moose-generic — Moose general discussions

Re: [moose-generic] MOOSE_installation_problem

[Vadim A <ast...@nc...>]

Also,   I am getting error when I just importing MOOSE :

import moose
on node 0, numNodes = 1, numCores = 16, numComputeThreads = 16
ImportError: numpy.core.multiarray failed to import
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/astakhov/moose/moose/moose/python/moose/__init__.py", line 201, in <module>
    from .moose import *
  File "/home/astakhov/moose/moose/moose/python/moose/moose.py", line 40, in <module>
    from . import _moose
ImportError: numpy.core.multiarray failed to import



>  . Sorry for bothering but it seems that we are still missing something.
> 
> 
> I exported PYTHONPATH and trying to run examples from Demo/snippets
> 
> but none of them work for me and I am getting errors like this 
> 
> 
> Traceback (most recent call last):
> 
> 
>   File "./Demos/snippets/compartment_net.py", line 53, in <module>
>     from pylab import *
> …...
>     import numpy as np
>   File "/home/diag/opt/python/lib64/python/numpy/__init__.py", line 130, in <module>
>     import add_newdocs
>   File "/home/diag/opt/python/lib64/python/numpy/add_newdocs.py", line 9, in <module>
>     from lib import add_newdoc
>   File "/home/diag/opt/python/lib64/python/numpy/lib/__init__.py", line 4, in <module>
>     from type_check import *
>   File "/home/diag/opt/python/lib64/python/numpy/lib/type_check.py", line 8, in <module>
>     import numpy.core.numeric as _nx
>   File "/home/diag/opt/python/lib64/python/numpy/core/__init__.py", line 5, in <module>
>     import multiarray
> 
> 
> ImportError: /home/diag/opt/python/lib64/python/numpy/core/multiarray.so: undefined symbol: Py_InitModule4
> 
> 
> 
> Do you know what we might need to adjust ?
> 
> 
>   Is there any other test examples which we can try ?
> 
> Thanks a lot in advance for any advice.
> 
> Vadim.
> 
> 
> On Mar 12, 2013, at 8:22 PM, Subhasis Ray wrote:
> 
>> 
>> 
>> 
>> On Wed, Mar 13, 2013 at 2:53 AM, Vadim A <ast...@nc...> wrote:
>> You saying that I don't really need to do "make install"  ?
>> 
>> after " make BUILD=release USE_HDF5=0"
>> 
>> return -> pymoose module built.
>> 
>> 
>> All I need to do just export PYTHONPATH, correct ?
>>  
>> Yes, that is all :)
>> 
> 
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Re: [moose-generic] MOOSE_installation_problem

[Vadim A <ast...@nc...>]

Hi Subha. Sorry for bothering but it seems that we are still missing something.


I exported PYTHONPATH and trying to run examples from Demo/snippets

but none of them work for me and I am getting errors like this 


Traceback (most recent call last):


  File "./Demos/snippets/compartment_net.py", line 53, in <module>
    from pylab import *
…...
    import numpy as np
  File "/home/diag/opt/python/lib64/python/numpy/__init__.py", line 130, in <module>
    import add_newdocs
  File "/home/diag/opt/python/lib64/python/numpy/add_newdocs.py", line 9, in <module>
    from lib import add_newdoc
  File "/home/diag/opt/python/lib64/python/numpy/lib/__init__.py", line 4, in <module>
    from type_check import *
  File "/home/diag/opt/python/lib64/python/numpy/lib/type_check.py", line 8, in <module>
    import numpy.core.numeric as _nx
  File "/home/diag/opt/python/lib64/python/numpy/core/__init__.py", line 5, in <module>
    import multiarray


ImportError: /home/diag/opt/python/lib64/python/numpy/core/multiarray.so: undefined symbol: Py_InitModule4



Do you know what we might need to adjust ?


Also, I see that those snippets use "matplotlib" which we do not have on cluster. Is there any other test examples which we can try ?

Thanks a lot in advance for any advice.

Vadim.


On Mar 12, 2013, at 8:22 PM, Subhasis Ray wrote:

> 
> 
> 
> On Wed, Mar 13, 2013 at 2:53 AM, Vadim A <ast...@nc...> wrote:
> You saying that I don't really need to do "make install"  ?
> 
> after " make BUILD=release USE_HDF5=0"
> 
> return -> pymoose module built.
> 
> 
> All I need to do just export PYTHONPATH, correct ?
>  
> Yes, that is all :)
> 

Re: [moose-generic] MOOSE_installation_problem

[Subhasis R. <ray...@gm...>]

On Wed, Mar 13, 2013 at 2:53 AM, Vadim A <ast...@nc...> wrote:

> You saying that I don't really need to do "make install"  ?
>
> after " make BUILD=release USE_HDF5=0"
>
> return -> pymoose module built.
>
>
> All I need to do just export PYTHONPATH, correct ?
>

Yes, that is all :)

Re: [moose-generic] MOOSE_installation_problem

[Vadim A <ast...@nc...>]

You saying that I don't really need to do "make install"  ?

after " make BUILD=release USE_HDF5=0"

return -> pymoose module built.


All I need to do just export PYTHONPATH, correct ?

Vadim.


 
On Mar 11, 2013, at 9:46 PM, Subhasis Ray wrote:

> 
> 
> 
> On Tue, Mar 12, 2013 at 12:21 AM, Vadim A <ast...@nc...> wrote:
> 
> I was able to BUILD release and now trying to compile the code with all ;attest configurations.
> 
> But it try to install moose on the cluster python folder which is not allowed.
> 
> 
> What is the way to provide a path for my home directory to install "MOOSE"  should I modify  Make script ?
> 
> 
> There is not much to install. Rest is just a matter of adding {moose-directory}/pythoon to your PYTHONPATH environment variable. In case of bash shell you can put:
> 
> export PYTHONPATH={moose-directory}/python:$PYTHONPATH
> 
> in your .bashrc file. This will allow you to import MOOSE in Python scripts. I have added relevant documentation in the top level README file in the moose source tree.
> 
> Best,
>   Subha

Re: [moose-generic] MOOSE_installation_problem

[Subhasis R. <ray...@gm...>]

On Tue, Mar 12, 2013 at 12:21 AM, Vadim A <ast...@nc...> wrote:

>
> I was able to BUILD release and now trying to compile the code with all
> ;attest configurations.
>
> But it try to install moose on the cluster python folder which is not
> allowed.
>
>
> What is the way to provide a path for my home directory to install "MOOSE"
>  should I modify  Make script ?
>
>
There is not much to install. Rest is just a matter of adding
{moose-directory}/pythoon to your PYTHONPATH environment variable. In case
of bash shell you can put:

export PYTHONPATH={moose-directory}/python:$PYTHONPATH

in your .bashrc file. This will allow you to import MOOSE in Python
scripts. I have added relevant documentation in the top level README file
in the moose source tree.

Best,
  Subha

Re: [moose-generic] MOOSE_installation_problem

[Vadim A <ast...@nc...>]

Hi Subha.

I was able to BUILD release and now trying to compile the code with all ;attest configurations.

But it try to install moose on the cluster python folder which is not allowed.


What is the way to provide a path for my home directory to install "MOOSE"  should I modify  Make script ?

Best,

Vadim.


On Mar 8, 2013, at 7:33 PM, Subhasis Ray wrote:

> Hi,
> You seem to have a non-standard location for Python library. You should update this:
> 
> PYTHON_LDFLAGS := -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic -L{location of libpython2.7.so}
> 
> Best,
>  Subha
> 
> 
> On Sat, Mar 9, 2013 at 5:36 AM, Vadim A <ast...@nc...> wrote:
> I add those paths in Makefile
> 
> PYTHON_INCLUDES := -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/include/
> 
> PYTHON_LDFLAGS := -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic
> 
> 
> Python.h and all numpy header are there
> 
> and build went through further
> 
> but now complain that "/usr/bin/ld: cannot find -lpython2.7"
> 
> 
> Is there another place where we should set some flags ?
> 
> 
> g++ -shared -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic  -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DPYMOOSE -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/include/ -o python/moose/_moose.so msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o pymoose/_pymoose.o basecode/_basecode_pymoose.o -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm
> 
> /usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
> /usr/bin/ld: skipping incompatible /usr/lib/libpthread.a when searching for -lpthread
> /usr/bin/ld: skipping incompatible /usr/lib/libdl.so when searching for -ldl
> /usr/bin/ld: skipping incompatible /usr/lib/libdl.a when searching for -ldl
> /usr/bin/ld: skipping incompatible /usr/lib/libutil.so when searching for -lutil
> /usr/bin/ld: skipping incompatible /usr/lib/libutil.a when searching for -lutil
> /usr/bin/ld: cannot find -lpython2.7
> 
> 
> 
> Thanks a lot in advance for any advice.
> 
> V.
> 
> On Mar 6, 2013, at 9:56 PM, Subhasis Ray wrote:
> 
>> Dear Vadim,
>>   You can change the following with the corresponding values for your system:
>> 
>> ~ Line # 339 and 340 ...
>> 
>> PYTHON_INCLUDES := $(shell python-config --includes)
>> PYTHON_LDFLAGS := $(shell python-config --ldflags)
>> 
>> And as I suspected, your system does not seems have python-config installed (standard locations are /usr/bin or /usr/local/bin) because that is the command we are using in the Makefile to get the flags. It is supposed to come with Python development library, which is also a prerequisite for building moose. So please make sure you have that installed (does locate Python.h show something like: /usr/include/python2.7/Python.h? ).
>> 
>> Best,
>>  Subha
>> 
>> 
>> On Thu, Mar 7, 2013 at 6:16 AM, Vadim A <ast...@nc...> wrote:
>> Also this example is not clear where you've mentioned
>> 
>> 
>> "...and add the following to LIBS (output of python-config --ldflags) updated according to local system paths:
>> 
>> -L/usr/lib/python2.7/config -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
>> 
>> "
>> 
>> 
>> I do not see  "python2.7/config" in our system
>> 
>> 
>> Vadim.
>> 
>> On Mar 6, 2013, at 4:31 PM, Vadim A wrote:
>> 
>>> Hi Subha. 
>>> 
>>> Just wan to clarify one think. We decided to concentrate on simples installation for now and do the following steps:
>>> 
>>> make clean
>>> make BUILD=release USE_HDF5=0
>>> 
>>> 
>>> And it still give me the error
>>> 
>>> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DPYMOOSE -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/include/python2.7 moosemodule.cpp -c
>>> 
>>> moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or directory
>>> 
>>> 
>>> 
>>> But we loaded that module and it is located in our system here : /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h
>>> 
>>> 
>>> You've suggested to add it to CXXFLAGS flags. But where in the Makefile should we do that ?
>>> 
>>> 
>>> Best regards,
>>> 
>>> Vadim.
>>> 
>>> 
>>> 
>>> On Mar 5, 2013, at 7:43 PM, Subhasis Ray wrote:
>>> 
>>>> Dear Vadim,
>>>>  Did you run "make clean" before rebuilding each time? If you specify USE_HDF5=0, then the entire content of HDF5 related files get excluded from the compilation process. But from the build log for the first case it seems the object files were compiled with HDF5 support but the linking is being done without.
>>>>  In the second case, is it possible that your version of HDF5 library is linked to a different MPI library than what you set in MOOSE Makefile? Otherwise, it is also possible that HDF5 lib is dynamically linked to MPI and when you are building MOOSE without MPI support the MPI-lib location is not passed to compiler. In that case you may want to use mpicxx as the compiler at line 250:
>>>> 
>>>> # Here we automagically change compilers to deal with MPI.
>>>> ifdef USE_MPI
>>>>     CXX = mpicxx
>>>> #    CXX = /usr/local/mvapich2/bin/mpicxx
>>>> #    PARALLEL_DIR = parallel
>>>> #    PARALLEL_LIB = parallel/parallel.o
>>>> else
>>>>     CXX = g++ # <-- replace with mpicxx
>>>> #    CXX = CC    # Choose between Solaris CC and g++ on a Solaris machine
>>>> endif
>>>> 
>>>> 
>>>>  For the third case, we use the command:
>>>> 
>>>> python-config --includes
>>>> 
>>>> in the Makefile in order to get the location of header files for numpy and python. Looks like that does not work on your system. So you need to explicitly add 
>>>> -I/usr/include/python2.7 -I/usr/include/python2.7
>>>> 
>>>> and 
>>>> 
>>>> -I{location of numpy/arrayobject.h}
>>>> 
>>>> to CXXFLAGS
>>>> 
>>>> and add the following to LIBS (output of python-config --ldflags) updated according to local system paths:
>>>> 
>>>> -L/usr/lib/python2.7/config -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
>>>> 
>>>> 
>>>> hth,
>>>>   Subha
>>>> 
>>>> 
>>>> On Wed, Mar 6, 2013 at 1:43 AM, Vadim A <ast...@nc...> wrote:
>>>> Dear Subha.
>>>> 
>>>> I was trying three different ways to install MOOSE: without HDF5, with HDF5 and with MPI
>>>> 
>>>> Unfortunatelly, I did fail in all. Here the list of problems which we have. We would very appreciate you comments or suggestions what we might missing here.
>>>> 
>>>> 
>>>> 
>>>> (1) First I did
>>>> 
>>>> make BUILD=release USE_HDF5=0
>>>> 
>>>> 
>>>> 
>>>> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -o moose
>>>> 
>>>> 
>>>> 
>>>> And getting a lot of error like this:
>>>> 
>>>> 
>>>> builtins/_builtins.o: In function `HDF5WriterBase::setMode(unsigned int)':
>>>> (.text+0x11f40): undefined reference to `H5check_version'
>>>> ……………….
>>>> 
>>>> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
>>>> collect2: ld returned 1 exit status
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> (2) Then 
>>>> 
>>>> We have installed  HDF5 1.8.9 and I was trying to do build release:  
>>>> 
>>>> 
>>>> make BUILD=release
>>>> 
>>>>  
>>>> It seems that all libs get compiled and it can find HDF5 1.8.9
>>>> 
>>>> 
>>>> All Libs compiled
>>>> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5 -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
>>>> 
>>>> 
>>>> 
>>>> but it complain about a lot of "undefined references like this:
>>>> 
>>>> 
>>>> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
>>>> collect2: ld returned 1 exit status
>>>> make: *** [moose] Error 1
>>>> 
>>>> Looks like we still missing something. Should we have exactly same HDF5 library as you are using -> libhdf5-serial   ?
>>>> 
>>>> 
>>>> 
>>>> 
>>>> (3)
>>>> 
>>>> Also I did try to compile with MPI:    
>>>> 
>>>> 
>>>> make BUILD=release USE_MPI=1
>>>> 
>>>> All Libs compiled
>>>> mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5 -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
>>>> 
>>>> 
>>>> 
>>>> But getting error:   
>>>> 
>>>> 
>>>> moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or directory
>>>> 
>>>> 
>>>> 
>>>> But We have "numpy 1.6" loaded.  Should we set some other flag or should we have different version of "numpy" ?
>>>> 
>>>> 
>>>> 
>>>> Thanks a lot in advance for any advice.
>>>> 
>>>> Vadim.
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Mar 2, 2013, at 10:58 PM, Subhasis Ray wrote:
>>>> 
>>>>> Hi,
>>>>> In the serial version, HDF5 1.8.9 should work fine. It is used in HDF5DataWriter class to incrementally dump data into an HDF5 file. It was implemented to reduce memory usage for long running simulations generating gigabytes of data.
>>>>> Best,
>>>>>   Subha
>>>>> 
>>>>> 
>>>>> On Sun, Mar 3, 2013 at 1:22 AM, Majumdar, Amitava <maj...@sd...> wrote:
>>>>> If HDF5 version is the only issue, we can make HDF51.8.0 or higher available (actually we have HDF5 1.8.9 available
>>>>> on another parallel computer at SDSC).
>>>>> 
>>>>> -Amitvai
>>>>> From: Subhasis Ray [ray...@gm...]
>>>>> Sent: Saturday, March 02, 2013 1:35 AM
>>>>> To: Vadim A
>>>>> 
>>>>> Cc: Niraj Dudani; Yoshimoto, Kenneth; Majumdar, Amitava; moo...@li...
>>>>> Subject: Re: [moose-generic] MOOSE_installation_problem
>>>>> 
>>>>> Dear Vadim,
>>>>>   I would recommend that you avoid the MPI build at this point. The errors again are due to a minor issue with HDF5 library that can vary from package to package. These functions were introduced in HDF5 1.8.0. Either you need the same or a newer version installed. Otherwise, you can skip HDF5 support (which is somewhat experimental anyways) altogether by passing USE_HDF5=0 to "make" command.
>>>>>   Hope this helps,
>>>>>     Subha
>>>>> 
>>>>> 
>>>>> On Sat, Mar 2, 2013 at 5:35 AM, Vadim A <ast...@nc...> wrote:
>>>>> Dear Subha.
>>>>> 
>>>>> I set CXXFLAG to include mpi.h in "ifeq ($(BUILD),release)"
>>>>> 
>>>>> 
>>>>> like you've suggested  and it seems that it can find all libraries now but unfortunately  
>>>>> 
>>>>> 
>>>>> make BUILD=release USE_MPI=1
>>>>> 
>>>>> 
>>>>> produce another error  
>>>>> 
>>>>> 
>>>>> mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I. -I../basecode -I../msg HDF5DataWriter.cpp -c
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> ../basecode/Conv.h:1009: warning: converting to 'unsigned int' from 'const double'
>>>>> HDF5DataWriter.cpp: In member function 'hid_t HDF5DataWriter::get_dataset(std::string)':
>>>>> HDF5DataWriter.cpp:222: error: 'H5Gcreate2' was not declared in this scope
>>>>> HDF5DataWriter.cpp:225: error: 'H5Gopen2' was not declared in this scope
>>>>> HDF5DataWriter.cpp:258: error: 'H5Dopen2' was not declared in this scope
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> HDF5  and openmpi  libraries included. Do I still missing something ?
>>>>> 
>>>>> Thanks a lot in advance for any comments.
>>>>> 
>>>>> Vadim.
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On Feb 28, 2013, at 7:37 PM, Subhasis Ray wrote:
>>>>> 
>>>>>>  
>>>>>> 
>>>>>> 
>>>>>> Do not enable MPI unless you want to try the parallel version. To enable MPI, you have to pass the argument "USE_MPI=1" to make command.
>>>>>>  
>>>>>> 
>>>>>> 
>>>>>> # Here we automagically change compilers to deal with MPI.
>>>>>> ifdef USE_MPI
>>>>>>         CXX = mpicxx
>>>>>> #       CXX = /usr/local/mvapich2/bin/mpicxx
>>>>>>         PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel 
>>>>>>         PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/   #parallel/parallel.o
>>>>>> else
>>>>>>         CXX = g++
>>>>>> #       CXX = CC        # Choose between Solaris CC and g++ on a Solaris machine
>>>>>> endif
>>>>>> 
>>>>>> 
>>>>>>  
>>>>>> In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source directory and object file for the parallel version. They are not to be modified.
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> We are using "openmpi" which does not have "parallel.o"
>>>>>> 
>>>>>> As mentioned above, parallel.o will be generated by the build process. It looks like your version of hdf5 includes mpi.h and the compiler cannot find it. So you have to add -I{location of mpi.h} to the CXXFLAGS variable somewhere.Depending on your build type, you can append this to the CXXFLAG assignment under :
>>>>>> 
>>>>>> ifeq ($(BUILD),debug)
>>>>>> 
>>>>>> and/or under 
>>>>>> 
>>>>>> ifeq ($(BUILD),release)
>>>>>> 
>>>>>> 
>>>>>> Best,
>>>>>>   Subha
>>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> 
>>> 
>> 
>> 
> 
> 

