Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

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Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

markaehlen
Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have used MacPorts in the past and found it very good ('secretarially') in keeping track of prerequisite libraries and insuring the latest libraries are used. I have tried several times to use it but am getting strange errors.

Before I ask specific questions about installation (I have also been following the guidance in the repast download files), should I / could I use MacPorts (it has entries for all of the pre-requisites: openmpi, mpich2, boost, netcdf, netcdf-cxx4), or should I really just do each pre-requisite manually? The problem appears to be that boost static libraries are not created, and certain header files (netcdfcpp.h) are not installed locally.

Just high-level question for now...

Thanks,

Mark
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

Murphy, John T.
Hi Mark,

My experience is skewed: I also use a Mac with an OS that has a name of a
big cat of some kind, but I basically started using it when I started
using Repast HPC. I didn't know much about 'MacPorts' at the time, and
still don't.

That said, I'm not too surprised by what you are reporting. The two most
difficult of Repast HPC's required libraries seem to be NetCDF and Boost.

With respect to NetCDF, I'm not entirely sure how the latest libraries
work. My own recent experience is with a Cygwin installation (because I
haven't changed the installation on my Mac in a long time). NetCDF has a
new structure for their libraries; this is apparent from their downloads
and from the options available in Cygwin setup, and exactly how MacPorts
will deal with these is something I can only guess. But I do know that
netcdfcpp.h isn't automatically created in the Cygwin installation.

In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the default
Cygwin (and possibly MacPorts) approach is to use the newer '4' versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h).

As for Boost, I'm not 100% sure you'll need the static libraries, but if
you do, I don't know how MacPorts can be told to build them. I always
build Boost manually. The steps aren't that hard:

./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
--with-libraries=system,filesystem,mpi,serialization

Add:

using mpi : mpicxx ;

to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file, where
mpicxx is your mpi compiler (full path if needed); make sure to include
the spaces!

./b2 --layout=tagged variant=release link=shared,static threading=multi
stage install

The options to the b2 install are viewable here:
http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.html

I would recommend copying the "boost" directory (with all the header
files) manually before using 'install'; for some reason boost copies each
file individually and this can take longer, when in fact all that happens
is this directory gets copied wholesale.

Hope this helps- best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]




On 8/20/12 1:10 PM, "markaehlen" <[hidden email]> wrote:

>
>Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have
>used
>MacPorts in the past and found it very good ('secretarially') in keeping
>track of prerequisite libraries and insuring the latest libraries are
>used.
>I have tried several times to use it but am getting strange errors.
>
>Before I ask specific questions about installation (I have also been
>following the guidance in the repast download files), should I / could I
>use
>MacPorts (it has entries for all of the pre-requisites: openmpi, mpich2,
>boost, netcdf, netcdf-cxx4), or should I really just do each pre-requisite
>manually? The problem appears to be that boost static libraries are not
>created, and certain header files (netcdfcpp.h) are not installed locally.
>
>Just high-level question for now...
>
>Thanks,
>
>Mark
>--
>View this message in context:
>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prerequ
>isite-Libraries-with-MacPort--tp34325774p34325774.html
>Sent from the repast-interest mailing list archive at Nabble.com.
>
>
>--------------------------------------------------------------------------
>----
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>threat landscape has changed and how IT managers can respond. Discussions
>will include endpoint security, mobile security and the latest in malware
>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>_______________________________________________
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>[hidden email]
>https://lists.sourceforge.net/lists/listinfo/repast-interest


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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

markaehlen
In reply to this post by markaehlen
Wow - thanks for the quick reply. I am in the middle of building (and the many variants it takes), so have some high-level thinking to do...will eventually install correctly, it just will when it does. In the meantime:

Its helpful to understand, from RepastHPC's standpoint (yes, the code), what it needs to compile. Some of the requirements are, I am assuming, runtime libraries and other things are specific header files. For example, it appears to want to find *actual files* such as boost/mpi.cpp and netcdfcpp.h. I'm not a deep compiler thinker, so pardon me if this sounds sophomoric, but which of the mpi/boost/netcdf/netcdf-cxx links need to be files and which need to be / can be compiled libraries? I'm learning this RepastHPC division/grouping the hard way, but that's okay. Macports, for example, just installs the needed libraries (and occasional executable code?), but by default probably does not install *any* source code, e.g., *.h files.

If you can harvest a question from the above, I look forward to an answer :)

Thanks again!

Mark


markaehlen wrote
Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have used MacPorts in the past and found it very good ('secretarially') in keeping track of prerequisite libraries and insuring the latest libraries are used. I have tried several times to use it but am getting strange errors.

Before I ask specific questions about installation (I have also been following the guidance in the repast download files), should I / could I use MacPorts (it has entries for all of the pre-requisites: openmpi, mpich2, boost, netcdf, netcdf-cxx4), or should I really just do each pre-requisite manually? The problem appears to be that boost static libraries are not created, and certain header files (netcdfcpp.h) are not installed locally.

Just high-level question for now...

Thanks,

Mark
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

markaehlen
In reply to this post by Murphy, John T.
Also, is there really no difference between using OpenMPI or using MPICH2? Do you recommend either for folks like me working hard to learn/achieve compilation?

M


Murphy, John T. wrote
Hi Mark,

My experience is skewed: I also use a Mac with an OS that has a name of a
big cat of some kind, but I basically started using it when I started
using Repast HPC. I didn't know much about 'MacPorts' at the time, and
still don't.

That said, I'm not too surprised by what you are reporting. The two most
difficult of Repast HPC's required libraries seem to be NetCDF and Boost.

With respect to NetCDF, I'm not entirely sure how the latest libraries
work. My own recent experience is with a Cygwin installation (because I
haven't changed the installation on my Mac in a long time). NetCDF has a
new structure for their libraries; this is apparent from their downloads
and from the options available in Cygwin setup, and exactly how MacPorts
will deal with these is something I can only guess. But I do know that
netcdfcpp.h isn't automatically created in the Cygwin installation.

In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the default
Cygwin (and possibly MacPorts) approach is to use the newer '4' versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h).

As for Boost, I'm not 100% sure you'll need the static libraries, but if
you do, I don't know how MacPorts can be told to build them. I always
build Boost manually. The steps aren't that hard:

./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
--with-libraries=system,filesystem,mpi,serialization

Add:

using mpi : mpicxx ;

to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file, where
mpicxx is your mpi compiler (full path if needed); make sure to include
the spaces!

./b2 --layout=tagged variant=release link=shared,static threading=multi
stage install

The options to the b2 install are viewable here:
http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.html

I would recommend copying the "boost" directory (with all the header
files) manually before using 'install'; for some reason boost copies each
file individually and this can take longer, when in fact all that happens
is this directory gets copied wholesale.

Hope this helps- best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
jtmurphy@anl.gov




On 8/20/12 1:10 PM, "markaehlen" <Markaehlen@gmail.com> wrote:

>
>Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have
>used
>MacPorts in the past and found it very good ('secretarially') in keeping
>track of prerequisite libraries and insuring the latest libraries are
>used.
>I have tried several times to use it but am getting strange errors.
>
>Before I ask specific questions about installation (I have also been
>following the guidance in the repast download files), should I / could I
>use
>MacPorts (it has entries for all of the pre-requisites: openmpi, mpich2,
>boost, netcdf, netcdf-cxx4), or should I really just do each pre-requisite
>manually? The problem appears to be that boost static libraries are not
>created, and certain header files (netcdfcpp.h) are not installed locally.
>
>Just high-level question for now...
>
>Thanks,
>
>Mark
>--
>View this message in context:
>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prerequ
>isite-Libraries-with-MacPort--tp34325774p34325774.html
>Sent from the repast-interest mailing list archive at Nabble.com.
>
>
>--------------------------------------------------------------------------
>----
>Live Security Virtual Conference
>Exclusive live event will cover all the ways today's security and
>threat landscape has changed and how IT managers can respond. Discussions
>will include endpoint security, mobile security and the latest in malware
>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>_______________________________________________
>Repast-interest mailing list
>Repast-interest@lists.sourceforge.net
>https://lists.sourceforge.net/lists/listinfo/repast-interest


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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

Murphy, John T.
In reply to this post by markaehlen
Mark,

In the simplest situation you get two pieces: .h files and a library like
libMYLIB.a.

The .h file (also, sometimes ".hpp", for c++ code) describes the functions
and classes in the library; the .a file is an archive of the compiled
versions of those functions and classes.

You might also get .c files (or .cpp, again for c++ code); these are the
source code that was used to generate the .a file. When you build the
libraries on your own machine, you get only the .c and .cpp files, and you
build the .a file.

After the .a file is created, you can (if you want) throw away the .c and
.cpp files. (It's good to keep them, but they're only good for reference.)

To use this library, you need to write code that includes the appropriate
.h files. This allows you to compile your code. To actually make it run,
you need to link to the library .a file. (Linking can be done as part of
compiling or during run-time.)

The first step in building the RepastHPC library uses the .h and .cpp
files from the other libraries like boost, netcdf, etc. The result is a
repasthpc.a library.

After that you can use the repast '.h' files (as well as any other
library's .h files) in your own code. When you link, you can link to the
other libraries and to the repasthpc.a library.

This is all an outcome of the separation of 'structure' from 'content':
the .h files describe what functions are available in the libraries; the
.cpp files actually have the code they need.

(There is also 'templated' code; this is code that is written at a generic
level and can't be compiled until its specifics are filled in; basically
there are .hpp files but no .cpp files.)

So the upshot is that Repast HPC will need the .h files and the .a files,
but shouldn't need the .cpp files. You should only need those if you're
building the libraries yourself.

Hope this makes sense.

Best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]




On 8/20/12 2:11 PM, "markaehlen" <[hidden email]> wrote:

>
>Wow - thanks for the quick reply. I am in the middle of building (and the
>many variants it takes), so have some high-level thinking to do...will
>eventually install correctly, it just will when it does. In the meantime:
>
>Its helpful to understand, from RepastHPC's standpoint (yes, the code),
>what
>it needs to compile. Some of the requirements are, I am assuming, runtime
>libraries and other things are specific header files. For example, it
>appears to want to find *actual files* such as boost/mpi.cpp and
>netcdfcpp.h. I'm not a deep compiler thinker, so pardon me if this sounds
>sophomoric, but which of the mpi/boost/netcdf/netcdf-cxx links need to be
>files and which need to be / can be compiled libraries? I'm learning this
>RepastHPC division/grouping the hard way, but that's okay. Macports, for
>example, just installs the needed libraries (and occasional executable
>code?), but by default probably does not install *any* source code, e.g.,
>*.h files.
>
>If you can harvest a question from the above, I look forward to an answer
>:)
>
>Thanks again!
>
>Mark
>
>
>
>markaehlen wrote:
>>
>> Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have
>> used MacPorts in the past and found it very good ('secretarially') in
>> keeping track of prerequisite libraries and insuring the latest
>>libraries
>> are used. I have tried several times to use it but am getting strange
>> errors.
>>
>> Before I ask specific questions about installation (I have also been
>> following the guidance in the repast download files), should I / could I
>> use MacPorts (it has entries for all of the pre-requisites: openmpi,
>> mpich2, boost, netcdf, netcdf-cxx4), or should I really just do each
>> pre-requisite manually? The problem appears to be that boost static
>> libraries are not created, and certain header files (netcdfcpp.h) are
>>not
>> installed locally.
>>
>> Just high-level question for now...
>>
>> Thanks,
>>
>> Mark
>>
>--
>View this message in context:
>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prerequ
>isite-Libraries-with-MacPort--tp34325774p34326062.html
>Sent from the repast-interest mailing list archive at Nabble.com.
>
>
>--------------------------------------------------------------------------
>----
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>threat landscape has changed and how IT managers can respond. Discussions
>will include endpoint security, mobile security and the latest in malware
>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>_______________________________________________
>Repast-interest mailing list
>[hidden email]
>https://lists.sourceforge.net/lists/listinfo/repast-interest


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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

Murphy, John T.
In reply to this post by markaehlen
Hi Mark,

"MPI" is a specification: it is a description of a set of functions that a
particular implementation should make available.

Both OpenMPI and MPICH2 follow the specification very closely; I don't
know of any differences between them. You can write code on one system
that has OpenMPI installed and use it on another with MPICH2, generally
without any problems. (My laptop has OpenMPI; I can run things on
Argonne's Blue Gene/P which has MPICH2 (somewhat customized), without any
issues.)

Of course, 'under-the-hood' they may be very different, but that doesn't
matter to you. (To put it in terms of the preceding email, the '.h' files
could be essentially the same for both, even if the underlying '.cpp'
files looked very different. This isn't really true, but it's a good way
to think about it.)

