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<body class='hmmessage'><div dir='ltr'><br><div><div>Hi,</div><div><br></div><div>Attached the log files.</div><div><br></div><div>these are my steps</div><div><br></div><div> 1- ./configure --disable-fortran<br>2- make all | tee make.log<br>3- make check </div><div><br></div><div>I tried running a simple mpi example it seems is not working anymore it is giving me the following</div><div><br></div><div>
<p class="p1">ld: can't write output file: mpi_hello_world 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: *** [mpi_hello_world] Error 1</p><p class="p1"><br></p><p class="p1">thanks.</p><p class="p1"><br></p></div><div><br></div><div>> From: vijay.m@gmail.com<br>> Date: Wed, 23 Jul 2014 19:33:56 -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>> clang is incompatible with the gfortran you have installed. The<br>> configuration and make went through fine according to your logs.Try<br>> configuring again with --disable-fortran explicitly specified.<br>> <br>> Vijay<br>> <br>> <br>> On Wed, Jul 23, 2014 at 7:20 PM, the lily <the.1.lily@hotmail.com> wrote:<br>> > Hi,<br>> ><br>> > Attached the config and make log files, this is what I have done.<br>> ><br>> > 1- download ftp://ftp.mcs.anl.gov/pub/fathom/moab-nightly.tar.gz<br>> > 2- unzip the file<br>> > 3- cd moab-4.7.0pre<br>> > 4- ./configure<br>> > 5- make all | tee make.log<br>> > 6- make check gave me the following<br>> ><br>> > make[4]: DHAVE_CONFIG_H: No such file or directory<br>> ><br>> > make[4]: [ScdMeshF90.o] Error 1 (ignored)<br>> ><br>> > /bin/sh ../../libtool --tag=FC --mode=link -O2 -o ScdMeshF90<br>> > ScdMeshF90.o libiMesh.la ../../src/libMOAB.la -lm<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>> > thanks.<br>> ><br>> ><br>> ><br>> >> From: vijay.m@gmail.com<br>> >> Date: Wed, 23 Jul 2014 18:26:29 -0500<br>> ><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>> >> You need autotools installed for your mac for autoreconf to work. If<br>> >> you have macports, this should be easy.<br>> >><br>> >> Meanwhile, you can try the nightly from here:<br>> >> ftp://ftp.mcs.anl.gov/pub/fathom/moab-nightly.tar.gz<br>> >><br>> >> Vijay<br>> >><br>> >> On Wed, Jul 23, 2014 at 4:52 PM, the lily <the.1.lily@hotmail.com> wrote:<br>> >> > Hi<br>> >> ><br>> >> > I tried before cloning moab from the git repository but it does not have<br>> >> > a<br>> >> > configure file and when I run autoreconf -fi I get the following<br>> >> ><br>> >> > bash: autoreconf: command not found<br>> >> ><br>> >> ><br>> >> > thanks.<br>> >> ><br>> >> ><br>> >> >> From: vijay.m@gmail.com<br>> >> >> Date: Tue, 22 Jul 2014 22:19:29 -0500<br>> >> ><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>> >> >> These error messages are incomplete. Please use make check | tee<br>> >> >> make.log and send us the make logs for us to help you better. Also I<br>> >> >> notice that you are using 4.6.3.<br>> >> >><br>> >> >> We are on the verge of the next big release and so if you want to work<br>> >> >> off the repository directly, we can make the appropriate fixes for<br>> >> >> clang 3.3 + OSX Mavericks and push those as part of the upcoming<br>> >> >> release. We haven't tested with this combination of compiler + OS and<br>> >> >> so its been hard to replicate so far.<br>> >> >><br>> >> >> Use:<br>> >> >> git clone https://bitbucket.org/fathomteam/moab.git moab<br>> >> >> autoreconf -fi<br>> >> >> ./configure --options<br>> >> >> make all | tee make.log<br>> >> >> make check<br>> >> >><br>> >> >> Then send us your config.log, make.log and test/test-suite.log<br>> >> >> appropriately as things fail.<br>> >> >><br>> >> >> Vijay<br>> >> >><br>> >> >> On Tue, Jul 22, 2014 at 8:36 PM, the lily <the.1.lily@hotmail.com><br>> >> >> wrote:<br>> >> >> ><br>> >> >> > Hi Vijya,<br>> >> >> ><br>> >> >> > 1) Can you check if you can run some simple MPI programs first. This<br>> >> >> > will<br>> >> >> > verify your MPI installation is correct<br>> >> >> ><br>> >> >> > I checked running a simple example and it is working.