On 21 Nov 2018, at 14:45, Miguel Zilhão miguel.zilhao.nogueira@tecnico.ulisboa.pt wrote:

hi all,

i'm compiling ET on a local cluster that uses the module system. on this system, once one does "module load <...>", the respective path is added to an environmental variable. for instance, doing

$ module load HDF5

sets the environmental variable $EBROOTHDF5:

$ echo $EBROOTHDF5 /home/share/easybuild/software/HDF5/1.8.20-GCC-7.3.0-2.30-generic

so i was trying to use these in my configuration file, by adding the lines

HDF5_DIR = $EBROOTHDF5 HDF5_LIB_DIRS = ${EBROOTHDF5}/lib HDF5_INC_DIRS = ${EBROOTHDF5}/include

etc, to it. however, these environmental variables don't seem to be correctly expanded, as i get things like the following:

Running configuration script for thorn HDF5: Additional requested language support: Fortran WARNING in HDF5 configuration: None of H5pubconf.h H5pubconf-64.h H5pubconf-32.h found in ${EBROOTHDF5}/lib ${EBROOTHDF5}/include Automatic detection of szip/zlib compression not possible Finished running configuration script for thorn HDF5.

but if i look into the folder ${EBROOTHDF5}/include, these files are clearly there. the compilation later fails because of this.

when i specify the full path explicitly in the config file:

HDF5_INC_DIRS = /home/share/easybuild/software/HDF5/1.8.20-GCC-7.3.0-2.30-generic/include

i get no such warnings, and the code proceeds to compile just fine. is this the expected behaviour? shouldn't the environmental variables be correctly expanded? if not, what would be the typical procedure to compile the code on systems with such module tools?

Hi Miguel,

No, environment variables are not expanded in that way, because optionlists are not evaluated by a shell. Yes, it would be nice if they were, however :) You can do it in parameter files, but not in optionlists. Usually, in this case, we either set the paths explicitly, resulting in a multitude of almost-identical optionlists, or let the external library automatically detect the location by finding an executable on the path (MPI does this, but I don't know if any others do).

I've never used it, but it looks like simfactory provides a solution. In simsubs.py SubAll, it looks like you can use @ENV(EBROOTHDF5)@. Let us know how you get on with that.