/sfu/SauceLabs
>> _______________________________________________
>> moose-devel mailing list
>> moo...@li...
>> https://lists.sourceforge.net/lists/listinfo/moose-devel
>>
>>
>
>
>------------------------------------------------------------------------------
>"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>Instantly run your Selenium tests across 300+ browser/OS combos. Get
>unparalleled scalability from the best Selenium testing platform available.
>Simple to use. Nothing to install. Get started now for free."
>http://p.sf.net/sfu/SauceLabs
>_______________________________________________
>moose-devel mailing list
>moo...@li...
>https://lists.sourceforge.net/lists/listinfo/moose-devel
|
|
From: Hugo C. <hug...@gm...> - 2014-05-01 09:14:27
|
Hi Dave, Upi and others, As Dave says, using hsolve comes with a significant performance improvement for event processing. I analysed the performance of event processing in Genesis-2 in depth a long time ago, but, really, cannot remember all the details. There are two elements that may be important: If I remember well the speedup of event processing with hsolve comes mostly from avoiding pointer indirections of the Genesis-2 action handling system in the Genesis-2 core. The implementation of Genesis-2 actions is similar to the implementation of C++ method invocation. So my guess is that Moose may benefit from similar optimizations. Although I want to be careful with such statements, because I don't know that much about Moose internals, and, also, CPUs use speculative execution techniques to optimize for C++ method invocation. The second element is the choice of data structure for event queuing. The event queue can either be centralized, which is the approach taken by most of the papers in discrete event simulation, or it can be distributed, which is what Genesis-2 does. >From memory of an in-depth analysis and benchmarking at the time, I can say, without remembering the details, that none of these two alternatives had significant advantages over the other. Even given that the literature of discrete event simulation mentions splay trees and calendar queues as optimal, I believe, this is not what I found for neural simulations. This may be due to the highly dynamical temporal structure of the event queue during a simulation. I hope this helps. Hugo On Thu, May 1, 2014 at 1:25 AM, Dave Beeman <db...@co...> wrote: > Hi Upi and other MOOSE developers, > > I will do my best to answer your questio of how GENESIS 2 hsolve > deals with spike delivery, but you will get a better answer from Hugo > Cornelis, who I have copied on this email.the > > Hugo wrote a detailed tutorial document on hsolve back in 2002 for the GUM > meeting. > > http://genesis-sim.org/GENESIS/UGTD/Tutorials/advanced-tutorials/hsolve- > cornelis/index.html > > The section on Synchan - hsolve coordination tells something of how it > works. It was only about two years ago that I got around to reading > the section on networks of cells that I tried using hsolve on my network > models. None of all the large GENESIS network models that I have seen use > hsolve, except in chanmode 0 or 1. > > I did not expect a significant speed improvement when I used hsolve > chanmode 4 with my cortical model of 9-compartment cells. The speedup > for the Purkinje cell model is only a factor of 4. I was amazed when > my simulations ran 10 to 12 times faster. Recently I reimplemented > the network benchmark that was used in the Brette et al 2007 paper > using hsolve. The cells are single compartment with only Na and K > channels, and the simulation ran 20 times faster. > > You can see an example of how hsolve is used in my auditory cortex model at > http://genesis-sim.org/GENESIS/ACnet2-GENESIS/ > > Evidently, when hsolve deals with the interactions between spiegens and > synchans it bypasses the overhead of the messaging, and that this overhead > is very large. I think it is important that MOOSE implement communication > in an efficient way to avoid this kind of speed penalty, whether it is done > within the hsolve implementation or with a separate solver. > > From my point of view as a modeler, the biggest limitation of GENESIS 2, > other than its lack of a Python interface, is the difficulty of using > hsolve for the non-expert, and the limitation on which objects can > be used with hsolve. If MOOSE can overcome these problems and give > speed equivalent to GENESIS 2, I would be happy to try my models > on MOOSE when it is ready enough to make the conversion simple. > > Dave > > > > On Wed, 30 Apr 2014, U.S.Bhalla wrote: > > Dear Dave, >> Perhaps you could remind me what the optimizations were that the >> Hsolve did for spike delivery in GENESIS. Was