Unable to compile PnetCDF: 'tst_rec_vars' test fails - c

Question

I am trying to install PnetCDF from source. I used the 1.12.2 version for installation. MPICH, Zlib, Szip, HDF5 and NetCDF-4 have been installed from source successfully (HDF5 and NetCDF-4 have been built with parallel I/O support).
MPICH is installed as follows (v3.4.2):
./configure --prefix=${DIR}/mpich --with-device=ch4:ofi CFLAGS="-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64" --enable-fortran
make
make check
make install
export PATH=${DIR}/mpich/bin:${PATH}
Where DIR is the root directory all the libraries are installed to (with their own directory).
Zlib (v1.2.11):
./configure --prefix=${DIR}/grib2
make
make check
make install
export CPPFLAGS="-I${DIR}/grib2/include"
export LDFLAGS="-L${DIR}/grib2/lib"
export LD_LIBRARY_PATH="${DIR}/grib2/lib:$LD_LIBRARY_PATH"
Szip (v2.1.1):
./configure --prefix=${DIR}/szip
CC=mpicc
make
make check
make install
export LD_LIBRARY_PATH="${DIR}/szip/lib:$LD_LIBRARY_PATH"
export CPPFLAGS="-I${DIR}/szip/include ${CPPFLAGS}"
export LDFLAGS="-L${DIR}/szip/lib ${LDFLAGS}"
HDF5 (v1.8.22):
export HDF5=${DIR}/hdf5
./configure --prefix=${HDF5} --with-szlib=${DIR}/szip --with-zlib=${DIR}/grib2 --enable-parallel CC=mpicc --enable-fortran FC=mpifort
make
make check
make install
export LD_LIBRARY_PATH="${HDF5}/lib:$LD_LIBRARY_PATH"
export CPPFLAGS="-I${HDF5}/include ${CPPFLAGS}"
export LDFLAGS="-L${HDF5}/lib ${LDFLAGS}"
export PATH="${HDF5}/bin:${PATH}"
NetCDF4-C (v4.8.0):
./configure --prefix=${DIR}/netcdf --disable-dap --enable-parallel-tests --enable-large-file-tests --disable-extreme-numbers CC=mpicc
make
make check
make install
export PATH="${NETCDF}/bin:${PATH}"
export LD_LIBRARY_PATH="${NETCDF}/lib:${LD_LIBRARY_PATH}"
export CPPFLAGS="-I${NETCDF}/include ${CPPFLAGS}"
export LDFLAGS="-L${NETCDF}/lib ${LDFLAGS}"
export LIBS="$(nc-config --libs) ${LIBS}"
NetCDF4-Fortran (v4.5.3):
./configure --prefix=${NETCDF} --enable-large-file-tests --enable-parallel-tests CC=${DIR}/mpich/bin/mpicc FC=mpifort F77=mpif77
make
make check
make install
The HDF5 configuration shown by h5pcc -showconfig is given below (only the part I think relevant is included):
Features:
---------
Parallel HDF5: yes
High-level library: yes
Build HDF5 Tests: yes
Build HDF5 Tools: yes
Threadsafety: no
Default API mapping: v18
With deprecated public symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
MPE:
Direct VFD: no
(Read-Only) S3 VFD: no
(Read-Only) HDFS VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function stack tracing: no
Strict file format checks: no
Optimization instrumentation: no
And the output of nc-config --all:
--cc -> /media/case/work/hwrf/libraries/mpich/bin/mpicc
--cflags -> -I/media/case/work/hwrf/libraries/netcdf/include -I/media/case/work/hwrf/libraries/hdf5/include -I/media/case/work/hwrf/libraries/szip/include -I/media/case/work/hwrf/libraries/grib2/include
--libs -> -L/media/case/work/hwrf/libraries/netcdf/lib -lnetcdf
--static -> -lhdf5_hl -lhdf5 -lm -ldl -lz -lcurl
--has-c++ -> no
--cxx ->
--has-c++4 -> no
--cxx4 ->
--has-fortran -> yes
--fc -> mpifort
--fflags -> -I/media/case/work/hwrf/libraries/netcdf/include -I/media/case/work/hwrf/libraries/netcdf/include
--flibs -> -L/media/case/work/hwrf/libraries/netcdf/lib -lnetcdff
--has-f90 ->
--has-f03 -> yes
--has-dap -> no
--has-dap2 -> no
--has-dap4 -> no
--has-nc2 -> yes
--has-nc4 -> yes
--has-hdf5 -> yes
--has-hdf4 -> no
--has-logging -> no
--has-pnetcdf -> no
--has-szlib -> yes
--has-cdf5 -> yes
--has-parallel4 -> yes
--has-parallel -> yes
--has-nczarr -> no
--prefix -> /media/case/work/hwrf/libraries/netcdf
--includedir -> /media/case/work/hwrf/libraries/netcdf/include
--libdir -> /media/case/work/hwrf/libraries/netcdf/lib
--version -> netCDF 4.8.0
So far, so good. Everything was installed without any failure. All make checks have been passed.
The trouble arises when I try to compile PnetCDF from source. I tried PnetCDF version 1.11.2 for installation (in fact, I triedd several older versions as well, more on that later). The installation is attempted as following:
./configure --prefix=${DIR}/pnetcdf --enable-large-single-req --enable-netcdf4 --enable-shared=yes --with-netcdf4="${DIR}/netcdf" MPICC=mpicc MPIF77=mpif77 MPIF90=mpif90 MPICC=mpicc MPIF77=mpif77 MPIF90=mpif90
make
make tests
make check
make ptest
make ptests
But, it fails at make ptest. The failed test is tst_rec_vars.c and the error message is:
Error at line 78 of tst_rec_vars.c: expect dim X len 4 but got 3
Error at line 78 of tst_rec_vars.c: expect dim X len 4 but got 3 fail with 2 mismatches
make[2]: *** [Makefile:1354: ptest4] Error 1
make[2]: Leaving directory '/media/case/work/hwrf/libraries/source/pnetcdf-1.12.2/test/nc4'
make[1]: *** [Makefile:780: ptests] Error 1
make[1]: Leaving directory '/media/case/work/hwrf/libraries/source/pnetcdf-1.12.2/test'
make: *** [Makefile:965: ptests] Error 1
Heres the test that is failing (GitHub link): tst_rec_vars.c
It seems that the test is checking a NetCDF file for the lenth of dimension in it. I assume the NetCDF file it is checking is tst_rec_vars.nc. The output of ncdump -h on this file is given below:
netcdf tst_rec_vars {
dimensions:
X = UNLIMITED ; // (4 currently)
variables:
int U(X) ;
int V(X) ;
}
That is, the NetCDF file's X dimension indeed has a length 4, although the test program beleives it is only 3. But, if I were to run the test manually as ./tst_rec_vars, it runs correctly.
*** TESTING C tst_rec_vars for record variables to NetCDF4 file ------ pass
Could it be due to parallel processing/threading? The test in question is run under a section titled test/nc4: Parallel testing on 4 MPI processes. I assume the NetCDF file was tested before it was formed completely, which could explain why I got a length 1 X dimension in the NetCDF file from ncdump at one point.
>>>ncdump -h tst_rec_vars.nc
netcdf tst_rec_vars {
dimensions:
X = UNLIMITED ; // (1 currently)
variables:
int U(X) ;
int V(X) ;
}
What exactly is going on here? How do I fix it?
Edit:
I'm trying to install it on CentOS 7, since I was encountering the above mentioned issue, I tried to install it on a Debian 11 system. But I am getting the very exact error in both systems.