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* rugnux now tells you whether a crystal diffracts anisotropically and how far it reaches in each direction, without a second program: a new `9. DIFFRACTION ANISOTROPY` section in `<prefix>_report.txt` and matching `_reflns.pdbx_aniso_B_tensor_*` / `_reflns.jfjoch_aniso_*` items in the merged mmCIF report the anisotropic deltaB, the diffraction limit along each principal direction, and a `NOT DETECTED` / `DETECTED` / `CANNOT DETERMINE` verdict measured against the data set's own systematic error. It is a description only - no intensity is corrected, no reflection is removed, and the merged data do not depend on direction.
* rugnux can hand its integrated observations to another scaling program: `--export-unmerged` writes `<prefix>_unmerged.mtz`, an unmerged MTZ readable by aimless, pointless, careless and `iotbx.merging_statistics`, in `--mode mx` and `--mode scale` alike. Each rotation reflection's partials are summed into one full; `--export-unmerged-partials` writes one row per image instead. Intensities carry the Lorentz-polarization factor and nothing else, since those programs scale the data themselves. Lattice-centring absences are not written; screw and glide absences are.
* rugnux integrates crystals with broad spots better - where it changes anything, per-shell mean I/sigma improves by up to 31% and R_meas by up to 24% - because on rotation data the integration signal radius is now taken from the crystal's own measured spot width instead of a fixed 4 px. `--adaptive-integration-radius=off` restores the fixed radius and an explicit `--integration-radius` still overrides both. The widened radius applies to the final integration pass only, and a pattern too dense for it is re-integrated at 4 px with a note in the log.
* rugnux discards fewer stills reflections for want of a background ring, improving per-shell R_meas over most of the signal-bearing range: the stills background ring now runs to 14 px instead of 12. The gain reverses in shells below a mean I/sigma of about 4.
* rugnux determines the space group with thresholds that mean the same thing on a weak crystal as on a strong one: symmetry operators are scored on resolution-normalised intensities (E squared) instead of raw merged intensities, and a reflection counts as genuinely present on its counting significance instead of on the merged I/sigma, which saturates at the merge's own ISa. The search resolution cut is no longer able to move the answer, and the twin-law H bound moves from 1.70 to 1.85, which stops one class of correct high-symmetry assignment being refused as twinning.
* rugnux says what the space-group search tested and what it could not: the twin-law disagreement H is printed for every operator together with the adopted point group's H ratio and its bound; alternatives that are not on the reported lattice are named with how their cell differs; and a lattice centring the data could not test - the crystal having been integrated on the primitive sub-cell, so the reflections it extinguishes were never measured - is marked `UNTESTED` and warned about where it is adopted, as coming from the lattice metric rather than from the intensities.
* rugnux `--mode scale` re-merges a `_process.h5` in the right symmetry without being told it: the file now records the space group on every run - a two-pass rotation run wrote none before, so re-merging defaulted to P1 - together with the change of basis under `/entry/MX/reindexMatrix` where the lattice was re-seated, and `--mode scale` also reports the Wilson B-factor estimate instead of `WILSON_B= nan`. A file written before this stops with a message naming the two cells and the override to use, instead of failing inside the merge. A third-party reader of a `_process.h5` must apply `reindexMatrix` where it is present.
* rugnux installs on its own, as a package called `rugnux` - `dnf install rugnux` or `apt install rugnux` - instead of arriving inside `jfjoch-viewer`. It pulls in none of the acquisition stack, so a machine that only processes data no longer has to carry the broker, the detector libraries or Qt to get it. Installing it over a `jfjoch-viewer` from rc.163 or earlier, which still owns `/usr/bin/rugnux`, upgrades cleanly rather than failing on the duplicate file.
* rugnux is also a standalone download, built for arm64 as well as x86_64: `rugnux-<version>-linux-{x86_64|aarch64}-cuda<major>.tgz` and `rugnux-<version>-win64-cuda<major>.zip` on the release page, for machines that are not managed by a package manager. The aarch64 build targets GH200 and DGX Spark, and is untested on hardware.