it simply that when the >> spike event occurred, it directly went and called the spike delivery >> methods of the target synapses, which were themselves under Hsolve? >> >> In any event, the current MOOSE implementation uses regular messaging to >> handle spike events. There is some optimization of messaging for >> multinode models, but we haven't yet looked at putting the entire >> network under a solver. First step would be to ask how much time is >> actually spent delivering the spikes. Then it would be interesting to >> compare with an equivalent model. Any suggestions? >> >> Best, >> Upi >> >> On Wednesday 30 April 2014 01:34 AM, Dave Beeman wrote: >> >>> I will be very interested in trying out the MOOSE Python implemention >>> of hsolved when it is fully ready. >>> >>> In GENESIS 2, hsolve performs both the functions of a Hines method >>> compartmental solver, and of a Discrete Event Solver for the efficient >>> delivery of spike messages. Ideally, these should be in separate >>> solvers, >>> as they are in GENESIS 3 (unfortunately still under development). >>> >>> How is this being handled in MOOSE? Can networks of hsolved cells >>> in MOOSE benefit from equivalent optimizations in spike delivery that >>> GENESIS hsolve gives? Or is a separate mechanism used for spike >>> delivery? >>> >>> On Tue, 29 Apr 2014, Dilawar Singh wrote: >>> >>> Hi Saeed, >>>> >>>> We are in process of integrating 'hsolve' into async13 branch. >>>> Only today, I >>>> got some sanity check of hsolve working. I am not sure how long it >>>> will take >>>> to get hsolve properly integrated with python. >>>> >>>> For time being -- if you want to use async13 branch -- you can >>>> change the >>>> solver to 'ee' from 'hsolve'. >>>> >>>> I'll let you know as soon as hsolve is ready. >>>> >>>> Dilawar >>>> >>> ------------------------------------------------------------ >>> ------------------ >>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >>> Instantly run your Selenium tests across 300+ browser/OS combos. Get >>> unparalleled scalability from the best Selenium testing platform >>> available. >>> Simple to use. Nothing to install. Get started now for free." >>> http://p.sf.net/sfu/SauceLabs >>> _______________________________________________ >>> moose-devel mailing list >>> moo...@li... >>> https://lists.sourceforge.net/lists/listinfo/moose-devel >>> >> >> >> ------------------------------------------------------------ >> ------------------ >> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >> Instantly run your Selenium tests across 300+ browser/OS combos. Get >> unparalleled scalability from the best Selenium testing platform >> available. >> Simple to use. Nothing to install. Get started now for free." >> http://p.sf.net/sfu/SauceLabs >> _______________________________________________ >> moose-devel mailing list >> moo...@li... >> https://lists.sourceforge.net/lists/listinfo/moose-devel >> >> -- Hugo -- Hugo Cornelis Ph.D. GENESIS-3 -- lead architect http://www.genesis-sim.org/ Neurospaces Project Architect http://www.neurospaces.org/ |
|
From: Subhasis R. <ray...@gm...> - 2014-05-01 05:15:00
|
On Wed, Apr 30, 2014 at 11:51 PM, Saeed <sa...@gn...> wrote: > > It would be my great pleasure if you could tell me which kind of test > cases you have used for testing the parallel execution. For example if > one of the snippets are suitable for these test, would be great. Also, > do you know any revision of the async13 which is working and suitable > for parallel test? > Look inside tests/python/mpi. I have done this on a single host with a multicore CPU. You may want to change the hostfile for your specific case. Best, Subhasis |
|
From: Dilawar S. <dil...@nc...> - 2014-05-01 04:36:49
|
Hi Saeed,
Fixed. Added missing files.
Also there is a cmake based build system. I'd be happy if you can test it on
your system and let me know how it went. You need to install cmake and do the
following in async branch.
$ cd buildMooseUsingCmake
$ ./build_me.sh
Dilawar
|
|
From: Dilawar S. <dil...@nc...> - 2014-05-01 04:32:32
|
>For example the last code of async13 has some missed files such as
>boost, global.cpp, etc. I just added files from other branches and I do
>not know are they correct version or not. By the way it compiled, but in
>simulation the below errors occur:
>
> bin: 101
> Error: bin:101t: 1921.01 currTime_ 1920 dt_: 0.01
> Simulated till 1930. Left: 70. 10 of simulation took: 0.016554 s
> bin: 101
> Error: bin:101t: 1931.01 currTime_ 1930 dt_: 0.01
> Simulated till 1940. Left: 60. 10 of simulation took: 0.016555 s
> bin: 101
> Error: bin:101t: 1941.01 currTime_ 1940 dt_: 0.01
>
>It can be possibly the result of changes which I made in the code.
