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

[Vijay S. Mahadevan]

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.