[MOAB-dev] make check returns error when installing moab

[the lily]

Hi
I tried before cloning moab from the git repository but it does not have a configure file and when I run autoreconf -fi I get the following
bash: autoreconf: command not found
thanks.
> From: vijay.m at gmail.com
> Date: Tue, 22 Jul 2014 22:19:29 -0500
> Subject: Re: [MOAB-dev] make check returns error when installing moab
> To: the.1.lily at hotmail.com
> CC: iulian at mcs.anl.gov; moab-dev at mcs.anl.gov
> 
> These error messages are incomplete. Please use make check | tee
> make.log and send us the make logs for us to help you better. Also I
> notice that you are using 4.6.3.
> 
> We are on the verge of the next big release and so if you want to work
> off the repository directly, we can make the appropriate fixes for
> clang 3.3 + OSX Mavericks and push those as part of the upcoming
> release. We haven't tested with this combination of compiler + OS and
> so its been hard to replicate so far.
> 
> Use:
> git clone https://bitbucket.org/fathomteam/moab.git moab
> autoreconf -fi
> ./configure --options
> make all | tee make.log
> make check
> 
> Then send us your config.log, make.log and test/test-suite.log
> appropriately as things fail.
> 
> Vijay
> 
> On Tue, Jul 22, 2014 at 8:36 PM, the lily <the.1.lily at hotmail.com> wrote:
> >
> > Hi Vijya,
> >
> > 1) Can you check if you can run some simple MPI programs first. This will
> > verify your MPI installation is correct
> >
> > I checked running a simple example and it is working.
> >
> > 2) Configure MOAB without MPI (with --disable-fortran). See if make check
> > passes
> >
> > This is what I tried ./configure --with-hdf5=/usr/local/hdf5
> > --disable-fortran
> >
> > I get the following when I do make check
> >
> > Making check in doc
> >
> > make[1]: Nothing to be done for `check'.
> >
> >
> >  3) Specify the MPI installation directory when specifying
> > --with-mpi=<MPI_DIR> and try again
> >
> > ./configure --with-mpi=/usr/local --with-hdf5=/usr/local/hdf5
> > --prefix=/Users/lab/Documents/Code/moab-4.6.3 --disable-fortran
> >
> > a(iMesh_MOAB.o)
> >
> >       _iMesh_save in libiMesh.a(iMesh_MOAB.o)
> >
> >       _iMesh_getEntitiesRec in libiMesh.a(iMesh_MOAB.o)
> >
> >       _iMesh_getVtxArrCoords in libiMesh.a(iMesh_MOAB.o)
> >
> >       _iMesh_getEntArrAdj in libiMesh.a(iMesh_MOAB.o)
> >
> > ld: symbol(s) not found for architecture x86_64
> >
> > clang: error: linker command failed with exit code 1 (use -v to see
> > invocation)
> >
> > make[1]: *** [example] Error 1
> >
> > make: *** [check] Error 2
> >
> >
> >
> > 4) Add HDF5 dependency -- make sure HDF5 is configured with
> > --enable-parallel
> >
> > ./configure --with-hdf5=/usr/local/hdf5 --enable-parallel --disable-fortran
> >
> > The output of make check:
> >
> > Making check in doc
> >
> > make[1]: Nothing to be done for `check'.
> >
> >
> > thank you.
> >
> >
> >
> >> From: vijay.m at gmail.com
> >> Date: Tue, 22 Jul 2014 19:26:36 -0500
> >
> >> Subject: Re: [MOAB-dev] make check returns error when installing moab
> >> To: the.1.lily at hotmail.com
> >> CC: iulian at mcs.anl.gov; moab-dev at mcs.anl.gov
> >>
> >> Couple of things for your to check:
> >>
> >> 1) Can you check if you can run some simple MPI programs first. This
> >> will verify your MPI installation is correct
> >> 2) Configure MOAB without MPI (with --disable-fortran). See if make check
> >> passes
> >> 3) Specify the MPI installation directory when specifying
> >> --with-mpi=<MPI_DIR> and try again
> >> 4) Add HDF5 dependency -- make sure HDF5 is configured with
> >> --enable-parallel
> >>
> >> Let us know which of these steps fail.