Re: [moose-generic] MOOSE_installation_problem

[Subhasis R. <ray...@gm...>]

Hi,
You seem to have a non-standard location for Python library. You should
update this:

PYTHON_LDFLAGS := -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker
-export-dynamic* -L{location of libpython2.7.so}*

Best,
 Subha


On Sat, Mar 9, 2013 at 5:36 AM, Vadim A <ast...@nc...> wrote:

> I add those paths in Makefile
>
> PYTHON_INCLUDES := -I/home/diag/opt/python2.7/include/python2.7
> -I/home/diag/opt/python2.7/include/python2.7
> -I/home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/include/
>
> PYTHON_LDFLAGS := -lpthread -ldl -lutil -lm *-lpython2.7* -Xlinker
> -export-dynamic
>
>
> Python.h and all numpy header are there
>
> and build went through further
>
> but now complain that "/usr/bin/ld: cannot find -lpython2.7"
>
>
> Is there another place where we should set some flags ?
>
>
> g++ -shared -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic
>  -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long
> -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
> -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DPYMOOSE
> -I/home/diag/opt/python2.7/include/python2.7
> -I/home/diag/opt/python2.7/include/python2.7
> -I/home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/include/
> -o python/moose/_moose.so msg/_msg.o shell/_shell.o
> biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o
> scheduling/_scheduling.o builtins/_builtins.o device/_device.o
> kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o
> utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o
> signeur/_signeur.o pymoose/_pymoose.o basecode/_basecode_pymoose.o
> -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib
> -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm
>
> /usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching
> for -lpthread
> /usr/bin/ld: skipping incompatible /usr/lib/libpthread.a when searching
> for -lpthread
> /usr/bin/ld: skipping incompatible /usr/lib/libdl.so when searching for
> -ldl
> /usr/bin/ld: skipping incompatible /usr/lib/libdl.a when searching for -ldl
> /usr/bin/ld: skipping incompatible /usr/lib/libutil.so when searching for
> -lutil
> /usr/bin/ld: skipping incompatible /usr/lib/libutil.a when searching for
> -lutil
> /usr/bin/ld: cannot find -lpython2.7
>
>
>
> Thanks a lot in advance for any advice.
>
> V.
>
> On Mar 6, 2013, at 9:56 PM, Subhasis Ray wrote:
>
> Dear Vadim,
>   You can change the following with the corresponding values for your
> system:
>
> ~ Line # 339 and 340 ...
>
> PYTHON_INCLUDES := $(shell python-config --includes)
> PYTHON_LDFLAGS := $(shell python-config --ldflags)
>
> And as I suspected, your system does not seems have python-config
> installed (standard locations are /usr/bin or /usr/local/bin) because that
> is the command we are using in the Makefile to get the flags. It is
> supposed to come with Python development library, which is also a
> prerequisite for building moose. So please make sure you have that
> installed (does locate Python.h show something like:
> /usr/include/python2.7/Python.h? ).
>
> Best,
>  Subha
>
>
> On Thu, Mar 7, 2013 at 6:16 AM, Vadim A <ast...@nc...> wrote:
>
>> Also this example is not clear where you've mentioned
>>
>>
>> "...and add the following to LIBS (output of python-config --ldflags)
>> updated according to local system paths:
>>
>> -L/usr/lib/python2.7/config -lpthread -ldl -lutil -lm -lpython2.7
>> -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
>>
>> "
>>
>>
>> I do not see  "python2.7/config" in our system
>>
>>
>> Vadim.
>>
>> On Mar 6, 2013, at 4:31 PM, Vadim A wrote:
>>
>> Hi Subha.
>>
>> Just wan to clarify one think. We decided to concentrate on simples
>> installation for now and do the following steps:
>>
>> make clean
>> make BUILD=release USE_HDF5=0
>>
>>
>> And it still give me the error
>>
>> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>> -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DPYMOOSE
>> -I/home/diag/opt/python2.7/include/python2.7
>> -I/home/diag/opt/python2.7/include/python2.7 moosemodule.cpp -c
>>
>> moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or
>> directory
>>
>>
>>
>> But we loaded that module and it is located in our system here :
>> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h
>>
>>
>> You've suggested to add it to CXXFLAGS flags. But where in the Makefile
>> should we do that ?
>>
>>
>> Best regards,
>>
>> Vadim.
>>
>>
>>
>> On Mar 5, 2013, at 7:43 PM, Subhasis Ray wrote:
>>
>> Dear Vadim,
>>  Did you run "make clean" before rebuilding each time? If you specify
>> USE_HDF5=0, then the entire content of HDF5 related files get excluded from
>> the compilation process. But from the build log for the first case it seems
>> the object files were compiled with HDF5 support but the linking is being
>> done without.
>>  In the second case, is it possible that your version of HDF5 library is
>> linked to a different MPI library than what you set in MOOSE Makefile?
>> Otherwise, it is also possible that HDF5 lib is dynamically linked to MPI
>> and when you are building MOOSE without MPI support the MPI-lib location is
>> not passed to compiler. In that case you may want to use mpicxx as the
>> compiler at line 250:
>>
>> # Here we automagically change compilers to deal with MPI.
>> ifdef USE_MPI
>>     CXX = mpicxx
>> #    CXX = /usr/local/mvapich2/bin/mpicxx
>> #    PARALLEL_DIR = parallel
>> #    PARALLEL_LIB = parallel/parallel.o
>> else
>>     CXX = g++ # <-- replace with mpicxx
>> #    CXX = CC    # Choose between Solaris CC and g++ on a Solaris machine
>> endif
>>
>>
>>  For the third case, we use the command:
>>
>> python-config --includes
>>
>> in the Makefile in order to get the location of header files for numpy
>> and python. Looks like that does not work on your system. So you need to
>> explicitly add
>> -I/usr/include/python2.7 -I/usr/include/python2.7
>>
>> and
>>
>> -I{location of numpy/arrayobject.h}
>>
>> to CXXFLAGS
>>
>> and add the following to LIBS (output of python-config --ldflags) updated
>> according to local system paths:
>>
>> -L/usr/lib/python2.7/config -lpthread -ldl -lutil -lm -lpython2.7
>> -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
>>
>>
>> hth,
>>   Subha
>>
>>
>> On Wed, Mar 6, 2013 at 1:43 AM, Vadim A <ast...@nc...> wrote:
>>
>>> Dear Subha.
>>>
>>> I was trying three different ways to install MOOSE: without HDF5, with
>>> HDF5 and with MPI
>>>
>>> Unfortunatelly, I did fail in all. Here the list of problems which we
>>> have. We would very appreciate you comments or suggestions what we might
>>> missing here.
>>>
>>>
>>>
>>> (1) First I did
>>>
>>> make BUILD=release USE_HDF5=0
>>>
>>>
>>>
>>> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>>> -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    basecode/_basecode.o
>>> msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o
>>> randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o
>>> device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o
>>> regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o
>>> manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib
>>> -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib
>>> -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -o moose
>>>
>>>
>>>
>>> And getting a lot of error like this:
>>>
>>>
>>> builtins/_builtins.o: In function `HDF5WriterBase::setMode(unsigned
>>> int)':
>>> (.text+0x11f40): undefined reference to `H5check_version'
>>> ……………….
>>>
>>> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for
>>> MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
>>> collect2: ld returned 1 exit status
>>>
>>>
>>>
>>>
>>>
>>>
>>> (2) Then
>>>
>>> We have installed  HDF5 1.8.9 and I was trying to do build release:
>>>
>>>
>>> make BUILD=release
>>>
>>>
>>> It seems that all libs get compiled and it can find HDF5 1.8.9
>>>
>>>
>>> All Libs compiled
>>> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>>> -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>>>  -DH5_NO_DEPRECATED_SYMBOLS -*I
>>>  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include* basecode/_basecode.o
>>> msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o
>>> randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o
>>> device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o
>>> regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o
>>> manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib
>>> -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib
>>> -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5
>>> -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
>>>
>>>
>>>
>>> but it complain about a lot of "undefined references like this:
>>>
>>>
>>> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for
>>> MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
>>> collect2: ld returned 1 exit status
>>> make: *** [moose] Error 1
>>>
>>> Looks like we still missing something. Should we have exactly same HDF5
>>> library as you are using -> *libhdf5-serial   ?*
>>>
>>>
>>>
>>>
>>> (3)
>>>
>>> Also I did try to compile with MPI:
>>>
>>>
>>> make BUILD=release USE_MPI=1
>>>
>>> All Libs compiled
>>> mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>>> -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I
>>> /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>>>  -DH5_NO_DEPRECATED_SYMBOLS -I
>>>  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include basecode/_basecode.o
>>> msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o
>>> randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o
>>> device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o
>>> regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o
>>> manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib
>>> -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib
>>> -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5
>>> -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
>>>
>>>
>>>
>>> But getting error:
>>>
>>>
>>> moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or
>>> directory
>>>
>>>
>>>
>>> But We have "numpy 1.6" loaded.  Should we set some other flag or should
>>> we have different version of "numpy" ?
>>>
>>>
>>>
>>> Thanks a lot in advance for any advice.
>>>
>>> Vadim.
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On Mar 2, 2013, at 10:58 PM, Subhasis Ray wrote:
>>>
>>> Hi,
>>> In the serial version, HDF5 1.8.9 should work fine. It is used in
>>> HDF5DataWriter class to incrementally dump data into an HDF5 file. It was
>>> implemented to reduce memory usage for long running simulations generating
>>> gigabytes of data.
>>> Best,
>>>   Subha
>>>
>>>
>>> On Sun, Mar 3, 2013 at 1:22 AM, Majumdar, Amitava <maj...@sd...>wrote:
>>>
>>>>  If HDF5 version is the only issue, we can make HDF51.8.0 or higher
>>>> available (actually we have HDF5 1.8.9 available
>>>> on another parallel computer at SDSC).
>>>>
>>>> -Amitvai
>>>>  ------------------------------
>>>> *From:* Subhasis Ray [ray...@gm...]
>>>> *Sent:* Saturday, March 02, 2013 1:35 AM
>>>> *To:* Vadim A
>>>>
>>>> *Cc:* Niraj Dudani; Yoshimoto, Kenneth; Majumdar, Amitava;
>>>> moo...@li...
>>>> *Subject:* Re: [moose-generic] MOOSE_installation_problem
>>>>
>>>>    Dear Vadim,
>>>>    I would recommend that you avoid the MPI build at this point. The
>>>> errors again are due to a minor issue with HDF5 library that can vary from
>>>> package to package. These functions were introduced in HDF5 1.8.0. Either
>>>> you need the same or a newer version installed. Otherwise, you can skip
>>>> HDF5 support (which is somewhat experimental anyways) altogether by passing
>>>> USE_HDF5=0 to "make" command.
>>>>    Hope this helps,
>>>>      Subha
>>>>
>>>>
>>>> On Sat, Mar 2, 2013 at 5:35 AM, Vadim A <ast...@nc...>wrote:
>>>>
>>>>> Dear Subha.
>>>>>
>>>>>  I set CXXFLAG to include mpi.h in "ifeq ($(BUILD),release)"
>>>>>
>>>>>
>>>>>  like you've suggested  and it seems that it can find all libraries
>>>>> now but unfortunately
>>>>>
>>>>>
>>>>>  make BUILD=release USE_MPI=1
>>>>>
>>>>>
>>>>>  produce another error
>>>>>
>>>>>
>>>>>  mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>>>>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>>>>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>>>>> -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I
>>>>> /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>>>>>  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I.
>>>>> -I../basecode -I../msg HDF5DataWriter.cpp -c
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>  ../basecode/Conv.h:1009: warning: converting to 'unsigned int' from
>>>>> 'const double'
>>>>> HDF5DataWriter.cpp: In member function 'hid_t
>>>>> HDF5DataWriter::get_dataset(std::string)':
>>>>> HDF5DataWriter.cpp:222: error: 'H5Gcreate2' was not declared in this
>>>>> scope
>>>>> HDF5DataWriter.cpp:225: error: 'H5Gopen2' was not declared in this
>>>>> scope
>>>>> HDF5DataWriter.cpp:258: error: 'H5Dopen2' was not declared in this
>>>>> scope
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>  HDF5  and openmpi  libraries included. Do I still missing something ?
>>>>>
>>>>>  Thanks a lot in advance for any comments.
>>>>>
>>>>>  Vadim.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>  On Feb 28, 2013, at 7:37 PM, Subhasis Ray wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Do not enable MPI unless you want to try the parallel version. To
>>>>> enable MPI, you have to pass the argument "USE_MPI=1" to make command.
>>>>>
>>>>>
>>>>>>
>>>>>>
>>>>>>  # Here we automagically change compilers to deal with MPI.
>>>>>> ifdef USE_MPI
>>>>>>         CXX = mpicxx
>>>>>> #       CXX = /usr/local/mvapich2/bin/mpicxx
>>>>>>         PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel
>>>>>>          PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/
>>>>>> #parallel/parallel.o
>>>>>> else
>>>>>>         CXX = g++
>>>>>> #       CXX = CC        # Choose between Solaris CC and g++ on a
>>>>>> Solaris machine
>>>>>> endif
>>>>>>
>>>>>>
>>>>>>
>>>>>  In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source
>>>>> directory and object file for the parallel version. They are not to be
>>>>> modified.
>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>  We are using "openmpi" which does not have "parallel.o"
>>>>>>
>>>>>
>>>>>  As mentioned above, parallel.o will be generated by the build
>>>>> process. It looks like your version of hdf5 includes mpi.h and the compiler
>>>>> cannot find it. So you have to add -I{location of mpi.h} to the CXXFLAGS
>>>>> variable somewhere.Depending on your build type, you can append this to the
>>>>> CXXFLAG assignment under :
>>>>>
>>>>> ifeq ($(BUILD),debug)
>>>>>
>>>>>  and/or under
>>>>>
>>>>> ifeq ($(BUILD),release)
>>>>>
>>>>>
>>>>>  Best,
>>>>>    Subha
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>>
>>
>
>