Best,
John

--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]




On 8/20/12 2:17 PM, "markaehlen" <[hidden email]> wrote:

>
>Also, is there really no difference between using OpenMPI or using
>MPICH2? Do
>you recommend either for folks like me working hard to learn/achieve
>compilation?
>
>M
>
>
>
>Murphy, John T. wrote:
>>
>> Hi Mark,
>>
>> My experience is skewed: I also use a Mac with an OS that has a name of
>>a
>> big cat of some kind, but I basically started using it when I started
>> using Repast HPC. I didn't know much about 'MacPorts' at the time, and
>> still don't.
>>
>> That said, I'm not too surprised by what you are reporting. The two most
>> difficult of Repast HPC's required libraries seem to be NetCDF and
>>Boost.
>>
>> With respect to NetCDF, I'm not entirely sure how the latest libraries
>> work. My own recent experience is with a Cygwin installation (because I
>> haven't changed the installation on my Mac in a long time). NetCDF has a
>> new structure for their libraries; this is apparent from their downloads
>> and from the options available in Cygwin setup, and exactly how MacPorts
>> will deal with these is something I can only guess. But I do know that
>> netcdfcpp.h isn't automatically created in the Cygwin installation.
>>
>> In this case, it seems to be because NetCDF is split 2 x 2 ways: With
>> respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
>> also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
>>only
>> use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
>>C++
>> 4 doesn't use the same netcdfcpp.h file, and my hunch is that the
>>default
>> Cygwin (and possibly MacPorts) approach is to use the newer '4'
>>versions.
>> Repast HPC expects the '3' versions (and has to have netcdfcpp.h).
>>
>> As for Boost, I'm not 100% sure you'll need the static libraries, but if
>> you do, I don't know how MacPorts can be told to build them. I always
>> build Boost manually. The steps aren't that hard:
>>
>> ./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
>> --with-libraries=system,filesystem,mpi,serialization
>>
>> Add:
>>
>> using mpi : mpicxx ;
>>
>> to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file, where
>> mpicxx is your mpi compiler (full path if needed); make sure to include
>> the spaces!
>>
>> ./b2 --layout=tagged variant=release link=shared,static threading=multi
>> stage install
>>
>> The options to the b2 install are viewable here:
>> http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.html
>>
>> I would recommend copying the "boost" directory (with all the header
>> files) manually before using 'install'; for some reason boost copies
>>each
>> file individually and this can take longer, when in fact all that
>>happens
>> is this directory gets copied wholesale.
>>
>> Hope this helps- best,
>> John
>>
>>
>>
>> --
>> John T. Murphy
>> Computational Postdoctoral Fellow
>> Decision and Information Sciences and
>> Argonne Leadership Computing Facility
>> Argonne National Laboratory
>> [hidden email]
>>
>>
>>
>>
>> On 8/20/12 1:10 PM, "markaehlen" <[hidden email]> wrote:
>>
>>>
>>>Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have
>>>used
>>>MacPorts in the past and found it very good ('secretarially') in keeping
>>>track of prerequisite libraries and insuring the latest libraries are
>>>used.
>>>I have tried several times to use it but am getting strange errors.
>>>
>>>Before I ask specific questions about installation (I have also been
>>>following the guidance in the repast download files), should I / could I
>>>use
>>>MacPorts (it has entries for all of the pre-requisites: openmpi, mpich2,
>>>boost, netcdf, netcdf-cxx4), or should I really just do each
>>>pre-requisite
>>>manually? The problem appears to be that boost static libraries are not
>>>created, and certain header files (netcdfcpp.h) are not installed
>>>locally.
>>>
>>>Just high-level question for now...
>>>
>>>Thanks,
>>>
>>>Mark
>>>--
>>>View this message in context:
>>>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prere
>>>qu
>>>isite-Libraries-with-MacPort--tp34325774p34325774.html
>>>Sent from the repast-interest mailing list archive at Nabble.com.
>>>
>>>
>>>------------------------------------------------------------------------
>>>--
>>>----
>>>Live Security Virtual Conference
>>>Exclusive live event will cover all the ways today's security and
>>>threat landscape has changed and how IT managers can respond.
>>>Discussions
>>>will include endpoint security, mobile security and the latest in
>>>malware
>>>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>_______________________________________________
>>>Repast-interest mailing list
>>>[hidden email]
>>>https://lists.sourceforge.net/lists/listinfo/repast-interest
>>
>>
>>
>>-------------------------------------------------------------------------
>>-----
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond.
>>Discussions
>> will include endpoint security, mobile security and the latest in
>>malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Repast-interest mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/repast-interest
>>
>>
>
>--
>View this message in context:
>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prerequ
>isite-Libraries-with-MacPort--tp34325774p34326086.html
>Sent from the repast-interest mailing list archive at Nabble.com.
>
>
>--------------------------------------------------------------------------
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>threat landscape has changed and how IT managers can respond. Discussions
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

markaehlen
This post was updated on .
In reply to this post by Murphy, John T.
Hey John - you are incredibly helpful; thanks. My knowledge is starting to catch up to current installation challenges, which has everything to do with knowing where things should be installed and testing testing testing.

I have stepped away from the MacPorts approach because some basic intermediate capabilities are not working. For example, I can't type "mpicc" after installation of OpenMPI via MacPorts, and "sudo find / -name mpicc" obtains nothing. The regular OpenMPI configure/make/install does, so I'm going with that approach for everything. Boost and OpenMPI are installed; NetCDF and NetCDF C++ are next.

I naively skipped over an important statement you made previously and want to revisit so I understand the next step clearly:

"In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the default
Cygwin (and possibly MacPorts) approach is to use the newer '4' versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h)."

1. To install what Repast HPC wants, should I install the NetCDF (NOT 4) and NetCDF C++ (legacy), that is, the "3" versions? I was using the "4" versions before.
2. NetCDF says I don't have HDF5 installed; is there a particular version I should install? I think the same question holds for zlib...

Thanks for all your help; is invaluable. I really need to get this installed.

Cheers,

Mark

Murphy, John T. wrote
Hi Mark,

My experience is skewed: I also use a Mac with an OS that has a name of a
big cat of some kind, but I basically started using it when I started
using Repast HPC. I didn't know much about 'MacPorts' at the time, and
still don't.

That said, I'm not too surprised by what you are reporting. The two most
difficult of Repast HPC's required libraries seem to be NetCDF and Boost.

With respect to NetCDF, I'm not entirely sure how the latest libraries
work. My own recent experience is with a Cygwin installation (because I
haven't changed the installation on my Mac in a long time). NetCDF has a
new structure for their libraries; this is apparent from their downloads
and from the options available in Cygwin setup, and exactly how MacPorts
will deal with these is something I can only guess. But I do know that
netcdfcpp.h isn't automatically created in the Cygwin installation.

In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the default
Cygwin (and possibly MacPorts) approach is to use the newer '4' versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h).

As for Boost, I'm not 100% sure you'll need the static libraries, but if
you do, I don't know how MacPorts can be told to build them. I always
build Boost manually. The steps aren't that hard:

./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
--with-libraries=system,filesystem,mpi,serialization

Add:

using mpi : mpicxx ;

to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file, where
mpicxx is your mpi compiler (full path if needed); make sure to include
the spaces!

./b2 --layout=tagged variant=release link=shared,static threading=multi
stage install

The options to the b2 install are viewable here:
http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.html

I would recommend copying the "boost" directory (with all the header
files) manually before using 'install'; for some reason boost copies each
file individually and this can take longer, when in fact all that happens
is this directory gets copied wholesale.

Hope this helps- best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
jtmurphy@anl.gov




On 8/20/12 1:10 PM, "markaehlen" <Markaehlen@gmail.com> wrote:

>
>Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have
>used
>MacPorts in the past and found it very good ('secretarially') in keeping
>track of prerequisite libraries and insuring the latest libraries are
>used.
>I have tried several times to use it but am getting strange errors.
>
>Before I ask specific questions about installation (I have also been
>following the guidance in the repast download files), should I / could I
>use
>MacPorts (it has entries for all of the pre-requisites: openmpi, mpich2,
>boost, netcdf, netcdf-cxx4), or should I really just do each pre-requisite
>manually? The problem appears to be that boost static libraries are not
>created, and certain header files (netcdfcpp.h) are not installed locally.
>
>Just high-level question for now...
>
>Thanks,
>
>Mark
>--
>View this message in context:
>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prerequ
>isite-Libraries-with-MacPort--tp34325774p34325774.html
>Sent from the repast-interest mailing list archive at Nabble.com.
>
>
>--------------------------------------------------------------------------
>----
>Live Security Virtual Conference
>Exclusive live event will cover all the ways today's security and
>threat landscape has changed and how IT managers can respond. Discussions
>will include endpoint security, mobile security and the latest in malware
>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>_______________________________________________
>Repast-interest mailing list
>Repast-interest@lists.sourceforge.net
>https://lists.sourceforge.net/lists/listinfo/repast-interest


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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

markaehlen
One more question:

3. Is this the right set of "3" installs to download?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-4_1_3/index.jsp

Thanks again!

Mark


markaehlen wrote
Hey John - you are incredibly helpful; thanks. My knowledge is starting to catch up to current installation challenges, which has everything to do with knowing where things should be installed and testing testing testing.

I have stepped away from the MacPorts approach because some basic intermediate capabilities are not working. For example, I can't type "mpicc" after installation of OpenMPI via MacPorts, and "sudo find / -name mpicc" obtains nothing. The regular OpenMPI configure/make/install does, so I'm going with that approach for everything. Boost and OpenMPI are installed; NetCDF and NetCDF C++ are next.

I skipped over an important statement you made previously and want to revisit so I understand the next step clearly:

"In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the default
Cygwin (and possibly MacPorts) approach is to use the newer '4' versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h)."

1. To install what Repast HPC wants, should I install the NetCDF (NOT 4) and NetCDF C++ (legacy), that is, the "3" versions? I was using the "4" versions before.
2. NetCDF says I don't have HDF5 installed; is there a particular version I should install? I think the same question holds for zlib...

Thanks for all your help; is invaluable. I really need to get this installed.

Cheers,

Mark

Murphy, John T. wrote
Hi Mark,

My experience is skewed: I also use a Mac with an OS that has a name of a
big cat of some kind, but I basically started using it when I started
using Repast HPC. I didn't know much about 'MacPorts' at the time, and
still don't.

That said, I'm not too surprised by what you are reporting. The two most
difficult of Repast HPC's required libraries seem to be NetCDF and Boost.

With respect to NetCDF, I'm not entirely sure how the latest libraries
work. My own recent experience is with a Cygwin installation (because I
haven't changed the installation on my Mac in a long time). NetCDF has a
new structure for their libraries; this is apparent from their downloads
and from the options available in Cygwin setup, and exactly how MacPorts
will deal with these is something I can only guess. But I do know that
netcdfcpp.h isn't automatically created in the Cygwin installation.

In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the default
Cygwin (and possibly MacPorts) approach is to use the newer '4' versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h).

As for Boost, I'm not 100% sure you'll need the static libraries, but if
you do, I don't know how MacPorts can be told to build them. I always
build Boost manually. The steps aren't that hard:

./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
--with-libraries=system,filesystem,mpi,serialization

Add:

using mpi : mpicxx ;

to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file, where
mpicxx is your mpi compiler (full path if needed); make sure to include
the spaces!

./b2 --layout=tagged variant=release link=shared,static threading=multi
stage install

The options to the b2 install are viewable here:
http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.html

I would recommend copying the "boost" directory (with all the header
files) manually before using 'install'; for some reason boost copies each
file individually and this can take longer, when in fact all that happens
is this directory gets copied wholesale.

Hope this helps- best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
jtmurphy@anl.gov




On 8/20/12 1:10 PM, "markaehlen" <Markaehlen@gmail.com> wrote:

>
>Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have
>used
>MacPorts in the past and found it very good ('secretarially') in keeping
>track of prerequisite libraries and insuring the latest libraries are
>used.
>I have tried several times to use it but am getting strange errors.
>
>Before I ask specific questions about installation (I have also been
>following the guidance in the repast download files), should I / could I
>use
>MacPorts (it has entries for all of the pre-requisites: openmpi, mpich2,
>boost, netcdf, netcdf-cxx4), or should I really just do each pre-requisite
>manually? The problem appears to be that boost static libraries are not
>created, and certain header files (netcdfcpp.h) are not installed locally.
>
>Just high-level question for now...
>
>Thanks,
>
>Mark
>--
>View this message in context:
>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prerequ
>isite-Libraries-with-MacPort--tp34325774p34325774.html
>Sent from the repast-interest mailing list archive at Nabble.com.
>
>
>--------------------------------------------------------------------------
>----
>Live Security Virtual Conference
>Exclusive live event will cover all the ways today's security and
>threat landscape has changed and how IT managers can respond. Discussions
>will include endpoint security, mobile security and the latest in malware
>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>_______________________________________________
>Repast-interest mailing list
>Repast-interest@lists.sourceforge.net
>https://lists.sourceforge.net/lists/listinfo/repast-interest


------------------------------------------------------------------------------
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threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

markaehlen
Or this one?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3_6_3/index.jsp

Thanks,

Mark

markaehlen wrote
One more question:

3. Is this the right set of "3" installs to download?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-4_1_3/index.jsp

Thanks again!

Mark


markaehlen wrote
Hey John - you are incredibly helpful; thanks. My knowledge is starting to catch up to current installation challenges, which has everything to do with knowing where things should be installed and testing testing testing.

I have stepped away from the MacPorts approach because some basic intermediate capabilities are not working. For example, I can't type "mpicc" after installation of OpenMPI via MacPorts, and "sudo find / -name mpicc" obtains nothing. The regular OpenMPI configure/make/install does, so I'm going with that approach for everything. Boost and OpenMPI are installed; NetCDF and NetCDF C++ are next.

I skipped over an important statement you made previously and want to revisit so I understand the next step clearly:

"In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the default
Cygwin (and possibly MacPorts) approach is to use the newer '4' versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h)."

1. To install what Repast HPC wants, should I install the NetCDF (NOT 4) and NetCDF C++ (legacy), that is, the "3" versions? I was using the "4" versions before.
2. NetCDF says I don't have HDF5 installed; is there a particular version I should install? I think the same question holds for zlib...

Thanks for all your help; is invaluable. I really need to get this installed.

Cheers,

Mark

Murphy, John T. wrote
Hi Mark,

My experience is skewed: I also use a Mac with an OS that has a name of a
big cat of some kind, but I basically started using it when I started
using Repast HPC. I didn't know much about 'MacPorts' at the time, and
still don't.

That said, I'm not too surprised by what you are reporting. The two most
difficult of Repast HPC's required libraries seem to be NetCDF and Boost.

With respect to NetCDF, I'm not entirely sure how the latest libraries
work. My own recent experience is with a Cygwin installation (because I
haven't changed the installation on my Mac in a long time). NetCDF has a
new structure for their libraries; this is apparent from their downloads
and from the options available in Cygwin setup, and exactly how MacPorts
will deal with these is something I can only guess. But I do know that
netcdfcpp.h isn't automatically created in the Cygwin installation.

In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the default
Cygwin (and possibly MacPorts) approach is to use the newer '4' versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h).

As for Boost, I'm not 100% sure you'll need the static libraries, but if
you do, I don't know how MacPorts can be told to build them. I always
build Boost manually. The steps aren't that hard:

./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
--with-libraries=system,filesystem,mpi,serialization

Add:

using mpi : mpicxx ;

to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file, where
mpicxx is your mpi compiler (full path if needed); make sure to include
the spaces!

./b2 --layout=tagged variant=release link=shared,static threading=multi
stage install

The options to the b2 install are viewable here:
http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.html

I would recommend copying the "boost" directory (with all the header
files) manually before using 'install'; for some reason boost copies each
file individually and this can take longer, when in fact all that happens
is this directory gets copied wholesale.

