Basic troubleshooting and common errors.

A small collection of common errors users have seen, and how to beat them. If you run into more exotic errors, let me know and I'll add them here.

Makefile errors

If running 'make' doesn't compile the code, or you get a "nothing to be done" or an error like:

make: *** No rule to make target '/main.o', needed by 'ampsci'. Stop.

you might be using an out-of-date Makefile. Either re-run configure.sh or manually re-copy the updated makefile:

./configure.sh

or

cp ./doc/Makefile .

make

and try again.

libgfortran error

Error linking to gfortran/lapack, may be something like this:

ld: .../liblapack.a(xerbla.o): undefined reference to symbol '_gfortran_string_len_trim@@GFORTRAN_8'
ld: .../libgfortran.so.5: error adding symbols: DSO missing from command line
make: *** [build/buildTargets.mk:66: ampsci] Error 1

Sometimes occurs on certain systems (e.g., bunya). In these cases, the fortran libraries need to be linked to explicitely. This can be done by adding -lgfortran to the LDLIBS option in the Makefile

LDLIBS += -lgfortran

OpenMP errors

error: unsupported option -fopenmp
error: could not find <omp.h>
openmp (used for parallelisation) is not working. See Compilation Details for some possible solutions.
Quick fix: change 'OMPLIB=-fopenmp' to 'OMPLIB=' in Makefile, which turns off OpenMP

GSL Errors

fatal error: gsl/<...>.h: No such file or directory (or similar)
gsl related linking/compilation error:
Could not find required GSL libraries. Either they are not installed, or you need to link to them
1) Ensure GSL is installed (see above for instructions)
1) If GSL library is not installed in _/usr/local/_, you have to tell the compiler where to find the GSL files. Do this by setting the GSL_PATH option in Makefile. Common examples:
- GSL_PATH=/opt/gsl/2.1/gnu # For UQ's getafix cluster
- GSL_PATH=/usr/local/opt/gnu-scientific-library # For my macbook
- Note: the exact path may differ for you, depending on where GSL was installed
error: too few arguments to function ‘int gsl_bspline_deriv_eval
This is because the code is linking to a very old version of GSL. You might need to update GSL. If you have updated GSL (to at least version 2.0) and still get the message, the code is probably linking against the wrong version of GSL; see above to point the compiler to the correct version
On HPC cluster, this might be because you haven't loaded the gsl module module load gsl (after loading the gcc compiler)

ld: Assertion failed: (resultIndex < sectData.atoms.size())

Full error message may look something like:

0x102497648  __assert_rtn + 72
0x1023cbfac  ld::AtomPlacement::findAtom(unsigned char, unsigned long long, ld::AtomPlacement::AtomLoc const*&, long long&) const + 1204
0x1023e1924  ld::InputFiles::SliceParser::parseObjectFile(mach_o::Header const*) const + 15164
0x1023eee30  ld::InputFiles::parseAllFiles(void (ld::AtomFile const*) block_pointer)::$_7::operator()(unsigned long, ld::FileInfo const&) const + 420
0x185a37950  _dispatch_client_callout2 + 20
0x185a4aba0  _dispatch_apply_invoke + 176
0x185a37910  _dispatch_client_callout + 20
0x185a493cc  _dispatch_root_queue_drain + 864
0x185a49a04  _dispatch_worker_thread2 + 156
0x185be10d8  _pthread_wqthread + 228
ld: Assertion failed: (resultIndex < sectData.atoms.size()), function findAtom, file Relocations.cpp, line 1336.
collect2: error: ld returned 1 exit status

This seems to be a bug with M1/M2 mac linker implementation with CommandLineTools version 15.0 (see developer.apple.com/forums/thread/737707)
See also: github.com/Homebrew/homebrew-core/issues/145991
This issue seems to have been resolved in version 15.1 - so run an update if you can.
If you can't update, it seems this can be fixed by adding the following to the Makefile:

LARGS=-Wl,-ld_classic

You shouldn't need to make clean first, but if it doesn't work, try that too.

Others

Sometimes, the compiler will not be able to find the correct libraries (particular, e.g., on clusters). In this case, there are two options in the Makfefile: CARGS ?= and LARGS ?=