Hi Saeed,
I made these changes for debugging purpose. Unfortunately I committed them
without protecting the original code with suitable macros.
There is some problem is bin-size, it is getting bigger than MAXBIN size
when you execute testHsolve.py file. If you pass smaller time to
moose.start() then this problem goes away.
There is also some issue with paths in hsolve folder. I am trying to resolve
it.
Dilawar
|
|
From: Saeed S. <sa...@gn...> - 2014-05-01 01:13:08
|
There is some missed files in async13 branch which cause problem for compiling. async13/external/debug/print_function.cc async13/external/debug/assert.cpp async13/basecode/global.cpp For example, I could not find any implementation for MOOSE_CURRENT_FUNCTION or MOOSE_ASSERT_MSG macros which are necessary for the compilation. |
|
From: Dave B. <db...@Co...> - 2014-04-30 23:25:50
|
Hi Upi and other MOOSE developers, I will do my best to answer your questio of how GENESIS 2 hsolve deals with spike delivery, but you will get a better answer from Hugo Cornelis, who I have copied on this email. Hugo wrote a detailed tutorial document on hsolve back in 2002 for the GUM meeting. http://genesis-sim.org/GENESIS/UGTD/Tutorials/advanced-tutorials/hsolve-cornelis/index.html The section on Synchan - hsolve coordination tells something of how it works. It was only about two years ago that I got around to reading the section on networks of cells that I tried using hsolve on my network models. None of all the large GENESIS network models that I have seen use hsolve, except in chanmode 0 or 1. I did not expect a significant speed improvement when I used hsolve chanmode 4 with my cortical model of 9-compartment cells. The speedup for the Purkinje cell model is only a factor of 4. I was amazed when my simulations ran 10 to 12 times faster. Recently I reimplemented the network benchmark that was used in the Brette et al 2007 paper using hsolve. The cells are single compartment with only Na and K channels, and the simulation ran 20 times faster. You can see an example of how hsolve is used in my auditory cortex model at http://genesis-sim.org/GENESIS/ACnet2-GENESIS/ Evidently, when hsolve deals with the interactions between spiegens and synchans it bypasses the overhead of the messaging, and that this overhead is very large. I think it is important that MOOSE implement communication in an efficient way to avoid this kind of speed penalty, whether it is done within the hsolve implementation or with a separate solver. >From my point of view as a modeler, the biggest limitation of GENESIS 2, other than its lack of a Python interface, is the difficulty of using hsolve for the non-expert, and the limitation on which objects can be used with hsolve. If MOOSE can overcome these problems and give speed equivalent to GENESIS 2, I would be happy to try my models on MOOSE when it is ready enough to make the conversion simple. Dave On Wed, 30 Apr 2014, U.S.Bhalla wrote: > Dear Dave, > Perhaps you could remind me what the optimizations were that the > Hsolve did for spike delivery in GENESIS. Was it simply that when the > spike event occurred, it directly went and called the spike delivery > methods of the target synapses, which were themselves under Hsolve? > > In any event, the current MOOSE implementation uses regular messaging to > handle spike events. There is some optimization of messaging for > multinode models, but we haven't yet looked at putting the entire > network under a solver. First step would be to ask how much time is > actually spent delivering the spikes. Then it would be interesting to > compare with an equivalent model. Any suggestions? > > Best, > Upi > > On Wednesday 30 April 2014 01:34 AM, Dave Beeman wrote: >> I will be very interested in trying out the MOOSE Python implemention >> of hsolved when it is fully ready. >> >> In GENESIS 2, hsolve performs both the functions of a Hines method >> compartmental solver, and of a Discrete Event Solver for the efficient >> delivery of spike messages. Ideally, these should be in separate solvers, >> as they are in GENESIS 3 (unfortunately still under development). >> >> How is this being handled in MOOSE? Can networks of hsolved cells >> in MOOSE benefit from equivalent optimizations in spike delivery that >> GENESIS hsolve gives? Or is a separate mechanism used for spike delivery? >> >> On Tue, 29 Apr 2014, Dilawar Singh wrote: >> >>> Hi Saeed, >>> >>> We are in process of integrating 'hsolve' into async13 branch. Only