error building pnetcdf

[Wei-keng Liao]

You don’t need to set environment variables CC, FC, CXX, CPPFLAGS, or LDFLAGS.
Could you try the following command and let me know?

MPIF77=mpiifort MPIF90=mpiifort MPICC=mpiicc MPICXX=mpiicpc ./configure --prefix=/mnt/nfs/home/b4064989/library/netcdf-parallel/intel/1.9.0 --enable-shared

Wei-keng

> On May 8, 2018, at 2:44 PM, Estanislao Gavilan Pascual-Ahuir (PGR) <E.Gavilan-Pascual-Ahuir1 at newcastle.ac.uk> wrote:
> 
> Hi Robb,
> 
> I think you were right. It seems openmpi is linked with munge. So I decided to use intel compilers intead of GNU. The building works quite smoothly until it reaches the ncmpigen  where it says that :
> 
> ./../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_cpystr'
> ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_allocate'
> ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_dealloc_allocatable'
> ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_cpstr'
> ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_alloc_allocatable'
> ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_len_trim'
> ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_array_copy_in'
> ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_trim'
> ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_contig_array'
> ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_check_mult_overflow64'
> ../../../src/libs/.libs/libpnetcdf.so: undefined reference to `for_array_copy_out'
> 
> I think these function are related to the fortran libraries. However, I am not sure how to add the library path in the ./configuration line. This is the configuration that I am setting
> 
> MPIF77=mpiifort MPIF90=mpiifort MPICC=mpiicc MPICXX=mpiicpc CC=mpiicc FC=mpiifort CXX=mpiicpc CPPFLAGS="-I/mnt/nfs/home/b4064989/library/zlib/intel/1.2.11/include -I/mnt/nfs/home/b4064989/library/hdf5/intel/1.10.2/include" LDFLAGS="-L/mnt/nfs/home/b4064989/library/zlib/intel/1.2.11/lib -L/mnt/nfs/home/b4064989/library/hdf5/intel/1.10.2/lib" ./configure --prefix=/mnt/nfs/home/b4064989/library/netcdf-parallel/intel/1.9.0 --enable-shared
> 
> Am I missing something? Thanks so much for your help. 
> 
> Estanis
> 
> 
> From: Latham, Robert J. <robl at mcs.anl.gov>
> Sent: 07 May 2018 19:53:53
> To: parallel-netcdf at mcs.anl.gov; Estanislao Gavilan Pascual-Ahuir (PGR)
> Subject: Re: error building pnetcdf
>  
> On Mon, 2018-05-07 at 14:13 +0000, Estanislao Gavilan Pascual-Ahuir
> (PGR) wrote:
> > Good afternoon,
> > 
> > I am trying to build the pnetcdf with shared enable. I am having this
> > error (attach picture). Do I need the libmunge for pnetcdf? I have
> > even tried to add the path to libmunge (/lib64) but I
> > cannot solve the problem. Am I missing something? Thanks in advance
> > for your help.
> 
> I don't know where 'libmunge' came from.  That's not part of parallel-
> netcdf.  Can you double-check your environment and figure out what
> wants to use that library?
> 
> ==rob

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