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<body class='hmmessage'><div dir='ltr'><div><br></div><div>Hi Vijya,</div><div><br></div><div>1) Can you check if you can run some simple MPI programs first. This will verify your MPI installation is correct</div><div><br></div><div>I checked running a simple example and it is working.</div><div><br></div><div>2) Configure MOAB without MPI (with --disable-fortran). See if make check passes</div><div><br></div><div>This is what I tried ./configure --with-hdf5=/usr/local/hdf5 --disable-fortran</div><div><br></div><div>I get the following when I do make check</div><div>
<p class="p1">Making check in doc</p>
<p class="p1">make[1]: Nothing to be done for `check'.</p></div><div><br></div><div> 3) Specify the MPI installation directory when specifying --with-mpi=<MPI_DIR> and try again</div><div><br></div><div>./configure --with-mpi=/usr/local --with-hdf5=/usr/local/hdf5 --prefix=/Users/lab/Documents/Code/moab-4.6.3 --disable-fortran</div><div><br></div>
<p class="p1">a(iMesh_MOAB.o)</p><p class="p1"> _iMesh_save in libiMesh.a(iMesh_MOAB.o)</p><p class="p1"> _iMesh_getEntitiesRec in libiMesh.a(iMesh_MOAB.o)</p><p class="p1"> _iMesh_getVtxArrCoords in libiMesh.a(iMesh_MOAB.o)</p><p class="p1">
</p><p class="p1"> _iMesh_getEntArrAdj in libiMesh.a(iMesh_MOAB.o)</p>
<p class="p1">ld: symbol(s) not found for architecture x86_64</p>
<p class="p1">clang: error: linker command failed with exit code 1 (use -v to see invocation)</p>
<p class="p1">make[1]: *** [example] Error 1</p>
<p class="p1">make: *** [check] Error 2</p><div><br></div><div><br></div>4) Add HDF5 dependency -- make sure HDF5 is configured with --enable-parallel<div><br></div><div>./configure --with-hdf5=/usr/local/hdf5 --enable-parallel --disable-fortran</div><div><br></div><div>The output of make check:</div><div><br></div><div>
<p class="p1">Making check in doc</p>
<p class="p1">make[1]: Nothing to be done for `check'.</p><p class="p1"><br></p><p class="p1">thank you.</p><p class="p1"><br></p></div><div><br><div>> From: vijay.m@gmail.com<br>> Date: Tue, 22 Jul 2014 19:26:36 -0500<br>> Subject: Re: [MOAB-dev] make check returns error when installing moab<br>> To: the.1.lily@hotmail.com<br>> CC: iulian@mcs.anl.gov; moab-dev@mcs.anl.gov<br>> <br>> Couple of things for your to check:<br>> <br>> 1) Can you check if you can run some simple MPI programs first. This<br>> will verify your MPI installation is correct<br>> 2) Configure MOAB without MPI (with --disable-fortran). See if make check passes<br>> 3) Specify the MPI installation directory when specifying<br>> --with-mpi=<MPI_DIR> and try again<br>> 4) Add HDF5 dependency -- make sure HDF5 is configured with --enable-parallel<br>> <br>> Let us know which of these steps fail.<br>> <br>> Vijay<br>> <br>> On Tue, Jul 22, 2014 at 7:23 PM, the lily <the.1.lily@hotmail.com> wrote:<br>> ><br>> > Hi Everyone,<br>> ><br>> > I'm trying to install moab to use it with DIY<br>> > http://www.mcs.anl.gov/~tpeterka/<br>> > I tried the following commands to install moab<br>> ><br>> > ./configure --with-mpi --with-hdf5=/usr/local/hdf5<br>> > --prefix=/Users/lab/Documents/Code/moab-4.6.3/bld --disable-fortran<br>> > make<br>> > make check but until now I was not able to install moab and Im getting the<br>> > following