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[netCDF #IKM-527849]: netcdf parallel compilation: nc_test fail

Subject: [netCDF #IKM-527849]: netcdf parallel compilation: nc_test fail
Date: Tue, 24 Sep 2013 08:18:22 -0600
Michael,

Rather than gfortran, you need to use mpif90 and mpif77, which are mpich 
wrappers for gfortran (or whatever Fortran compiler you're using).  So
try rerunning configure and then make check with

 F77=mpif77 FC=mpif90 F90=mpif90 CC=mpicc 

and if CPPFLAGS=-DgFortran doesn't work due to unsatisfied externals from
the netCDF C library (such as nc_open_ or nc_open__), use

 CPPFLAGS=-DpgiFortran

as instructed in step 4 of the building netcdf-Fortran instructions
under "Building with static libraries":

  http://www.unidata.ucar.edu/netcdf/docs/netcdf-fortran-install.html

instead.  Please let us know if this doesn't work.

--Russ

> Ok. After talking to supprt for HDF I built a later version of MPICH2
> (1.4.1p). which allowed me to build HDF5 1.8.11, and after that netCDF-C
> 4.3.0. Now I'm running into trouble, again, trying to build
> netCDF-Fortran. I've followed the intructions : "Building with static
> libraries"
> (http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-fortran-install.html).
> 
> export CPPFLAGS="-I/local/opt/netcdf/include -I/local/opt/hdf5/include"
> export LD_LIBRARY_PATH=/local/opt/netcdf/lib:/local/opt/hdf5/lib
> export LDFLAGS="-L/local/opt/netcdf/lib -L/local/opt/hdf5/lib"
> export LIBS="-lnetcdf -lhdf5_hl -lhdf5 -lz -lcurl"
> export CFLAGS=-Dgfortran
> 
> ./configure --prefix=/local/opt/netcdf-fortran --disable-shared
> --enable-parallel-tests
> 
> Configure works fine but make check gives me errors. I've attached the
> config.log and the output from make check.
> 
> ========================================================================================================================================================================
> If it helps:
> mpich2 was built with a simple "./configure"
> hdf-1.8.11 with "CC=mpicc ./configure --prefix=/local/opt/hdf5
> --disable-shared --enable-parallel"
> NetCDF-C by:
> 
> declare -x H5DIR=/local/build/hdf5-1.8.11/hdf5
> declare -x CPPFLAGS="-I/local/build/hdf5-1.8.11/hdf5/include"
> declare -x CC=mpicc
> declare -x LDFLAGS=-L/local/build/hdf5-1.8.11/hdf5/lib/
> declare -x LIBS=-ldl
> 
> ./configure --prefix=/local/opt/netcdf --disable-shared
> --enable-parallel-tests
> ==================================================================
> 
> > Michael,
> >
> >> I actually tried and failed building hdf5 first, I think I've tried it
> >> in 10-20 different ways, some more subtle than others. The last attempt
> >> was after reinstalling the system and adding:
> >>
> >> mpich2 libmpich2-1.2 libmpich2-dev libmpich1.0-dev libmpich1.0gf
> >> gfortran g++ libstdc++6-4.4-dev zlib1g zlib1g-dev
> >>
> >> then unpacking hdf5-1.8.11 and running: ./configure
> >> --prefix=/local/opt/hdf5 --enable-fortran --disable-shared 
> >> --enable-parallel
> > If you're just building HDF5 for netCDF-4, there's no need to 
> > --enable-fortran,
> > as neither the netCDF C or netCDF Fortran libraries depend on the HDF5 
> > Fortran
> > API.  However, I don't think that's relevant to the problem you encountered.
> >
> >> I've attached the config.log and make check install output. I know hdf5
> >> is not yours to support, but maybe you can have a look at it anyhow.
> > The error you encountered is in testing HDF5 parallel I/O using the mpich
> > library:
> >
> >    Testing  -- test lower dim size comp in span tree to mpi derived type 
> > (tldsc)
> >    *** glibc detected *** ./testphdf5: double free or corruption (!prev): 
> > 0x00000000016f9450 ***
> >    *** glibc detected *** ./testphdf5: double free or corruption (!prev): 
> > 0x000000000174ae30 ***
> >    ======= Backtrace: =========
> >    /lib/libc.so.6(+0x78bb6)[0x7f207733fbb6]
> >    /lib/libc.so.6(cfree+0x73)[0x7f2077346483]
> >    
> > /usr/lib/libmpich.so.1.2(MPID_Dataloop_create_struct+0x8e2)[0x7f2077b1f632]
> >
> > First, do you really need parallel I/O for what you intend to do with 
> > netCDF-4?
> > If so, you'll have to send your question to HDF5 support, as we have little
