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

the lily the.1.lily at hotmail.com
Wed Jul 23 19:44:34 CDT 2014 

Hi,
Attached the log files.
these are my steps
 1- ./configure --disable-fortran
2- make all | tee make.log
3- make check 
I tried running a simple mpi example it seems is not working anymore it is giving me the following








ld: can't write output file: mpi_hello_world for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [mpi_hello_world] Error 1
thanks.

> From: vijay.m at gmail.com
> Date: Wed, 23 Jul 2014 19:33:56 -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
> 
> clang is incompatible with the gfortran you have installed. The
> configuration and make went through fine according to your logs.Try
> configuring again with --disable-fortran explicitly specified.
> 
> Vijay
> 
> 
> On Wed, Jul 23, 2014 at 7:20 PM, the lily <the.1.lily at hotmail.com> wrote:
> > Hi,
> >
> > Attached the config and make log files, this is what I have done.
> >
> > 1- download ftp://ftp.mcs.anl.gov/pub/fathom/moab-nightly.tar.gz
> > 2- unzip the file
> > 3- cd moab-4.7.0pre
> > 4- ./configure
> > 5- make all | tee make.log
> > 6- make check gave me the following
> >
> > make[4]: DHAVE_CONFIG_H: No such file or directory
> >
> > make[4]: [ScdMeshF90.o] Error 1 (ignored)
> >
> > /bin/sh ../../libtool  --tag=FC   --mode=link   -O2   -o ScdMeshF90
> > ScdMeshF90.o libiMesh.la ../../src/libMOAB.la   -lm
> >
> > 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
> >
> >
> > thanks.
> >
> >
> >
> >> From: vijay.m at gmail.com
> >> Date: Wed, 23 Jul 2014 18:26:29 -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
> >>
> >> You need autotools installed for your mac for autoreconf to work. If
> >> you have macports, this should be easy.
> >>
> >> Meanwhile, you can try the nightly from here:
> >> ftp://ftp.mcs.anl.gov/pub/fathom/moab-nightly.tar.gz
> >>
> >> Vijay
> >>
> >> On Wed, Jul 23, 2014 at 4:52 PM, the lily <the.1.lily at hotmail.com> wrote:
> >> > 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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