Re: [moose-generic] MOOSE_installation_problem

[Vadim A <ast...@nc...>]

I add those paths in Makefile

PYTHON_INCLUDES := -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/include/

PYTHON_LDFLAGS := -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic


Python.h and all numpy header are there

and build went through further

but now complain that "/usr/bin/ld: cannot find -lpython2.7"


Is there another place where we should set some flags ?


g++ -shared -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic  -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DPYMOOSE -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/include/ -o python/moose/_moose.so msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o pymoose/_pymoose.o basecode/_basecode_pymoose.o -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm

/usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/libpthread.a when searching for -lpthread
/usr/bin/ld: skipping incompatible /usr/lib/libdl.so when searching for -ldl
/usr/bin/ld: skipping incompatible /usr/lib/libdl.a when searching for -ldl
/usr/bin/ld: skipping incompatible /usr/lib/libutil.so when searching for -lutil
/usr/bin/ld: skipping incompatible /usr/lib/libutil.a when searching for -lutil
/usr/bin/ld: cannot find -lpython2.7



Thanks a lot in advance for any advice.

V.

On Mar 6, 2013, at 9:56 PM, Subhasis Ray wrote:

> Dear Vadim,
>   You can change the following with the corresponding values for your system:
> 
> ~ Line # 339 and 340 ...
> 
> PYTHON_INCLUDES := $(shell python-config --includes)
> PYTHON_LDFLAGS := $(shell python-config --ldflags)
> 
> And as I suspected, your system does not seems have python-config installed (standard locations are /usr/bin or /usr/local/bin) because that is the command we are using in the Makefile to get the flags. It is supposed to come with Python development library, which is also a prerequisite for building moose. So please make sure you have that installed (does locate Python.h show something like: /usr/include/python2.7/Python.h? ).
> 
> Best,
>  Subha
> 
> 
> On Thu, Mar 7, 2013 at 6:16 AM, Vadim A <ast...@nc...> wrote:
> Also this example is not clear where you've mentioned
> 
> 
> "...and add the following to LIBS (output of python-config --ldflags) updated according to local system paths:
> 
> -L/usr/lib/python2.7/config -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
> 
> "
> 
> 
> I do not see  "python2.7/config" in our system
> 
> 
> Vadim.
> 
> On Mar 6, 2013, at 4:31 PM, Vadim A wrote:
> 
>> Hi Subha. 
>> 
>> Just wan to clarify one think. We decided to concentrate on simples installation for now and do the following steps:
>> 
>> make clean
>> make BUILD=release USE_HDF5=0
>> 
>> 
>> And it still give me the error
>> 
>> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DPYMOOSE -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/include/python2.7 moosemodule.cpp -c
>> 
>> moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or directory
>> 
>> 
>> 
>> But we loaded that module and it is located in our system here : /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h
>> 
>> 
>> You've suggested to add it to CXXFLAGS flags. But where in the Makefile should we do that ?
>> 
>> 
>> Best regards,
>> 
>> Vadim.
>> 
>> 
>> 
>> On Mar 5, 2013, at 7:43 PM, Subhasis Ray wrote:
>> 
>>> Dear Vadim,
>>>  Did you run "make clean" before rebuilding each time? If you specify USE_HDF5=0, then the entire content of HDF5 related files get excluded from the compilation process. But from the build log for the first case it seems the object files were compiled with HDF5 support but the linking is being done without.
>>>  In the second case, is it possible that your version of HDF5 library is linked to a different MPI library than what you set in MOOSE Makefile? Otherwise, it is also possible that HDF5 lib is dynamically linked to MPI and when you are building MOOSE without MPI support the MPI-lib location is not passed to compiler. In that case you may want to use mpicxx as the compiler at line 250:
>>> 
>>> # Here we automagically change compilers to deal with MPI.
>>> ifdef USE_MPI
>>>     CXX = mpicxx
>>> #    CXX = /usr/local/mvapich2/bin/mpicxx
>>> #    PARALLEL_DIR = parallel
>>> #    PARALLEL_LIB = parallel/parallel.o
>>> else
>>>     CXX = g++ # <-- replace with mpicxx
>>> #    CXX = CC    # Choose between Solaris CC and g++ on a Solaris machine
>>> endif
>>> 
>>> 
>>>  For the third case, we use the command:
>>> 
>>> python-config --includes
>>> 
>>> in the Makefile in order to get the location of header files for numpy and python. Looks like that does not work on your system. So you need to explicitly add 
>>> -I/usr/include/python2.7 -I/usr/include/python2.7
>>> 
>>> and 
>>> 
>>> -I{location of numpy/arrayobject.h}
>>> 
>>> to CXXFLAGS
>>> 
>>> and add the following to LIBS (output of python-config --ldflags) updated according to local system paths:
>>> 
>>> -L/usr/lib/python2.7/config -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
>>> 
>>> 
>>> hth,
>>>   Subha
>>> 
>>> 
>>> On Wed, Mar 6, 2013 at 1:43 AM, Vadim A <ast...@nc...> wrote:
>>> Dear Subha.
>>> 
>>> I was trying three different ways to install MOOSE: without HDF5, with HDF5 and with MPI
>>> 
>>> Unfortunatelly, I did fail in all. Here the list of problems which we have. We would very appreciate you comments or suggestions what we might missing here.
>>> 
>>> 
>>> 
>>> (1) First I did
>>> 
>>> make BUILD=release USE_HDF5=0
>>> 
>>> 
>>> 
>>> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -o moose
>>> 
>>> 
>>> 
>>> And getting a lot of error like this:
>>> 
>>> 
>>> builtins/_builtins.o: In function `HDF5WriterBase::setMode(unsigned int)':
>>> (.text+0x11f40): undefined reference to `H5check_version'
>>> ……………….
>>> 
>>> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
>>> collect2: ld returned 1 exit status
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> (2) Then 
>>> 
>>> We have installed  HDF5 1.8.9 and I was trying to do build release:  
>>> 
>>> 
>>> make BUILD=release
>>> 
>>>  
>>> It seems that all libs get compiled and it can find HDF5 1.8.9
>>> 
>>> 
>>> All Libs compiled
>>> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5 -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
>>> 
>>> 
>>> 
>>> but it complain about a lot of "undefined references like this:
>>> 
>>> 
>>> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
>>> collect2: ld returned 1 exit status
>>> make: *** [moose] Error 1
>>> 
>>> Looks like we still missing something. Should we have exactly same HDF5 library as you are using -> libhdf5-serial   ?
>>> 
>>> 
>>> 
>>> 
>>> (3)
>>> 
>>> Also I did try to compile with MPI:    
>>> 
>>> 
>>> make BUILD=release USE_MPI=1
>>> 
>>> All Libs compiled
>>> mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5 -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
>>> 
>>> 
>>> 
>>> But getting error:   
>>> 
>>> 
>>> moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or directory
>>> 
>>> 
>>> 
>>> But We have "numpy 1.6" loaded.  Should we set some other flag or should we have different version of "numpy" ?
>>> 
>>> 
>>> 
>>> Thanks a lot in advance for any advice.
>>> 
>>> Vadim.
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Mar 2, 2013, at 10:58 PM, Subhasis Ray wrote:
>>> 
>>>> Hi,
>>>> In the serial version, HDF5 1.8.9 should work fine. It is used in HDF5DataWriter class to incrementally dump data into an HDF5 file. It was implemented to reduce memory usage for long running simulations generating gigabytes of data.
>>>> Best,
>>>>   Subha
>>>> 
>>>> 
>>>> On Sun, Mar 3, 2013 at 1:22 AM, Majumdar, Amitava <maj...@sd...> wrote:
>>>> If HDF5 version is the only issue, we can make HDF51.8.0 or higher available (actually we have HDF5 1.8.9 available
>>>> on another parallel computer at SDSC).
>>>> 
>>>> -Amitvai
>>>> From: Subhasis Ray [ray...@gm...]
>>>> Sent: Saturday, March 02, 2013 1:35 AM
>>>> To: Vadim A
>>>> 
>>>> Cc: Niraj Dudani; Yoshimoto, Kenneth; Majumdar, Amitava; moo...@li...
>>>> Subject: Re: [moose-generic] MOOSE_installation_problem
>>>> 
>>>> Dear Vadim,
>>>>   I would recommend that you avoid the MPI build at this point. The errors again are due to a minor issue with HDF5 library that can vary from package to package. These functions were introduced in HDF5 1.8.0. Either you need the same or a newer version installed. Otherwise, you can skip HDF5 support (which is somewhat experimental anyways) altogether by passing USE_HDF5=0 to "make" command.
>>>>   Hope this helps,
>>>>     Subha
>>>> 
>>>> 
>>>> On Sat, Mar 2, 2013 at 5:35 AM, Vadim A <ast...@nc...> wrote:
>>>> Dear Subha.
>>>> 
>>>> I set CXXFLAG to include mpi.h in "ifeq ($(BUILD),release)"
>>>> 
>>>> 
>>>> like you've suggested  and it seems that it can find all libraries now but unfortunately  
>>>> 
>>>> 
>>>> make BUILD=release USE_MPI=1
>>>> 
>>>> 
>>>> produce another error  
>>>> 
>>>> 
>>>> mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/     -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I. -I../basecode -I../msg HDF5DataWriter.cpp -c
>>>> 
>>>> 
>>>> 
>>>> 
>>>> ../basecode/Conv.h:1009: warning: converting to 'unsigned int' from 'const double'
>>>> HDF5DataWriter.cpp: In member function 'hid_t HDF5DataWriter::get_dataset(std::string)':
>>>> HDF5DataWriter.cpp:222: error: 'H5Gcreate2' was not declared in this scope
>>>> HDF5DataWriter.cpp:225: error: 'H5Gopen2' was not declared in this scope
>>>> HDF5DataWriter.cpp:258: error: 'H5Dopen2' was not declared in this scope
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> HDF5  and openmpi  libraries included. Do I still missing something ?
>>>> 
>>>> Thanks a lot in advance for any comments.
>>>> 
>>>> Vadim.
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On Feb 28, 2013, at 7:37 PM, Subhasis Ray wrote:
>>>> 
>>>>>  
>>>>> 
>>>>> 
>>>>> Do not enable MPI unless you want to try the parallel version. To enable MPI, you have to pass the argument "USE_MPI=1" to make command.
>>>>>  
>>>>> 
>>>>> 
>>>>> # Here we automagically change compilers to deal with MPI.
>>>>> ifdef USE_MPI
>>>>>         CXX = mpicxx
>>>>> #       CXX = /usr/local/mvapich2/bin/mpicxx
>>>>>         PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel 
>>>>>         PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/   #parallel/parallel.o
>>>>> else
>>>>>         CXX = g++
>>>>> #       CXX = CC        # Choose between Solaris CC and g++ on a Solaris machine
>>>>> endif
>>>>> 
>>>>> 
>>>>>  
>>>>> In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source directory and object file for the parallel version. They are not to be modified.
>>>>> 
>>>>> 
>>>>> 
>>>>> We are using "openmpi" which does not have "parallel.o"
>>>>> 
>>>>> As mentioned above, parallel.o will be generated by the build process. It looks like your version of hdf5 includes mpi.h and the compiler cannot find it. So you have to add -I{location of mpi.h} to the CXXFLAGS variable somewhere.Depending on your build type, you can append this to the CXXFLAG assignment under :
>>>>> 
>>>>> ifeq ($(BUILD),debug)
>>>>> 
>>>>> and/or under 
>>>>> 
>>>>> ifeq ($(BUILD),release)
>>>>> 
>>>>> 
>>>>> Best,
>>>>>   Subha
>>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>> 
> 
> 

Re: [moose-generic] MOOSE_installation_problem

[Subhasis R. <ray...@gm...>]

Dear Vadim,
  You can change the following with the corresponding values for your
system:

~ Line # 339 and 340 ...

PYTHON_INCLUDES := $(shell python-config --includes)
PYTHON_LDFLAGS := $(shell python-config --ldflags)

And as I suspected, your system does not seems have python-config installed
(standard locations are /usr/bin or /usr/local/bin) because that is the
command we are using in the Makefile to get the flags. It is supposed to
come with Python development library, which is also a prerequisite for
building moose. So please make sure you have that installed (does locate
Python.h show something like: /usr/include/python2.7/Python.h? ).