<br>> >> >> ><br>> >> >> > 2) Configure MOAB without MPI (with --disable-fortran). See if make<br>> >> >> > check<br>> >> >> > passes<br>> >> >> ><br>> >> >> > This is what I tried ./configure --with-hdf5=/usr/local/hdf5<br>> >> >> > --disable-fortran<br>> >> >> ><br>> >> >> > I get the following when I do make check<br>> >> >> ><br>> >> >> > Making check in doc<br>> >> >> ><br>> >> >> > make[1]: Nothing to be done for `check'.<br>> >> >> ><br>> >> >> ><br>> >> >> > 3) Specify the MPI installation directory when specifying<br>> >> >> > --with-mpi=<MPI_DIR> and try again<br>> >> >> ><br>> >> >> > ./configure --with-mpi=/usr/local --with-hdf5=/usr/local/hdf5<br>> >> >> > --prefix=/Users/lab/Documents/Code/moab-4.6.3 --disable-fortran<br>> >> >> ><br>> >> >> > a(iMesh_MOAB.o)<br>> >> >> ><br>> >> >> > _iMesh_save in libiMesh.a(iMesh_MOAB.o)<br>> >> >> ><br>> >> >> > _iMesh_getEntitiesRec in libiMesh.a(iMesh_MOAB.o)<br>> >> >> ><br>> >> >> > _iMesh_getVtxArrCoords in libiMesh.a(iMesh_MOAB.o)<br>> >> >> ><br>> >> >> > _iMesh_getEntArrAdj in libiMesh.a(iMesh_MOAB.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[1]: *** [example] Error 1<br>> >> >> ><br>> >> >> > make: *** [check] Error 2<br>> >> >> ><br>> >> >> ><br>> >> >> ><br>> >> >> > 4) Add HDF5 dependency -- make sure HDF5 is configured with<br>> >> >> > --enable-parallel<br>> >> >> ><br>> >> >> > ./configure --with-hdf5=/usr/local/hdf5 --enable-parallel<br>> >> >> > --disable-fortran<br>> >> >> ><br>> >> >> > The output of make check:<br>> >> >> ><br>> >> >> > Making check in doc<br>> >> >> ><br>> >> >> > make[1]: Nothing to be done for `check'.<br>> >> >> ><br>> >> >> ><br>> >> >> > thank you.<br>> >> >> ><br>> >> >> ><br>> >> >> ><br>> >> >> >> From: vijay.m@gmail.com<br>> >> >> >> Date: Tue, 22 Jul 2014 19:26:36 -0500<br>> >> >> ><br>> >> >> >> Subject: Re: [MOAB-dev] make check returns error when installing<br>> >> >> >> 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<br>> >> >> >> check<br>> >> >> >> 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<br>> >> >> >> --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><br>> >> >> >> 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<br>> >> >> >> > --disable-fortran<br>> >> >> >> > make<br>> >> >> >> > make check but until now I was not able to install moab and Im<br>> >> >> >> > getting<br>> >> >> >> > 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<br>> >> >> >> > 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<br>> >> >> >> > do<br>> >> >> >> > 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<br>> >> >> >> > 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<br>> >> >> >> > 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<br>> >> >> >> > 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<br>> >> >> >> > make<br>> >> >> >> > 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<br>> >> >> >> > 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<br>> >> >> >> >> 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<br>> >> >> >> >> OpenMPI<br>> >> >> >> >> installation. That is perfectly fine. We will have to disable<br>> >> >> >> >> 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<br>> >> >> >> >> --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<br>> >> >> >> >> <the.1.lily@hotmail.com><br>> >> >> >> >> 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<br>> >> >> >> >> > installing<br>> >> >> >> >> > 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<br>> >> >> >> >> > [moab-dev-bounces@mcs.anl.gov]<br>> >> >> >> >> > 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<br>> >> >> >> >> > moab<br>> >> >> >> >> ><br>> >> >> >> >> > Hi everyone,<br>> >> >> >> >> ><br>> >> >> >> >> > I keep getting an error when I try to install moab, here are<br>> >> >> >> >> > the<br>> >> >> >> >> > 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>> >> >> >> >> ><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>> >> >> >> >> ><br>> >> >> >> >> > *************************************************************************<br>> >> >> >> >> ><br>> >> >> >> >> > configure: WARNING:<br>> >> >> >> >> ><br>> >> >> >> >> ><br>> >> >> >> >> ><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<br>> >> >> >> >> > disabled!<br>> >> >> >> >> ><br>> >> >> >> >> ><br>> >> >> >> >> ><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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