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

[Vijay S. Mahadevan]

I still don't see any issues with your logs. Did make check with all
the tests pass completely ? If not, send us the log of "make check |
tee check.log".

> 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)

How are you trying to link your simple example with MOAB ? What
arguments do you pass to the linker for your example ? clang doesn't
like your linker arguments.

In the git repo, the example folder has a simple makefile that you can
use to link your own examples after you install the build somewhere.

./configure --prefix=INSTALL_DIR --disable-fortran
make check
make install

Create your makefile with something that resembles:

#------------------------------------
# MOAB_DIR points to top-level install dir, below which MOAB's lib/
and include/ are located
MOAB_DIR=<INSTALL_DIR specified to prefix>
include ${MOAB_DIR}/lib/moab.make
include ${MOAB_DIR}/lib/iMesh-Defs.inc

.SUFFIXES: .o .cpp .F90

mpi_hello_world: mpi_hello_world.o ${MOAB_LIBDIR}/libMOAB.la
  ${MOAB_CXX} -o $@ $< ${MOAB_LIBS_LINK}
#------------------------------------

Now you can run

make mpi_hello_world

and your program should link against MOAB properly.

Vijay

On Wed, Jul 23, 2014 at 7:44 PM, the lily <the.1.lily at hotmail.com> wrote:
>
> 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.