Hope this helps- best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
jtmurphy@anl.gov




On 8/20/12 1:10 PM, "markaehlen" <Markaehlen@gmail.com> wrote:

>
>Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have
>used
>MacPorts in the past and found it very good ('secretarially') in keeping
>track of prerequisite libraries and insuring the latest libraries are
>used.
>I have tried several times to use it but am getting strange errors.
>
>Before I ask specific questions about installation (I have also been
>following the guidance in the repast download files), should I / could I
>use
>MacPorts (it has entries for all of the pre-requisites: openmpi, mpich2,
>boost, netcdf, netcdf-cxx4), or should I really just do each pre-requisite
>manually? The problem appears to be that boost static libraries are not
>created, and certain header files (netcdfcpp.h) are not installed locally.
>
>Just high-level question for now...
>
>Thanks,
>
>Mark
>--
>View this message in context:
>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prerequ
>isite-Libraries-with-MacPort--tp34325774p34325774.html
>Sent from the repast-interest mailing list archive at Nabble.com.
>
>
>--------------------------------------------------------------------------
>----
>Live Security Virtual Conference
>Exclusive live event will cover all the ways today's security and
>threat landscape has changed and how IT managers can respond. Discussions
>will include endpoint security, mobile security and the latest in malware
>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>_______________________________________________
>Repast-interest mailing list
>Repast-interest@lists.sourceforge.net
>https://lists.sourceforge.net/lists/listinfo/repast-interest


------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

markaehlen
Hey John - last message on this thread, at least for today:

When installed the following two versions of netcdf - netcdf-3.6.3, netcdf-cxx-4.2) - I get the following error on "make all":

mv -f .deps/librepast_hpc_1_0_1_la-logger.Tpo .deps/librepast_hpc_1_0_1_la-logger.Plo
/bin/sh ../../libtool  --tag=CXX   --mode=compile mpic++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF .deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c -o librepast_hpc_1_0_1_la-NCDataSet.lo `test -f 'NCDataSet.cpp' || echo './'`NCDataSet.cpp
libtool: compile:  mpic++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF .deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c NCDataSet.cpp  -fno-common -DPIC -o .libs/librepast_hpc_1_0_1_la-NCDataSet.o
NCDataSet.cpp: In constructor 'repast::NCDataSet::NCDataSet(std::string, const repast::Schedule&)':
NCDataSet.cpp:68: error: conversion from 'boost::filesystem::path' to non-scalar type 'std::basic_string<char, std::char_traits<char>, std::allocator<char> >' requested
make[2]: *** [librepast_hpc_1_0_1_la-NCDataSet.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Any insights would be GREATLY appreciated!

Mark

markaehlen wrote
Or this one?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3_6_3/index.jsp

Thanks,

Mark

markaehlen wrote
One more question:

3. Is this the right set of "3" installs to download?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-4_1_3/index.jsp

Thanks again!

Mark


markaehlen wrote
Hey John - you are incredibly helpful; thanks. My knowledge is starting to catch up to current installation challenges, which has everything to do with knowing where things should be installed and testing testing testing.

I have stepped away from the MacPorts approach because some basic intermediate capabilities are not working. For example, I can't type "mpicc" after installation of OpenMPI via MacPorts, and "sudo find / -name mpicc" obtains nothing. The regular OpenMPI configure/make/install does, so I'm going with that approach for everything. Boost and OpenMPI are installed; NetCDF and NetCDF C++ are next.

I skipped over an important statement you made previously and want to revisit so I understand the next step clearly:

"In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the default
Cygwin (and possibly MacPorts) approach is to use the newer '4' versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h)."

1. To install what Repast HPC wants, should I install the NetCDF (NOT 4) and NetCDF C++ (legacy), that is, the "3" versions? I was using the "4" versions before.
2. NetCDF says I don't have HDF5 installed; is there a particular version I should install? I think the same question holds for zlib...

Thanks for all your help; is invaluable. I really need to get this installed.

Cheers,

Mark

Murphy, John T. wrote
Hi Mark,

My experience is skewed: I also use a Mac with an OS that has a name of a
big cat of some kind, but I basically started using it when I started
using Repast HPC. I didn't know much about 'MacPorts' at the time, and
still don't.

That said, I'm not too surprised by what you are reporting. The two most
difficult of Repast HPC's required libraries seem to be NetCDF and Boost.

With respect to NetCDF, I'm not entirely sure how the latest libraries
work. My own recent experience is with a Cygwin installation (because I
haven't changed the installation on my Mac in a long time). NetCDF has a
new structure for their libraries; this is apparent from their downloads
and from the options available in Cygwin setup, and exactly how MacPorts
will deal with these is something I can only guess. But I do know that
netcdfcpp.h isn't automatically created in the Cygwin installation.

In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the default
Cygwin (and possibly MacPorts) approach is to use the newer '4' versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h).

As for Boost, I'm not 100% sure you'll need the static libraries, but if
you do, I don't know how MacPorts can be told to build them. I always
build Boost manually. The steps aren't that hard:

./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
--with-libraries=system,filesystem,mpi,serialization

Add:

using mpi : mpicxx ;

to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file, where
mpicxx is your mpi compiler (full path if needed); make sure to include
the spaces!

./b2 --layout=tagged variant=release link=shared,static threading=multi
stage install

The options to the b2 install are viewable here:
http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.html

I would recommend copying the "boost" directory (with all the header
files) manually before using 'install'; for some reason boost copies each
file individually and this can take longer, when in fact all that happens
is this directory gets copied wholesale.

Hope this helps- best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
jtmurphy@anl.gov




On 8/20/12 1:10 PM, "markaehlen" <Markaehlen@gmail.com> wrote:

>
>Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have
>used
>MacPorts in the past and found it very good ('secretarially') in keeping
>track of prerequisite libraries and insuring the latest libraries are
>used.
>I have tried several times to use it but am getting strange errors.
>
>Before I ask specific questions about installation (I have also been
>following the guidance in the repast download files), should I / could I
>use
>MacPorts (it has entries for all of the pre-requisites: openmpi, mpich2,
>boost, netcdf, netcdf-cxx4), or should I really just do each pre-requisite
>manually? The problem appears to be that boost static libraries are not
>created, and certain header files (netcdfcpp.h) are not installed locally.
>
>Just high-level question for now...
>
>Thanks,
>
>Mark
>--
>View this message in context:
>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prerequ
>isite-Libraries-with-MacPort--tp34325774p34325774.html
>Sent from the repast-interest mailing list archive at Nabble.com.
>
>
>--------------------------------------------------------------------------
>----
>Live Security Virtual Conference
>Exclusive live event will cover all the ways today's security and
>threat landscape has changed and how IT managers can respond. Discussions
>will include endpoint security, mobile security and the latest in malware
>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>_______________________________________________
>Repast-interest mailing list
>Repast-interest@lists.sourceforge.net
>https://lists.sourceforge.net/lists/listinfo/repast-interest


------------------------------------------------------------------------------
Live Security Virtual Conference
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

Murphy, John T.
In reply to this post by markaehlen
Mark,

Sorry for the NetCDF Confusion.

For the 'C' portion of NetCDF, you can use the most current version, which
is at:

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-4_2_1_1/index.jsp

However, when it is installed, there are build options like
"--enable-netcdf-4" or "--disable-netcdf-4" that are used to specify which
version (or, probably more correctly, which feature set) of netcdf is
built. See
http://www.unidata.ucar.edu/downloads/netcdf/netcdf-4_0/index.jsp and
http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-install/Configure.h
tml for some more information (and let me know if I'm off-base; I have
only worked with this a little bit.) Without the -4 feature set I don't
think you'll need HDF5.

It sounds like MacPorts is bringing in portions of OpenMPI that can be
used by other pre-compiled things, but not the compilers, etc. needed for
building new MPI applications.

One thing to be very careful about, though, is that if you have two
versions of OpenMPI on your machine, things can get confusing: for
example, if one version compiles the application but then- possibly
without you being fully aware- the other version is being called when you
invoke mpirun, you can get some very confusing error messages. Make sure
you are using the same version of all executable components (the compiler
and the libraries) and headers for both compilation and execution by
making sure everything is on the correct search and invocation paths.

Best,
John


--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]




On 8/21/12 8:41 AM, "markaehlen" <[hidden email]> wrote:

>
>Hey John - you are incredibly helpful; thanks. My knowledge is starting to
>catch up to current installation challenges, which has everything to do
>with
>knowing where things should be installed and testing testing testing.
>
>I have stepped away from the MacPorts approach because some basic
>intermediate capabilities are not working. For example, I can't type
>"mpicc"
>after installation of OpenMPI via MacPorts, and "sudo find / -name mpicc"
>obtains nothing. The regular OpenMPI configure/make/install does, so I'm
>going with that approach for everything. Boost and OpenMPI are installed;
>NetCDF and NetCDF C++ are next.
>
>I skipped over an important statement you made previously and want to
>revisit so I understand the next step clearly:
>
>"In this case, it seems to be because NetCDF is split 2 x 2 ways: With
>respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
>also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
>only
>use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF C++
>4 doesn't use the same netcdfcpp.h file, and my hunch is that the default
>Cygwin (and possibly MacPorts) approach is to use the newer '4' versions.
>Repast HPC expects the '3' versions (and has to have netcdfcpp.h)."
>
>1. To install what Repast HPC wants, should I install the NetCDF (NOT 4)
>and
>NetCDF C++ (legacy), that is, the "3" versions? I was using the "4"
>versions
>before.
>2. NetCDF says I don't have HDF5 installed; is there a particular version
>I
>should install? I think the same question holds for zlib...
>
>Thanks for all your help; is invaluable. I really need to get this
>installed.
>
>Cheers,
>
>Mark
>
>
>Murphy, John T. wrote:
>>
>> Hi Mark,
>>
>> My experience is skewed: I also use a Mac with an OS that has a name of
>>a
>> big cat of some kind, but I basically started using it when I started
>> using Repast HPC. I didn't know much about 'MacPorts' at the time, and
>> still don't.
>>
>> That said, I'm not too surprised by what you are reporting. The two most
>> difficult of Repast HPC's required libraries seem to be NetCDF and
>>Boost.
>>
>> With respect to NetCDF, I'm not entirely sure how the latest libraries
>> work. My own recent experience is with a Cygwin installation (because I
>> haven't changed the installation on my Mac in a long time). NetCDF has a
>> new structure for their libraries; this is apparent from their downloads
>> and from the options available in Cygwin setup, and exactly how MacPorts
>> will deal with these is something I can only guess. But I do know that
>> netcdfcpp.h isn't automatically created in the Cygwin installation.
>>
>> In this case, it seems to be because NetCDF is split 2 x 2 ways: With
>> respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
>> also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
>>only
>> use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
>>C++
>> 4 doesn't use the same netcdfcpp.h file, and my hunch is that the
>>default
>> Cygwin (and possibly MacPorts) approach is to use the newer '4'
>>versions.
>> Repast HPC expects the '3' versions (and has to have netcdfcpp.h).
>>
>> As for Boost, I'm not 100% sure you'll need the static libraries, but if
>> you do, I don't know how MacPorts can be told to build them. I always
>> build Boost manually. The steps aren't that hard:
>>
>> ./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
>> --with-libraries=system,filesystem,mpi,serialization
>>
>> Add:
>>
>> using mpi : mpicxx ;
>>
>> to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file, where
>> mpicxx is your mpi compiler (full path if needed); make sure to include
>> the spaces!
>>
>> ./b2 --layout=tagged variant=release link=shared,static threading=multi
>> stage install
>>
>> The options to the b2 install are viewable here:
>> http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.html
>>
>> I would recommend copying the "boost" directory (with all the header
>> files) manually before using 'install'; for some reason boost copies
>>each
>> file individually and this can take longer, when in fact all that
>>happens
>> is this directory gets copied wholesale.
>>
>> Hope this helps- best,
>> John
>>
>>
>>
>> --
>> John T. Murphy
>> Computational Postdoctoral Fellow
>> Decision and Information Sciences and
>> Argonne Leadership Computing Facility
>> Argonne National Laboratory
>> [hidden email]
>>
>>
>>
>>
>> On 8/20/12 1:10 PM, "markaehlen" <[hidden email]> wrote:
>>
>>>
>>>Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have
>>>used
>>>MacPorts in the past and found it very good ('secretarially') in keeping
>>>track of prerequisite libraries and insuring the latest libraries are
>>>used.
>>>I have tried several times to use it but am getting strange errors.
>>>
>>>Before I ask specific questions about installation (I have also been
>>>following the guidance in the repast download files), should I / could I
>>>use
>>>MacPorts (it has entries for all of the pre-requisites: openmpi, mpich2,
>>>boost, netcdf, netcdf-cxx4), or should I really just do each
>>>pre-requisite
>>>manually? The problem appears to be that boost static libraries are not
>>>created, and certain header files (netcdfcpp.h) are not installed
>>>locally.
>>>
>>>Just high-level question for now...
>>>
>>>Thanks,
>>>
>>>Mark
>>>--
>>>View this message in context:
>>>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prere
>>>qu
>>>isite-Libraries-with-MacPort--tp34325774p34325774.html
>>>Sent from the repast-interest mailing list archive at Nabble.com.
>>>
>>>
>>>------------------------------------------------------------------------
>>>--
>>>----
>>>Live Security Virtual Conference
>>>Exclusive live event will cover all the ways today's security and
>>>threat landscape has changed and how IT managers can respond.
>>>Discussions
>>>will include endpoint security, mobile security and the latest in
>>>malware
>>>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>_______________________________________________
>>>Repast-interest mailing list
>>>[hidden email]
>>>https://lists.sourceforge.net/lists/listinfo/repast-interest
>>
>>
>>
>>-------------------------------------------------------------------------
>>-----
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond.
>>Discussions
>> will include endpoint security, mobile security and the latest in
>>malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Repast-interest mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/repast-interest
>>
>>
>--
>View this message in context:
>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prerequ
>isite-Libraries-with-MacPort--tp34325774p34329214.html
>Sent from the repast-interest mailing list archive at Nabble.com.
>
>
>--------------------------------------------------------------------------
>----
>Live Security Virtual Conference
>Exclusive live event will cover all the ways today's security and
>threat landscape has changed and how IT managers can respond. Discussions
>will include endpoint security, mobile security and the latest in malware
>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>_______________________________________________
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

Murphy, John T.
In reply to this post by markaehlen
Hi Mark,

This looks like you are using one of the recent versions of Boost. They
just released version 1.51 this morning (!), but Repast HPC is only
guaranteed to work through 1.48. (I've used 1.49 without problems, but
Boost's docs suggest this is iffy, so to be on the safe side, stick with
1.48.)

