# undefined reference to \`H5Pset\_fapl\_mpiposix'

**URL:** <https://forum.hdfgroup.org/t/undefined-reference-to-h5pset-fapl-mpiposix/3217>\
**Category:** Hdf-forum archives\
**Created:** [May 15, 2014, 7:09pm UTC](https://forum.hdfgroup.org/t/undefined-reference-to-h5pset-fapl-mpiposix/3217 "2014-05-15T19:09:50Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Timothy\_Stitt](https://forum.hdfgroup.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@Timothy\_Stitt](https://forum.hdfgroup.org/u/Timothy_Stitt)\
**Post date:** [May 15, 2014, 7:09pm UTC](https://forum.hdfgroup.org/t/undefined-reference-to-h5pset-fapl-mpiposix/3217/1 "2014-05-15T19:09:50Z")

</div>

HDF Forum,

I’m actually trying to build NETCDF-4 (with parallel I/O) but I keep running into the following link error which appears to be related to HDF5 v1.8.13:

libtool: link: mpicc -g -O2 -o ncgen3 main.o load.o escapes.o getfill.o init.o genlib.o ncgentab.o -L/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/ ../liblib/.libs/libnetcdf.a /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5\_hl.so /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5.so -lz -ldl -lm -lcurl -Wl,-rpath -Wl,/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib -Wl,-rpath -Wl,/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib  
../liblib/.libs/libnetcdf.a(libnetcdf4\_la-nc4file.o): In function `nc4\_open\_file':  
/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/netcdf-4.3.2/libsrc4/nc4file.c:2174: undefined reference to `H5Pset\_fapl\_mpiposix’

I have built HDF5 v1.8.13 using MPICH v3 and GCC v4.4.7 on a RHEL6 Linux system. My HDF5 configure options are as follows:

./configure --prefix=/my/install/path CC=mpicc FC=mpif90 CXX=mpicxx --enable-static --enable-shared --enable-parallel

Is there something I am doing wrong that prevents H5Pset\_fapl\_mpiposix from being built?

Thanks in advance,

Tim.

---

<div class="post-metadata">

**Author:** ![epourmal](https://forum.hdfgroup.org/letter_avatar_proxy/v4/letter/e/c67d28/32.png) [@epourmal](https://forum.hdfgroup.org/u/epourmal)\
**Post date:** [May 15, 2014, 7:45pm UTC](https://forum.hdfgroup.org/t/undefined-reference-to-h5pset-fapl-mpiposix/3217/2 "2014-05-15T19:45:43Z")

</div>

MPI POSIX VFD was removed from HDF5 1.8.13. We submitted a patch to netCDF folks.

See [Account for the HDF5 library not having the MPI-POSIX VFD configured in. · Unidata/netcdf-c@435d8a0 · GitHub](https://github.com/Unidata/netcdf-c/commit/435d8a03ed28bb5ad63aff12cbc6ab91531b6bc8)

Elena

> **···**
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  
> Elena Pourmal The HDF Group [http://hdfgroup.org](http://hdfgroup.org)  
> 1800 So. Oak St., Suite 203, Champaign IL 61820  
> 217.531.6112  
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> On May 15, 2014, at 2:09 PM, Timothy Stitt \<Timothy.Stitt.9@nd.edu\> wrote:
> 
> > HDF Forum,
> > 
> > I’m actually trying to build NETCDF-4 (with parallel I/O) but I keep running into the following link error which appears to be related to HDF5 v1.8.13:
> > 
> > libtool: link: mpicc -g -O2 -o ncgen3 main.o load.o escapes.o getfill.o init.o genlib.o ncgentab.o -L/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/ ../liblib/.libs/libnetcdf.a /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5\_hl.so /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5.so -lz -ldl -lm -lcurl -Wl,-rpath -Wl,/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib -Wl,-rpath -Wl,/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib  
> > ../liblib/.libs/libnetcdf.a(libnetcdf4\_la-nc4file.o): In function `nc4\_open\_file':  
> > /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/netcdf-4.3.2/libsrc4/nc4file.c:2174: undefined reference to `H5Pset\_fapl\_mpiposix’
> > 
> > I have built HDF5 v1.8.13 using MPICH v3 and GCC v4.4.7 on a RHEL6 Linux system. My HDF5 configure options are as follows:
> > 
> > ./configure --prefix=/my/install/path CC=mpicc FC=mpif90 CXX=mpicxx --enable-static --enable-shared --enable-parallel
> > 
> > Is there something I am doing wrong that prevents H5Pset\_fapl\_mpiposix from being built?
> > 
> > Thanks in advance,
> > 
> > Tim.
> > 
> > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_  
> > Hdf-forum is for HDF software users discussion.  
> > Hdf-forum@lists.hdfgroup.org  
> > [http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum\_lists.hdfgroup.org](http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org)

---

<div class="post-metadata">

**Author:** ![Timothy\_Stitt](https://forum.hdfgroup.org/letter_avatar_proxy/v4/letter/t/8e7dd6/32.png) [@Timothy\_Stitt](https://forum.hdfgroup.org/u/Timothy_Stitt)\
**Post date:** [May 19, 2014, 3:42am UTC](https://forum.hdfgroup.org/t/undefined-reference-to-h5pset-fapl-mpiposix/3217/3 "2014-05-19T03:42:59Z")

</div>

Thanks Elena, the git version did the trick. Much appreciated.