errors<br>> ><br>> > ld: symbol(s) not found for architecture x86_64<br>> ><br>> > clang: error: linker command failed with exit code 1 (use -v to see<br>> > invocation)<br>> ><br>> > make[4]: *** [testc_cbind] Error 1<br>> ><br>> > make[3]: *** [check-am] Error 2<br>> ><br>> > make[2]: *** [check] Error 2<br>> ><br>> > make[1]: *** [check-recursive] Error 1<br>> ><br>> > make: *** [check-recursive] Error 1<br>> ><br>> ><br>> ><br>> > and now even diy is not working and I think it is something has to do with<br>> > mpi because I'm trying to run a code that include some mpi call<br>> ><br>> > and I'm getting the following errors<br>> ><br>> ><br>> > MPI::Op::Init(void (*)(void const*, void*, int, MPI::Datatype const&),<br>> > bool) in merge.o<br>> ><br>> > ld: symbol(s) not found for architecture x86_64<br>> ><br>> > clang: error: linker command failed with exit code 1 (use -v to see<br>> > invocation)<br>> ><br>> > make: *** [merge] Error 1<br>> ><br>> ><br>> > I hope someone call help me to fix this<br>> ><br>> > ________________________________<br>> > From: the.1.lily@hotmail.com<br>> > To: vijay.m@gmail.com<br>> > CC: iulian@mcs.anl.gov; moab-dev@mcs.anl.gov<br>> ><br>> > Subject: RE: [MOAB-dev] make check returns error when installing moab<br>> > Date: Tue, 22 Jul 2014 02:11:45 +0300<br>> ><br>> ><br>> > when I run config I do not get any errors but when I do make and make check<br>> > I get the following<br>> ><br>> > ld: symbol(s) not found for architecture x86_64<br>> ><br>> > clang: error: linker command failed with exit code 1 (use -v to see<br>> > invocation)<br>> ><br>> > make[4]: *** [testc_cbind] Error 1<br>> ><br>> > make[3]: *** [check-am] Error 2<br>> ><br>> > make[2]: *** [check] Error 2<br>> ><br>> > make[1]: *** [check-recursive] Error 1<br>> ><br>> > make: *** [check-recursive] Error 1<br>> ><br>> ><br>> > Thanks.<br>> ><br>> ><br>> >> From: vijay.m@gmail.com<br>> >> Date: Mon, 21 Jul 2014 17:48:42 -0500<br>> >> Subject: Re: [MOAB-dev] make check returns error when installing moab<br>> >> To: the.1.lily@hotmail.com<br>> >> CC: iulian@mcs.anl.gov; moab-dev@mcs.anl.gov<br>> >><br>> >> The log shows that the fortran compiler is invalid in your OpenMPI<br>> >> installation. That is perfectly fine. We will have to disable fortran<br>> >> support if an appropriate compiler is not found.<br>> >><br>> >> Can you try again with ./configure --with-mpi<br>> >> --with-hdf5=/usr/local/hdf5<br>> >> --prefix=/Users/lab/Documents/Code/moab-4.6.3/bld --disable-fortran<br>> >><br>> >> Let us know if configure still fails, along with config logs.<br>> >><br>> >> Vijay<br>> >><br>> >> On Mon, Jul 21, 2014 at 5:41 PM, the lily <the.1.lily@hotmail.com> wrote:<br>> >> > Hi Grindeanu,<br>> >> ><br>> >> > Thank you for your help. Attached the config.log<br>> >> ><br>> >> > Thank you.<br>> >> ><br>> >> ><br>> >> ><br>> >> > ________________________________<br>> >> > From: iulian@mcs.anl.gov<br>> >> ><br>> >> > To: the.1.lily@hotmail.com; moab-dev@mcs.anl.gov<br>> >> > Subject: RE: [MOAB-dev] make check returns error when installing moab<br>> >> > Date: Mon, 21 Jul 2014 14:12:47 +0000<br>> >> ><br>> >> ><br>> >> > what version of moab did you try?<br>> >> > checkout a fresh clone from master<br>> >> > (git@bitbucket.org:fathomteam/moab.git)<br>> >> ><br>> >> > can you send your config.log ?