The change to make Repast HPC compatible with 1.50 (I haven't tested 1.51
yet, of course) is trivial and is included in the next release; if I
recall, it's nothing more than adding ".string()" to the end of the
boost::filesystem::path elements in about six places in the code. But it's
probably best to stick with the version of Boost that is known to have no
problems.

Best,
John
--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]




On 8/21/12 9:06 AM, "markaehlen" <[hidden email]> wrote:

>
>Hey John - last message on this thread, at least for today:
>
>When installed the following two versions of netcdf - netcdf-3.6.3,
>netcdf-cxx-4.2) - I get the following error on "make all":
>
>mv -f .deps/librepast_hpc_1_0_1_la-logger.Tpo
>.deps/librepast_hpc_1_0_1_la-logger.Plo
>/bin/sh ../../libtool  --tag=CXX   --mode=compile mpic++ -DHAVE_CONFIG_H
>-I.
>-I../..     -g -O2 -MT librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF
>.deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c -o
>librepast_hpc_1_0_1_la-NCDataSet.lo `test -f 'NCDataSet.cpp' || echo
>'./'`NCDataSet.cpp
>libtool: compile:  mpic++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT
>librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF
>.deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c NCDataSet.cpp  -fno-common
>-DPIC -o .libs/librepast_hpc_1_0_1_la-NCDataSet.o
>NCDataSet.cpp: In constructor 'repast::NCDataSet::NCDataSet(std::string,
>const repast::Schedule&)':
>NCDataSet.cpp:68: error: conversion from 'boost::filesystem::path' to
>non-scalar type 'std::basic_string<char, std::char_traits<char>,
>std::allocator<char> >' requested
>make[2]: *** [librepast_hpc_1_0_1_la-NCDataSet.lo] Error 1
>make[1]: *** [all-recursive] Error 1
>make: *** [all] Error 2
>
>Any insights would be GREATLY appreciated!
>
>Mark
>
>
>markaehlen wrote:
>>
>> Or this one?
>>
>> http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3_6_3/index.jsp
>>
>> Thanks,
>>
>> Mark
>>
>>
>> markaehlen wrote:
>>>
>>> One more question:
>>>
>>> 3. Is this the right set of "3" installs to download?
>>>
>>> http://www.unidata.ucar.edu/downloads/netcdf/netcdf-4_1_3/index.jsp
>>>
>>> Thanks again!
>>>
>>> Mark
>>>
>>>
>>>
>>> markaehlen wrote:
>>>>
>>>> Hey John - you are incredibly helpful; thanks. My knowledge is
>>>>starting
>>>> to catch up to current installation challenges, which has everything
>>>>to
>>>> do with knowing where things should be installed and testing testing
>>>> testing.
>>>>
>>>> I have stepped away from the MacPorts approach because some basic
>>>> intermediate capabilities are not working. For example, I can't type
>>>> "mpicc" after installation of OpenMPI via MacPorts, and "sudo find /
>>>> -name mpicc" obtains nothing. The regular OpenMPI
>>>>configure/make/install
>>>> does, so I'm going with that approach for everything. Boost and
>>>>OpenMPI
>>>> are installed; NetCDF and NetCDF C++ are next.
>>>>
>>>> I skipped over an important statement you made previously and want to
>>>> revisit so I understand the next step clearly:
>>>>
>>>> "In this case, it seems to be because NetCDF is split 2 x 2 ways:
>>>>With
>>>> respect to the base, C version, you can use NetCDF or 'NetCDF4'; you
>>>>can
>>>> also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
>>>> only
>>>> use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
>>>> C++
>>>> 4 doesn't use the same netcdfcpp.h file, and my hunch is that the
>>>> default
>>>> Cygwin (and possibly MacPorts) approach is to use the newer '4'
>>>> versions.
>>>> Repast HPC expects the '3' versions (and has to have netcdfcpp.h)."
>>>>
>>>> 1. To install what Repast HPC wants, should I install the NetCDF (NOT
>>>>4)
>>>> and NetCDF C++ (legacy), that is, the "3" versions? I was using the
>>>>"4"
>>>> versions before.
>>>> 2. NetCDF says I don't have HDF5 installed; is there a particular
>>>> version I should install? I think the same question holds for zlib...
>>>>
>>>> Thanks for all your help; is invaluable. I really need to get this
>>>> installed.
>>>>
>>>> Cheers,
>>>>
>>>> Mark
>>>>
>>>>
>>>> Murphy, John T. wrote:
>>>>>
>>>>> Hi Mark,
>>>>>
>>>>> My experience is skewed: I also use a Mac with an OS that has a name
>>>>>of
>>>>> a
>>>>> big cat of some kind, but I basically started using it when I started
>>>>> using Repast HPC. I didn't know much about 'MacPorts' at the time,
>>>>>and
>>>>> still don't.
>>>>>
>>>>> That said, I'm not too surprised by what you are reporting. The two
>>>>> most
>>>>> difficult of Repast HPC's required libraries seem to be NetCDF and
>>>>> Boost.
>>>>>
>>>>> With respect to NetCDF, I'm not entirely sure how the latest
>>>>>libraries
>>>>> work. My own recent experience is with a Cygwin installation
>>>>>(because I
>>>>> haven't changed the installation on my Mac in a long time). NetCDF
>>>>>has
>>>>> a
>>>>> new structure for their libraries; this is apparent from their
>>>>> downloads
>>>>> and from the options available in Cygwin setup, and exactly how
>>>>> MacPorts
>>>>> will deal with these is something I can only guess. But I do know
>>>>>that
>>>>> netcdfcpp.h isn't automatically created in the Cygwin installation.
>>>>>
>>>>> In this case, it seems to be because NetCDF is split 2 x 2 ways: With
>>>>> respect to the base, C version, you can use NetCDF or 'NetCDF4'; you
>>>>> can
>>>>> also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
>>>>> only
>>>>> use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
>>>>> C++
>>>>> 4 doesn't use the same netcdfcpp.h file, and my hunch is that the
>>>>> default
>>>>> Cygwin (and possibly MacPorts) approach is to use the newer '4'
>>>>> versions.
>>>>> Repast HPC expects the '3' versions (and has to have netcdfcpp.h).
>>>>>
>>>>> As for Boost, I'm not 100% sure you'll need the static libraries, but
>>>>> if
>>>>> you do, I don't know how MacPorts can be told to build them. I always
>>>>> build Boost manually. The steps aren't that hard:
>>>>>
>>>>> ./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
>>>>> --with-libraries=system,filesystem,mpi,serialization
>>>>>
>>>>> Add:
>>>>>
>>>>> using mpi : mpicxx ;
>>>>>
>>>>> to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file,
>>>>>where
>>>>> mpicxx is your mpi compiler (full path if needed); make sure to
>>>>>include
>>>>> the spaces!
>>>>>
>>>>> ./b2 --layout=tagged variant=release link=shared,static
>>>>>threading=multi
>>>>> stage install
>>>>>
>>>>> The options to the b2 install are viewable here:
>>>>>
>>>>>http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.ht
>>>>>ml
>>>>>
>>>>> I would recommend copying the "boost" directory (with all the header
>>>>> files) manually before using 'install'; for some reason boost copies
>>>>> each
>>>>> file individually and this can take longer, when in fact all that
>>>>> happens
>>>>> is this directory gets copied wholesale.
>>>>>
>>>>> Hope this helps- best,
>>>>> John
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> John T. Murphy
>>>>> Computational Postdoctoral Fellow
>>>>> Decision and Information Sciences and
>>>>> Argonne Leadership Computing Facility
>>>>> Argonne National Laboratory
>>>>> [hidden email]
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 8/20/12 1:10 PM, "markaehlen" <[hidden email]> wrote:
>>>>>
>>>>>>
>>>>>>Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I
>>>>>>have
>>>>>>used
>>>>>>MacPorts in the past and found it very good ('secretarially') in
>keeping
>>>>>>track of prerequisite libraries and insuring the latest libraries are
>>>>>>used.
>>>>>>I have tried several times to use it but am getting strange errors.
>>>>>>
>>>>>>Before I ask specific questions about installation (I have also been
>>>>>>following the guidance in the repast download files), should I /
>>>>>>could
>I
>>>>>>use
>>>>>>MacPorts (it has entries for all of the pre-requisites: openmpi,
>mpich2,
>>>>>>boost, netcdf, netcdf-cxx4), or should I really just do each
>pre-requisite
>>>>>>manually? The problem appears to be that boost static libraries are
>>>>>>not
>>>>>>created, and certain header files (netcdfcpp.h) are not installed
>locally.
>>>>>>
>>>>>>Just high-level question for now...
>>>>>>
>>>>>>Thanks,
>>>>>>
>>>>>>Mark
>>>>>>--
>>>>>>View this message in context:
>>>>>>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Pr
>>>>>>erequ
>>>>>>isite-Libraries-with-MacPort--tp34325774p34325774.html
>>>>>>Sent from the repast-interest mailing list archive at Nabble.com.
>>>>>>
>>>>>>
>>>>>>---------------------------------------------------------------------
>>>>>>-----
>>>>>>----
>>>>>>Live Security Virtual Conference
>>>>>>Exclusive live event will cover all the ways today's security and
>>>>>>threat landscape has changed and how IT managers can respond.
>Discussions
>>>>>>will include endpoint security, mobile security and the latest in
>malware
>>>>>>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>>>_______________________________________________
>>>>>>Repast-interest mailing list
>>>>>>[hidden email]
>>>>>>https://lists.sourceforge.net/lists/listinfo/repast-interest
>>>>>
>>>>>
>>>>>
>>>>>----------------------------------------------------------------------
>>>>>--------
>>>>> Live Security Virtual Conference
>>>>> Exclusive live event will cover all the ways today's security and
>>>>> threat landscape has changed and how IT managers can respond.
>>>>> Discussions
>>>>> will include endpoint security, mobile security and the latest in
>>>>> malware
>>>>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>>> _______________________________________________
>>>>> Repast-interest mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/repast-interest
>>>>>
>>>>>
>>>>
>>>
>>
>--
>View this message in context:
>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prerequ
>isite-Libraries-with-MacPort--tp34325774p34329338.html
>Sent from the repast-interest mailing list archive at Nabble.com.
>
>
>--------------------------------------------------------------------------
>----
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>Exclusive live event will cover all the ways today's security and
>threat landscape has changed and how IT managers can respond. Discussions
>will include endpoint security, mobile security and the latest in malware
>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>_______________________________________________
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

Jon Cline-2
In reply to this post by markaehlen
Mark,

I recently configured and installed RepastHPC on a Mac running Mountain Lion.

I installed the required packages via home brew (http://mxcl.github.com/homebrew/ – yes, macports was driving me to drink):


RepastHPC, as you have learned, will not compile with the  new netcdf-c++ api. In addition to replacing <netcdfcpp.h> with <netcdf>, and "-lnetcdf_c++" with "-lnetcdf_c++4", some patching of the repast_hpc is required – here is a brief summary of my notes from conversion attempt:

Converting from NetCDF C++ legacy api to NetCDF C++4

NetCDF C++ legacy NetCDF C++ 4.1.4 Description (from http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-cxx/Class-NcVar.htm)
NcVar* NcFile::get_var(NcToken varname) const NcVar NcGroup::getVar(const std::string& varname) const Gets the named NcVar object.
NcBool NcVar::set_cur(long c0-1, long c1=-1, long c2=-1, long c3=-1, long c4=-1)

NcBool NcVar::set_cur(long* cur)
<none> Resets the starting corner to the values supplied. Resets the starting corner to the values supplied. The first form works for a variable of dimensionality from scalar to 5 dimensions. For more than five dimensions, use the second form, in which the number of longs supplied must match the rank of the variable.
NcBool NcVar::NcBool put(const double* vals, long c0, long c1, long c2, long c3, long c4)

NcBool NcVar::put(const double* vals, const long* counts)
void NcVar::putVar(      const std::vector< size_t > &  startp,
const std::vector< size_t > &  countp,
const double* dataVals)
Write scalar or 1 to 5-dimensional arrays by providing enough arguments. The vals argument points to a contiguous block of values in memory to be written. For more than five dimensions, use the second form.
NcDim* NcFile::add_dim(NcToken dimname)

NcDim* NcFile::add_dim(NcToken dimname, long dimsize)
NcDim NcGroup::addDim (const std::string &name) const

NcDim NcGroup::addDim (const std::string &name, size_t dimSize) const 
Add an unlimited dimension named dimname to the netCDF file.

Add a dimension named dimname of size dimsize.


I was able to compile repast hoc with netcdf-c++4 (the new api), but ran into problems running the zombie example. So I downloaded and installed netcdf-c++-4.2 (http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx-4.2.tar.gz), the legacy netcdf c++ api from source (will install on top to netcdf-4.2.1.1 – should also work with macports). After completing the installation of the legacy netcdf c++, I was able to configure and install the unpatched repast hpc source and run the zombie example.

Then I upgraded to boost 1.50 (this morning). With this upgrade, Boost.Filesystem V2 is no longer supported, so repast hpc no longer compiles. Fortunately, minor changes to NCDataSet.cpp and SVDataSet.cpp fix the problem.

  • Change (NCDataSet.cpp:49 and SVDataSet.cpp:45) 
    • From "#define BOOST_FILESYSTEM_VERSION 2"
    • To "#define BOOST_FILESYSTEM_VERSION 3"
  • Change (NCDataSet.cpp:68 and SVDataSet.cpp:64)
    • From "std::string stem = filepath.stem()"
    • To "std::string stem = filepath.stem().string()"

It would be nice to get repast hpc to work with netcdf-c++4, but the zombie example now works for me.

Hope this helps.