> **···**
>
> \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_  
> Tim Stitt PhD  
> User Support Manager (CRC)  
> Research Assistant Professor (Computer Science & Engineering)  
> Room 108, Center for Research Computing, University of Notre Dame, IN 46556  
> Email: tstitt@nd.edu\<[mailto:tstitt@nd.edu](mailto:tstitt@nd.edu)\>
> 
> From: Elena Pourmal \<[epourmal@hdfgroup.org](mailto:epourmal@hdfgroup.org)\<[mailto:epourmal@hdfgroup.org](mailto:epourmal@hdfgroup.org)\>\>  
> Reply-To: HDF Users Discussion List \<[hdf-forum@lists.hdfgroup.org](mailto:hdf-forum@lists.hdfgroup.org)\<[mailto:hdf-forum@lists.hdfgroup.org](mailto:hdf-forum@lists.hdfgroup.org)\>\>  
> Date: Thursday, May 15, 2014 at 3:45 PM  
> To: HDF Users Discussion List \<[hdf-forum@lists.hdfgroup.org](mailto:hdf-forum@lists.hdfgroup.org)\<[mailto:hdf-forum@lists.hdfgroup.org](mailto:hdf-forum@lists.hdfgroup.org)\>\>  
> Subject: Re: [Hdf-forum] undefined reference to `H5Pset\_fapl\_mpiposix'
> 
> MPI POSIX VFD was removed from HDF5 1.8.13. We submitted a patch to netCDF folks.
> 
> See [https://github.com/Unidata/netcdf-c/commit/435d8a03ed28bb5ad63aff12cbc6ab91531b6bc8](https://github.com/Unidata/netcdf-c/commit/435d8a03ed28bb5ad63aff12cbc6ab91531b6bc8)
> 
> Elena  
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  
> Elena Pourmal The HDF Group [http://hdfgroup.org](http://hdfgroup.org)  
> 1800 So. Oak St., Suite 203, Champaign IL 61820  
> 217.531.6112  
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 
> On May 15, 2014, at 2:09 PM, Timothy Stitt \<Timothy.Stitt.9@nd.edu\<[mailto:Timothy.Stitt.9@nd.edu](mailto:Timothy.Stitt.9@nd.edu)\>\> wrote:
> 
> HDF Forum,
> 
> I’m actually trying to build NETCDF-4 (with parallel I/O) but I keep running into the following link error which appears to be related to HDF5 v1.8.13:
> 
> libtool: link: mpicc -g -O2 -o ncgen3 main.o load.o escapes.o getfill.o init.o genlib.o ncgentab.o -L/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/\<[http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/](http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/)\> ../liblib/.libs/libnetcdf.a /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5\_hl.so\<[http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5\_hl.so](http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5_hl.so)\> /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5.so\<[http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5.so](http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5.so)\> -lz -ldl -lm -lcurl -Wl,-rpath -Wl,/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib\<[http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib](http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib)\> -Wl,-rpath -Wl,/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib\<[http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib](http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib)\>  
> ../liblib/.libs/libnetcdf.a(libnetcdf4\_la-nc4file.o): In function `nc4\_open\_file':  
> /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/netcdf-4.3.2/libsrc4/nc4file.c:2174:\<[http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/netcdf-4.3.2/libsrc4/nc4file.c:2174:](http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/netcdf-4.3.2/libsrc4/nc4file.c:2174:)\> undefined reference to `H5Pset\_fapl\_mpiposix’
> 
> I have built HDF5 v1.8.13 using MPICH v3 and GCC v4.4.7 on a RHEL6 Linux system. My HDF5 configure options are as follows:
> 
> ./configure --prefix=/my/install/path CC=mpicc FC=mpif90 CXX=mpicxx --enable-static --enable-shared --enable-parallel
> 
> Is there something I am doing wrong that prevents H5Pset\_fapl\_mpiposix from being built?
> 
> Thanks in advance,
> 
> Tim.
> 
> \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_  
> Hdf-forum is for HDF software users discussion.  
> [Hdf-forum@lists.hdfgroup.org](mailto:Hdf-forum@lists.hdfgroup.org)\<[mailto:Hdf-forum@lists.hdfgroup.org](mailto:Hdf-forum@lists.hdfgroup.org)\>  
> [http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum\_lists.hdfgroup.org](http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org)