Best,
 Subha


On Thu, Mar 7, 2013 at 6:16 AM, Vadim A <ast...@nc...> wrote:

> Also this example is not clear where you've mentioned
>
>
> "...and add the following to LIBS (output of python-config --ldflags)
> updated according to local system paths:
>
> -L/usr/lib/python2.7/config -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker
> -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
>
> "
>
>
> I do not see  "python2.7/config" in our system
>
>
> Vadim.
>
> On Mar 6, 2013, at 4:31 PM, Vadim A wrote:
>
> Hi Subha.
>
> Just wan to clarify one think. We decided to concentrate on simples
> installation for now and do the following steps:
>
> make clean
> make BUILD=release USE_HDF5=0
>
>
> And it still give me the error
>
> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
> -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DPYMOOSE
> -I/home/diag/opt/python2.7/include/python2.7
> -I/home/diag/opt/python2.7/include/python2.7 moosemodule.cpp -c
>
> moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or
> directory
>
>
>
> But we loaded that module and it is located in our system here :
> /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h
>
>
> You've suggested to add it to CXXFLAGS flags. But where in the Makefile
> should we do that ?
>
>
> Best regards,
>
> Vadim.
>
>
>
> On Mar 5, 2013, at 7:43 PM, Subhasis Ray wrote:
>
> Dear Vadim,
>  Did you run "make clean" before rebuilding each time? If you specify
> USE_HDF5=0, then the entire content of HDF5 related files get excluded from
> the compilation process. But from the build log for the first case it seems
> the object files were compiled with HDF5 support but the linking is being
> done without.
>  In the second case, is it possible that your version of HDF5 library is
> linked to a different MPI library than what you set in MOOSE Makefile?
> Otherwise, it is also possible that HDF5 lib is dynamically linked to MPI
> and when you are building MOOSE without MPI support the MPI-lib location is
> not passed to compiler. In that case you may want to use mpicxx as the
> compiler at line 250:
>
> # Here we automagically change compilers to deal with MPI.
> ifdef USE_MPI
>     CXX = mpicxx
> #    CXX = /usr/local/mvapich2/bin/mpicxx
> #    PARALLEL_DIR = parallel
> #    PARALLEL_LIB = parallel/parallel.o
> else
>     CXX = g++ # <-- replace with mpicxx
> #    CXX = CC    # Choose between Solaris CC and g++ on a Solaris machine
> endif
>
>
>  For the third case, we use the command:
>
> python-config --includes
>
> in the Makefile in order to get the location of header files for numpy and
> python. Looks like that does not work on your system. So you need to
> explicitly add
> -I/usr/include/python2.7 -I/usr/include/python2.7
>
> and
>
> -I{location of numpy/arrayobject.h}
>
> to CXXFLAGS
>
> and add the following to LIBS (output of python-config --ldflags) updated
> according to local system paths:
>
> -L/usr/lib/python2.7/config -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker
> -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
>
>
> hth,
>   Subha
>
>
> On Wed, Mar 6, 2013 at 1:43 AM, Vadim A <ast...@nc...> wrote:
>
>> Dear Subha.
>>
>> I was trying three different ways to install MOOSE: without HDF5, with
>> HDF5 and with MPI
>>
>> Unfortunatelly, I did fail in all. Here the list of problems which we
>> have. We would very appreciate you comments or suggestions what we might
>> missing here.
>>
>>
>>
>> (1) First I did
>>
>> make BUILD=release USE_HDF5=0
>>
>>
>>
>> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>> -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    basecode/_basecode.o
>> msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o
>> randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o
>> device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o
>> regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o
>> manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib
>> -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib
>> -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -o moose
>>
>>
>>
>> And getting a lot of error like this:
>>
>>
>> builtins/_builtins.o: In function `HDF5WriterBase::setMode(unsigned int)':
>> (.text+0x11f40): undefined reference to `H5check_version'
>> ……………….
>>
>> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for
>> MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
>> collect2: ld returned 1 exit status
>>
>>
>>
>>
>>
>>
>> (2) Then
>>
>> We have installed  HDF5 1.8.9 and I was trying to do build release:
>>
>>
>> make BUILD=release
>>
>>
>> It seems that all libs get compiled and it can find HDF5 1.8.9
>>
>>
>> All Libs compiled
>> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>> -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>>  -DH5_NO_DEPRECATED_SYMBOLS -*I
>>  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include* basecode/_basecode.o
>> msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o
>> randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o
>> device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o
>> regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o
>> manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib
>> -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib
>> -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5
>> -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
>>
>>
>>
>> but it complain about a lot of "undefined references like this:
>>
>>
>> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for
>> MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
>> collect2: ld returned 1 exit status
>> make: *** [moose] Error 1
>>
>> Looks like we still missing something. Should we have exactly same HDF5
>> library as you are using -> *libhdf5-serial   ?*
>>
>>
>>
>>
>> (3)
>>
>> Also I did try to compile with MPI:
>>
>>
>> make BUILD=release USE_MPI=1
>>
>> All Libs compiled
>> mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>> -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I
>> /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>>  -DH5_NO_DEPRECATED_SYMBOLS -I
>>  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include basecode/_basecode.o
>> msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o
>> randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o
>> device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o
>> regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o
>> manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib
>> -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib
>> -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5
>> -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
>>
>>
>>
>> But getting error:
>>
>>
>> moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or
>> directory
>>
>>
>>
>> But We have "numpy 1.6" loaded.  Should we set some other flag or should
>> we have different version of "numpy" ?
>>
>>
>>
>> Thanks a lot in advance for any advice.
>>
>> Vadim.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Mar 2, 2013, at 10:58 PM, Subhasis Ray wrote:
>>
>> Hi,
>> In the serial version, HDF5 1.8.9 should work fine. It is used in
>> HDF5DataWriter class to incrementally dump data into an HDF5 file. It was
>> implemented to reduce memory usage for long running simulations generating
>> gigabytes of data.
>> Best,
>>   Subha
>>
>>
>> On Sun, Mar 3, 2013 at 1:22 AM, Majumdar, Amitava <maj...@sd...>wrote:
>>
>>>  If HDF5 version is the only issue, we can make HDF51.8.0 or higher
>>> available (actually we have HDF5 1.8.9 available
>>> on another parallel computer at SDSC).
>>>
>>> -Amitvai
>>>  ------------------------------
>>> *From:* Subhasis Ray [ray...@gm...]
>>> *Sent:* Saturday, March 02, 2013 1:35 AM
>>> *To:* Vadim A
>>>
>>> *Cc:* Niraj Dudani; Yoshimoto, Kenneth; Majumdar, Amitava;
>>> moo...@li...
>>> *Subject:* Re: [moose-generic] MOOSE_installation_problem
>>>
>>>    Dear Vadim,
>>>    I would recommend that you avoid the MPI build at this point. The
>>> errors again are due to a minor issue with HDF5 library that can vary from
>>> package to package. These functions were introduced in HDF5 1.8.0. Either
>>> you need the same or a newer version installed. Otherwise, you can skip
>>> HDF5 support (which is somewhat experimental anyways) altogether by passing
>>> USE_HDF5=0 to "make" command.
>>>    Hope this helps,
>>>      Subha
>>>
>>>
>>> On Sat, Mar 2, 2013 at 5:35 AM, Vadim A <ast...@nc...> wrote:
>>>
>>>> Dear Subha.
>>>>
>>>>  I set CXXFLAG to include mpi.h in "ifeq ($(BUILD),release)"
>>>>
>>>>
>>>>  like you've suggested  and it seems that it can find all libraries
>>>> now but unfortunately
>>>>
>>>>
>>>>  make BUILD=release USE_MPI=1
>>>>
>>>>
>>>>  produce another error
>>>>
>>>>
>>>>  mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>>>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>>>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>>>> -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I
>>>> /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>>>>  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I.
>>>> -I../basecode -I../msg HDF5DataWriter.cpp -c
>>>>
>>>>
>>>>
>>>>
>>>>  ../basecode/Conv.h:1009: warning: converting to 'unsigned int' from
>>>> 'const double'
>>>> HDF5DataWriter.cpp: In member function 'hid_t
>>>> HDF5DataWriter::get_dataset(std::string)':
>>>> HDF5DataWriter.cpp:222: error: 'H5Gcreate2' was not declared in this
>>>> scope
>>>> HDF5DataWriter.cpp:225: error: 'H5Gopen2' was not declared in this scope
>>>> HDF5DataWriter.cpp:258: error: 'H5Dopen2' was not declared in this scope
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>  HDF5  and openmpi  libraries included. Do I still missing something ?
>>>>
>>>>  Thanks a lot in advance for any comments.
>>>>
>>>>  Vadim.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>  On Feb 28, 2013, at 7:37 PM, Subhasis Ray wrote:
>>>>
>>>>
>>>>
>>>>
>>>> Do not enable MPI unless you want to try the parallel version. To
>>>> enable MPI, you have to pass the argument "USE_MPI=1" to make command.
>>>>
>>>>
>>>>>
>>>>>
>>>>>  # Here we automagically change compilers to deal with MPI.
>>>>> ifdef USE_MPI
>>>>>         CXX = mpicxx
>>>>> #       CXX = /usr/local/mvapich2/bin/mpicxx
>>>>>         PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel
>>>>>          PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/
>>>>> #parallel/parallel.o
>>>>> else
>>>>>         CXX = g++
>>>>> #       CXX = CC        # Choose between Solaris CC and g++ on a
>>>>> Solaris machine
>>>>> endif
>>>>>
>>>>>
>>>>>
>>>>  In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source
>>>> directory and object file for the parallel version. They are not to be
>>>> modified.
>>>>
>>>>>
>>>>>
>>>>>
>>>>>  We are using "openmpi" which does not have "parallel.o"
>>>>>
>>>>
>>>>  As mentioned above, parallel.o will be generated by the build
>>>> process. It looks like your version of hdf5 includes mpi.h and the compiler
>>>> cannot find it. So you have to add -I{location of mpi.h} to the CXXFLAGS
>>>> variable somewhere.Depending on your build type, you can append this to the
>>>> CXXFLAG assignment under :
>>>>
>>>> ifeq ($(BUILD),debug)
>>>>
>>>>  and/or under
>>>>
>>>> ifeq ($(BUILD),release)
>>>>
>>>>
>>>>  Best,
>>>>    Subha
>>>>
>>>>
>>>>
>>>
>>
>>
>
>
>

Re: [moose-generic] MOOSE_installation_problem

[Vadim A <ast...@nc...>]

Hi Subha. 

Just wan to clarify one think. We decided to concentrate on simples installation for now and do the following steps:

make clean
make BUILD=release USE_HDF5=0


And it still give me the error

g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DPYMOOSE -I/home/diag/opt/python2.7/include/python2.7 -I/home/diag/opt/python2.7/include/python2.7 moosemodule.cpp -c

moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or directory



But we loaded that module and it is located in our system here : /home/diag/opt/python2.7/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h


You've suggested to add it to CXXFLAGS flags. But where in the Makefile should we do that ?


Best regards,

Vadim.



On Mar 5, 2013, at 7:43 PM, Subhasis Ray wrote:

> Dear Vadim,
>  Did you run "make clean" before rebuilding each time? If you specify USE_HDF5=0, then the entire content of HDF5 related files get excluded from the compilation process. But from the build log for the first case it seems the object files were compiled with HDF5 support but the linking is being done without.
>  In the second case, is it possible that your version of HDF5 library is linked to a different MPI library than what you set in MOOSE Makefile? Otherwise, it is also possible that HDF5 lib is dynamically linked to MPI and when you are building MOOSE without MPI support the MPI-lib location is not passed to compiler. In that case you may want to use mpicxx as the compiler at line 250:
> 
> # Here we automagically change compilers to deal with MPI.
> ifdef USE_MPI
>     CXX = mpicxx
> #    CXX = /usr/local/mvapich2/bin/mpicxx
> #    PARALLEL_DIR = parallel
> #    PARALLEL_LIB = parallel/parallel.o
> else
>     CXX = g++ # <-- replace with mpicxx
> #    CXX = CC    # Choose between Solaris CC and g++ on a Solaris machine
> endif
> 
> 
>  For the third case, we use the command:
> 
> python-config --includes
> 
> in the Makefile in order to get the location of header files for numpy and python. Looks like that does not work on your system. So you need to explicitly add 
> -I/usr/include/python2.7 -I/usr/include/python2.7
> 
> and 
> 
> -I{location of numpy/arrayobject.h}
> 
> to CXXFLAGS
> 
> and add the following to LIBS (output of python-config --ldflags) updated according to local system paths:
> 
> -L/usr/lib/python2.7/config -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
> 
> 
> hth,
>   Subha
> 
> 
> On Wed, Mar 6, 2013 at 1:43 AM, Vadim A <ast...@nc...> wrote:
> Dear Subha.
> 
> I was trying three different ways to install MOOSE: without HDF5, with HDF5 and with MPI
> 
> Unfortunatelly, I did fail in all. Here the list of problems which we have. We would very appreciate you comments or suggestions what we might missing here.
> 
> 
> 
> (1) First I did
> 
> make BUILD=release USE_HDF5=0
> 
> 
> 
> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -o moose
> 
> 
> 
> And getting a lot of error like this:
> 
> 
> builtins/_builtins.o: In function `HDF5WriterBase::setMode(unsigned int)':
> (.text+0x11f40): undefined reference to `H5check_version'
> ……………….
> 
> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
> collect2: ld returned 1 exit status
> 
> 
> 
> 
> 
> 
> (2) Then 
> 
> We have installed  HDF5 1.8.9 and I was trying to do build release:  
> 
> 
> make BUILD=release
> 
>  
> It seems that all libs get compiled and it can find HDF5 1.8.9
> 
> 
> All Libs compiled
> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5 -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
> 
> 
> 
> but it complain about a lot of "undefined references like this:
> 
> 
> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
> collect2: ld returned 1 exit status
> make: *** [moose] Error 1
> 
> Looks like we still missing something. Should we have exactly same HDF5 library as you are using -> libhdf5-serial   ?
> 
> 
> 
> 
> (3)
> 
> Also I did try to compile with MPI:    
> 
> 
> make BUILD=release USE_MPI=1
> 
> All Libs compiled
> mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5 -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
> 
> 
> 
> But getting error:   
> 
> 
> moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or directory
> 
> 
> 
> But We have "numpy 1.6" loaded.  Should we set some other flag or should we have different version of "numpy" ?
> 
> 
> 
> Thanks a lot in advance for any advice.
> 
> Vadim.
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On Mar 2, 2013, at 10:58 PM, Subhasis Ray wrote:
> 
>> Hi,
>> In the serial version, HDF5 1.8.9 should work fine. It is used in HDF5DataWriter class to incrementally dump data into an HDF5 file. It was implemented to reduce memory usage for long running simulations generating gigabytes of data.
>> Best,
>>   Subha
>> 
>> 
>> On Sun, Mar 3, 2013 at 1:22 AM, Majumdar, Amitava <maj...@sd...> wrote:
>> If HDF5 version is the only issue, we can make HDF51.8.0 or higher available (actually we have HDF5 1.8.9 available
>> on another parallel computer at SDSC).
>> 
>> -Amitvai
>> From: Subhasis Ray [ray...@gm...]
>> Sent: Saturday, March 02, 2013 1:35 AM
>> To: Vadim A
>> 
>> Cc: Niraj Dudani; Yoshimoto, Kenneth; Majumdar, Amitava; moo...@li...
>> Subject: Re: [moose-generic] MOOSE_installation_problem
>> 
>> Dear Vadim,
>>   I would recommend that you avoid the MPI build at this point. The errors again are due to a minor issue with HDF5 library that can vary from package to package. These functions were introduced in HDF5 1.8.0. Either you need the same or a newer version installed. Otherwise, you can skip HDF5 support (which is somewhat experimental anyways) altogether by passing USE_HDF5=0 to "make" command.
>>   Hope this helps,
>>     Subha
>> 
>> 
>> On Sat, Mar 2, 2013 at 5:35 AM, Vadim A <ast...@nc...> wrote:
>> Dear Subha.
>> 
>> I set CXXFLAG to include mpi.h in "ifeq ($(BUILD),release)"
>> 
>> 
>> like you've suggested  and it seems that it can find all libraries now but unfortunately  
>> 
>> 
>> make BUILD=release USE_MPI=1
>> 
>> 
>> produce another error  
>> 
>> 
>> mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I. -I../basecode -I../msg HDF5DataWriter.cpp -c
>> 
>> 
>> 
>> 
>> ../basecode/Conv.h:1009: warning: converting to 'unsigned int' from 'const double'
>> HDF5DataWriter.cpp: In member function 'hid_t HDF5DataWriter::get_dataset(std::string)':
>> HDF5DataWriter.cpp:222: error: 'H5Gcreate2' was not declared in this scope
>> HDF5DataWriter.cpp:225: error: 'H5Gopen2' was not declared in this scope
>> HDF5DataWriter.cpp:258: error: 'H5Dopen2' was not declared in this scope
>> 
>> 
>> 
>> 
>> 
>> HDF5  and openmpi  libraries included. Do I still missing something ?
>> 
>> Thanks a lot in advance for any comments.
>> 
>> Vadim.
>> 
>> 
>> 
>> 
>> 
>> On Feb 28, 2013, at 7:37 PM, Subhasis Ray wrote:
>> 
>>>  
>>> 
>>> 
>>> Do not enable MPI unless you want to try the parallel version. To enable MPI, you have to pass the argument "USE_MPI=1" to make command.
>>>  
>>> 
>>> 
>>> # Here we automagically change compilers to deal with MPI.
>>> ifdef USE_MPI
>>>         CXX = mpicxx
>>> #       CXX = /usr/local/mvapich2/bin/mpicxx
>>>         PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel 
>>>         PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/   #parallel/parallel.o
>>> else
>>>         CXX = g++
>>> #       CXX = CC        # Choose between Solaris CC and g++ on a Solaris machine
>>> endif
>>> 
>>> 
>>>  
>>> In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source directory and object file for the parallel version. They are not to be modified.
>>> 
>>> 
>>> 
>>> We are using "openmpi" which does not have "parallel.o"
>>> 
>>> As mentioned above, parallel.o will be generated by the build process. It looks like your version of hdf5 includes mpi.h and the compiler cannot find it. So you have to add -I{location of mpi.h} to the CXXFLAGS variable somewhere.Depending on your build type, you can append this to the CXXFLAG assignment under :
>>> 
>>> ifeq ($(BUILD),debug)
>>> 
>>> and/or under 
>>> 
>>> ifeq ($(BUILD),release)
>>> 
>>> 
>>> Best,
>>>   Subha
>>> 
>> 
>> 
>> 
> 
> 