Cheers,
Jon

Jon C. Cline, Ph.D. | The MITRE Corporation | Information Sys Eng, Sr
Center for Connected Government – Modeling & Analytics 
[hidden email] | o. (703) 983 9529 | c. (202) 617 8226



On Aug 21, 2012, at 9:41 AM, markaehlen <[hidden email]> wrote:


Hey John - you are incredibly helpful; thanks. My knowledge is starting to
catch up to current installation challenges, which has everything to do with
knowing where things should be installed and testing testing testing.

I have stepped away from the MacPorts approach because some basic
intermediate capabilities are not working. For example, I can't type "mpicc"
after installation of OpenMPI via MacPorts, and "sudo find / -name mpicc"
obtains nothing. The regular OpenMPI configure/make/install does, so I'm
going with that approach for everything. Boost and OpenMPI are installed;
NetCDF and NetCDF C++ are next.

I skipped over an important statement you made previously and want to
revisit so I understand the next step clearly:

"In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the default
Cygwin (and possibly MacPorts) approach is to use the newer '4' versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h)."

1. To install what Repast HPC wants, should I install the NetCDF (NOT 4) and
NetCDF C++ (legacy), that is, the "3" versions? I was using the "4" versions
before.
2. NetCDF says I don't have HDF5 installed; is there a particular version I
should install? I think the same question holds for zlib...

Thanks for all your help; is invaluable. I really need to get this
installed.

Cheers,

Mark


Murphy, John T. wrote:

Hi Mark,

My experience is skewed: I also use a Mac with an OS that has a name of a
big cat of some kind, but I basically started using it when I started
using Repast HPC. I didn't know much about 'MacPorts' at the time, and
still don't.

That said, I'm not too surprised by what you are reporting. The two most
difficult of Repast HPC's required libraries seem to be NetCDF and Boost.

With respect to NetCDF, I'm not entirely sure how the latest libraries
work. My own recent experience is with a Cygwin installation (because I
haven't changed the installation on my Mac in a long time). NetCDF has a
new structure for their libraries; this is apparent from their downloads
and from the options available in Cygwin setup, and exactly how MacPorts
will deal with these is something I can only guess. But I do know that
netcdfcpp.h isn't automatically created in the Cygwin installation.

In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the default
Cygwin (and possibly MacPorts) approach is to use the newer '4' versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h).

As for Boost, I'm not 100% sure you'll need the static libraries, but if
you do, I don't know how MacPorts can be told to build them. I always
build Boost manually. The steps aren't that hard:

./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
--with-libraries=system,filesystem,mpi,serialization

Add:

using mpi : mpicxx ;

to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file, where
mpicxx is your mpi compiler (full path if needed); make sure to include
the spaces!

./b2 --layout=tagged variant=release link=shared,static threading=multi
stage install

The options to the b2 install are viewable here:
http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.html

I would recommend copying the "boost" directory (with all the header
files) manually before using 'install'; for some reason boost copies each
file individually and this can take longer, when in fact all that happens
is this directory gets copied wholesale.

Hope this helps- best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]




On 8/20/12 1:10 PM, "markaehlen" <[hidden email]> wrote:


Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have
used
MacPorts in the past and found it very good ('secretarially') in keeping
track of prerequisite libraries and insuring the latest libraries are
used.
I have tried several times to use it but am getting strange errors.

Before I ask specific questions about installation (I have also been
following the guidance in the repast download files), should I / could I
use
MacPorts (it has entries for all of the pre-requisites: openmpi, mpich2,
boost, netcdf, netcdf-cxx4), or should I really just do each pre-requisite
manually? The problem appears to be that boost static libraries are not
created, and certain header files (netcdfcpp.h) are not installed locally.

Just high-level question for now...

Thanks,

Mark
--
View this message in context:
http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prerequ
isite-Libraries-with-MacPort--tp34325774p34325774.html
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

Jon Cline-2
In reply to this post by Murphy, John T.
John,

Any chance this change will be made available via subversion or git?

Jon

Jon C. Cline, Ph.D. | The MITRE Corporation | Information Sys Eng, Sr
Center for Connected Government – Modeling & Analytics 
[hidden email] | o. (703) 983 9529 | c. (202) 617 8226


On Aug 21, 2012, at 10:18 AM, "Murphy, John T." <[hidden email]> wrote:

Hi Mark,

This looks like you are using one of the recent versions of Boost. They
just released version 1.51 this morning (!), but Repast HPC is only
guaranteed to work through 1.48. (I've used 1.49 without problems, but
Boost's docs suggest this is iffy, so to be on the safe side, stick with
1.48.)

The change to make Repast HPC compatible with 1.50 (I haven't tested 1.51
yet, of course) is trivial and is included in the next release; if I
recall, it's nothing more than adding ".string()" to the end of the
boost::filesystem::path elements in about six places in the code. But it's
probably best to stick with the version of Boost that is known to have no
problems.

Best,
John
--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]




On 8/21/12 9:06 AM, "markaehlen" <[hidden email]> wrote:


Hey John - last message on this thread, at least for today:

When installed the following two versions of netcdf - netcdf-3.6.3,
netcdf-cxx-4.2) - I get the following error on "make all":

mv -f .deps/librepast_hpc_1_0_1_la-logger.Tpo
.deps/librepast_hpc_1_0_1_la-logger.Plo
/bin/sh ../../libtool  --tag=CXX   --mode=compile mpic++ -DHAVE_CONFIG_H
-I.
-I../..     -g -O2 -MT librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF
.deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c -o
librepast_hpc_1_0_1_la-NCDataSet.lo `test -f 'NCDataSet.cpp' || echo
'./'`NCDataSet.cpp
libtool: compile:  mpic++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT
librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF
.deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c NCDataSet.cpp  -fno-common
-DPIC -o .libs/librepast_hpc_1_0_1_la-NCDataSet.o
NCDataSet.cpp: In constructor 'repast::NCDataSet::NCDataSet(std::string,
const repast::Schedule&)':
NCDataSet.cpp:68: error: conversion from 'boost::filesystem::path' to
non-scalar type 'std::basic_string<char, std::char_traits<char>,
std::allocator<char> >' requested
make[2]: *** [librepast_hpc_1_0_1_la-NCDataSet.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Any insights would be GREATLY appreciated!

Mark


markaehlen wrote:

Or this one?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3_6_3/index.jsp

Thanks,

Mark


markaehlen wrote:

One more question:

3. Is this the right set of "3" installs to download?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-4_1_3/index.jsp

Thanks again!

Mark



markaehlen wrote:

Hey John - you are incredibly helpful; thanks. My knowledge is
starting
to catch up to current installation challenges, which has everything
to
do with knowing where things should be installed and testing testing
testing.

I have stepped away from the MacPorts approach because some basic
intermediate capabilities are not working. For example, I can't type
"mpicc" after installation of OpenMPI via MacPorts, and "sudo find /
-name mpicc" obtains nothing. The regular OpenMPI
configure/make/install
does, so I'm going with that approach for everything. Boost and
OpenMPI
are installed; NetCDF and NetCDF C++ are next.

I skipped over an important statement you made previously and want to
revisit so I understand the next step clearly:

"In this case, it seems to be because NetCDF is split 2 x 2 ways:
With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you
can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the
default
Cygwin (and possibly MacPorts) approach is to use the newer '4'
versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h)."

1. To install what Repast HPC wants, should I install the NetCDF (NOT
4)
and NetCDF C++ (legacy), that is, the "3" versions? I was using the
"4"
versions before.
2. NetCDF says I don't have HDF5 installed; is there a particular
version I should install? I think the same question holds for zlib...

Thanks for all your help; is invaluable. I really need to get this
installed.

Cheers,

Mark


Murphy, John T. wrote:

Hi Mark,

My experience is skewed: I also use a Mac with an OS that has a name
of
a
big cat of some kind, but I basically started using it when I started
using Repast HPC. I didn't know much about 'MacPorts' at the time,
and
still don't.

That said, I'm not too surprised by what you are reporting. The two
most
difficult of Repast HPC's required libraries seem to be NetCDF and
Boost.

With respect to NetCDF, I'm not entirely sure how the latest
libraries
work. My own recent experience is with a Cygwin installation
(because I
haven't changed the installation on my Mac in a long time). NetCDF
has
a
new structure for their libraries; this is apparent from their
downloads
and from the options available in Cygwin setup, and exactly how
MacPorts
will deal with these is something I can only guess. But I do know
that
netcdfcpp.h isn't automatically created in the Cygwin installation.

In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you
can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the
default
Cygwin (and possibly MacPorts) approach is to use the newer '4'
versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h).

As for Boost, I'm not 100% sure you'll need the static libraries, but
if
you do, I don't know how MacPorts can be told to build them. I always
build Boost manually. The steps aren't that hard:

./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
--with-libraries=system,filesystem,mpi,serialization

Add:

using mpi : mpicxx ;

to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file,
where
mpicxx is your mpi compiler (full path if needed); make sure to
include
the spaces!

./b2 --layout=tagged variant=release link=shared,static
threading=multi
stage install

The options to the b2 install are viewable here:

http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.ht
ml

I would recommend copying the "boost" directory (with all the header
files) manually before using 'install'; for some reason boost copies
each
file individually and this can take longer, when in fact all that
happens
is this directory gets copied wholesale.

Hope this helps- best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]




On 8/20/12 1:10 PM, "markaehlen" <[hidden email]> wrote:


Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I
have
used
MacPorts in the past and found it very good ('secretarially') in
keeping
track of prerequisite libraries and insuring the latest libraries are
used.
I have tried several times to use it but am getting strange errors.

Before I ask specific questions about installation (I have also been
following the guidance in the repast download files), should I /
could
I
use
MacPorts (it has entries for all of the pre-requisites: openmpi,
mpich2,
boost, netcdf, netcdf-cxx4), or should I really just do each
pre-requisite
manually? The problem appears to be that boost static libraries are
not
created, and certain header files (netcdfcpp.h) are not installed
locally.

Just high-level question for now...

Thanks,

Mark
--
View this message in context:
http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Pr
erequ
isite-Libraries-with-MacPort--tp34325774p34325774.html
Sent from the repast-interest mailing list archive at Nabble.com.


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Discussions
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

Murphy, John T.
Jon,

We occasionally issue releases with bug fixes and other small changes in them. There is a git repository for Repast HPC under repast on SourceForge. I have a number of changes, including the boost filesystem change, that I haven't merged with the central repository; I'll try to do that soon.

Best,
John
--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]

From: Jon Cline <[hidden email]<mailto:[hidden email]>>
Date: Tuesday, August 21, 2012 9:43 AM
To: "Murphy, John T." <[hidden email]<mailto:[hidden email]>>
Cc: markaehlen <[hidden email]<mailto:[hidden email]>>, "[hidden email]<mailto:[hidden email]>" <[hidden email]<mailto:[hidden email]>>
Subject: Re: [Repast-interest] Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

John,

Any chance this change will be made available via subversion or git?

Jon

Jon C. Cline, Ph.D. | The MITRE Corporation | Information Sys Eng, Sr
Center for Connected Government – Modeling & Analytics
[hidden email]<mailto:[hidden email]> | o. (703) 983 9529 | c. (202) 617 8226


On Aug 21, 2012, at 10:18 AM, "Murphy, John T." <[hidden email]<mailto:[hidden email]>> wrote:

Hi Mark,

This looks like you are using one of the recent versions of Boost. They
just released version 1.51 this morning (!), but Repast HPC is only
guaranteed to work through 1.48. (I've used 1.49 without problems, but
Boost's docs suggest this is iffy, so to be on the safe side, stick with
1.48.)

The change to make Repast HPC compatible with 1.50 (I haven't tested 1.51
yet, of course) is trivial and is included in the next release; if I
recall, it's nothing more than adding ".string()" to the end of the
boost::filesystem::path elements in about six places in the code. But it's
probably best to stick with the version of Boost that is known to have no
problems.

Best,
John
--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]<mailto:[hidden email]>




On 8/21/12 9:06 AM, "markaehlen" <[hidden email]<mailto:[hidden email]>> wrote:


Hey John - last message on this thread, at least for today:

When installed the following two versions of netcdf - netcdf-3.6.3,
netcdf-cxx-4.2) - I get the following error on "make all":

mv -f .deps/librepast_hpc_1_0_1_la-logger.Tpo
.deps/librepast_hpc_1_0_1_la-logger.Plo
/bin/sh ../../libtool  --tag=CXX   --mode=compile mpic++ -DHAVE_CONFIG_H
-I.
-I../..     -g -O2 -MT librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF
.deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c -o
librepast_hpc_1_0_1_la-NCDataSet.lo `test -f 'NCDataSet.cpp' || echo
'./'`NCDataSet.cpp
libtool: compile:  mpic++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT
librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF
.deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c NCDataSet.cpp  -fno-common
-DPIC -o .libs/librepast_hpc_1_0_1_la-NCDataSet.o
NCDataSet.cpp: In constructor 'repast::NCDataSet::NCDataSet(std::string,
const repast::Schedule&)':
NCDataSet.cpp:68: error: conversion from 'boost::filesystem::path' to
non-scalar type 'std::basic_string<char, std::char_traits<char>,
std::allocator<char> >' requested
make[2]: *** [librepast_hpc_1_0_1_la-NCDataSet.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Any insights would be GREATLY appreciated!

Mark


markaehlen wrote:

Or this one?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3_6_3/index.jsp

Thanks,

Mark


markaehlen wrote:

One more question:

3. Is this the right set of "3" installs to download?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-4_1_3/index.jsp

Thanks again!

Mark



markaehlen wrote:

Hey John - you are incredibly helpful; thanks. My knowledge is
starting
to catch up to current installation challenges, which has everything
to
do with knowing where things should be installed and testing testing
testing.

I have stepped away from the MacPorts approach because some basic
intermediate capabilities are not working. For example, I can't type
"mpicc" after installation of OpenMPI via MacPorts, and "sudo find /
-name mpicc" obtains nothing. The regular OpenMPI
configure/make/install
does, so I'm going with that approach for everything. Boost and
OpenMPI
are installed; NetCDF and NetCDF C++ are next.

I skipped over an important statement you made previously and want to
revisit so I understand the next step clearly:

"In this case, it seems to be because NetCDF is split 2 x 2 ways:
With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you
can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the
default
Cygwin (and possibly MacPorts) approach is to use the newer '4'
versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h)."