> > expertise in that area.  If not, you could omit the --enable-parallel from 
> > the
> > HDF5 configure invocation.
> >
> > Here's the way I invoked configure the last time I built parallel 
> > HDF5-1.8.11
> > successfully on a Linux Fedora platform, in a debug configuration:
> >
> >    env CC=mpicc ../configure --disable-shared --enable-debug 
> > --disable-production --enable-parallel --enable-build-all 
> > --prefix=/machine/russ/installs/h5_1811_db && make all && make check && 
> > make install
> >
> > and it worked.  Note that CC=mpicc is necessary, but you could omit 
> > --enable-debug,
> > --disable-production, --enable-build-all, and use your own --prefix= ...
> >
> > --Russ
> >
> >>> Hi Michael,
> >>>
> >>>> I read in another thread that you wanted config.log and output from the
> >>>> make check, so here you have that aswell.
> >>> I think the problem is the old version of HDF5 (1.8.4) you are using with
> >>> a new version of netCDF (4.3.0).  We didn't test netCDF 4.3.0 with 
> >>> versions
> >>> of HDF5 before 1.8.9, and recommend using it with HDF5 1.8.11.  Earlier
> >>> versions of HDF5 had bugs that affected netCDF, which tests that those
> >>> bugs have been fixed when "make check" is invoked. I just tried building
> >>> netCDF-4.3.0 with HDF5-1.8.4p1, and it got an error from "make check"
> >>> similar to what you are seeing.
> >>>
> >>> I recommend building HDF5-1.8.11 from source and installing that before
> >>> trying to build netCDF-4.3.0.  The HDF5 build is very robust and builds
> >>> on most systems with no problems.  You can just use all the defaults for
> >>> configure except you should add --enable-parallel and use CC=mpicc if you
> >>> want parallel HDF5, required for parallel netCDF-4.
> >>>
> >>> Here's instructions:
> >>>
> >>>     http://www.unidata.ucar.edu/netcdf/docs/build_default.html
> >>>     http://www.unidata.ucar.edu/netcdf/docs/build_parallel.html
> >>>
> >>> --Russ
> >>>
> >>>> -------- Original Message --------
> >>>> Subject:         Fwd: netcdf parallel compilation: nc_test fail
> >>>> Date:    Wed, 18 Sep 2013 11:58:42 +0200
> >>>> From:    Michael Burger <address@hidden>
> >>>> Reply-To:        address@hidden
> >>>> To:      address@hidden
> >>>>
> >>>>
> >>>>
> >>>> I forgot to mention that I also set:
> >>>>
> >>>> declare -x H5DIR=/usr
> >>>> declare -x CPPFLAGS="-I/usr/inlude"
> >>>> declare -x CC=mpicc
> >>>> declare -x LDFLAGS=-L/usr/lib
> >>>> declare -x LIBS=-ldl
> >>>>
> >>>>
> >>>> -------- Original Message --------
> >>>> Subject:         netcdf parallel compilation: nc_test fail
> >>>> Date:    Wed, 18 Sep 2013 11:53:35 +0200
> >>>> From:    Michael Burger <address@hidden>
> >>>> Reply-To:        address@hidden
> >>>> To:      address@hidden
> >>>>
> >>>>
> >>>>
> >>>> I installed Ubuntu 10.04 LTS (amd64) and added:
> >>>>
> >>>> mpich2
> >>>> mpich-bin
> >>>> libmpich2-1.2
> >>>> libmpich2-dev
> >>>> zlib1g
> >>>> zlib1g-dev
> >>>> gfortran
> >>>> g++
> >>>> libstdc++6-4.4-dev
> >>>> hdf5-tools
> >>>> libhdf5-mpich-1.8.4
> >>>> libhdf5-mpich-dev
> >>>> libjpeg62-dev
> >>>> libmpich1.0-dev
> >>>> libmpich1.0gf
> >>>> libhdf5-doc
> >>>> mpi-doc
> >>>>
> >>>> uname -a:
> >>>>
> >>>> Linux misu197 2.6.32-51-generic #113-Ubuntu SMP Wed Aug 21 19:46:35 UTC
> >>>> 2013 x86_64 GNU/Linux
> >>>>
> >>>> Unpacked netcdf-4.3.0.tar.gz
> >>>> ./configure --prefix=/local/opt/netcdf --disable-shared
> >>>> --enable-parallel-tests
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>> Russ Rew                                         UCAR Unidata Program
> >>> address@hidden                      http://www.unidata.ucar.edu
> >>>
> >>>
> >>>
> >>> Ticket Details
> >>> ===================
> >>> Ticket ID: IKM-527849
> >>> Department: Support netCDF
> >>> Priority: Normal
> >>> Status: Closed
> >>>
> >>
> >>
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                      http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: IKM-527849
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> 
> 
> 
Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: IKM-527849
Department: Support netCDF
Priority: Normal
Status: Closed
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