hpc
Cannot build with backends other than default ones
I'm trying to build IOR with some backends. So far I tried HDF5, Parallel NetCDF, and AIO, and I don't manage to compile IOR with any of them.
HDF5
I have the hdf5 package installed via spack and loaded, with the +mpi variant.
If I do
$ ../configure --with-hdf5`
The configure process runs without any error, however the make command fails with this error:
Making all in .
CC ior-aiori-HDF5.o
../../src/aiori-HDF5.c:25:10: fatal error: hdf5.h: No such file or directory
25 | #include <hdf5.h>
If I do
$ ../configure --with-hdf5=`spack location -i hdf5`
Then IOR simply doesn't compile ior-aiori-HDF5.c and the HDF5 backend isn't available when running IOR.
Note that spack location -i hdf5 correctly gives me the location where HDF5 is installed.
The latter seems normal per the configure.ac file, which has AM_CONDITIONAL([USE_HDF5_AIORI], [test x$with_hdf5 = xyes]), so it doesn't expect a path, only "yes" or "no" (or just --with-hdf5) however I don't know why it doesn't find HDF5 when it's loaded.
With the former (just passing --with-hdf5, I can see this in the log:
checking for H5Pset_all_coll_metadata_ops... no
which corresponds to this in the configure.ac file:
AM_COND_IF([USE_HDF5_AIORI],[
AC_DEFINE([USE_HDF5_AIORI], [], [Build HDF5 backend AIORI])
AC_SEARCH_LIBS([H5Pset_all_coll_metadata_ops], [hdf5])
AC_CHECK_FUNCS([H5Pset_all_coll_metadata_ops])
])
Yes I can confirm with nm that the installed hdf5 library does have this symbol, and it's in the headers as well.
Parallel NetCDF
I have the parallel-netcdf package install via spack and loaded.
If I do
$ ../configure --with-ncmpi
The configure command fails with this error:
configure: error: --with-ncmpi was given but pnetcdf.h not found
If I do
../configure --with-ncmpi=`spack location -i parallel-netcdf`
The configure command runs fine, but aiori-NCMPI.c is not compiled and the NetCDF backend isn't available to IOR.
Once again, it seems that the configure.ac file is not expecting a path, and even though Parallel NetCDF is installed, IOR does not find it when passing just --with-ncmpi.
AIO
I have the libaio package installed via spack, and loaded.
If I do
$ ../configure --with-aio
The configure command runs fine, but the make command fails with this error:
../../src/aiori-aio.c:10:10: fatal error: libaio.h: No such file or directory
10 | #include <libaio.h>
Once again, if I provide the path to libaio as --with-aio=... then configure runs fine but does not compile the AIO backend.
Can you have a look at ./testing/build-pnetcdf.sh file? That shows how pnetcdf can be compiled -> needs to be run in the top-level dir. Arguably, it does set CFLAGS and LDFLAGS. Still I agree, the auto-detection should be fixed.
Indeed, this works:
$ ../configure --with-hdf5 CFLAGS=-I`spack location -i hdf5`/include LDFLAGS="-L`spack location -i hdf5`/lib -lhdf5"
I think it would be a good idea to use pkg-config to locate dependencies when possible, or to have a way of specifying the path if pkg-config is not an option.