Hello Jared,
new clusters are always tricky. We have a bit of a guide on our wiki: https://docs.einsteintoolkit.org/et-docs/Configuring_a_new_machine though your best start is usually to pick an option list from a cluster similar to yours and modify it.
In your case, as you say the numa library is not properly linked in, which can happen if hwloc is statically linked (hwloc.a) but numa is dynamic linked (since it is a system library). It could (doing my own google search) be an ordering issues in the libraries.
In both cases, you may likely (I cannot test this) be able to fix this by adding the following line to your option list file:
HWLOC_EXTRA_LIBS = numa
then recompile (from scratch).
The best way to be sure that there are no leftover parts is to completely wipe the current configuration:
rm -rf configs/sim
and then start over with "simfactory/bin/sim build --optionlist youroptionlist.cfg --thornlist manifest/einsteintoolkit.th"
Yours, Roland
Hello! I've just started using the Einstein toolkit and I'm new to the whole cactus and thorn way of compiling code, so forgive me if these questions seem stupid.
I downloaded the code onto my laptop and followed the new users Jupyter notebook instructions to compile it, and it worked like a charm. I then downloaded the code to my University's compute cluster to try and run some of the test problems.
When compiling, at the very end, I get an error about DSO not being found. As far as I can tell from Google, this is a linker error where the proper library (libnuma, it appears) has not been correctly linked. I was just wondering if this is the case and, if so, where I tell the code which libraries to link? I'm used to more traditional makefiles, so I was unsure where this sort of thing should go.
The relevant part of the error message is as follows:
1 /usr/bin/ld: /path/to/einsteintoolkit/Cactus/con figs/sim/scratch/external/hwloc/lib/libhwloc.a(topology-linux.o): undefined refe rence to symbol 'mbind@@libnuma_1.1' 2 //usr/lib64/libnuma.so.1: error adding symbols: DSO missing from command line 3 collect2: error: ld returned 1 exit status
I just went with the default ./simfactory/bin/sim setup-silent
So I'm not sure if that needs to change (since I saw there are versions for other clusters).
Thank you!
Sincerely, -Jared