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CrystFEL 0.11
This is not part of the tutorial; this is my notes on installation and results of initial evaluation.
SACLA HPC does not have direct internet access. Thus, compilation with Meson is tricky.
wget https://github.com/mesonbuild/meson/releases/download/1.4.0/meson-1.4.0.tar.gz
wget https://www.desy.de/~twhite/crystfel/crystfel-0.11.0.tar.gz
# then rsync to the HPC
tar xzvf meson-1.4.0.tar.gz
ninja-linux.zip
mv ninja ~/local/bin/With CMake, specifying which HDF5 libraries to use is easy; just set the HDF5_ROOT variable.
It is harder with Meson.
Older Meson could find HDF5 by h5cc but this feature was
deleted in 2020 (why?).
Meson needs pkg-config's *.pc files.
These are created only when the HDF5 library is built with CMake, but not with Autotools.
This missing feature is one of the earliest issues (#8 out of > 4400) in their GitHub, but has not been addressed. In summary, we have to build HDF5lib with CMake.
Building HDF5 with CMake is very tricky! Carefully follow guidances in release_docs/INSTALL_CMake.txt.
It is essential that all files and directories have the exact name.
For example, zlib-1.3.1.tar.gz is not picked up by the build script and the resulting library lacks deflate filter support.
wget https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_1.14.4.2.tar.gz
# rsync to the HPC
wget https://github.com/HDFGroup/hdf5_plugins/archive/refs/tags/hdf5-1.14.4.tar.gz
# rsync to the HPC and RENAME this to hdf5_plugins.tar.gz
# Why do they name this as "hdf5" not "hdf5_plugins"? Very confusing.
wget https://github.com/madler/zlib/releases/download/v1.3.1/zlib-1.3.1.tar.gz
# rsync to the HPC and RENAME this to zlib-1.3.tar.gz
mkdir hdf5-1.14.4.2-build
cd hdf5-1.14.4.2-build
# put hdf5_plugins.tar.gz and zlib-1.3.tar.gz here
tar xzvf hdf5_1.14.4.2.tar.gz
# The directory name must be EXACTLY like this!
# I would say this is a packaging error.
mv hdf5-hdf5_1.14.4.2 hdf5-1.14.4-2
cp hdf5-1.14.4-2/config/cmake/scripts/CTestScript.cmake .
cp hdf5-1.14.4-2/config/cmake/scripts/HDF5config.cmake .
cp hdf5-1.14.4-2/config/cmake/scripts/HDF5options.cmake .
module load cmake/3.20.3_gcc-4.8.5
INSTALLDIR=/home/sacla_sfx_app/local ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix -C Release -VV -O hdf5.log
cd ~/local
bash ../packages/hdf5-1.14.4.2-build/build/HDF5-1.14.4.2-Linux.sh
# say No to "Do you want to include the subdirectory HDF5-1.14.4.2-Linux?"After all this hussle, the pkg-config files are broken!
We have to fix the path.
cd /home/sacla_sfx_app/local/HDF_Group/HDF5/1.14.4.2/lib/pkgconfig
sed -i.bak -e s,packages/hdf5-1.14.4.2-build/HDF_Group/HDF5/1.14.4,local/HDF_Group/HDF5/1.14.4.2,g *.pc
# This replaces the wrong prefix
# prefix=/home/sacla_sfx_app/packages/hdf5-1.14.4.2-build/HDF_Group/HDF5/1.14.4
# into
# prefix=/home/sacla_sfx_app/local/HDF_Group/HDF5/1.14.4.2
A good new is that HDF5 libraries built in this way can read EIGER HDF5 files without setting HDF5_PLUGIN_PATH.
This can be confirmed by:
h5dump -d /entry/data/data -s 0 -S 1 -c 1 -k 1 some_EIGER_dataset_data_000001.h5
Because we do not have internet access, we have to disable automatic downloading of dependencies.
wget https://www.desy.de/~twhite/crystfel/crystfel-0.11.0.tar.gz
# rsync to the HPC
tar xzvf crystfel-0.11.0.tar.gz
cd crystfel-0.11.0
# module load gsl/2.7_gcc-4.8.5
# Meson uses pkg-config. The SALCA-provided module sets
# CPATH, LD_LIBRARY_PATH, LIBRARY_PATH but not PKG_CONFIG_PATH.
# Thus one ends up using GSL 2.7's header but linking to the system provided GSL 1.15!
module load python/3.8.10_gcc-4.8.5
export PKG_CONFIG_PATH=/home/sacla_sfx_app/local/HDF_Group/HDF5/1.14.4.2/lib/pkgconfig:/home/sacla_sfx_app/local/lib64/pkgconfig:/home/software/local/gsl-2.7_gcc-4.8.5/lib/pkgconfig:/usr/share/pkgconfig
~/packages/meson-1.4.0/meson.py setup build --wrap-mode=nodownload
ninja -C buildWe do not "install" this, because Ninja install strips rpath and causes various problems.
This shows following missing libraries but they are inconsequential:
- We do not use on-the-fly related features.
- We can export MTZ files via
create-mtz. - Millepede can be built separately (see below).
Found CMake: NO
Run-time dependency libzmq found: NO (tried pkgconfig and cmake)
Run-time dependency libasapo-producer found: NO (tried pkgconfig and cmake)
Run-time dependency seedee found: NO (tried pkgconfig and cmake)
Run-time dependency libccp4c found: NO (tried pkgconfig and cmake)
Run-time dependency msgpack-c found: NO (tried pkgconfig and cmake)
Run-time dependency msgpack found: NO (tried pkgconfig and cmake)
Subproject millepede is buildable: NO (disabling)
Program pandoc found: NO
Program pandoc found: NO
wget https://gitlab.desy.de/claus.kleinwort/millepede-ii/-/archive/V04-16-01/millepede-ii-V04-16-01.tar.gz
# rsync to the HPC
tar xzvf millepede-ii-V04-16-01.tar.gz
cd millepede-ii-V04-16-01/
make # do not use -jX!
cp pede ~/local/binFor unknown reasons, compilation was unsuccessful with newer GCCs, saying "undefined reference to `_gfortran_os_error_at'".
We have to comment out these lines:
;mask_good = 0x00 ; instead, we can specify bad regions below if necessary
;mask_bad = 0xFF
Otherwise CrystFEL 0.11.0 complains: "You have specified good/bad bits for mask 0 of panel q1, but not the mask location."
Add this after panels are defined to enable geometry refinement by Millipede:
group_all = q1,q2,q3,q4,q5,q6,q7,q8
Unlike rigid groups, groups cannot be defined before its panels are defined.