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

Tue Jul 22 22:19:29 CDT 2014

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.