1. To install what Repast HPC wants, should I install the NetCDF (NOT
4)
and NetCDF C++ (legacy), that is, the "3" versions? I was using the
"4"
versions before.
2. NetCDF says I don't have HDF5 installed; is there a particular
version I should install? I think the same question holds for zlib...

Thanks for all your help; is invaluable. I really need to get this
installed.

Cheers,

Mark


Murphy, John T. wrote:

Hi Mark,

My experience is skewed: I also use a Mac with an OS that has a name
of
a
big cat of some kind, but I basically started using it when I started
using Repast HPC. I didn't know much about 'MacPorts' at the time,
and
still don't.

That said, I'm not too surprised by what you are reporting. The two
most
difficult of Repast HPC's required libraries seem to be NetCDF and
Boost.

With respect to NetCDF, I'm not entirely sure how the latest
libraries
work. My own recent experience is with a Cygwin installation
(because I
haven't changed the installation on my Mac in a long time). NetCDF
has
a
new structure for their libraries; this is apparent from their
downloads
and from the options available in Cygwin setup, and exactly how
MacPorts
will deal with these is something I can only guess. But I do know
that
netcdfcpp.h isn't automatically created in the Cygwin installation.

In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you
can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the
default
Cygwin (and possibly MacPorts) approach is to use the newer '4'
versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h).

As for Boost, I'm not 100% sure you'll need the static libraries, but
if
you do, I don't know how MacPorts can be told to build them. I always
build Boost manually. The steps aren't that hard:

./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
--with-libraries=system,filesystem,mpi,serialization

Add:

using mpi : mpicxx ;

to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file,
where
mpicxx is your mpi compiler (full path if needed); make sure to
include
the spaces!

./b2 --layout=tagged variant=release link=shared,static
threading=multi
stage install

The options to the b2 install are viewable here:

http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.ht
ml

I would recommend copying the "boost" directory (with all the header
files) manually before using 'install'; for some reason boost copies
each
file individually and this can take longer, when in fact all that
happens
is this directory gets copied wholesale.

Hope this helps- best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]<mailto:[hidden email]>




On 8/20/12 1:10 PM, "markaehlen" <[hidden email]<mailto:[hidden email]>> wrote:


Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I
have
used
MacPorts in the past and found it very good ('secretarially') in
keeping
track of prerequisite libraries and insuring the latest libraries are
used.
I have tried several times to use it but am getting strange errors.

Before I ask specific questions about installation (I have also been
following the guidance in the repast download files), should I /
could
I
use
MacPorts (it has entries for all of the pre-requisites: openmpi,
mpich2,
boost, netcdf, netcdf-cxx4), or should I really just do each
pre-requisite
manually? The problem appears to be that boost static libraries are
not
created, and certain header files (netcdfcpp.h) are not installed
locally.

Just high-level question for now...

Thanks,

Mark
--
View this message in context:
http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Pr
erequ
isite-Libraries-with-MacPort--tp34325774p34325774.html
Sent from the repast-interest mailing list archive at Nabble.com.


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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

Jon Cline-2
John,

I've checked out source from both the git and subversion repositories, but did not see any recent changes.

Also, I may have spoken too soon about (successfully) running repast hpc on my mac. The netcdf generated by my attempt to run the zombie model:

$ mpirun -np 4 ./zombie_model config.props model.props

is not recognized as a valid netcdf file by my local installation of ncdump (the csv file looks file).

Thanks for your prompt response.

Jon

Jon C. Cline, Ph.D. | The MITRE Corporation | Information Sys Eng, Sr
Center for Connected Government – Modeling & Analytics 
[hidden email] | o. (703) 983 9529 | c. (202) 617 8226


On Aug 21, 2012, at 11:07 AM, "Murphy, John T." <[hidden email]> wrote:

Jon,

We occasionally issue releases with bug fixes and other small changes in them. There is a git repository for Repast HPC under repast on SourceForge. I have a number of changes, including the boost filesystem change, that I haven't merged with the central repository; I'll try to do that soon.

Best,
John
--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]

From: Jon Cline <[hidden email]<mailto:[hidden email]>>
Date: Tuesday, August 21, 2012 9:43 AM
To: "Murphy, John T." <[hidden email]<mailto:[hidden email]>>
Cc: markaehlen <[hidden email]<mailto:[hidden email]>>, "[hidden email]<mailto:[hidden email]>" <[hidden email]<mailto:[hidden email]>>
Subject: Re: [Repast-interest] Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

John,

Any chance this change will be made available via subversion or git?

Jon

Jon C. Cline, Ph.D. | The MITRE Corporation | Information Sys Eng, Sr
Center for Connected Government – Modeling & Analytics
[hidden email]<mailto:[hidden email]> | o. (703) 983 9529 | c. (202) 617 8226


On Aug 21, 2012, at 10:18 AM, "Murphy, John T." <[hidden email]<mailto:[hidden email]>> wrote:

Hi Mark,

This looks like you are using one of the recent versions of Boost. They
just released version 1.51 this morning (!), but Repast HPC is only
guaranteed to work through 1.48. (I've used 1.49 without problems, but
Boost's docs suggest this is iffy, so to be on the safe side, stick with
1.48.)

The change to make Repast HPC compatible with 1.50 (I haven't tested 1.51
yet, of course) is trivial and is included in the next release; if I
recall, it's nothing more than adding ".string()" to the end of the
boost::filesystem::path elements in about six places in the code. But it's
probably best to stick with the version of Boost that is known to have no
problems.

Best,
John
--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]<mailto:[hidden email]>




On 8/21/12 9:06 AM, "markaehlen" <[hidden email]<mailto:[hidden email]>> wrote:


Hey John - last message on this thread, at least for today:

When installed the following two versions of netcdf - netcdf-3.6.3,
netcdf-cxx-4.2) - I get the following error on "make all":

mv -f .deps/librepast_hpc_1_0_1_la-logger.Tpo
.deps/librepast_hpc_1_0_1_la-logger.Plo
/bin/sh ../../libtool  --tag=CXX   --mode=compile mpic++ -DHAVE_CONFIG_H
-I.
-I../..     -g -O2 -MT librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF
.deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c -o
librepast_hpc_1_0_1_la-NCDataSet.lo `test -f 'NCDataSet.cpp' || echo
'./'`NCDataSet.cpp
libtool: compile:  mpic++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT
librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF
.deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c NCDataSet.cpp  -fno-common
-DPIC -o .libs/librepast_hpc_1_0_1_la-NCDataSet.o
NCDataSet.cpp: In constructor 'repast::NCDataSet::NCDataSet(std::string,
const repast::Schedule&)':
NCDataSet.cpp:68: error: conversion from 'boost::filesystem::path' to
non-scalar type 'std::basic_string<char, std::char_traits<char>,
std::allocator<char> >' requested
make[2]: *** [librepast_hpc_1_0_1_la-NCDataSet.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Any insights would be GREATLY appreciated!

Mark


markaehlen wrote:

Or this one?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3_6_3/index.jsp

Thanks,

Mark


markaehlen wrote:

One more question:

3. Is this the right set of "3" installs to download?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-4_1_3/index.jsp

Thanks again!

Mark



markaehlen wrote:

Hey John - you are incredibly helpful; thanks. My knowledge is
starting
to catch up to current installation challenges, which has everything
to
do with knowing where things should be installed and testing testing
testing.

I have stepped away from the MacPorts approach because some basic
intermediate capabilities are not working. For example, I can't type
"mpicc" after installation of OpenMPI via MacPorts, and "sudo find /
-name mpicc" obtains nothing. The regular OpenMPI
configure/make/install
does, so I'm going with that approach for everything. Boost and
OpenMPI
are installed; NetCDF and NetCDF C++ are next.

I skipped over an important statement you made previously and want to
revisit so I understand the next step clearly:

"In this case, it seems to be because NetCDF is split 2 x 2 ways:
With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you
can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the
default
Cygwin (and possibly MacPorts) approach is to use the newer '4'
versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h)."

1. To install what Repast HPC wants, should I install the NetCDF (NOT
4)
and NetCDF C++ (legacy), that is, the "3" versions? I was using the
"4"
versions before.
2. NetCDF says I don't have HDF5 installed; is there a particular
version I should install? I think the same question holds for zlib...

Thanks for all your help; is invaluable. I really need to get this
installed.

Cheers,

Mark


Murphy, John T. wrote:

Hi Mark,

My experience is skewed: I also use a Mac with an OS that has a name
of
a
big cat of some kind, but I basically started using it when I started
using Repast HPC. I didn't know much about 'MacPorts' at the time,
and
still don't.

That said, I'm not too surprised by what you are reporting. The two
most
difficult of Repast HPC's required libraries seem to be NetCDF and
Boost.

With respect to NetCDF, I'm not entirely sure how the latest
libraries
work. My own recent experience is with a Cygwin installation
(because I
haven't changed the installation on my Mac in a long time). NetCDF
has
a
new structure for their libraries; this is apparent from their
downloads
and from the options available in Cygwin setup, and exactly how
MacPorts
will deal with these is something I can only guess. But I do know
that
netcdfcpp.h isn't automatically created in the Cygwin installation.

In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you
can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the
default
Cygwin (and possibly MacPorts) approach is to use the newer '4'
versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h).

As for Boost, I'm not 100% sure you'll need the static libraries, but
if
you do, I don't know how MacPorts can be told to build them. I always
build Boost manually. The steps aren't that hard:

./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
--with-libraries=system,filesystem,mpi,serialization

Add:

using mpi : mpicxx ;

to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file,
where
mpicxx is your mpi compiler (full path if needed); make sure to
include
the spaces!

./b2 --layout=tagged variant=release link=shared,static
threading=multi
stage install

The options to the b2 install are viewable here:

http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.ht
ml

I would recommend copying the "boost" directory (with all the header
files) manually before using 'install'; for some reason boost copies
each
file individually and this can take longer, when in fact all that
happens
is this directory gets copied wholesale.

Hope this helps- best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]<mailto:[hidden email]>




On 8/20/12 1:10 PM, "markaehlen" <[hidden email]<mailto:[hidden email]>> wrote:


Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I
have
used
MacPorts in the past and found it very good ('secretarially') in
keeping
track of prerequisite libraries and insuring the latest libraries are
used.
I have tried several times to use it but am getting strange errors.

Before I ask specific questions about installation (I have also been
following the guidance in the repast download files), should I /
could
I
use
MacPorts (it has entries for all of the pre-requisites: openmpi,
mpich2,
boost, netcdf, netcdf-cxx4), or should I really just do each
pre-requisite
manually? The problem appears to be that boost static libraries are
not
created, and certain header files (netcdfcpp.h) are not installed
locally.

Just high-level question for now...

Thanks,

Mark
--
View this message in context:
http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Pr
erequ
isite-Libraries-with-MacPort--tp34325774p34325774.html
Sent from the repast-interest mailing list archive at Nabble.com.


---------------------------------------------------------------------
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Discussions
will include endpoint security, mobile security and the latest in
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_______________________________________________
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Discussions
will include endpoint security, mobile security and the latest in
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--
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isite-Libraries-with-MacPort--tp34325774p34329338.html
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

Murphy, John T.
Jon,

Thanks for this; I haven't looked at the NetCDF output in a while, but I'll check it out in light of the changes to NetCDF that have happened since the code in Repast HPC was first written.

Best,
John
--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]

From: Jon Cline <[hidden email]<mailto:[hidden email]>>
Date: Tuesday, August 21, 2012 10:16 AM
To: "Murphy, John T." <[hidden email]<mailto:[hidden email]>>
Cc: "[hidden email]<mailto:[hidden email]>" <[hidden email]<mailto:[hidden email]>>
Subject: Re: [Repast-interest] Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

John,

I've checked out source from both the git and subversion repositories, but did not see any recent changes.

Also, I may have spoken too soon about (successfully) running repast hpc on my mac. The netcdf generated by my attempt to run the zombie model:

$ mpirun -np 4 ./zombie_model config.props model.props

is not recognized as a valid netcdf file by my local installation of ncdump (the csv file looks file).

Thanks for your prompt response.

Jon

Jon C. Cline, Ph.D. | The MITRE Corporation | Information Sys Eng, Sr
Center for Connected Government – Modeling & Analytics
[hidden email]<mailto:[hidden email]> | o. (703) 983 9529 | c. (202) 617 8226


On Aug 21, 2012, at 11:07 AM, "Murphy, John T." <[hidden email]<mailto:[hidden email]>> wrote:

Jon,

We occasionally issue releases with bug fixes and other small changes in them. There is a git repository for Repast HPC under repast on SourceForge. I have a number of changes, including the boost filesystem change, that I haven't merged with the central repository; I'll try to do that soon.

Best,
John
--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]<mailto:[hidden email]>

From: Jon Cline <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>>
Date: Tuesday, August 21, 2012 9:43 AM
To: "Murphy, John T." <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>>
Cc: markaehlen <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>>, "[hidden email]<mailto:[hidden email]><mailto:[hidden email]>" <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>>
Subject: Re: [Repast-interest] Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

John,

Any chance this change will be made available via subversion or git?

Jon

Jon C. Cline, Ph.D. | The MITRE Corporation | Information Sys Eng, Sr
Center for Connected Government – Modeling & Analytics
[hidden email]<mailto:[hidden email]><mailto:[hidden email]> | o. (703) 983 9529 | c. (202) 617 8226


On Aug 21, 2012, at 10:18 AM, "Murphy, John T." <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:

Hi Mark,

This looks like you are using one of the recent versions of Boost. They
just released version 1.51 this morning (!), but Repast HPC is only
guaranteed to work through 1.48. (I've used 1.49 without problems, but
Boost's docs suggest this is iffy, so to be on the safe side, stick with
1.48.)

The change to make Repast HPC compatible with 1.50 (I haven't tested 1.51
yet, of course) is trivial and is included in the next release; if I
recall, it's nothing more than adding ".string()" to the end of the
boost::filesystem::path elements in about six places in the code. But it's
probably best to stick with the version of Boost that is known to have no
problems.