> >>
> >> Vijay
> >>
> >> On Tue, Jul 22, 2014 at 7:23 PM, the lily <the.1.lily at hotmail.com> wrote:
> >> >
> >> > Hi Everyone,
> >> >
> >> > I'm trying to install moab to use it with DIY
> >> > http://www.mcs.anl.gov/~tpeterka/
> >> > I tried the following commands to install moab
> >> >
> >> > ./configure --with-mpi --with-hdf5=/usr/local/hdf5
> >> > --prefix=/Users/lab/Documents/Code/moab-4.6.3/bld --disable-fortran
> >> > make
> >> > make check but until now I was not able to install moab and Im getting
> >> > the
> >> > following errors
> >> >
> >> > ld: symbol(s) not found for architecture x86_64
> >> >
> >> > clang: error: linker command failed with exit code 1 (use -v to see
> >> > invocation)
> >> >
> >> > make[4]: *** [testc_cbind] Error 1
> >> >
> >> > make[3]: *** [check-am] Error 2
> >> >
> >> > make[2]: *** [check] Error 2
> >> >
> >> > make[1]: *** [check-recursive] Error 1
> >> >
> >> > make: *** [check-recursive] Error 1
> >> >
> >> >
> >> >
> >> > and now even diy is not working and I think it is something has to do
> >> > with
> >> > mpi because I'm trying to run a code that include some mpi call
> >> >
> >> > and I'm getting the following errors
> >> >
> >> >
> >> > MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&),
> >> > bool) in merge.o
> >> >
> >> > ld: symbol(s) not found for architecture x86_64
> >> >
> >> > clang: error: linker command failed with exit code 1 (use -v to see
> >> > invocation)
> >> >
> >> > make: *** [merge] Error 1
> >> >
> >> >
> >> > I hope someone call help me to fix this
> >> >
> >> > ________________________________
> >> > From: the.1.lily at hotmail.com
> >> > To: vijay.m at gmail.com
> >> > CC: iulian at mcs.anl.gov; moab-dev at mcs.anl.gov
> >> >
> >> > Subject: RE: [MOAB-dev] make check returns error when installing moab
> >> > Date: Tue, 22 Jul 2014 02:11:45 +0300
> >> >
> >> >
> >> > when I run config I do not get any errors but when I do make and make
> >> > check
> >> > I get the following
> >> >
> >> > ld: symbol(s) not found for architecture x86_64
> >> >
> >> > clang: error: linker command failed with exit code 1 (use -v to see
> >> > invocation)
> >> >
> >> > make[4]: *** [testc_cbind] Error 1
> >> >
> >> > make[3]: *** [check-am] Error 2
> >> >
> >> > make[2]: *** [check] Error 2
> >> >
> >> > make[1]: *** [check-recursive] Error 1
> >> >
> >> > make: *** [check-recursive] Error 1
> >> >
> >> >
> >> > Thanks.
> >> >
> >> >
> >> >> From: vijay.m at gmail.com
> >> >> Date: Mon, 21 Jul 2014 17:48:42 -0500
> >> >> Subject: Re: [MOAB-dev] make check returns error when installing moab
> >> >> To: the.1.lily at hotmail.com
> >> >> CC: iulian at mcs.anl.gov; moab-dev at mcs.anl.gov
> >> >>
> >> >> The log shows that the fortran compiler is invalid in your OpenMPI
> >> >> installation. That is perfectly fine. We will have to disable fortran
> >> >> support if an appropriate compiler is not found.
> >> >>
> >> >> Can you try again with ./configure --with-mpi
> >> >> --with-hdf5=/usr/local/hdf5
> >> >> --prefix=/Users/lab/Documents/Code/moab-4.6.3/bld --disable-fortran
> >> >>
> >> >> Let us know if configure still fails, along with config logs.
> >> >>
> >> >> Vijay
> >> >>
> >> >> On Mon, Jul 21, 2014 at 5:41 PM, the lily <the.1.lily at hotmail.com>
> >> >> wrote:
> >> >> > Hi Grindeanu,
> >> >> >
> >> >> > Thank you for your help. Attached the config.log
> >> >> >
> >> >> > Thank you.
> >> >> >
> >> >> >
> >> >> >
> >> >> > ________________________________
> >> >> > From: iulian at mcs.anl.gov
> >> >> >
> >> >> > To: the.1.lily at hotmail.com; moab-dev at mcs.anl.gov
> >> >> > Subject: RE: [MOAB-dev] make check returns error when installing moab
> >> >> > Date: Mon, 21 Jul 2014 14:12:47 +0000
> >> >> >
> >> >> >
> >> >> > what version of moab did you try?