Re: [moose-generic] MOOSE_installation_problem

[Subhasis R. <ray...@gm...>]

Dear Vadim,
 Did you run "make clean" before rebuilding each time? If you specify
USE_HDF5=0, then the entire content of HDF5 related files get excluded from
the compilation process. But from the build log for the first case it seems
the object files were compiled with HDF5 support but the linking is being
done without.
 In the second case, is it possible that your version of HDF5 library is
linked to a different MPI library than what you set in MOOSE Makefile?
Otherwise, it is also possible that HDF5 lib is dynamically linked to MPI
and when you are building MOOSE without MPI support the MPI-lib location is
not passed to compiler. In that case you may want to use mpicxx as the
compiler at line 250:

# Here we automagically change compilers to deal with MPI.
ifdef USE_MPI
    CXX = mpicxx
#    CXX = /usr/local/mvapich2/bin/mpicxx
#    PARALLEL_DIR = parallel
#    PARALLEL_LIB = parallel/parallel.o
else
    CXX = g++ # <-- replace with mpicxx
#    CXX = CC    # Choose between Solaris CC and g++ on a Solaris machine
endif


 For the third case, we use the command:

python-config --includes

in the Makefile in order to get the location of header files for numpy and
python. Looks like that does not work on your system. So you need to
explicitly add
-I/usr/include/python2.7 -I/usr/include/python2.7

and

-I{location of numpy/arrayobject.h}

to CXXFLAGS

and add the following to LIBS (output of python-config --ldflags) updated
according to local system paths:

-L/usr/lib/python2.7/config -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker
-export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions


hth,
  Subha


On Wed, Mar 6, 2013 at 1:43 AM, Vadim A <ast...@nc...> wrote:

> Dear Subha.
>
> I was trying three different ways to install MOOSE: without HDF5, with
> HDF5 and with MPI
>
> Unfortunatelly, I did fail in all. Here the list of problems which we
> have. We would very appreciate you comments or suggestions what we might
> missing here.
>
>
>
> (1) First I did
>
> make BUILD=release USE_HDF5=0
>
>
>
> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
> -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    basecode/_basecode.o
> msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o
> randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o
> device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o
> regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o
> manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib
> -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib
> -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -o moose
>
>
>
> And getting a lot of error like this:
>
>
> builtins/_builtins.o: In function `HDF5WriterBase::setMode(unsigned int)':
> (.text+0x11f40): undefined reference to `H5check_version'
> ……………….
>
> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for
> MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
> collect2: ld returned 1 exit status
>
>
>
>
>
>
> (2) Then
>
> We have installed  HDF5 1.8.9 and I was trying to do build release:
>
>
> make BUILD=release
>
>
> It seems that all libs get compiled and it can find HDF5 1.8.9
>
>
> All Libs compiled
> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
> -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>  -DH5_NO_DEPRECATED_SYMBOLS -*I
>  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include* basecode/_basecode.o
> msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o
> randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o
> device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o
> regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o
> manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib
> -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib
> -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5
> -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
>
>
>
> but it complain about a lot of "undefined references like this:
>
>
> builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for
> MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
> collect2: ld returned 1 exit status
> make: *** [moose] Error 1
>
> Looks like we still missing something. Should we have exactly same HDF5
> library as you are using -> *libhdf5-serial   ?*
>
>
>
>
> (3)
>
> Also I did try to compile with MPI:
>
>
> make BUILD=release USE_MPI=1
>
> All Libs compiled
> mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
> -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I
> /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>  -DH5_NO_DEPRECATED_SYMBOLS -I
>  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include basecode/_basecode.o
> msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o
> randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o
> device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o
> regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o
> manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib
> -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib
> -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5
> -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose
>
>
>
> But getting error:
>
>
> moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or
> directory
>
>
>
> But We have "numpy 1.6" loaded.  Should we set some other flag or should
> we have different version of "numpy" ?
>
>
>
> Thanks a lot in advance for any advice.
>
> Vadim.
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> On Mar 2, 2013, at 10:58 PM, Subhasis Ray wrote:
>
> Hi,
> In the serial version, HDF5 1.8.9 should work fine. It is used in
> HDF5DataWriter class to incrementally dump data into an HDF5 file. It was
> implemented to reduce memory usage for long running simulations generating
> gigabytes of data.
> Best,
>   Subha
>
>
> On Sun, Mar 3, 2013 at 1:22 AM, Majumdar, Amitava <maj...@sd...>wrote:
>
>>  If HDF5 version is the only issue, we can make HDF51.8.0 or higher
>> available (actually we have HDF5 1.8.9 available
>> on another parallel computer at SDSC).
>>
>> -Amitvai
>>  ------------------------------
>> *From:* Subhasis Ray [ray...@gm...]
>> *Sent:* Saturday, March 02, 2013 1:35 AM
>> *To:* Vadim A
>>
>> *Cc:* Niraj Dudani; Yoshimoto, Kenneth; Majumdar, Amitava;
>> moo...@li...
>> *Subject:* Re: [moose-generic] MOOSE_installation_problem
>>
>>    Dear Vadim,
>>    I would recommend that you avoid the MPI build at this point. The
>> errors again are due to a minor issue with HDF5 library that can vary from
>> package to package. These functions were introduced in HDF5 1.8.0. Either
>> you need the same or a newer version installed. Otherwise, you can skip
>> HDF5 support (which is somewhat experimental anyways) altogether by passing
>> USE_HDF5=0 to "make" command.
>>    Hope this helps,
>>      Subha
>>
>>
>> On Sat, Mar 2, 2013 at 5:35 AM, Vadim A <ast...@nc...> wrote:
>>
>>> Dear Subha.
>>>
>>>  I set CXXFLAG to include mpi.h in "ifeq ($(BUILD),release)"
>>>
>>>
>>>  like you've suggested  and it seems that it can find all libraries now
>>> but unfortunately
>>>
>>>
>>>  make BUILD=release USE_MPI=1
>>>
>>>
>>>  produce another error
>>>
>>>
>>>  mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>>> -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I
>>> /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>>>  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I.
>>> -I../basecode -I../msg HDF5DataWriter.cpp -c
>>>
>>>
>>>
>>>
>>>  ../basecode/Conv.h:1009: warning: converting to 'unsigned int' from
>>> 'const double'
>>> HDF5DataWriter.cpp: In member function 'hid_t
>>> HDF5DataWriter::get_dataset(std::string)':
>>> HDF5DataWriter.cpp:222: error: 'H5Gcreate2' was not declared in this
>>> scope
>>> HDF5DataWriter.cpp:225: error: 'H5Gopen2' was not declared in this scope
>>> HDF5DataWriter.cpp:258: error: 'H5Dopen2' was not declared in this scope
>>>
>>>
>>>
>>>
>>>
>>>  HDF5  and openmpi  libraries included. Do I still missing something ?
>>>
>>>  Thanks a lot in advance for any comments.
>>>
>>>  Vadim.
>>>
>>>
>>>
>>>
>>>
>>>  On Feb 28, 2013, at 7:37 PM, Subhasis Ray wrote:
>>>
>>>
>>>
>>>
>>> Do not enable MPI unless you want to try the parallel version. To enable
>>> MPI, you have to pass the argument "USE_MPI=1" to make command.
>>>
>>>
>>>>
>>>>
>>>>  # Here we automagically change compilers to deal with MPI.
>>>> ifdef USE_MPI
>>>>         CXX = mpicxx
>>>> #       CXX = /usr/local/mvapich2/bin/mpicxx
>>>>         PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel
>>>>          PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/
>>>> #parallel/parallel.o
>>>> else
>>>>         CXX = g++
>>>> #       CXX = CC        # Choose between Solaris CC and g++ on a
>>>> Solaris machine
>>>> endif
>>>>
>>>>
>>>>
>>>  In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source
>>> directory and object file for the parallel version. They are not to be
>>> modified.
>>>
>>>>
>>>>
>>>>
>>>>  We are using "openmpi" which does not have "parallel.o"
>>>>
>>>
>>>  As mentioned above, parallel.o will be generated by the build process.
>>> It looks like your version of hdf5 includes mpi.h and the compiler cannot
>>> find it. So you have to add -I{location of mpi.h} to the CXXFLAGS variable
>>> somewhere.Depending on your build type, you can append this to the CXXFLAG
>>> assignment under :
>>>
>>> ifeq ($(BUILD),debug)
>>>
>>>  and/or under
>>>
>>> ifeq ($(BUILD),release)
>>>
>>>
>>>  Best,
>>>    Subha
>>>
>>>
>>>
>>
>
>

Re: [moose-generic] MOOSE_installation_problem

[Vadim A <ast...@nc...>]

Dear Subha.

I was trying three different ways to install MOOSE: without HDF5, with HDF5 and with MPI

Unfortunatelly, I did fail in all. Here the list of problems which we have. We would very appreciate you comments or suggestions what we might missing here.



(1) First I did

make BUILD=release USE_HDF5=0



g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -o moose



And getting a lot of error like this:


builtins/_builtins.o: In function `HDF5WriterBase::setMode(unsigned int)':
(.text+0x11f40): undefined reference to `H5check_version'
……………….

builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
collect2: ld returned 1 exit status






(2) Then 

We have installed  HDF5 1.8.9 and I was trying to do build release:  


make BUILD=release

 
It seems that all libs get compiled and it can find HDF5 1.8.9


All Libs compiled
g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5 -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose



but it complain about a lot of "undefined references like this:


builtins/_builtins.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[vtable for MPI::Datatype]+0x78): undefined reference to `MPI::Datatype::Free()'
collect2: ld returned 1 exit status
make: *** [moose] Error 1

Looks like we still missing something. Should we have exactly same HDF5 library as you are using -> libhdf5-serial   ?




(3)

Also I did try to compile with MPI:    


make BUILD=release USE_MPI=1

All Libs compiled
mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.8.9/gnu/openmpi/include basecode/_basecode.o msg/_msg.o shell/_shell.o biophysics/_biophysics.o hsolve/_hsolve.o randnum/_randnum.o scheduling/_scheduling.o builtins/_builtins.o device/_device.o kinetics/_kinetics.o ksolve/_ksolve.o regressionTests/_rt.o utility/_utility.o geom/_geom.o mesh/_mesh.o manager/_manager.o signeur/_signeur.o     -L/usr/lib -L/usr/local/lib -lpthread -L/lib64 -L/usr/lib64 -L/usr/lib -L/home/diag/opt/gsl/1.15/gnu/lib/ -lgsl -lgslcblas -lm -lhdf5 -L/home/diag/opt/hdf5/1.8.9/gnu/openmpi/lib    -o moose



But getting error:   


moosemodule.cpp:80:31: error: numpy/arrayobject.h: No such file or directory



But We have "numpy 1.6" loaded.  Should we set some other flag or should we have different version of "numpy" ?



Thanks a lot in advance for any advice.

Vadim.

























On Mar 2, 2013, at 10:58 PM, Subhasis Ray wrote:

> Hi,
> In the serial version, HDF5 1.8.9 should work fine. It is used in HDF5DataWriter class to incrementally dump data into an HDF5 file. It was implemented to reduce memory usage for long running simulations generating gigabytes of data.
> Best,
>   Subha
> 
> 
> On Sun, Mar 3, 2013 at 1:22 AM, Majumdar, Amitava <maj...@sd...> wrote:
> If HDF5 version is the only issue, we can make HDF51.8.0 or higher available (actually we have HDF5 1.8.9 available
> on another parallel computer at SDSC).
> 
> -Amitvai
> From: Subhasis Ray [ray...@gm...]
> Sent: Saturday, March 02, 2013 1:35 AM
> To: Vadim A
> 
> Cc: Niraj Dudani; Yoshimoto, Kenneth; Majumdar, Amitava; moo...@li...
> Subject: Re: [moose-generic] MOOSE_installation_problem
> 
> Dear Vadim,
>   I would recommend that you avoid the MPI build at this point. The errors again are due to a minor issue with HDF5 library that can vary from package to package. These functions were introduced in HDF5 1.8.0. Either you need the same or a newer version installed. Otherwise, you can skip HDF5 support (which is somewhat experimental anyways) altogether by passing USE_HDF5=0 to "make" command.
>   Hope this helps,
>     Subha
> 
> 
> On Sat, Mar 2, 2013 at 5:35 AM, Vadim A <ast...@nc...> wrote:
> Dear Subha.
> 
> I set CXXFLAG to include mpi.h in "ifeq ($(BUILD),release)"
> 
> 
> like you've suggested  and it seems that it can find all libraries now but unfortunately  
> 
> 
> make BUILD=release USE_MPI=1
> 
> 
> produce another error  
> 
> 
> mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I. -I../basecode -I../msg HDF5DataWriter.cpp -c
> 
> 
> 
> 
> ../basecode/Conv.h:1009: warning: converting to 'unsigned int' from 'const double'
> HDF5DataWriter.cpp: In member function 'hid_t HDF5DataWriter::get_dataset(std::string)':
> HDF5DataWriter.cpp:222: error: 'H5Gcreate2' was not declared in this scope
> HDF5DataWriter.cpp:225: error: 'H5Gopen2' was not declared in this scope
> HDF5DataWriter.cpp:258: error: 'H5Dopen2' was not declared in this scope
> 
> 
> 
> 
> 
> HDF5  and openmpi  libraries included. Do I still missing something ?
> 
> Thanks a lot in advance for any comments.
> 
> Vadim.
> 
> 
> 
> 
> 
> On Feb 28, 2013, at 7:37 PM, Subhasis Ray wrote:
> 
>>  
>> 
>> 
>> Do not enable MPI unless you want to try the parallel version. To enable MPI, you have to pass the argument "USE_MPI=1" to make command.
>>  
>> 
>> 
>> # Here we automagically change compilers to deal with MPI.
>> ifdef USE_MPI
>>         CXX = mpicxx
>> #       CXX = /usr/local/mvapich2/bin/mpicxx
>>         PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel 
>>         PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/   #parallel/parallel.o
>> else
>>         CXX = g++
>> #       CXX = CC        # Choose between Solaris CC and g++ on a Solaris machine
>> endif
>> 
>> 
>>  
>> In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source directory and object file for the parallel version. They are not to be modified.
>> 
>> 
>> 
>> We are using "openmpi" which does not have "parallel.o"
>> 
>> As mentioned above, parallel.o will be generated by the build process. It looks like your version of hdf5 includes mpi.h and the compiler cannot find it. So you have to add -I{location of mpi.h} to the CXXFLAGS variable somewhere.Depending on your build type, you can append this to the CXXFLAG assignment under :
>> 
>> ifeq ($(BUILD),debug)
>> 
>> and/or under 
>> 
>> ifeq ($(BUILD),release)
>> 
>> 
>> Best,
>>   Subha
>> 
> 
> 
> 

Re: [moose-generic] MOOSE_installation_problem

[Subhasis R. <ray...@gm...>]

Hi,
In the serial version, HDF5 1.8.9 should work fine. It is used in
HDF5DataWriter class to incrementally dump data into an HDF5 file. It was
implemented to reduce memory usage for long running simulations generating
gigabytes of data.
Best,
  Subha


On Sun, Mar 3, 2013 at 1:22 AM, Majumdar, Amitava <maj...@sd...> wrote:

>  If HDF5 version is the only issue, we can make HDF51.8.0 or higher
> available (actually we have HDF5 1.8.9 available
> on another parallel computer at SDSC).
>
> -Amitvai
>  ------------------------------
> *From:* Subhasis Ray [ray...@gm...]
> *Sent:* Saturday, March 02, 2013 1:35 AM
> *To:* Vadim A
>
> *Cc:* Niraj Dudani; Yoshimoto, Kenneth; Majumdar, Amitava;
> moo...@li...
> *Subject:* Re: [moose-generic] MOOSE_installation_problem
>
>    Dear Vadim,
>    I would recommend that you avoid the MPI build at this point. The
> errors again are due to a minor issue with HDF5 library that can vary from
> package to package. These functions were introduced in HDF5 1.8.0. Either
> you need the same or a newer version installed. Otherwise, you can skip
> HDF5 support (which is somewhat experimental anyways) altogether by passing
> USE_HDF5=0 to "make" command.
>    Hope this helps,
>      Subha
>
>
> On Sat, Mar 2, 2013 at 5:35 AM, Vadim A <ast...@nc...> wrote:
>
>> Dear Subha.
>>
>>  I set CXXFLAG to include mpi.h in "ifeq ($(BUILD),release)"
>>
>>
>>  like you've suggested  and it seems that it can find all libraries now
>> but unfortunately
>>
>>
>>  make BUILD=release USE_MPI=1
>>
>>
>>  produce another error
>>
>>
>>  mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>> -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I
>> /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>>  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I.
>> -I../basecode -I../msg HDF5DataWriter.cpp -c
>>
>>
>>
>>
>>  ../basecode/Conv.h:1009: warning: converting to 'unsigned int' from
>> 'const double'
>> HDF5DataWriter.cpp: In member function 'hid_t
>> HDF5DataWriter::get_dataset(std::string)':
>> HDF5DataWriter.cpp:222: error: 'H5Gcreate2' was not declared in this scope
>> HDF5DataWriter.cpp:225: error: 'H5Gopen2' was not declared in this scope
>> HDF5DataWriter.cpp:258: error: 'H5Dopen2' was not declared in this scope
>>
>>
>>
>>
>>
>>  HDF5  and openmpi  libraries included. Do I still missing something ?
>>
>>  Thanks a lot in advance for any comments.
>>
>>  Vadim.
>>
>>
>>
>>
>>
>>  On Feb 28, 2013, at 7:37 PM, Subhasis Ray wrote:
>>
>>
>>
>>
>> Do not enable MPI unless you want to try the parallel version. To enable
>> MPI, you have to pass the argument "USE_MPI=1" to make command.
>>
>>
>>>
>>>
>>>  # Here we automagically change compilers to deal with MPI.
>>> ifdef USE_MPI
>>>         CXX = mpicxx
>>> #       CXX = /usr/local/mvapich2/bin/mpicxx
>>>         PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel
>>>          PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/
>>> #parallel/parallel.o
>>> else
>>>         CXX = g++
>>> #       CXX = CC        # Choose between Solaris CC and g++ on a Solaris
>>> machine
>>> endif
>>>
>>>
>>>
>>  In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source
>> directory and object file for the parallel version. They are not to be
>> modified.
>>
>>>
>>>
>>>
>>>  We are using "openmpi" which does not have "parallel.o"
>>>
>>
>>  As mentioned above, parallel.o will be generated by the build process.
>> It looks like your version of hdf5 includes mpi.h and the compiler cannot
>> find it. So you have to add -I{location of mpi.h} to the CXXFLAGS variable
>> somewhere.Depending on your build type, you can append this to the CXXFLAG
>> assignment under :
>>
>> ifeq ($(BUILD),debug)
>>
>>  and/or under
>>
>> ifeq ($(BUILD),release)
>>
>>
>>  Best,
>>    Subha
>>
>>
>>
>

Re: [moose-generic] MOOSE_installation_problem

[Subhasis R. <ray...@gm...>]

I was suggesting that you avoid the MPI version altogether unless you want
to specifically try it. This is because it is not stable and different
approaches are still being tried out on the parallel front.

Best,
  Subha


On Sat, Mar 2, 2013 at 11:38 PM, Vadim Astakhov <ast...@nc...>wrote:

> Thank you for information. It seems that we need mpi version because we
> are installing software on cluster. Thus it make more since to have
> parallel version.
> Please let me clarify that, you do not suggest to install mpi version at
> all or we can proceed just installing appropriate hdf5.?
> Vadim
>
>
> Subhasis Ray <ray...@gm...> wrote:
>
> Dear Vadim,
>   I would recommend that you avoid the MPI build at this point. The errors
> again are due to a minor issue with HDF5 library that can vary from package
> to package. These functions were introduced in HDF5 1.8.0. Either you need
> the same or a newer version installed. Otherwise, you can skip HDF5 support
> (which is somewhat experimental anyways) altogether by passing USE_HDF5=0
> to "make" command.
>   Hope this helps,
>     Subha
>
>
> On Sat, Mar 2, 2013 at 5:35 AM, Vadim A <ast...@nc...> wrote:
>
>> Dear Subha.
>>
>> I set CXXFLAG to include mpi.h in "ifeq ($(BUILD),release)"
>>
>>
>> like you've suggested  and it seems that it can find all libraries now
>> but unfortunately
>>
>>
>> make BUILD=release USE_MPI=1
>>
>>
>> produce another error
>>
>>
>> mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
>> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
>> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
>> -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I
>> /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>>  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I.
>> -I../basecode -I../msg HDF5DataWriter.cpp -c
>>
>>
>>
>>
>> ../basecode/Conv.h:1009: warning: converting to 'unsigned int' from
>> 'const double'
>> HDF5DataWriter.cpp: In member function 'hid_t
>> HDF5DataWriter::get_dataset(std::string)':
>> HDF5DataWriter.cpp:222: error: 'H5Gcreate2' was not declared in this scope
>> HDF5DataWriter.cpp:225: error: 'H5Gopen2' was not declared in this scope
>> HDF5DataWriter.cpp:258: error: 'H5Dopen2' was not declared in this scope
>>
>>
>>
>>
>>
>> HDF5  and openmpi  libraries included. Do I still missing something ?
>>
>> Thanks a lot in advance for any comments.
>>
>> Vadim.
>>
>>
>>
>>
>>
>> On Feb 28, 2013, at 7:37 PM, Subhasis Ray wrote:
>>
>>
>>
>>
>> Do not enable MPI unless you want to try the parallel version. To enable
>> MPI, you have to pass the argument "USE_MPI=1" to make command.
>>
>>
>>>
>>>
>>> # Here we automagically change compilers to deal with MPI.
>>> ifdef USE_MPI
>>>         CXX = mpicxx
>>> #       CXX = /usr/local/mvapich2/bin/mpicxx
>>>         PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel
>>>         PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/
>>> #parallel/parallel.o
>>> else
>>>         CXX = g++
>>> #       CXX = CC        # Choose between Solaris CC and g++ on a Solaris
>>> machine
>>> endif
>>>
>>>
>>>
>> In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source
>> directory and object file for the parallel version. They are not to be
>> modified.
>>
>>>
>>>
>>>
>>> We are using "openmpi" which does not have "parallel.o"
>>>
>>
>> As mentioned above, parallel.o will be generated by the build process. It
>> looks like your version of hdf5 includes mpi.h and the compiler cannot find
>> it. So you have to add -I{location of mpi.h} to the CXXFLAGS variable
>> somewhere.Depending on your build type, you can append this to the CXXFLAG
>> assignment under :
>>
>> ifeq ($(BUILD),debug)
>>
>> and/or under
>>
>> ifeq ($(BUILD),release)
>>
>>
>> Best,
>>   Subha
>>
>>
>>
>

Re: [moose-generic] MOOSE_installation_problem

[Vadim A. <ast...@nc...>]

Thank you for information. It seems that we need mpi version because we are installing software on cluster. Thus it make more since to have parallel version. 
Please let me clarify that, you do not suggest to install mpi version at all or we can proceed just installing appropriate hdf5.?
Vadim

Subhasis Ray <ray...@gm...> wrote:

>Dear Vadim,
>
>  I would recommend that you avoid the MPI build at this point. The errors again are due to a minor issue with HDF5 library that can vary from package to package. These functions were introduced in HDF5 1.8.0. Either you need the same or a newer version installed. Otherwise, you can skip HDF5 support (which is somewhat experimental anyways) altogether by passing USE_HDF5=0 to "make" command.
>
>  Hope this helps,
>
>    Subha
>
>
>
>On Sat, Mar 2, 2013 at 5:35 AM, Vadim A <ast...@nc...> wrote:
>
>Dear Subha.
>
>
>I set CXXFLAG to include mpi.h in "ifeq ($(BUILD),release)"
>
>
>
>like you've suggested  and it seems that it can find all libraries now but unfortunately  
>
>
>
>make BUILD=release USE_MPI=1
>
>
>
>produce another error  
>
>
>
>mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I. -I../basecode -I../msg HDF5DataWriter.cpp -c
>
>
>
>
>
>../basecode/Conv.h:1009: warning: converting to 'unsigned int' from 'const double'
>
>HDF5DataWriter.cpp: In member function 'hid_t HDF5DataWriter::get_dataset(std::string)':
>
>HDF5DataWriter.cpp:222: error: 'H5Gcreate2' was not declared in this scope
>
>HDF5DataWriter.cpp:225: error: 'H5Gopen2' was not declared in this scope
>
>HDF5DataWriter.cpp:258: error: 'H5Dopen2' was not declared in this scope
>
>
>
>
>
>
>HDF5  and openmpi  libraries included. Do I still missing something ?
>
>
>Thanks a lot in advance for any comments.
>
>
>Vadim.
>
>
>
>
>
>
>On Feb 28, 2013, at 7:37 PM, Subhasis Ray wrote:
>
>
> 
>
>
>
>Do not enable MPI unless you want to try the parallel version. To enable MPI, you have to pass the argument "USE_MPI=1" to make command.
> 
>
>
>
># Here we automagically change compilers to deal with MPI.
>
>ifdef USE_MPI
>
>        CXX = mpicxx
>
>#       CXX = /usr/local/mvapich2/bin/mpicxx
>
>        PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel 
>
>        PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/   #parallel/parallel.o
>
>else
>
>        CXX = g++
>
>#       CXX = CC        # Choose between Solaris CC and g++ on a Solaris machine
>
>endif
>
>
>
> 
>
>In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source directory and object file for the parallel version. They are not to be modified.
>
>
>
>
>We are using "openmpi" which does not have "parallel.o"
>
>
>As mentioned above, parallel.o will be generated by the build process. It looks like your version of hdf5 includes mpi.h and the compiler cannot find it. So you have to add -I{location of mpi.h} to the CXXFLAGS variable somewhere.Depending on your build type, you can append this to the CXXFLAG assignment under :
>
>ifeq ($(BUILD),debug)
>
>and/or under 
>
>ifeq ($(BUILD),release)
>
>
>Best,
>
>  Subha
>
>
>
>

Re: [moose-generic] MOOSE_installation_problem

[Subhasis R. <ray...@gm...>]

Dear Vadim,
  I would recommend that you avoid the MPI build at this point. The errors
again are due to a minor issue with HDF5 library that can vary from package
to package. These functions were introduced in HDF5 1.8.0. Either you need
the same or a newer version installed. Otherwise, you can skip HDF5 support
(which is somewhat experimental anyways) altogether by passing USE_HDF5=0
to "make" command.
  Hope this helps,
    Subha


On Sat, Mar 2, 2013 at 5:35 AM, Vadim A <ast...@nc...> wrote:

> Dear Subha.
>
> I set CXXFLAG to include mpi.h in "ifeq ($(BUILD),release)"
>
>
> like you've suggested  and it seems that it can find all libraries now but
> unfortunately
>
>
> make BUILD=release USE_MPI=1
>
>
> produce another error
>
>
> mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I
> /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX
> -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I
> /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I.
> -I../basecode -I../msg HDF5DataWriter.cpp -c
>
>
>
>
> ../basecode/Conv.h:1009: warning: converting to 'unsigned int' from 'const
> double'
> HDF5DataWriter.cpp: In member function 'hid_t
> HDF5DataWriter::get_dataset(std::string)':
> HDF5DataWriter.cpp:222: error: 'H5Gcreate2' was not declared in this scope
> HDF5DataWriter.cpp:225: error: 'H5Gopen2' was not declared in this scope
> HDF5DataWriter.cpp:258: error: 'H5Dopen2' was not declared in this scope
>
>
>
>
>
> HDF5  and openmpi  libraries included. Do I still missing something ?
>
> Thanks a lot in advance for any comments.
>
> Vadim.
>
>
>
>
>
> On Feb 28, 2013, at 7:37 PM, Subhasis Ray wrote:
>
>
>
>
> Do not enable MPI unless you want to try the parallel version. To enable
> MPI, you have to pass the argument "USE_MPI=1" to make command.
>
>
>>
>>
>> # Here we automagically change compilers to deal with MPI.
>> ifdef USE_MPI
>>         CXX = mpicxx
>> #       CXX = /usr/local/mvapich2/bin/mpicxx
>>         PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel
>>         PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/
>> #parallel/parallel.o
>> else
>>         CXX = g++
>> #       CXX = CC        # Choose between Solaris CC and g++ on a Solaris
>> machine
>> endif
>>
>>
>>
> In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source directory
> and object file for the parallel version. They are not to be modified.
>
>>
>>
>>
>> We are using "openmpi" which does not have "parallel.o"
>>
>
> As mentioned above, parallel.o will be generated by the build process. It
> looks like your version of hdf5 includes mpi.h and the compiler cannot find
> it. So you have to add -I{location of mpi.h} to the CXXFLAGS variable
> somewhere.Depending on your build type, you can append this to the CXXFLAG
> assignment under :
>
> ifeq ($(BUILD),debug)
>
> and/or under
>
> ifeq ($(BUILD),release)
>
>
> Best,
>   Subha
>
>
>

Re: [moose-generic] MOOSE_installation_problem

[Vadim A <ast...@nc...>]

Dear Subha.

I set CXXFLAG to include mpi.h in "ifeq ($(BUILD),release)"


like you've suggested  and it seems that it can find all libraries now but unfortunately  


make BUILD=release USE_MPI=1


produce another error  


mpicxx -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -I /home/diag/opt/openmpi/1.4.3/gnu/include  -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_MPI -DMPICH_IGNORE_CXX_SEEK -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I. -I../basecode -I../msg HDF5DataWriter.cpp -c




../basecode/Conv.h:1009: warning: converting to 'unsigned int' from 'const double'
HDF5DataWriter.cpp: In member function 'hid_t HDF5DataWriter::get_dataset(std::string)':
HDF5DataWriter.cpp:222: error: 'H5Gcreate2' was not declared in this scope
HDF5DataWriter.cpp:225: error: 'H5Gopen2' was not declared in this scope
HDF5DataWriter.cpp:258: error: 'H5Dopen2' was not declared in this scope





HDF5  and openmpi  libraries included. Do I still missing something ?

Thanks a lot in advance for any comments.

Vadim.