* Every portable Linux binary is now a single self-contained file: cuFFT is linked statically instead of being shipped beside the executable and found through an rpath, so `rugnux` and `jfjoch_viewer` need nothing but an NVIDIA driver, and only to use the GPU. The `.rpm`/`.deb` continue to take cuFFT from the distribution. The developer utilities `jfjoch_extract_hkl` and `jfjoch_recompress` are no longer packaged anywhere.
* Jungfraujoch needs six fewer shared libraries on the machine - libopenblas and libmetis, and libgfortran, libquadmath, libgomp and libz behind them - because the Ceres LAPACK, METIS and SuiteSparse back-ends are no longer built. Nothing in the code ever selected them, and results are unchanged.
* The PCIe driver DKMS package builds for the kernel it is being installed for instead of the running one, so a module built while a kernel update is being applied loads after the reboot.
* The PCIe driver builds on RHEL 9.5 and later, and on their CentOS Stream, Rocky and AlmaLinux equivalents, where the `vm_flags` kernel interface was backported into the 5.14 kernel.
* A data collection started with `async_start` that fails to start - a writer refusing to overwrite an existing file, for instance - is reported as an error by `/wait_until_running` and `/wait_till_done` instead of as a timeout and a successful collection respectively. The error message is the one the writer gave.
* A calibration that is cancelled or that fails to collect its pedestals is no longer reported as a successful one. The broker goes to `Inactive` with an error message and has to be initialized again, instead of sitting in `Idle` looking ready to measure while holding partial pedestals - data collected in that state was silently mis-converted.
* A failed `/initialize` is reported to `/wait_until_running` and `/wait_till_done` as soon as it happens, instead of when their timeout expires.
* `space_group_number` accepts space groups up to 230 in the API schema, so cubic space groups can be recorded. The broker always accepted them; the generated clients rejected them before the request was sent.
* The results report's `REPORT_VERSION` is 3, two sections having been added. Existing key names and table columns are unchanged.
* The merged statistics table has **9** resolution shells instead of 10, which is what XDS reports. The bins were already XDS's - equal steps in 1/d^2 between the lowest- and the highest-resolution reflection the merge kept - so at the same resolution limits the two tables now have the same shell boundaries and can be read row for row. `--resolution-shells` sets a different count.
* `rugnux --model` now settles the frame the merged reflections are written in, not only the frame the R-factors and the maps are computed in: the `.mtz`/`.cif`/`.hkl` come out in the model's indexing, and where the data were merged in the model's enantiomorph they take the model's hand and space group - which on anomalous data puts I(+) and I(-) the right way round. The indexing choice is logged with the winning R-free and the runner-up, so a decision made within noise is visible.
* `rugnux --model` can resolve the indexing ambiguity of a **serial stills** run, which a model could not do before: structure factors computed from the model become the per-image reference, the same role a reference MTZ plays. It needs the cell and space group up front (`-C` / `-S`). Without one or the other, a merohedral serial run still merges both hands together and says so.
* The rugnux documentation opens with a quick start - the default run, and runs with a reference MTZ, with a model, or with the space group and cell pinned - and explains the indexing ambiguity: what it costs on rotation and on serial data, and which of `-z` / `--model` resolves it in each case. The long reference pages now carry a table of contents.
Reviewed-on: #74
Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
104 lines
5.4 KiB
Markdown
104 lines
5.4 KiB
Markdown
# FPGA PCIe driver
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## Compilation
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To compile kernel module type:
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```
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make
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```
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## Installation
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To install kernel module, you need to have root permissions and run:
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```
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sudo make install
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```
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## Loading driver into kernel
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After installing the kernel driver, it should be possible to insert it into the kernel via:
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```
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modprobe jfjoch
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```
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## Ownership of the character devices
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By default, character devices `/dev/jfjoch<device number>` are owned by root (user/group) and are not accessible by others.
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This means that `jfjoch_broker` must be running as superuser, which might not be optimal for security reasons in most cases.
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The behavior can be changed by creating `udev` rules. Create a file called `/etc/udev/rules.d/99-jfjoch.rules`
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with the following content:
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```
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KERNEL=="jfjoch*" OWNER="<UNIX username>" GROUP="<UNIX group>"
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```
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It is OK to provide only group, for example to make the devices accessible by group `jungfrau`:
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```
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KERNEL=="jfjoch*" GROUP="jungfrau"
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```
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## DKMS
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To avoid problems with updating the kernel, it is possible to use DKMS to autobuild Jungfraujoch kernel
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module, when new kernel is installed. For RHEL 8 it is well tested to use the RPM module built automatically from Jungfraujoch source.