today, I >>> got some sanity check of hsolve working. I am not sure how long it will take >>> to get hsolve properly integrated with python. >>> >>> For time being -- if you want to use async13 branch -- you can change the >>> solver to 'ee' from 'hsolve'. >>> >>> I'll let you know as soon as hsolve is ready. >>> >>> Dilawar >> ------------------------------------------------------------------------------ >> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE >> Instantly run your Selenium tests across 300+ browser/OS combos. Get >> unparalleled scalability from the best Selenium testing platform available. >> Simple to use. Nothing to install. Get started now for free." >> http://p.sf.net/sfu/SauceLabs >> _______________________________________________ >> moose-devel mailing list >> moo...@li... >> https://lists.sourceforge.net/lists/listinfo/moose-devel > > > ------------------------------------------------------------------------------ > "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE > Instantly run your Selenium tests across 300+ browser/OS combos. Get > unparalleled scalability from the best Selenium testing platform available. > Simple to use. Nothing to install. Get started now for free." > http://p.sf.net/sfu/SauceLabs > _______________________________________________ > moose-devel mailing list > moo...@li... > https://lists.sourceforge.net/lists/listinfo/moose-devel > |
|
From: Saeed <sa...@gn...> - 2014-04-30 18:21:51
|
Thank you Subhasis, It was very helpful.
I know that the code is under development and I should not expect
correct execution at this moment. But my problem is that I suggested to
some students to have performance analysis on the Moose for their class
project. Their deadline is quite close and I want to give them a small
model and a version of Moose that is work enough for applying
performance tests.
It would be my great pleasure if you could tell me which kind of test
cases you have used for testing the parallel execution. For example if
one of the snippets are suitable for these test, would be great. Also,
do you know any revision of the async13 which is working and suitable
for parallel test?
For example the last code of async13 has some missed files such as
boost, global.cpp, etc. I just added files from other branches and I do
not know are they correct version or not. By the way it compiled, but in
simulation the below errors occur:
bin: 101
Error: bin:101t: 1921.01 currTime_ 1920 dt_: 0.01
Simulated till 1930. Left: 70. 10 of simulation took: 0.016554 s
bin: 101
Error: bin:101t: 1931.01 currTime_ 1930 dt_: 0.01
Simulated till 1940. Left: 60. 10 of simulation took: 0.016555 s
bin: 101
Error: bin:101t: 1941.01 currTime_ 1940 dt_: 0.01
It can be possibly the result of changes which I made in the code.
Thank you very much in advance
On 30-04-2014 02:41, Subhasis Ray wrote:
> Hi,
> More specifically the error is due to incorrect field name, as the error
> message suggests. The field name is 'spikeOut' and the snippet had not been
> updated to reflect the change in naming.
>
> Please note that we have settled on some naming conventions for fields
> since async13 branch.
> In particular, all source fields are suffixed 'Out' unless the field name
> itself is output. Many of the old snippets and demos have been copied over
> to the async13 branch but not yet updated to follow the new naming
> convention and hence this error.
>
> You can check the available field names using moose.doc() function in
> Python which displays the class documentation and a list of fields, like
> this:
>
>>>> moose.doc('Compartment')
> If you want to display the documentation for a particular field, then
> append the field name with a dot as separator:
>
>>>> moose.doc('Compartment.Vm')
> I made some fixes to docstring generation, so please update before reading
> the docs.
>
> Best,
> - Subhasis
> ( ʃʊbʱaːʃɪʃ )
>
>
> On Tue, Apr 29, 2014 at 11:32 PM, Dilawar Singh <dil...@nc...>wrote:
>
>> Hi Saeed,
>>
>> We are in process of integrating 'hsolve' into async13 branch. Only
>> today, I
>> got some sanity check of hsolve working. I am not sure how long it
>> will take
>> to get hsolve properly integrated with python.
>>
>> For time being -- if you want to use async13 branch -- you can change
>> the
>> solver to 'ee' from 'hsolve'.
>>
>> I'll let you know as soon as hsolve is ready.
>>
>> Dilawar
>>
>> On Tue, Apr 29, 2014 at 02:58:28PM -0300, Saeed wrote:
>>> Sure, Sorry for the lack of information.