On Feb 28, 2013, at 7:37 PM, Subhasis Ray wrote:

>  
> 
> 
> Do not enable MPI unless you want to try the parallel version. To enable MPI, you have to pass the argument "USE_MPI=1" to make command.
>  
> 
> 
> # Here we automagically change compilers to deal with MPI.
> ifdef USE_MPI
>         CXX = mpicxx
> #       CXX = /usr/local/mvapich2/bin/mpicxx
>         PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel 
>         PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/   #parallel/parallel.o
> else
>         CXX = g++
> #       CXX = CC        # Choose between Solaris CC and g++ on a Solaris machine
> endif
> 
> 
>  
> In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source directory and object file for the parallel version. They are not to be modified.
> 
> 
> 
> We are using "openmpi" which does not have "parallel.o"
> 
> As mentioned above, parallel.o will be generated by the build process. It looks like your version of hdf5 includes mpi.h and the compiler cannot find it. So you have to add -I{location of mpi.h} to the CXXFLAGS variable somewhere.Depending on your build type, you can append this to the CXXFLAG assignment under :
> 
> ifeq ($(BUILD),debug)
> 
> and/or under 
> 
> ifeq ($(BUILD),release)
> 
> 
> Best,
>   Subha
> 

Re: [moose-generic] MOOSE_installation_problem

[Subhasis R. <ray...@gm...>]

On Fri, Mar 1, 2013 at 4:59 AM, Vadim A <ast...@nc...> wrote:

> Actually , we found the problem with  GSL lib (it was mis-typed letter)
>
> But we still straggling with configuring MPI.
>
>
>
> I am getting this error:
>
>
>
> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall
> -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER
> -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I
> /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5
>  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I.
> -I../basecode -I../msg HDF5WriterBase.cpp -c
> In file included from /home/diag/opt/hdf5/1.6/gnu/include/hdf5.h:23,
>                  from HDF5WriterBase.cpp:33:
>
> /home/diag/opt/hdf5/1.6/gnu/include/H5public.h:54:20: error: mpi.h: No
> such file or directory
>
>

This is possibly an issue with your HDF5 installation, not MOOSE. HDF5
comes in multiple flavours like libhdf5-lam, libhdf5-mpich, libhdf5-openmi.
We are using libhdf5-serial which does not require MPI or any other
parallel library.


>
>
>
>
> Even, I set flags for MPI in the Makefile.   Could you please advise what
> might be missing ?
>


Do not enable MPI unless you want to try the parallel version. To enable
MPI, you have to pass the argument "USE_MPI=1" to make command.


>
>
> # Here we automagically change compilers to deal with MPI.
> ifdef USE_MPI
>         CXX = mpicxx
> #       CXX = /usr/local/mvapich2/bin/mpicxx
>         PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel
>         PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/
> #parallel/parallel.o
> else
>         CXX = g++
> #       CXX = CC        # Choose between Solaris CC and g++ on a Solaris
> machine
> endif
>
>
>
In the above, the PARALLEL_DIR and PARALLEL_LIB are MOOSE source directory
and object file for the parallel version. They are not to be modified.

>
>
>
> We are using "openmpi" which does not have "parallel.o"
>

As mentioned above, parallel.o will be generated by the build process. It
looks like your version of hdf5 includes mpi.h and the compiler cannot find
it. So you have to add -I{location of mpi.h} to the CXXFLAGS variable
somewhere.Depending on your build type, you can append this to the CXXFLAG
assignment under :

ifeq ($(BUILD),debug)

and/or under

ifeq ($(BUILD),release)


Best,
  Subha

Re: [moose-generic] MOOSE_installation_problem

[Vadim A <ast...@nc...>]

Actually , we found the problem with  GSL lib (it was mis-typed letter) 

But we still straggling with configuring MPI.



I am getting this error:



g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -I /home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I. -I../basecode -I../msg HDF5WriterBase.cpp -c
In file included from /home/diag/opt/hdf5/1.6/gnu/include/hdf5.h:23,
                 from HDF5WriterBase.cpp:33:

/home/diag/opt/hdf5/1.6/gnu/include/H5public.h:54:20: error: mpi.h: No such file or directory






Even, I set flags for MPI in the Makefile.   Could you please advise what might be missing ?


# Here we automagically change compilers to deal with MPI.
ifdef USE_MPI
        CXX = mpicxx
#       CXX = /usr/local/mvapich2/bin/mpicxx
        PARALLEL_DIR = /home/diag/opt/openmpi/1.4.3/gnu/  #parallel
        PARALLEL_LIB = /home/diag/opt/openmpi/1.4.3/gnu/lib/   #parallel/parallel.o
else
        CXX = g++
#       CXX = CC        # Choose between Solaris CC and g++ on a Solaris machine
endif





We are using "openmpi" which does not have "parallel.o"


Thanks a lot in advance for any suggestions,

Vadim.




> 
> 
> 
> Also, 
> 
> I having error about MPI
> 
> /home/diag/opt/hdf5/1.6/gnu/include/H5public.h:54:20: error: mpi.h: No such file or directory
> 
> , should I set some more flags ?  I see one for mpicxx - but it is commented.
> 
> 
> 
> 
> Here the error log:
> 
> g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -l/home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I. -I../basecode -I../msg HDF5WriterBase.cpp -c
> In file included from /home/diag/opt/hdf5/1.6/gnu/include/hdf5.h:23,
>                  from HDF5WriterBase.cpp:33:
> /home/diag/opt/hdf5/1.6/gnu/include/H5public.h:54:20: error: mpi.h: No such file or directory
> /home/diag/opt/hdf5/1.6/gnu/include/H5public.h:56:21: error: mpio.h: No such file or directory
> 
> 
> 
> 
>> 
>> Subhasis Ray <ray...@gm...> wrote:
>> 
>> Hi, 
>>  Just expanding on what Niraj mentioned briefly: The errors indicate that the compiler could not find the gsl/gsl_errno.h and hdf5.h in its include path. We put the common locations of HDF and GSL libraries on Debian based systems in the Makefile, but it seems you need to update that with your local settings.
>> 
>> For hdf5, search for "DUSE_HDF5" in the Makefile and replace the line:
>> 
>> CXXFLAGS+= -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I/usr/local/hdf5/include
>> 
>> with 
>> CXXFLAGS+= -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I{path of directory containing hdf5.h on your system}
>> 
>> and in the next line:
>> 
>>     LIBS+= -lhdf5 -L/usr/local/hdf5/lib
>> 
>> with
>> 
>>     LIBS+= -lhdf5 -L{path directory containing libhdf5.so on your system}
>> 
>> Similarly for GSL, search for "ifdef USE_GSL" in the Makefile and in that section replace:
>> 
>> LIBS+= -L/usr/lib -lgsl -lgslcblas -lm
>> 
>> with
>> 
>> LIBS+= -L/usr/lib -L{path to directory containing libgsl.so on your system} -lgsl -lgslcblas -lm
>> 
>> and replace 
>> 
>> CXXFLAGS+= -DUSE_GSL
>> 
>> with
>> 
>> CXXFLAGS+= -DUSE_GSL -I{path to directory containing gsl/gsl_cblas.h}
>> 
>> Note that in the above the directory should be "/usr/include" when gsl_cblas.h located in /usr/include/gsl. If you have the 'locate' utility installed you can use that to find the location of the above mentioned files.
>> 
>> Hope this helps,
>> 
>>    Subha
>> 
>> 
>> On Thu, Feb 28, 2013 at 11:03 AM, Niraj Dudani <ni...@nc...> wrote:
>> Hi Vadim,
>> 
>> Thanks for your mail: it appears that your mails were stuck in the spam filter, because
>> you're not subscribed to the mailing list. To avoid this the next time, you could
>> subscribe to the mailing list here:
>> https://lists.sourceforge.net/lists/listinfo/moose-generic.
>> 
>> The errors you reported seem to be due to path issues. Can you check where the GSL and
>> HDF5 libraries have been installed? You may have to edit the Makefile to get it to work.
>> The library path has to be appended to the LIBS variable, and the include path to the
>> CXXFLAGS variable. In the current revision (r4433), the GSL section of the Makefile is
>> on line numbers 208-209, and the HDF5 section is at line numbers 262-263.
>> 
>> Best,
>> Niraj
>> 
>> >
>> > Hi
>> > I have python-2.7 with GSL and HDF5 libraries installed    but I am getting  a lot of
>> > errors every time I try to do "make BUILD=release" on CentOS 5.5  x86_64 x86_64 x86_64
>> > GNU/Linux
>> > We are trying to have it installed on the cluster and using "module" commands to load
>> > all libraries.
>> >
>> > Can somebody advice what might be missing ?  Thanks a lot in advance.
>> > Vadim.
>> >
>> > Here the error:
>> >
>> >
>> > MarkovChannel.cpp:16:27: error: gsl/gsl_errno.h: No such file or directory***
>> > [MarkovChannel.o] Error 1
>> >
>> > HDF5WriterBase.cpp:33:18: error: hdf5.h: No such file or directorymake[1]: ***
>> > [HDF5WriterBase.o] Error 1
>> >
>> > Stoich.cpp:42:27: error: gsl/gsl_errno.h: No such file or directorymake[1]: ***
>> > [Stoich.o] Error 1
>> >
>> > rtMultiCompartment.cpp:11:27: error: gsl/gsl_errno.h: No such file or
>> > directoryrtMultiCompartment.cpp:12:28: error: gsl/gsl_matrix.h: No such file or
>> > directoryrtMultiCompartment.cpp:13:27: error: gsl/gsl_odeiv.h: No such file or directory
>> > ../ksolve/OdeSystem.h:51: warning: ISO C++ forbids declaration of 'gsl_odeiv_step_type'
>> > with no type../ksolve/OdeSystem.h:51: error: expected ';' before '*'
>> > token../ksolve/OdeSystem.h:52: warning: ISO C++ forbids declaration of 'gsl_odeiv_step'
>> > with no type../ksolve/OdeSystem.h:52: error: expected ';' before '*'
>> > token../ksolve/OdeSystem.h:53: warning: ISO C++ forbids declaration of
>> > 'gsl_odeiv_control' with no type../ksolve/OdeSystem.h:53: error: expected ';' before '*'
>> > token../ksolve/OdeSystem.h:54: warning: ISO C++ forbids declaration of
>> > 'gsl_odeiv_evolve' with no type../ksolve/OdeSystem.h:54: error: expected ';' before '*'
>> > token../ksolve/OdeSystem.h:55: error: 'gsl_odeiv_system' does not name a type
>> > [rtMultiCompartment.o] Error 1No rule to make target `biophysics/_biophysics.o', needed
>> > by `moose'.  Stop.
>> > ------------------------------------------------------------------------------
>> > Everyone hates slow websites. So do we.
>> > Make your web apps faster with AppDynamics
>> > Download AppDynamics Lite for free today:
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>> > moose-generic mailing list
>> > moo...@li...
>> > https://lists.sourceforge.net/lists/listinfo/moose-generic
>> >
>> 
>> 
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_feb
>> _______________________________________________
>> moose-generic mailing list
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>> 
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>> moose-generic mailing list
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>> https://lists.sourceforge.net/lists/listinfo/moose-generic
> 
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> moose-generic mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-generic

Re: [moose-generic] MOOSE_installation_problem

[Vadim A <ast...@nc...>]

Thanks you for your suggestions,  I've set those flags and one for HDF5 seems work 


but GSL does not and gives me an error:

g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -l/home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include   -I.. -I../basecode -I../msg -I../kinetics -I../mesh Stoich.cpp -c
Stoich.cpp:42:27: error: gsl/gsl_errno.h: No such file or directory



Looks like it can not find "gel/gsl_errno.h" in  -DUSE_GSL -l/home/diag/opt/gsl/1.15/gnu/include/

but it is here when I do "ls"


[astakhov@trestles-login1 moose]$ ls /home/diag/opt/gsl/1.15/gnu/include/gsl/gsl_errno.h 
/home/diag/opt/gsl/1.15/gnu/include/gsl/gsl_errno.h



Am I missing something ?



Also, 

I having error about MPI

/home/diag/opt/hdf5/1.6/gnu/include/H5public.h:54:20: error: mpi.h: No such file or directory

, should I set some more flags ?  I see one for mpicxx - but it is commented.




Here the error log:

g++ -O3 -pthread -fpermissive -fno-strict-aliasing -fPIC -Wall -Wno-long-long -pedantic -DNDEBUG -DUSE_GENESIS_PARSER -DSVN_REVISION=\"4401M\" -DLINUX -DUSE_GSL -l/home/diag/opt/gsl/1.15/gnu/include/    -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I  /home/diag/opt/hdf5/1.6/gnu/include  -I. -I../basecode -I../msg HDF5WriterBase.cpp -c
In file included from /home/diag/opt/hdf5/1.6/gnu/include/hdf5.h:23,
                 from HDF5WriterBase.cpp:33:
/home/diag/opt/hdf5/1.6/gnu/include/H5public.h:54:20: error: mpi.h: No such file or directory
/home/diag/opt/hdf5/1.6/gnu/include/H5public.h:56:21: error: mpio.h: No such file or directory




> 
> Subhasis Ray <ray...@gm...> wrote:
> 
> Hi, 
>  Just expanding on what Niraj mentioned briefly: The errors indicate that the compiler could not find the gsl/gsl_errno.h and hdf5.h in its include path. We put the common locations of HDF and GSL libraries on Debian based systems in the Makefile, but it seems you need to update that with your local settings.
> 
> For hdf5, search for "DUSE_HDF5" in the Makefile and replace the line:
> 
> CXXFLAGS+= -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I/usr/local/hdf5/include
> 
> with 
> CXXFLAGS+= -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I{path of directory containing hdf5.h on your system}
> 
> and in the next line:
> 
>     LIBS+= -lhdf5 -L/usr/local/hdf5/lib
> 
> with
> 
>     LIBS+= -lhdf5 -L{path directory containing libhdf5.so on your system}
> 
> Similarly for GSL, search for "ifdef USE_GSL" in the Makefile and in that section replace:
> 
> LIBS+= -L/usr/lib -lgsl -lgslcblas -lm
> 
> with
> 
> LIBS+= -L/usr/lib -L{path to directory containing libgsl.so on your system} -lgsl -lgslcblas -lm
> 
> and replace 
> 
> CXXFLAGS+= -DUSE_GSL
> 
> with
> 
> CXXFLAGS+= -DUSE_GSL -I{path to directory containing gsl/gsl_cblas.h}
> 
> Note that in the above the directory should be "/usr/include" when gsl_cblas.h located in /usr/include/gsl. If you have the 'locate' utility installed you can use that to find the location of the above mentioned files.
> 
> Hope this helps,
> 
>    Subha
> 
> 
> On Thu, Feb 28, 2013 at 11:03 AM, Niraj Dudani <ni...@nc...> wrote:
> Hi Vadim,
> 
> Thanks for your mail: it appears that your mails were stuck in the spam filter, because
> you're not subscribed to the mailing list. To avoid this the next time, you could
> subscribe to the mailing list here:
> https://lists.sourceforge.net/lists/listinfo/moose-generic.
> 
> The errors you reported seem to be due to path issues. Can you check where the GSL and
> HDF5 libraries have been installed? You may have to edit the Makefile to get it to work.
> The library path has to be appended to the LIBS variable, and the include path to the
> CXXFLAGS variable. In the current revision (r4433), the GSL section of the Makefile is
> on line numbers 208-209, and the HDF5 section is at line numbers 262-263.
> 
> Best,
> Niraj
> 
> >
> > Hi
> > I have python-2.7 with GSL and HDF5 libraries installed    but I am getting  a lot of
> > errors every time I try to do "make BUILD=release" on CentOS 5.5  x86_64 x86_64 x86_64
> > GNU/Linux
> > We are trying to have it installed on the cluster and using "module" commands to load
> > all libraries.
> >
> > Can somebody advice what might be missing ?  Thanks a lot in advance.
> > Vadim.
> >
> > Here the error:
> >
> >
> > MarkovChannel.cpp:16:27: error: gsl/gsl_errno.h: No such file or directory***
> > [MarkovChannel.o] Error 1
> >
> > HDF5WriterBase.cpp:33:18: error: hdf5.h: No such file or directorymake[1]: ***
> > [HDF5WriterBase.o] Error 1
> >
> > Stoich.cpp:42:27: error: gsl/gsl_errno.h: No such file or directorymake[1]: ***
> > [Stoich.o] Error 1
> >
> > rtMultiCompartment.cpp:11:27: error: gsl/gsl_errno.h: No such file or
> > directoryrtMultiCompartment.cpp:12:28: error: gsl/gsl_matrix.h: No such file or
> > directoryrtMultiCompartment.cpp:13:27: error: gsl/gsl_odeiv.h: No such file or directory
> > ../ksolve/OdeSystem.h:51: warning: ISO C++ forbids declaration of 'gsl_odeiv_step_type'
> > with no type../ksolve/OdeSystem.h:51: error: expected ';' before '*'
> > token../ksolve/OdeSystem.h:52: warning: ISO C++ forbids declaration of 'gsl_odeiv_step'
> > with no type../ksolve/OdeSystem.h:52: error: expected ';' before '*'
> > token../ksolve/OdeSystem.h:53: warning: ISO C++ forbids declaration of
> > 'gsl_odeiv_control' with no type../ksolve/OdeSystem.h:53: error: expected ';' before '*'
> > token../ksolve/OdeSystem.h:54: warning: ISO C++ forbids declaration of
> > 'gsl_odeiv_evolve' with no type../ksolve/OdeSystem.h:54: error: expected ';' before '*'
> > token../ksolve/OdeSystem.h:55: error: 'gsl_odeiv_system' does not name a type
> > [rtMultiCompartment.o] Error 1No rule to make target `biophysics/_biophysics.o', needed
> > by `moose'.  Stop.
> > ------------------------------------------------------------------------------
> > Everyone hates slow websites. So do we.
> > Make your web apps faster with AppDynamics
> > Download AppDynamics Lite for free today:
> > http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> > moose-generic mailing list
> > moo...@li...
> > https://lists.sourceforge.net/lists/listinfo/moose-generic
> >
> 
> 
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> moose-generic mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-generic
> 
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> moose-generic mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-generic

Re: [moose-generic] MOOSE_installation_problem

[Vadim A. <ast...@nc...>]

Thank you. I will set those flags and will try again.
Vadim.