Best,
John
--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]<mailto:[hidden email]><mailto:[hidden email]>




On 8/21/12 9:06 AM, "markaehlen" <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:


Hey John - last message on this thread, at least for today:

When installed the following two versions of netcdf - netcdf-3.6.3,
netcdf-cxx-4.2) - I get the following error on "make all":

mv -f .deps/librepast_hpc_1_0_1_la-logger.Tpo
.deps/librepast_hpc_1_0_1_la-logger.Plo
/bin/sh ../../libtool  --tag=CXX   --mode=compile mpic++ -DHAVE_CONFIG_H
-I.
-I../..     -g -O2 -MT librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF
.deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c -o
librepast_hpc_1_0_1_la-NCDataSet.lo `test -f 'NCDataSet.cpp' || echo
'./'`NCDataSet.cpp
libtool: compile:  mpic++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT
librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF
.deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c NCDataSet.cpp  -fno-common
-DPIC -o .libs/librepast_hpc_1_0_1_la-NCDataSet.o
NCDataSet.cpp: In constructor 'repast::NCDataSet::NCDataSet(std::string,
const repast::Schedule&)':
NCDataSet.cpp:68: error: conversion from 'boost::filesystem::path' to
non-scalar type 'std::basic_string<char, std::char_traits<char>,
std::allocator<char> >' requested
make[2]: *** [librepast_hpc_1_0_1_la-NCDataSet.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Any insights would be GREATLY appreciated!

Mark


markaehlen wrote:

Or this one?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3_6_3/index.jsp

Thanks,

Mark


markaehlen wrote:

One more question:

3. Is this the right set of "3" installs to download?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-4_1_3/index.jsp

Thanks again!

Mark



markaehlen wrote:

Hey John - you are incredibly helpful; thanks. My knowledge is
starting
to catch up to current installation challenges, which has everything
to
do with knowing where things should be installed and testing testing
testing.

I have stepped away from the MacPorts approach because some basic
intermediate capabilities are not working. For example, I can't type
"mpicc" after installation of OpenMPI via MacPorts, and "sudo find /
-name mpicc" obtains nothing. The regular OpenMPI
configure/make/install
does, so I'm going with that approach for everything. Boost and
OpenMPI
are installed; NetCDF and NetCDF C++ are next.

I skipped over an important statement you made previously and want to
revisit so I understand the next step clearly:

"In this case, it seems to be because NetCDF is split 2 x 2 ways:
With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you
can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the
default
Cygwin (and possibly MacPorts) approach is to use the newer '4'
versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h)."

1. To install what Repast HPC wants, should I install the NetCDF (NOT
4)
and NetCDF C++ (legacy), that is, the "3" versions? I was using the
"4"
versions before.
2. NetCDF says I don't have HDF5 installed; is there a particular
version I should install? I think the same question holds for zlib...

Thanks for all your help; is invaluable. I really need to get this
installed.

Cheers,

Mark


Murphy, John T. wrote:

Hi Mark,

My experience is skewed: I also use a Mac with an OS that has a name
of
a
big cat of some kind, but I basically started using it when I started
using Repast HPC. I didn't know much about 'MacPorts' at the time,
and
still don't.

That said, I'm not too surprised by what you are reporting. The two
most
difficult of Repast HPC's required libraries seem to be NetCDF and
Boost.

With respect to NetCDF, I'm not entirely sure how the latest
libraries
work. My own recent experience is with a Cygwin installation
(because I
haven't changed the installation on my Mac in a long time). NetCDF
has
a
new structure for their libraries; this is apparent from their
downloads
and from the options available in Cygwin setup, and exactly how
MacPorts
will deal with these is something I can only guess. But I do know
that
netcdfcpp.h isn't automatically created in the Cygwin installation.

In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you
can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the
default
Cygwin (and possibly MacPorts) approach is to use the newer '4'
versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h).

As for Boost, I'm not 100% sure you'll need the static libraries, but
if
you do, I don't know how MacPorts can be told to build them. I always
build Boost manually. The steps aren't that hard:

./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
--with-libraries=system,filesystem,mpi,serialization

Add:

using mpi : mpicxx ;

to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file,
where
mpicxx is your mpi compiler (full path if needed); make sure to
include
the spaces!

./b2 --layout=tagged variant=release link=shared,static
threading=multi
stage install

The options to the b2 install are viewable here:

http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.ht
ml

I would recommend copying the "boost" directory (with all the header
files) manually before using 'install'; for some reason boost copies
each
file individually and this can take longer, when in fact all that
happens
is this directory gets copied wholesale.

Hope this helps- best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]<mailto:[hidden email]><mailto:[hidden email]>




On 8/20/12 1:10 PM, "markaehlen" <[hidden email]<mailto:[hidden email]><mailto:[hidden email]>> wrote:


Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I
have
used
MacPorts in the past and found it very good ('secretarially') in
keeping
track of prerequisite libraries and insuring the latest libraries are
used.
I have tried several times to use it but am getting strange errors.

Before I ask specific questions about installation (I have also been
following the guidance in the repast download files), should I /
could
I
use
MacPorts (it has entries for all of the pre-requisites: openmpi,
mpich2,
boost, netcdf, netcdf-cxx4), or should I really just do each
pre-requisite
manually? The problem appears to be that boost static libraries are
not
created, and certain header files (netcdfcpp.h) are not installed
locally.

Just high-level question for now...

Thanks,

Mark
--
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

markaehlen
Thanks John and Jon for your help. Installation went flawlessly with the following files:

drwxr-xr-x@ 27 markehlen  staff    918 Aug 21 19:14 boost_1_48_0
drwxr-xr-x@ 54 markehlen  staff   1836 Aug 21 19:19 netcdf-4.2.1.1
drwxr-xr-x@ 26 markehlen  staff    884 Aug 21 19:20 netcdf-cxx-4.2
drwxr-xr-x@ 30 markehlen  staff   1020 Aug 21 19:04 openmpi-1.6
drwxr-xr-x@ 31 markehlen  staff   1054 Aug 21 19:28 repasthpc-1.0.1

Onward!

M
Murphy, John T. wrote
Jon,

Thanks for this; I haven't looked at the NetCDF output in a while, but I'll check it out in light of the changes to NetCDF that have happened since the code in Repast HPC was first written.

Best,
John
--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
jtmurphy@anl.gov

From: Jon Cline <clinej@alumni.stanford.edu<mailto:clinej@alumni.stanford.edu>>
Date: Tuesday, August 21, 2012 10:16 AM
To: "Murphy, John T." <jtmurphy@anl.gov<mailto:jtmurphy@anl.gov>>
Cc: "repast-interest@lists.sourceforge.net<mailto:repast-interest@lists.sourceforge.net>" <repast-interest@lists.sourceforge.net<mailto:repast-interest@lists.sourceforge.net>>
Subject: Re: [Repast-interest] Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

John,

I've checked out source from both the git and subversion repositories, but did not see any recent changes.

Also, I may have spoken too soon about (successfully) running repast hpc on my mac. The netcdf generated by my attempt to run the zombie model:

$ mpirun -np 4 ./zombie_model config.props model.props

is not recognized as a valid netcdf file by my local installation of ncdump (the csv file looks file).

Thanks for your prompt response.

Jon

Jon C. Cline, Ph.D. | The MITRE Corporation | Information Sys Eng, Sr
Center for Connected Government – Modeling & Analytics
Jcline@mitre.org<mailto:Jcline@mitre.org> | o. (703) 983 9529 | c. (202) 617 8226


On Aug 21, 2012, at 11:07 AM, "Murphy, John T." <jtmurphy@anl.gov<mailto:jtmurphy@anl.gov>> wrote:

Jon,

We occasionally issue releases with bug fixes and other small changes in them. There is a git repository for Repast HPC under repast on SourceForge. I have a number of changes, including the boost filesystem change, that I haven't merged with the central repository; I'll try to do that soon.

Best,
John
--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
jtmurphy@anl.gov<mailto:jtmurphy@anl.gov>

From: Jon Cline <clinej@alumni.stanford.edu<mailto:clinej@alumni.stanford.edu><mailto:clinej@alumni.stanford.edu>>
Date: Tuesday, August 21, 2012 9:43 AM
To: "Murphy, John T." <jtmurphy@anl.gov<mailto:jtmurphy@anl.gov><mailto:jtmurphy@anl.gov>>
Cc: markaehlen <Markaehlen@gmail.com<mailto:Markaehlen@gmail.com><mailto:Markaehlen@gmail.com>>, "repast-interest@lists.sourceforge.net<mailto:repast-interest@lists.sourceforge.net><mailto:repast-interest@lists.sourceforge.net>" <repast-interest@lists.sourceforge.net<mailto:repast-interest@lists.sourceforge.net><mailto:repast-interest@lists.sourceforge.net>>
Subject: Re: [Repast-interest] Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

John,

Any chance this change will be made available via subversion or git?

Jon

Jon C. Cline, Ph.D. | The MITRE Corporation | Information Sys Eng, Sr
Center for Connected Government – Modeling & Analytics
Jcline@mitre.org<mailto:Jcline@mitre.org><mailto:Jcline@mitre.org> | o. (703) 983 9529 | c. (202) 617 8226


On Aug 21, 2012, at 10:18 AM, "Murphy, John T." <jtmurphy@anl.gov<mailto:jtmurphy@anl.gov><mailto:jtmurphy@anl.gov>> wrote:

Hi Mark,

This looks like you are using one of the recent versions of Boost. They
just released version 1.51 this morning (!), but Repast HPC is only
guaranteed to work through 1.48. (I've used 1.49 without problems, but
Boost's docs suggest this is iffy, so to be on the safe side, stick with
1.48.)

The change to make Repast HPC compatible with 1.50 (I haven't tested 1.51
yet, of course) is trivial and is included in the next release; if I
recall, it's nothing more than adding ".string()" to the end of the
boost::filesystem::path elements in about six places in the code. But it's
probably best to stick with the version of Boost that is known to have no
problems.

Best,
John
--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
jtmurphy@anl.gov<mailto:jtmurphy@anl.gov><mailto:jtmurphy@anl.gov>




On 8/21/12 9:06 AM, "markaehlen" <Markaehlen@gmail.com<mailto:Markaehlen@gmail.com><mailto:Markaehlen@gmail.com>> wrote:


Hey John - last message on this thread, at least for today:

When installed the following two versions of netcdf - netcdf-3.6.3,
netcdf-cxx-4.2) - I get the following error on "make all":

mv -f .deps/librepast_hpc_1_0_1_la-logger.Tpo
.deps/librepast_hpc_1_0_1_la-logger.Plo
/bin/sh ../../libtool  --tag=CXX   --mode=compile mpic++ -DHAVE_CONFIG_H
-I.
-I../..     -g -O2 -MT librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF
.deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c -o
librepast_hpc_1_0_1_la-NCDataSet.lo `test -f 'NCDataSet.cpp' || echo
'./'`NCDataSet.cpp
libtool: compile:  mpic++ -DHAVE_CONFIG_H -I. -I../.. -g -O2 -MT
librepast_hpc_1_0_1_la-NCDataSet.lo -MD -MP -MF
.deps/librepast_hpc_1_0_1_la-NCDataSet.Tpo -c NCDataSet.cpp  -fno-common
-DPIC -o .libs/librepast_hpc_1_0_1_la-NCDataSet.o
NCDataSet.cpp: In constructor 'repast::NCDataSet::NCDataSet(std::string,
const repast::Schedule&)':
NCDataSet.cpp:68: error: conversion from 'boost::filesystem::path' to
non-scalar type 'std::basic_string<char, std::char_traits<char>,
std::allocator<char> >' requested
make[2]: *** [librepast_hpc_1_0_1_la-NCDataSet.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Any insights would be GREATLY appreciated!

Mark


markaehlen wrote:

Or this one?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-3_6_3/index.jsp

Thanks,

Mark


markaehlen wrote:

One more question:

3. Is this the right set of "3" installs to download?

http://www.unidata.ucar.edu/downloads/netcdf/netcdf-4_1_3/index.jsp

Thanks again!

Mark



markaehlen wrote:

Hey John - you are incredibly helpful; thanks. My knowledge is
starting
to catch up to current installation challenges, which has everything
to
do with knowing where things should be installed and testing testing
testing.

I have stepped away from the MacPorts approach because some basic
intermediate capabilities are not working. For example, I can't type
"mpicc" after installation of OpenMPI via MacPorts, and "sudo find /
-name mpicc" obtains nothing. The regular OpenMPI
configure/make/install
does, so I'm going with that approach for everything. Boost and
OpenMPI
are installed; NetCDF and NetCDF C++ are next.

I skipped over an important statement you made previously and want to
revisit so I understand the next step clearly:

"In this case, it seems to be because NetCDF is split 2 x 2 ways:
With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you
can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the
default
Cygwin (and possibly MacPorts) approach is to use the newer '4'
versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h)."

1. To install what Repast HPC wants, should I install the NetCDF (NOT
4)
and NetCDF C++ (legacy), that is, the "3" versions? I was using the
"4"
versions before.
2. NetCDF says I don't have HDF5 installed; is there a particular
version I should install? I think the same question holds for zlib...

Thanks for all your help; is invaluable. I really need to get this
installed.

Cheers,

Mark


Murphy, John T. wrote:

Hi Mark,

My experience is skewed: I also use a Mac with an OS that has a name
of
a
big cat of some kind, but I basically started using it when I started
using Repast HPC. I didn't know much about 'MacPorts' at the time,
and
still don't.

That said, I'm not too surprised by what you are reporting. The two
most
difficult of Repast HPC's required libraries seem to be NetCDF and
Boost.

With respect to NetCDF, I'm not entirely sure how the latest
libraries
work. My own recent experience is with a Cygwin installation
(because I
haven't changed the installation on my Mac in a long time). NetCDF
has
a
new structure for their libraries; this is apparent from their
downloads
and from the options available in Cygwin setup, and exactly how
MacPorts
will deal with these is something I can only guess. But I do know
that
netcdfcpp.h isn't automatically created in the Cygwin installation.

In this case, it seems to be because NetCDF is split 2 x 2 ways: With
respect to the base, C version, you can use NetCDF or 'NetCDF4'; you
can
also use NetCDF C++ basic (legacy) or NetCDF C++ 4. Naturally you can
only
use C++4 with NetCDF4. I think- without tracking it 100%- that NetCDF
C++
4 doesn't use the same netcdfcpp.h file, and my hunch is that the
default
Cygwin (and possibly MacPorts) approach is to use the newer '4'
versions.
Repast HPC expects the '3' versions (and has to have netcdfcpp.h).