>>> As I found it happens in many of Demo files, for example at
>> "async13/Demos/snippets/testHsolve.py" the below error produces:
>>> =====================================
>>> on node 0, numNodes = 1, numCores = 12
>>> Info: Time to define moose classes:0
>>> Info: Time to initialize module:0.05
>>> Created 306 path=/n numData=1 isGlobal=0 baseType=Neutral
>>> Created 307 path=/n/compt numData=1 isGlobal=0 baseType=SymCompartment
>>> Created 308 path=/n/compt/Na numData=1 isGlobal=0 baseType=HHChannel
>>> Created 312 path=/n/compt/K numData=1 isGlobal=0 baseType=HHChannel
>>> Created 316 path=/n/compt/synInput numData=1 isGlobal=0 baseType=SpikeGen
>>> Created 317 path=/n[0]/shaft0 numData=1 isGlobal=0 baseType=SymCompartment
>>> Created 318 path=/n[0]/head0 numData=1 isGlobal=0 baseType=SymCompartment
>>> Created 319 path=/n[0]/head0[0]/gluR numData=1 isGlobal=0 baseType=SynChan
>>> Created 321 path=/n[0]/head0[0]/ca numData=1 isGlobal=0 baseType=CaConc
>>> 0: Shell::doAddMsg: Error: Failed to find field event on src: synInput
>>> Traceback (most recent call last):
>>> File "testHsolve.py", line 297, in <module>
>>> main()
>>> File "testHsolve.py", line 294, in main
>>> test_elec_alone()
>>> File "testHsolve.py", line 265, in test_elec_alone
>>> make_spiny_compt()
>>> File "testHsolve.py", line 243, in make_spiny_compt
>>> moose.connect( synInput, 'event', syn, 'addSpike', 'Single' )
>>> NameError: check field names and type compatibility.
>>>
>>> ======================================
>>>
>>> It seems that the finfoMap_ array at Cinfo.cpp:214 does not contains all
>> object names.
>>>
>>>
>>>> Upi
>>>> Dear Saeed,
>>>> Please give script snippet where this happens. Also you might wish
>>>> to look in Demos/snippets for examples of the correct use of the
>> function.
>>>> Best,
>>>> Upi
>>>> On Tuesday 29 April 2014 09:04 PM, Saeed Shariati wrote:
>>>>> Hi,
>>>>>
>>>>> At async13 branch, when it tries to use connect method, the below error
>>>>> throws away:
>>>>>
>>>>> 0: Shell::doAddMsg: Error: Failed to find field spike on src: cell_0
>>>>>
>>>>> It would be my please if you have a look at this.
>>>>>
>>>>> Bests,
>>>>> Saeed
>>>>>
>> ------------------------------------------------------------------------------
>>>>> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
>>>>> Instantly run your Selenium tests across 300+ browser/OS combos. Get
>>>>> unparalleled scalability from the best Selenium testing platform
>> available.
>>>>> Simple to use. Nothing to install. Get started now for free."
>>>>> http://p.sf.net/sfu/SauceLabs
>>>>> _______________________________________________
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From: Subhasis R. <ray...@gm...> - 2014-04-30 05:42:26
|
Hi,
More specifically the error is due to incorrect field name, as the error
message suggests. The field name is 'spikeOut' and the snippet had not been
updated to reflect the change in naming.
Please note that we have settled on some naming conventions for fields
since async13 branch.
In particular, all source fields are suffixed 'Out' unless the field name
itself is output. Many of the old snippets and demos have been copied over
to the async13 branch but not yet updated to follow the new naming
convention and hence this error.
You can check the available field names using moose.doc() function in
Python which displays the class documentation and a list of fields, like
this:
>>> moose.doc('Compartment')
If you want to display the documentation for a particular field, then
append the field name with a dot as separator:
>>> moose.doc('Compartment.Vm')
I made some fixes to docstring generation, so please update before reading
the docs.
Best,
- Subhasis
( ʃʊbʱaːʃɪʃ )
On Tue, Apr 29, 2014 at 11:32 PM, Dilawar Singh <dil...@nc...>wrote:
> Hi Saeed,
>
> We are in process of integrating 'hsolve' into async13 branch. Only
> today, I
> got some sanity check of hsolve working. I am not sure how long it
> will take
> to get hsolve properly integrated with python.