Niraj Dudani <ni...@nc...> wrote:

>Hi Vadim,
>
>Thanks for your mail: it appears that your mails were stuck in the spam filter, because
>you're not subscribed to the mailing list. To avoid this the next time, you could
>subscribe to the mailing list here:
>https://lists.sourceforge.net/lists/listinfo/moose-generic.
>
>The errors you reported seem to be due to path issues. Can you check where the GSL and
>HDF5 libraries have been installed? You may have to edit the Makefile to get it to work.
>The library path has to be appended to the LIBS variable, and the include path to the
>CXXFLAGS variable. In the current revision (r4433), the GSL section of the Makefile is
>on line numbers 208-209, and the HDF5 section is at line numbers 262-263.
>
>Best,
>Niraj
>
>>
>> Hi
>> I have python-2.7 with GSL and HDF5 libraries installed    but I am getting  a lot of
>> errors every time I try to do "make BUILD=release" on CentOS 5.5  x86_64 x86_64 x86_64
>> GNU/Linux
>> We are trying to have it installed on the cluster and using "module" commands to load
>> all libraries.
>>
>> Can somebody advice what might be missing ?  Thanks a lot in advance.
>> Vadim.
>>
>> Here the error:
>>
>>
>> MarkovChannel.cpp:16:27: error: gsl/gsl_errno.h: No such file or directory***
>> [MarkovChannel.o] Error 1
>>
>> HDF5WriterBase.cpp:33:18: error: hdf5.h: No such file or directorymake[1]: ***
>> [HDF5WriterBase.o] Error 1
>>
>> Stoich.cpp:42:27: error: gsl/gsl_errno.h: No such file or directorymake[1]: ***
>> [Stoich.o] Error 1
>>
>> rtMultiCompartment.cpp:11:27: error: gsl/gsl_errno.h: No such file or
>> directoryrtMultiCompartment.cpp:12:28: error: gsl/gsl_matrix.h: No such file or
>> directoryrtMultiCompartment.cpp:13:27: error: gsl/gsl_odeiv.h: No such file or directory
>> ../ksolve/OdeSystem.h:51: warning: ISO C++ forbids declaration of 'gsl_odeiv_step_type'
>> with no type../ksolve/OdeSystem.h:51: error: expected ';' before '*'
>> token../ksolve/OdeSystem.h:52: warning: ISO C++ forbids declaration of 'gsl_odeiv_step'
>> with no type../ksolve/OdeSystem.h:52: error: expected ';' before '*'
>> token../ksolve/OdeSystem.h:53: warning: ISO C++ forbids declaration of
>> 'gsl_odeiv_control' with no type../ksolve/OdeSystem.h:53: error: expected ';' before '*'
>> token../ksolve/OdeSystem.h:54: warning: ISO C++ forbids declaration of
>> 'gsl_odeiv_evolve' with no type../ksolve/OdeSystem.h:54: error: expected ';' before '*'
>> token../ksolve/OdeSystem.h:55: error: 'gsl_odeiv_system' does not name a type
>> [rtMultiCompartment.o] Error 1No rule to make target `biophysics/_biophysics.o', needed
>> by `moose'.  Stop.
>> ------------------------------------------------------------------------------
>> Everyone hates slow websites. So do we.
>> Make your web apps faster with AppDynamics
>> Download AppDynamics Lite for free today:
>> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
>> moose-generic mailing list
>> moo...@li...
>> https://lists.sourceforge.net/lists/listinfo/moose-generic
>>
>
>
>------------------------------------------------------------------------------
>Everyone hates slow websites. So do we.
>Make your web apps faster with AppDynamics
>Download AppDynamics Lite for free today:
>http://p.sf.net/sfu/appdyn_d2d_feb
>_______________________________________________
>moose-generic mailing list
>moo...@li...
>https://lists.sourceforge.net/lists/listinfo/moose-generic
>

Re: [moose-generic] MOOSE_installation_problem

[Vadim A. <ast...@nc...>]

Thanks a lot for commens
I will try and let you know.
Vadim.

Subhasis Ray <ray...@gm...> wrote:

>------------------------------------------------------------------------------
>Everyone hates slow websites. So do we.
>Make your web apps faster with AppDynamics
>Download AppDynamics Lite for free today:
>http://p.sf.net/sfu/appdyn_d2d_feb
>_______________________________________________
>moose-generic mailing list
>moo...@li...
>https://lists.sourceforge.net/lists/listinfo/moose-generic

Re: [moose-generic] MOOSE_installation_problem

[Subhasis R. <ray...@gm...>]

Hi,
 Just expanding on what Niraj mentioned briefly: The errors indicate that
the compiler could not find the gsl/gsl_errno.h and hdf5.h in its include
path. We put the common locations of HDF and GSL libraries on Debian based
systems in the Makefile, but it seems you need to update that with your
local settings.

For hdf5, search for "DUSE_HDF5" in the Makefile and replace the line:

CXXFLAGS+= -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I/usr/local/hdf5/include

with
CXXFLAGS+= -DUSE_HDF5  -DH5_NO_DEPRECATED_SYMBOLS -I{path of directory
containing hdf5.h on your system}

and in the next line:

    LIBS+= -lhdf5 -L/usr/local/hdf5/lib

with

    LIBS+= -lhdf5 -L{path directory containing libhdf5.so on your system}

Similarly for GSL, search for "ifdef USE_GSL" in the Makefile and in that
section replace:

LIBS+= -L/usr/lib -lgsl -lgslcblas -lm

with

LIBS+= -L/usr/lib -L{path to directory containing libgsl.so on your system}
-lgsl -lgslcblas -lm

and replace

CXXFLAGS+= -DUSE_GSL

with

CXXFLAGS+= -DUSE_GSL -I{path to directory containing gsl/gsl_cblas.h}

Note that in the above the directory should be "/usr/include" when
gsl_cblas.h located in /usr/include/gsl. If you have the 'locate' utility
installed you can use that to find the location of the above mentioned
files.

Hope this helps,

   Subha


On Thu, Feb 28, 2013 at 11:03 AM, Niraj Dudani <ni...@nc...> wrote:

> Hi Vadim,
>
> Thanks for your mail: it appears that your mails were stuck in the spam
> filter, because
> you're not subscribed to the mailing list. To avoid this the next time,
> you could
> subscribe to the mailing list here:
> https://lists.sourceforge.net/lists/listinfo/moose-generic.
>
> The errors you reported seem to be due to path issues. Can you check where
> the GSL and
> HDF5 libraries have been installed? You may have to edit the Makefile to
> get it to work.
> The library path has to be appended to the LIBS variable, and the include
> path to the
> CXXFLAGS variable. In the current revision (r4433), the GSL section of the
> Makefile is
> on line numbers 208-209, and the HDF5 section is at line numbers 262-263.
>
> Best,
> Niraj
>
> >
> > Hi
> > I have python-2.7 with GSL and HDF5 libraries installed    but I am
> getting  a lot of
> > errors every time I try to do "make BUILD=release" on CentOS 5.5  x86_64
> x86_64 x86_64
> > GNU/Linux
> > We are trying to have it installed on the cluster and using "module"
> commands to load
> > all libraries.
> >
> > Can somebody advice what might be missing ?  Thanks a lot in advance.
> > Vadim.
> >
> > Here the error:
> >
> >
> > MarkovChannel.cpp:16:27: error: gsl/gsl_errno.h: No such file or
> directory***
> > [MarkovChannel.o] Error 1
> >
> > HDF5WriterBase.cpp:33:18: error: hdf5.h: No such file or
> directorymake[1]: ***
> > [HDF5WriterBase.o] Error 1
> >
> > Stoich.cpp:42:27: error: gsl/gsl_errno.h: No such file or
> directorymake[1]: ***
> > [Stoich.o] Error 1
> >
> > rtMultiCompartment.cpp:11:27: error: gsl/gsl_errno.h: No such file or
> > directoryrtMultiCompartment.cpp:12:28: error: gsl/gsl_matrix.h: No such
> file or
> > directoryrtMultiCompartment.cpp:13:27: error: gsl/gsl_odeiv.h: No such
> file or directory
> > ../ksolve/OdeSystem.h:51: warning: ISO C++ forbids declaration of
> 'gsl_odeiv_step_type'
> > with no type../ksolve/OdeSystem.h:51: error: expected ';' before '*'
> > token../ksolve/OdeSystem.h:52: warning: ISO C++ forbids declaration of
> 'gsl_odeiv_step'
> > with no type../ksolve/OdeSystem.h:52: error: expected ';' before '*'
> > token../ksolve/OdeSystem.h:53: warning: ISO C++ forbids declaration of
> > 'gsl_odeiv_control' with no type../ksolve/OdeSystem.h:53: error:
> expected ';' before '*'
> > token../ksolve/OdeSystem.h:54: warning: ISO C++ forbids declaration of
> > 'gsl_odeiv_evolve' with no type../ksolve/OdeSystem.h:54: error: expected
> ';' before '*'
> > token../ksolve/OdeSystem.h:55: error: 'gsl_odeiv_system' does not name a
> type
> > [rtMultiCompartment.o] Error 1No rule to make target
> `biophysics/_biophysics.o', needed
> > by `moose'.  Stop.
> >
> ------------------------------------------------------------------------------
> > Everyone hates slow websites. So do we.
> > Make your web apps faster with AppDynamics
> > Download AppDynamics Lite for free today:
> >
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> > moose-generic mailing list
> > moo...@li...
> > https://lists.sourceforge.net/lists/listinfo/moose-generic
> >
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> _______________________________________________
> moose-generic mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-generic
>

Re: [moose-generic] MOOSE_installation_problem

[Niraj D. <ni...@nc...>]

Hi Vadim,

Thanks for your mail: it appears that your mails were stuck in the spam filter, because
you're not subscribed to the mailing list. To avoid this the next time, you could
subscribe to the mailing list here:
https://lists.sourceforge.net/lists/listinfo/moose-generic.

The errors you reported seem to be due to path issues. Can you check where the GSL and
HDF5 libraries have been installed? You may have to edit the Makefile to get it to work.
The library path has to be appended to the LIBS variable, and the include path to the
CXXFLAGS variable. In the current revision (r4433), the GSL section of the Makefile is
on line numbers 208-209, and the HDF5 section is at line numbers 262-263.

Best,
Niraj

>
> Hi
> I have python-2.7 with GSL and HDF5 libraries installed    but I am getting  a lot of
> errors every time I try to do "make BUILD=release" on CentOS 5.5  x86_64 x86_64 x86_64
> GNU/Linux
> We are trying to have it installed on the cluster and using "module" commands to load
> all libraries.
>
> Can somebody advice what might be missing ?  Thanks a lot in advance.
> Vadim.
>
> Here the error:
>
>
> MarkovChannel.cpp:16:27: error: gsl/gsl_errno.h: No such file or directory***
> [MarkovChannel.o] Error 1
>
> HDF5WriterBase.cpp:33:18: error: hdf5.h: No such file or directorymake[1]: ***
> [HDF5WriterBase.o] Error 1
>
> Stoich.cpp:42:27: error: gsl/gsl_errno.h: No such file or directorymake[1]: ***
> [Stoich.o] Error 1
>
> rtMultiCompartment.cpp:11:27: error: gsl/gsl_errno.h: No such file or
> directoryrtMultiCompartment.cpp:12:28: error: gsl/gsl_matrix.h: No such file or
> directoryrtMultiCompartment.cpp:13:27: error: gsl/gsl_odeiv.h: No such file or directory
> ../ksolve/OdeSystem.h:51: warning: ISO C++ forbids declaration of 'gsl_odeiv_step_type'
> with no type../ksolve/OdeSystem.h:51: error: expected ';' before '*'
> token../ksolve/OdeSystem.h:52: warning: ISO C++ forbids declaration of 'gsl_odeiv_step'
> with no type../ksolve/OdeSystem.h:52: error: expected ';' before '*'
> token../ksolve/OdeSystem.h:53: warning: ISO C++ forbids declaration of
> 'gsl_odeiv_control' with no type../ksolve/OdeSystem.h:53: error: expected ';' before '*'
> token../ksolve/OdeSystem.h:54: warning: ISO C++ forbids declaration of
> 'gsl_odeiv_evolve' with no type../ksolve/OdeSystem.h:54: error: expected ';' before '*'
> token../ksolve/OdeSystem.h:55: error: 'gsl_odeiv_system' does not name a type
> [rtMultiCompartment.o] Error 1No rule to make target `biophysics/_biophysics.o', needed
> by `moose'.  Stop.
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb_______________________________________________
> moose-generic mailing list
> moo...@li...
> https://lists.sourceforge.net/lists/listinfo/moose-generic
>

[moose-generic] MOOSE_installation_problem

[vadim a. <vad...@ho...>]

Hi
I have python-2.7 with GSL and HDF5 libraries installed    but I am getting  a lot of errors every time I try to do "make BUILD=release" on CentOS 5.5  x86_64 x86_64 x86_64 GNU/Linux
We are trying to have it installed on the cluster and using "module" commands to load all libraries.

Can somebody advice what might be missing ?  Thanks a lot in advance.
Vadim.

Here the error:


MarkovChannel.cpp:16:27: error: gsl/gsl_errno.h: No such file or directory*** [MarkovChannel.o] Error 1

HDF5WriterBase.cpp:33:18: error: hdf5.h: No such file or directorymake[1]: *** [HDF5WriterBase.o] Error 1

Stoich.cpp:42:27: error: gsl/gsl_errno.h: No such file or directorymake[1]: *** [Stoich.o] Error 1

rtMultiCompartment.cpp:11:27: error: gsl/gsl_errno.h: No such file or directoryrtMultiCompartment.cpp:12:28: error: gsl/gsl_matrix.h: No such file or directoryrtMultiCompartment.cpp:13:27: error: gsl/gsl_odeiv.h: No such file or directory
../ksolve/OdeSystem.h:51: warning: ISO C++ forbids declaration of 'gsl_odeiv_step_type' with no type../ksolve/OdeSystem.h:51: error: expected ';' before '*' token../ksolve/OdeSystem.h:52: warning: ISO C++ forbids declaration of 'gsl_odeiv_step' with no type../ksolve/OdeSystem.h:52: error: expected ';' before '*' token../ksolve/OdeSystem.h:53: warning: ISO C++ forbids declaration of 'gsl_odeiv_control' with no type../ksolve/OdeSystem.h:53: error: expected ';' before '*' token../ksolve/OdeSystem.h:54: warning: ISO C++ forbids declaration of 'gsl_odeiv_evolve' with no type../ksolve/OdeSystem.h:54: error: expected ';' before '*' token../ksolve/OdeSystem.h:55: error: 'gsl_odeiv_system' does not name a type
[rtMultiCompartment.o] Error 1No rule to make target `biophysics/_biophysics.o', needed by `moose'.  Stop.