<br>> >> ><br>> >> > Iulian<br>> >> > ________________________________<br>> >> > From: moab-dev-bounces@mcs.anl.gov [moab-dev-bounces@mcs.anl.gov] on<br>> >> > behalf<br>> >> > of the lily [the.1.lily@hotmail.com]<br>> >> > Sent: Monday, July 21, 2014 3:07 AM<br>> >> > To: moab-dev@mcs.anl.gov<br>> >> > Subject: [MOAB-dev] make check returns error when installing moab<br>> >> ><br>> >> > Hi everyone,<br>> >> ><br>> >> > I keep getting an error when I try to install moab, here are the steps I<br>> >> > did<br>> >> > and the output for each step,<br>> >> ><br>> >> > Step1: ./configure<br>> >> > output:<br>> >> ><br>> >> > configure: WARNING:<br>> >> ><br>> >> ><br>> >> > *************************************************************************<br>> >> ><br>> >> > * MOAB has been configured w/out the HDF5 library.<br>> >> ><br>> >> > * Support for native file format is disabled!<br>> >> ><br>> >> ><br>> >> > *************************************************************************<br>> >> ><br>> >> > configure: WARNING:<br>> >> ><br>> >> ><br>> >> > *************************************************************************<br>> >> ><br>> >> > * MOAB has been configured w/out the NetCDF library.<br>> >> ><br>> >> > * Support for ExodusII/Genesis and other file formats is disabled!<br>> >> ><br>> >> ><br>> >> > *************************************************************************<br>> >> ><br>> >> ><br>> >> > Step2: make<br>> >> ><br>> >> > output:<br>> >> ><br>> >> > make[3]: Nothing to be done for `all-am'.<br>> >> ><br>> >> > Making all in io<br>> >> ><br>> >> > make[3]: Nothing to be done for `all'.<br>> >> ><br>> >> > Making all in dual<br>> >> ><br>> >> > make[3]: Nothing to be done for `all'.<br>> >> ><br>> >> > Making all in obb<br>> >> ><br>> >> > make[3]: Nothing to be done for `all'.<br>> >> ><br>> >> > Making all in perf<br>> >> ><br>> >> > Making all in point_location<br>> >> ><br>> >> > make[4]: Nothing to be done for `all'.<br>> >> ><br>> >> > make[4]: Nothing to be done for `all-am'.<br>> >> ><br>> >> > Making all in dagmc<br>> >> ><br>> >> > make[3]: Nothing to be done for `all'.<br>> >> ><br>> >> > Making all in oldinc<br>> >> ><br>> >> > make[3]: Nothing to be done for `all'.<br>> >> ><br>> >> > Making all in doc<br>> >> ><br>> >> > make[2]: Nothing to be done for `all'.<br>> >> ><br>> >> > ./config.status --version | \<br>> >> ><br>> >> > sed -e 's/.*options "\(.*\)"/\1/p' -e 'd' | \<br>> >> ><br>> >> > tr "'" "\n" | \<br>> >> ><br>> >> > sed -e '/^ *$/d' > moab.config<br>> >> ><br>> >> ><br>> >> > Step3: make check<br>> >> ><br>> >> > output:<br>> >> ><br>> >> > libtool: link: unrecognized option `-O2'<br>> >> ><br>> >> > libtool: link: Try `libtool --help' for more information.<br>> >> ><br>> >> > make[4]: *** [ScdMeshF90] Error 1<br>> >> ><br>> >> > make[3]: *** [check-am] Error 2<br>> >> ><br>> >> > make[2]: *** [check] Error 2<br>> >> ><br>> >> > make[1]: *** [check-recursive] Error 1<br>> >> ><br>> >> > make: *** [check-recursive] Error 1<br>> >> ><br>> >> ><br>> >> ><br>> >> > I do not know what exactly went wrong, do I need to install any<br>> >> > libraries<br>> >> > before installing moab?<br>> >> ><br>> >> > Thank you.<br></div></div> </div></body>
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