Hello. I'm having trouble compiling Rosetta on an AWS Ubuntu 22.04 instance, using scons with the extras=hdf5 flag. The problem seems to be with finding the HDF5 libraries.
My question - how can I successfully compile Rosetta with the extras=hdf5 flag?
Below, I show how I set up the AWS instance, the compilation errors, and some checks I did on my HDF5 installation (including successful compilation of simple test code with h5c++).
AWS Instance General Software Install Commands
I performed the following install commands prior to attempting my Rosetta compile
sudo apt-get update
sudo apt-get update
sudo apt-get install zlib1g-dev
sudo apt-get install -y libhdf5-serial-dev
sudo apt-get install build-essential
sudo apt-get install python-is-python3
Rosetta Compilation Commands
I'm trying to compile Rosetta with the following command:
~/rosetta_src_2021.16.61629_bundle/main/source$ ./scons.py -j7 mode=release bin extras=hdf5
I first had to fix ~/rosetta*/main/source/src/protocols/features/ReaturesReporter.fwd.hh by adding an #include <cstdint>
After this fix, I still get the typical stream of g++: warning: switch '-ffor-scope' is no longer supported warnings.
More importantly, I have troubles with hdf5:
src/protocols/indexed_structure_store/H5FragmentStoreBackend.cc:22:10: fatal error: H5Cpp.h: No such file or directory
22 | #include "H5Cpp.h"
src/protocols/indexed_structure_store/H5StructureStoreBackend.hh:32:10: fatal error: H5Cpp.h: No such file or directory
32 | #include "H5Cpp.h"
Checking HDF5 installation
I checked for HDF5 library installation:
~/rosetta_src_2021.16.61629_bundle/main/source$ find / -iname "*hdf5.h*"
~/rosetta_src_2021.16.61629_bundle/main/source$ find / -iname "*H5Cpp.h*"
(ignoring a bunch of "Permission denied" outputs)
I also successfully compiled and ran a simple tutorial HDF5 C++ tutorial code (https://gist.github.com/YukiSakamoto/6319458 - after adding using namespace H5;) using h5c++.
Question - How can I successfully compile Rosetta with the "extras=hdf5" option, which seems required for my work? Do I need to modify SCons configuration set up to find my HDF5 installation?