error building pnetcdf

[Estanislao Gavilan Pascual-Ahuir (PGR)]

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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