>
> For time being -- if you want to use async13 branch -- you can change
> the
> solver to 'ee' from 'hsolve'.
>
> I'll let you know as soon as hsolve is ready.
>
> Dilawar
>
> On Tue, Apr 29, 2014 at 02:58:28PM -0300, Saeed wrote:
> >Sure, Sorry for the lack of information.
> >As I found it happens in many of Demo files, for example at
> "async13/Demos/snippets/testHsolve.py" the below error produces:
> >
> >=====================================
> >on node 0, numNodes = 1, numCores = 12
> >Info: Time to define moose classes:0
> >Info: Time to initialize module:0.05
> >Created 306 path=/n numData=1 isGlobal=0 baseType=Neutral
> >Created 307 path=/n/compt numData=1 isGlobal=0 baseType=SymCompartment
> >Created 308 path=/n/compt/Na numData=1 isGlobal=0 baseType=HHChannel
> >Created 312 path=/n/compt/K numData=1 isGlobal=0 baseType=HHChannel
> >Created 316 path=/n/compt/synInput numData=1 isGlobal=0 baseType=SpikeGen
> >Created 317 path=/n[0]/shaft0 numData=1 isGlobal=0 baseType=SymCompartment
> >Created 318 path=/n[0]/head0 numData=1 isGlobal=0 baseType=SymCompartment
> >Created 319 path=/n[0]/head0[0]/gluR numData=1 isGlobal=0 baseType=SynChan
> >Created 321 path=/n[0]/head0[0]/ca numData=1 isGlobal=0 baseType=CaConc
> >0: Shell::doAddMsg: Error: Failed to find field event on src: synInput
> >Traceback (most recent call last):
> > File "testHsolve.py", line 297, in <module>
> > main()
> > File "testHsolve.py", line 294, in main
> > test_elec_alone()
> > File "testHsolve.py", line 265, in test_elec_alone
> > make_spiny_compt()
> > File "testHsolve.py", line 243, in make_spiny_compt
> > moose.connect( synInput, 'event', syn, 'addSpike', 'Single' )
> >NameError: check field names and type compatibility.
> >
> >======================================
> >
> >It seems that the finfoMap_ array at Cinfo.cpp:214 does not contains all
> object names.
> >
> >
> >
> >>Upi
> >> Dear Saeed,
> >> Please give script snippet where this happens. Also you might wish
> >> to look in Demos/snippets for examples of the correct use of the
> function.
> >> Best,
> >> Upi
> >> On Tuesday 29 April 2014 09:04 PM, Saeed Shariati wrote:
> >>> Hi,
> >>>
> >>> At async13 branch, when it tries to use connect method, the below error
> >>> throws away:
> >>>
> >>> 0: Shell::doAddMsg: Error: Failed to find field spike on src: cell_0
> >>>
> >>> It would be my please if you have a look at this.
> >>>
> >>> Bests,
> >>> Saeed
> >>>
> ------------------------------------------------------------------------------
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> >>> unparalleled scalability from the best Selenium testing platform
> available.
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> >>>https://lists.sourceforge.net/lists/listinfo/moose-devel
> >
> >
>
> >------------------------------------------------------------------------------
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>
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|
|
From: U.S.Bhalla <bh...@nc...> - 2014-04-30 04:57:14
|
Dear Dave,
Perhaps you could remind me what the optimizations were that the
Hsolve did for spike delivery in GENESIS. Was it simply that when the
spike event occurred, it directly went and called the spike delivery
methods of the target synapses, which were themselves under Hsolve?
In any event, the current MOOSE implementation uses regular messaging to
handle spike events. There is some optimization of messaging for
multinode models, but we haven't yet looked at putting the entire
network under a solver. First step would be to ask how much time is
actually spent delivering the spikes. Then it would be interesting to
compare with an equivalent model. Any suggestions?
Best,
Upi
On Wednesday 30 April 2014 01:34 AM, Dave Beeman wrote:
> I will be very interested in trying out the MOOSE Python implemention
> of hsolved when it is fully ready.
>
> In GENESIS 2, hsolve performs both the functions of a Hines method
> compartmental solver, and of a Discrete Event Solver for the efficient
> delivery of spike messages. Ideally, these should be in separate solvers,
> as they are in GENESIS 3 (unfortunately still under development).