As for Boost, I'm not 100% sure you'll need the static libraries, but
if
you do, I don't know how MacPorts can be told to build them. I always
build Boost manually. The steps aren't that hard:

./bootstrap.sh --prefix=/WHEREVER/YOU/WANT
--with-libraries=system,filesystem,mpi,serialization

Add:

using mpi : mpicxx ;

to the end of the /BOOST_DIR/tools/build/v2/user-config.jam file,
where
mpicxx is your mpi compiler (full path if needed); make sure to
include
the spaces!

./b2 --layout=tagged variant=release link=shared,static
threading=multi
stage install

The options to the b2 install are viewable here:

http://www.boost.org/boost-build2/doc/html/bbv2/overview/invocation.ht
ml

I would recommend copying the "boost" directory (with all the header
files) manually before using 'install'; for some reason boost copies
each
file individually and this can take longer, when in fact all that
happens
is this directory gets copied wholesale.

Hope this helps- best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
jtmurphy@anl.gov<mailto:jtmurphy@anl.gov><mailto:jtmurphy@anl.gov>




On 8/20/12 1:10 PM, "markaehlen" <Markaehlen@gmail.com<mailto:Markaehlen@gmail.com><mailto:Markaehlen@gmail.com>> wrote:


Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I
have
used
MacPorts in the past and found it very good ('secretarially') in
keeping
track of prerequisite libraries and insuring the latest libraries are
used.
I have tried several times to use it but am getting strange errors.

Before I ask specific questions about installation (I have also been
following the guidance in the repast download files), should I /
could
I
use
MacPorts (it has entries for all of the pre-requisites: openmpi,
mpich2,
boost, netcdf, netcdf-cxx4), or should I really just do each
pre-requisite
manually? The problem appears to be that boost static libraries are
not
created, and certain header files (netcdfcpp.h) are not installed
locally.

Just high-level question for now...

Thanks,

Mark
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

markaehlen
In reply to this post by Murphy, John T.
Hey John - thanks again, you're a saint. I'm off to building a prototype off of the Rumor example that comes with the Repast HPC installation. I have a secretarial question: a PDF PPTX I found on the web describes the Rumor example with a lot of specifics, but when I open the RumorModel.{h,cpp} and main.cpp files that come with the installation, they appear to be missing some of this detail, such as the creation of complimentary edges. Am I not using the right RumorModel files? Where are the complete versions of these files. More broadly, is there a repository of simple examples that users have shared, that I can peruse?

Thanks again!

M


Murphy, John T. wrote
Mark,

In the simplest situation you get two pieces: .h files and a library like
libMYLIB.a.

The .h file (also, sometimes ".hpp", for c++ code) describes the functions
and classes in the library; the .a file is an archive of the compiled
versions of those functions and classes.

You might also get .c files (or .cpp, again for c++ code); these are the
source code that was used to generate the .a file. When you build the
libraries on your own machine, you get only the .c and .cpp files, and you
build the .a file.

After the .a file is created, you can (if you want) throw away the .c and
.cpp files. (It's good to keep them, but they're only good for reference.)

To use this library, you need to write code that includes the appropriate
.h files. This allows you to compile your code. To actually make it run,
you need to link to the library .a file. (Linking can be done as part of
compiling or during run-time.)

The first step in building the RepastHPC library uses the .h and .cpp
files from the other libraries like boost, netcdf, etc. The result is a
repasthpc.a library.

After that you can use the repast '.h' files (as well as any other
library's .h files) in your own code. When you link, you can link to the
other libraries and to the repasthpc.a library.

This is all an outcome of the separation of 'structure' from 'content':
the .h files describe what functions are available in the libraries; the
.cpp files actually have the code they need.

(There is also 'templated' code; this is code that is written at a generic
level and can't be compiled until its specifics are filled in; basically
there are .hpp files but no .cpp files.)

So the upshot is that Repast HPC will need the .h files and the .a files,
but shouldn't need the .cpp files. You should only need those if you're
building the libraries yourself.

Hope this makes sense.

Best,
John



--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
jtmurphy@anl.gov




On 8/20/12 2:11 PM, "markaehlen" <Markaehlen@gmail.com> wrote:

>
>Wow - thanks for the quick reply. I am in the middle of building (and the
>many variants it takes), so have some high-level thinking to do...will
>eventually install correctly, it just will when it does. In the meantime:
>
>Its helpful to understand, from RepastHPC's standpoint (yes, the code),
>what
>it needs to compile. Some of the requirements are, I am assuming, runtime
>libraries and other things are specific header files. For example, it
>appears to want to find *actual files* such as boost/mpi.cpp and
>netcdfcpp.h. I'm not a deep compiler thinker, so pardon me if this sounds
>sophomoric, but which of the mpi/boost/netcdf/netcdf-cxx links need to be
>files and which need to be / can be compiled libraries? I'm learning this
>RepastHPC division/grouping the hard way, but that's okay. Macports, for
>example, just installs the needed libraries (and occasional executable
>code?), but by default probably does not install *any* source code, e.g.,
>*.h files.
>
>If you can harvest a question from the above, I look forward to an answer
>:)
>
>Thanks again!
>
>Mark
>
>
>
>markaehlen wrote:
>>
>> Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have
>> used MacPorts in the past and found it very good ('secretarially') in
>> keeping track of prerequisite libraries and insuring the latest
>>libraries
>> are used. I have tried several times to use it but am getting strange
>> errors.
>>
>> Before I ask specific questions about installation (I have also been
>> following the guidance in the repast download files), should I / could I
>> use MacPorts (it has entries for all of the pre-requisites: openmpi,
>> mpich2, boost, netcdf, netcdf-cxx4), or should I really just do each
>> pre-requisite manually? The problem appears to be that boost static
>> libraries are not created, and certain header files (netcdfcpp.h) are
>>not
>> installed locally.
>>
>> Just high-level question for now...
>>
>> Thanks,
>>
>> Mark
>>
>--
>View this message in context:
>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prerequ
>isite-Libraries-with-MacPort--tp34325774p34326062.html
>Sent from the repast-interest mailing list archive at Nabble.com.
>
>
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Re: Installing RepastHPC on Mac: Can I Install Prerequisite Libraries with MacPort?

Murphy, John T.
Hi Mark,

I'd be curious to know where you found this pdf/pptx document; it would
make it easier to know exactly what the source of confusion is.

The call to createComplementaryEdges in the RumorModel code occurs in
RumorModel.cpp, line 127.

Please note that this call occurs in the most recently distributed version
of Repast HPC, version 1.0.1. The internal development code repository
contains newer versions of Repast HPC and of the RumorModel demo, and in
these the call to createComplementaryEdges may not be used. However, these
repository versions are not yet fully tested nor finalized for release,
nor is there any documentation of them. I would assume that any
documentation or commentary that you find will refer to the released
version- and I recommend you use the release version as well, if you are
not.

The RumorModel example in the release version (and in all other versions
that I know of) is complete in the three files that you mentioned. It and
the 'zombies' model are the two demonstration models that currently exist.
Keep in mind that some explanations of these demonstration models may
comment on both the elements that are handled by the code in the
demonstrations themselves and also on aspects that are handled 'under the
hood' by Repast HPC; Repast HPC is intended to do a lot of things without
requiring explicit calls in the user's code. The documentation and
comments may blur the lines between these, so that they discuss things
that occur in the RumorModel but that are actually handled by code
somewhere else in the Repast HPC library.

Along with the new versions of Repast HPC there is more documentation
being prepared, but the release date is not yet known.

Best,
John

--
John T. Murphy
Computational Postdoctoral Fellow
Decision and Information Sciences and
Argonne Leadership Computing Facility
Argonne National Laboratory
[hidden email]




On 11/25/12 8:47 AM, "markaehlen" <[hidden email]> wrote:

>
>Hey John - thanks again, you're a saint. I'm off to building a prototype
>off
>of the Rumor example that comes with the Repast HPC installation. I have a
>secretarial question: a PDF PPTX I found on the web describes the Rumor
>example with a lot of specifics, but when I open the RumorModel.{h,cpp}
>and
>main.cpp files that come with the installation, they appear to be missing
>some of this detail, such as the creation of complimentary edges. Am I not
>using the right RumorModel files? Where are the complete versions of these
>files. More broadly, is there a repository of simple examples that users
>have shared, that I can peruse?
>
>Thanks again!
>
>M
>
>
>
>Murphy, John T. wrote:
>>
>> Mark,
>>
>> In the simplest situation you get two pieces: .h files and a library
>>like
>> libMYLIB.a.
>>
>> The .h file (also, sometimes ".hpp", for c++ code) describes the
>>functions
>> and classes in the library; the .a file is an archive of the compiled
>> versions of those functions and classes.
>>
>> You might also get .c files (or .cpp, again for c++ code); these are the
>> source code that was used to generate the .a file. When you build the
>> libraries on your own machine, you get only the .c and .cpp files, and
>>you
>> build the .a file.
>>
>> After the .a file is created, you can (if you want) throw away the .c
>>and
>> .cpp files. (It's good to keep them, but they're only good for
>>reference.)
>>
>> To use this library, you need to write code that includes the
>>appropriate
>> .h files. This allows you to compile your code. To actually make it run,
>> you need to link to the library .a file. (Linking can be done as part of
>> compiling or during run-time.)
>>
>> The first step in building the RepastHPC library uses the .h and .cpp
>> files from the other libraries like boost, netcdf, etc. The result is a
>> repasthpc.a library.
>>
>> After that you can use the repast '.h' files (as well as any other
>> library's .h files) in your own code. When you link, you can link to the
>> other libraries and to the repasthpc.a library.
>>
>> This is all an outcome of the separation of 'structure' from 'content':
>> the .h files describe what functions are available in the libraries; the
>> .cpp files actually have the code they need.
>>
>> (There is also 'templated' code; this is code that is written at a
>>generic
>> level and can't be compiled until its specifics are filled in; basically
>> there are .hpp files but no .cpp files.)
>>
>> So the upshot is that Repast HPC will need the .h files and the .a
>>files,
>> but shouldn't need the .cpp files. You should only need those if you're
>> building the libraries yourself.
>>
>> Hope this makes sense.
>>
>> Best,
>> John
>>
>>
>>
>> --
>> John T. Murphy
>> Computational Postdoctoral Fellow
>> Decision and Information Sciences and
>> Argonne Leadership Computing Facility
>> Argonne National Laboratory
>> [hidden email]
>>
>>
>>
>>
>> On 8/20/12 2:11 PM, "markaehlen" <[hidden email]> wrote:
>>
>>>
>>>Wow - thanks for the quick reply. I am in the middle of building (and
>>>the
>>>many variants it takes), so have some high-level thinking to do...will
>>>eventually install correctly, it just will when it does. In the
>>>meantime:
>>>
>>>Its helpful to understand, from RepastHPC's standpoint (yes, the code),
>>>what
>>>it needs to compile. Some of the requirements are, I am assuming,
>>>runtime
>>>libraries and other things are specific header files. For example, it
>>>appears to want to find *actual files* such as boost/mpi.cpp and
>>>netcdfcpp.h. I'm not a deep compiler thinker, so pardon me if this
>>>sounds
>>>sophomoric, but which of the mpi/boost/netcdf/netcdf-cxx links need to
>>>be
>>>files and which need to be / can be compiled libraries? I'm learning
>>>this
>>>RepastHPC division/grouping the hard way, but that's okay. Macports, for
>>>example, just installs the needed libraries (and occasional executable
>>>code?), but by default probably does not install *any* source code,
>>>e.g.,
>>>*.h files.
>>>
>>>If you can harvest a question from the above, I look forward to an
>>>answer
>>>:)
>>>
>>>Thanks again!
>>>
>>>Mark
>>>
>>>
>>>
>>>markaehlen wrote:
>>>>
>>>> Hi - I'm installing Repast HPC on a new Mac with Mountain Lion. I have
>>>> used MacPorts in the past and found it very good ('secretarially') in
>>>> keeping track of prerequisite libraries and insuring the latest
>>>>libraries
>>>> are used. I have tried several times to use it but am getting strange
>>>> errors.
>>>>
>>>> Before I ask specific questions about installation (I have also been
>>>> following the guidance in the repast download files), should I /
>>>>could I
>>>> use MacPorts (it has entries for all of the pre-requisites: openmpi,
>>>> mpich2, boost, netcdf, netcdf-cxx4), or should I really just do each
>>>> pre-requisite manually? The problem appears to be that boost static
>>>> libraries are not created, and certain header files (netcdfcpp.h) are
>>>>not
>>>> installed locally.
>>>>
>>>> Just high-level question for now...
>>>>
>>>> Thanks,
>>>>
>>>> Mark
>>>>
>>>--
>>>View this message in context:
>>>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prere
>>>qu
>>>isite-Libraries-with-MacPort--tp34325774p34326062.html
>>>Sent from the repast-interest mailing list archive at Nabble.com.
>>>
>>>
>>>------------------------------------------------------------------------
>>>--
>>>----
>>>Live Security Virtual Conference
>>>Exclusive live event will cover all the ways today's security and
>>>threat landscape has changed and how IT managers can respond.
>>>Discussions
>>>will include endpoint security, mobile security and the latest in
>>>malware
>>>threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>>>_______________________________________________
>>>Repast-interest mailing list
>>>[hidden email]
>>>https://lists.sourceforge.net/lists/listinfo/repast-interest
>>
>>
>>
>>-------------------------------------------------------------------------
>>-----
>> Live Security Virtual Conference
>> Exclusive live event will cover all the ways today's security and
>> threat landscape has changed and how IT managers can respond.
>>Discussions
>> will include endpoint security, mobile security and the latest in
>>malware
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> _______________________________________________
>> Repast-interest mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/repast-interest
>>
>>
>
>--
>View this message in context:
>http://old.nabble.com/Installing-RepastHPC-on-Mac%3A-Can-I-Install-Prerequ
>isite-Libraries-with-MacPort--tp34325774p34719546.html
>Sent from the repast-interest mailing list archive at Nabble.com.
>
>
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