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
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