>
> How is this being handled in MOOSE? Can networks of hsolved cells
> in MOOSE benefit from equivalent optimizations in spike delivery that
> GENESIS hsolve gives? Or is a separate mechanism used for spike delivery?
>
> On Tue, 29 Apr 2014, Dilawar Singh wrote:
>
>> Hi Saeed,
>>
>> We are in process of integrating 'hsolve' into async13 branch. Only today, I
>> got some sanity check of hsolve working. I am not sure how long it will take
>> to get hsolve properly integrated with python.
>>
>> For time being -- if you want to use async13 branch -- you can change the
>> solver to 'ee' from 'hsolve'.
>>
>> I'll let you know as soon as hsolve is ready.
>>
>> Dilawar
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos. Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
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> _______________________________________________
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|
|
From: Saeed S. <sa...@gn...> - 2014-04-29 22:00:43
|
Dear Dave,
In my opinion, HSolve strategy in the Moose is different than
Genesis. It is more an integration algorithm than overall framework.
It applies to a part of the general simulation and communicate with
external objects. However, objects such as active and synaptic
channels are HSolvable, spike delivery serves outside of HSolve. The
good thing is that with this mechanism, it's possible to use HSolve
in a complex models that have non-HSolvabe objects.
Saeed
On 04/29/2014 05:04 PM, Dave Beeman wrote:
> I will be very interested in trying out the MOOSE Python implemention
> of hsolved when it is fully ready.
>
> In GENESIS 2, hsolve performs both the functions of a Hines method
> compartmental solver, and of a Discrete Event Solver for the efficient
> delivery of spike messages. Ideally, these should be in separate solvers,
> as they are in GENESIS 3 (unfortunately still under development).
>
> How is this being handled in MOOSE? Can networks of hsolved cells
> in MOOSE benefit from equivalent optimizations in spike delivery that
> GENESIS hsolve gives? Or is a separate mechanism used for spike delivery?
>
> On Tue, 29 Apr 2014, Dilawar Singh wrote:
>
>> Hi Saeed,
>>
>> We are in process of integrating 'hsolve' into async13 branch. Only today, I
>> got some sanity check of hsolve working. I am not sure how long it will take
>> to get hsolve properly integrated with python.
>>
>> For time being -- if you want to use async13 branch -- you can change the
>> solver to 'ee' from 'hsolve'.
>>
>> I'll let you know as soon as hsolve is ready.
>>
>> Dilawar
> ------------------------------------------------------------------------------
> "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
> Instantly run your Selenium tests across 300+ browser/OS combos. Get
> unparalleled scalability from the best Selenium testing platform available.
> Simple to use. Nothing to install. Get started now for free."
> http://p.sf.net/sfu/SauceLabs
> _______________________________________________
> moose-devel mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-devel
>
>
|
|
From: Jaeger, D. <dj...@em...> - 2014-04-29 20:24:04
|
Same interest here. -Dieter -----Original Message----- From: Dave Beeman [mailto:db...@Co...] Sent: Tuesday, April 29, 2014 4:05 PM To: Moose development issues Subject: Re: [moose-devel] Error in moose.connect method I will be very interested in trying out the MOOSE Python implemention of hsolved when it is fully ready. In GENESIS 2, hsolve performs both the functions of a Hines method compartmental solver, and of a Discrete Event Solver for the efficient delivery of spike messages. Ideally, these should be in separate solvers, as they are in GENESIS 3 (unfortunately still under development). How is this being handled in MOOSE? Can networks of hsolved cells in MOOSE benefit from equivalent optimizations in spike delivery that GENESIS hsolve gives? Or is a separate mechanism used for spike delivery? On Tue, 29 Apr 2014, Dilawar Singh wrote: > Hi Saeed, > > We are in process of integrating 'hsolve' into async13 branch. Only today, I > got some sanity check of hsolve working. I am not sure how long it will take > to get hsolve properly integrated with python. > > For time being -- if you want to use async13 branch -- you can change the > solver to 'ee' from 'hsolve'. > > I'll let you know as soon as hsolve is ready. > > Dilawar ------------------------------------------------------------------------------ "Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available. Simple to use. Nothing to install. Get started now for free." http://p.sf.net/sfu/SauceLabs _______________________________________________ moose-devel mailing list moo...@li... https://lists.sourceforge.net/lists/listinfo/moose-devel |
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