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For other systems, it is necessary to follow the procedure below, though it is not well tested.
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This first requires to install DKMS - for RHEL it is available via EPEL repository:
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```
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sudo dnf install dkms
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```
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Then use script provided in the driver directory to copy driver code to DKMS directory:
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```
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./install_dkms.sh
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```
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If upgrading the driver, please first remove current driver from DKMS system:
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```
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dkms remove jfjoch -v <version> --all
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```
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## Driver parameters
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Currently, there is one driver parameter `nbuffers`, that defines count of exchange buffers (see below).
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This can be adjusted in the modprobe operation, for example:
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```
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modprobe jfjoch nbuffers=1024
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```
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## Exchange buffers
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The parameter defines number of buffers used to exchange data between card and host application.
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Each buffer can hold one detector module (1024x512) in 16-bit or 32-bit mode + associated processing results and metadata.
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These buffers are used by both card-to-host and host-to-card operations.
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Buffers use special allocation, as they are continuous in physical address space, which helps the FPGA card to transfer all
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data associated with detector module in two DMA transfers (one data, one metadata).
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Useful buffer size is a bit more than 2 MiB, but given that kernel allocates physical memory in power of two, **4 MiB** is safe number for one buffer size.
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Buffer can be mapped into user space, but performing `mmap` system call on the `/dev/jfjoch<number of device>` character device.
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Buffer count can be adjusted by setting `nbuffers` parameter. There are two considerations for setting optimal value:
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1. For card-to-host transfers, minimal value is roughly
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`<number of threads in receiver> * <number of modules processed by thread; usually equal to number of modules per card>`,
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this way each thread can have enough data for operation. Default thread count for Jungfraujoch receiver is 64.
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2. For host-to-card transfers, full detector calibration has to fit into memory and one buffer accommodates one calibration set for one module.
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So minimal count is `<number of modules> * (3 + 3 * <number of storage cells>)`.
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Based on both rules, optimal number is 512 buffers (2 GiB), though this can be adjusted for particular system and configuration.
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## Known problems
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To avoid inconsistent behavior, this driver won't load if release number differs between the kernel driver and FPGA card.
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## CMake file
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While CMake file is present in the driver directory, it is only for the purpose of proper detection of the files in CLion IDE.
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It is not made for actual compilation of the kernel driver and should not be used for that purpose.
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## Character device access
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For each FPGA device a character device is created called `/dev/jfjoch<number of device>`.
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When device is opened two operations are possible:
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mmap() to map exchange buffers
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ioctl() to communicate with the cards
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Interfacing should be done through the JungfraujochDevice class in `fpga/host_library` directory.
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## Sysfs access
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Certain performance counters can be read through sysfs mechanism in the kernel.
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One needs to `cat` files in `/sys/class/misc/jfjoch<number of device>/` directory.
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## RHEL 9.5+ virtual memory flags
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RedHat Enterprise Linux 9.5 backported the `vm_flags_set` interface from Linux kernel 6.3 while still reporting kernel version 5.14, so a plain kernel-version test picks the wrong branch and the build fails.
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This is now detected automatically from `RHEL_RELEASE_CODE`, so the module builds unaided on RHEL 9.5 and later and on the CentOS Stream, Rocky and AlmaLinux equivalents, as well as on distributions that have not backported it.
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**No user action is needed.** The `HAVE_VM_FLAGS_SET` environment variable that earlier releases required is obsolete; it is still honoured if set, but setting it is no longer necessary and the DKMS packaging never passed it anyway.
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## Which kernel DKMS builds for
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The DKMS package builds the module for the kernel it is being **installed for**, not the one currently running, so a module built while a kernel update is being applied loads correctly after the reboot.
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Building by hand in `fpga/pcie_driver/` still defaults to the running kernel; pass `KDIR=/lib/modules/<version>/build` (or `KVER=<version>`) to target another one.
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