Instructions to build olex2 on linux

[sprock]

Hello,

I have built, at least partially, olex2 from github, specifically 119890c. The two binaries that built are olex2 and olex2_exe. When I look in the linux distribution I see a number of binaries:

hart, hart_mpi, olex2, olex2c and unirun.

I assume the olex2 I built corresponds to the file of the same name in the distribution, but I don't know what correspondence, if any, there is between olex2_exe and olex2c, nor do I know what the hart* are or how to build them. As for unirun, my build directory contains CMakeFiles/olex2.dir/unirun/main.cpp.o, but the binary did not get built.

I have copied olex2 and olex2_exe to the linux distribution. I can start the application using 'start' provided that ASAN_OPTIONS=alloc_dealloc_mismatch=0. However, upon attempting to open a file, the application crashes, so clearly something is missing or mis-compiled.

Are there, somewhere, some more complete build instructions for linux?

If it matters, I am building on gentoo linux.

Thank you for reading this.
sprock

[pcxod]

olex2 is all that you need (unirun does updates that will most probably destroy your build).
Make sure you define PYTHONHOME in the 'start' script. You will also need to build cctbx.

[sprock]

Can I install cctbx using conda (conda install -c conda-forge cctbx-base) or must I build it using the developer instructions?

[pcxod]

it should be built with the same Python as Olex2, Then I guess you can set OLEX2_CCTBX_DIR to point to it or re-bundle in the way Olex2 uses it using:

cd Olex2_dir
libtbx.python modules/cctbx_project/libtbx/bundle/copy_all.py cctbx

this will create cctbx/cctbx_build and cctbx/cctbx_sources directories as Olex2's normal distribution provides.
I have not tried the conda build myself though.

[pcxod]

oh, and in anyway (disregarding if you are using bootstrap or conda, you will need the following configuration:

export CXXFLAGS=-std=c++20
python3 modules/cctbx_project/libtbx/configure.py iotbx smtbx fast_linalg --enable_openmp_if_possible=true --use_environmet_flags

And do use my cctbx fork as sources as there have been a few deviations that are no tin the main branch yet...

[sprock]

Is your fork of cctbx in the directory inside the linux64 download?

[pcxod]

No, that is the bundle created with the commands above. It is on the same account as the Olex2 github.

[sprock]

Do you mean libtbx.python modules/cctbx_project/libtbx/bundle/copy_all.py cctbx

[pcxod]

yes, it leaves out all cpp sources and build intermediate files and makes a 'clean' distribution.

[sprock]

I have a directory called eolex2-sources, in which I compiled olex2. That directory does not contain any cctbx source code. I have another directory olex2-linux64 unpacked from the olex2-linux64 zip file. That directory contains the following:
cctbx_build cctbx_sources. The directory cctbx_build contains bin/libtbx.python. Is that the script I should call?

[pcxod]

You ca try following the cctbx build instructions (https://cctbx.github.io/installation.html)
Or simply, created a directory where you want to build cctbx, let's call it 'cctbx'
then cd cctbx
download this file to it
https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py
The script will collect all necessary dependencies to build cctbx. I am not sure which boost version it will fetch, but to build with Python 313 and later you will need 1.86 (you may need to replace it if build fails for whatever reason).
Then replace the modules cctbx_project with this repository:
https://github.com/pcxod/cctbx_project
create a directory "build" and cd into it (use same python as you used to compile Olex2):

export CXXFLAGS=-std=c++20
python3 ../modules/cctbx_project/libtbx/configure.py iotbx smtbx fast_linalg --enable_openmp_if_possible=true --use_environmet_flags

Once this has been completed successfully,

source setpaths.sh
libtbx.scons -j N

where 'N' is the number of simultaneous jobs... Once this has been done, you can use this:
export OLEX2_CCTBX_DIR=cctbx/build
This will instruct Olex2 to use your build instead of searching for "cctbx" dir next to itself.

[sprock]

I have been trying to install cctbx for several days, using bootstrap.py. My latest attempt, using python3.8 (same version used to build olex2) fails while building python3.7.2. I don't understand why building cctbx builds (yet another) python version. Is it really necessary to build python3.7.2?

[pcxod]

hmm, you can definitely skip that step and use your own Python!

[sprock]

python bootstrap.py --with-python=/home/rmason/miniforge3/envs/python3.8/bin/python

Collecting numpy==1.15.4...

× python setup.py bdist_wheel did not run successfully....

ModuleNotFoundError: No module named 'distutils.msvccompiler'

[pcxod]

Just use bootstrap to download the required dependencies. Then proceed with configure with your Python etc as I listed above. You will need numpy installed indeed in your Python. We use numpy 1.24.4 with Python 3.8.

[sprock]

Had to patch modules/boost/boost/thread/pthread/thread_data.hpp at line 60:

//#if PTHREAD_STACK_MIN > 0 
#ifdef PTHREAD_STACK_MIN

Had to patch modules/ccp4io/libccp4/ccp4/library_utils.c at line 143:

//int putenv ();

I'm stuck on this:

ccp4io_adaptbx/library_f.c:310:6: error: too many arguments to function ‘routne’; expected 0, have 2
  310 |     (* routne) (leng[1], pointer[1]);

That error is repeated several times for different line numbers. It originates from a case statement in modules/ccp4io/libccp4/fortran/library_f.c staring at line 307.

Any ideas?