> >> >> > checkout a fresh clone from master
> >> >> > (git at bitbucket.org:fathomteam/moab.git)
> >> >> >
> >> >> > can you send your config.log ?
> >> >> >
> >> >> > Iulian
> >> >> > ________________________________
> >> >> > From: moab-dev-bounces at mcs.anl.gov [moab-dev-bounces at mcs.anl.gov] on
> >> >> > behalf
> >> >> > of the lily [the.1.lily at hotmail.com]
> >> >> > Sent: Monday, July 21, 2014 3:07 AM
> >> >> > To: moab-dev at mcs.anl.gov
> >> >> > Subject: [MOAB-dev] make check returns error when installing moab
> >> >> >
> >> >> > Hi everyone,
> >> >> >
> >> >> > I keep getting an error when I try to install moab, here are the
> >> >> > steps I
> >> >> > did
> >> >> > and the output for each step,
> >> >> >
> >> >> > Step1: ./configure
> >> >> > output:
> >> >> >
> >> >> > configure: WARNING:
> >> >> >
> >> >> >
> >> >> >
> >> >> > *************************************************************************
> >> >> >
> >> >> > * MOAB has been configured w/out the HDF5 library.
> >> >> >
> >> >> > * Support for native file format is disabled!
> >> >> >
> >> >> >
> >> >> >
> >> >> > *************************************************************************
> >> >> >
> >> >> > configure: WARNING:
> >> >> >
> >> >> >
> >> >> >
> >> >> > *************************************************************************
> >> >> >
> >> >> > * MOAB has been configured w/out the NetCDF library.
> >> >> >
> >> >> > * Support for ExodusII/Genesis and other file formats is disabled!
> >> >> >
> >> >> >
> >> >> >
> >> >> > *************************************************************************
> >> >> >
> >> >> >
> >> >> > Step2: make
> >> >> >
> >> >> > output:
> >> >> >
> >> >> > make[3]: Nothing to be done for `all-am'.
> >> >> >
> >> >> > Making all in io
> >> >> >
> >> >> > make[3]: Nothing to be done for `all'.
> >> >> >
> >> >> > Making all in dual
> >> >> >
> >> >> > make[3]: Nothing to be done for `all'.
> >> >> >
> >> >> > Making all in obb
> >> >> >
> >> >> > make[3]: Nothing to be done for `all'.
> >> >> >
> >> >> > Making all in perf
> >> >> >
> >> >> > Making all in point_location
> >> >> >
> >> >> > make[4]: Nothing to be done for `all'.
> >> >> >
> >> >> > make[4]: Nothing to be done for `all-am'.
> >> >> >
> >> >> > Making all in dagmc
> >> >> >
> >> >> > make[3]: Nothing to be done for `all'.
> >> >> >
> >> >> > Making all in oldinc
> >> >> >
> >> >> > make[3]: Nothing to be done for `all'.
> >> >> >
> >> >> > Making all in doc
> >> >> >
> >> >> > make[2]: Nothing to be done for `all'.
> >> >> >
> >> >> > ./config.status --version | \
> >> >> >
> >> >> > sed -e 's/.*options "\(.*\)"/\1/p' -e 'd' | \
> >> >> >
> >> >> > tr "'" "\n" | \
> >> >> >
> >> >> > sed -e '/^ *$/d' > moab.config
> >> >> >
> >> >> >
> >> >> > Step3: make check
> >> >> >
> >> >> > output:
> >> >> >
> >> >> > libtool: link: unrecognized option `-O2'
> >> >> >
> >> >> > libtool: link: Try `libtool --help' for more information.
> >> >> >
> >> >> > make[4]: *** [ScdMeshF90] Error 1
> >> >> >
> >> >> > make[3]: *** [check-am] Error 2
> >> >> >
> >> >> > make[2]: *** [check] Error 2
> >> >> >
> >> >> > make[1]: *** [check-recursive] Error 1
> >> >> >
> >> >> > make: *** [check-recursive] Error 1
> >> >> >
> >> >> >
> >> >> >
> >> >> > I do not know what exactly went wrong, do I need to install any
> >> >> > libraries
> >> >> > before installing moab?
> >> >> >
> >> >> > Thank you.
 		 	   		  
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