README: drop a run disturbed by another process on the GPU; capsid device memory about 12 GB

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HVeDQsU5a8AJUdJPgWevAK
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leonarski_fandClaude Opus 5.5 committed 2026-11-10 17:07:10 +01:00
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@@ -59,7 +59,7 @@ stage has a CPU implementation and a CUDA build on a machine without a GPU or dr
CPU, about 20 times slower on the demo below. Device memory, measured on the demo at the default
worker count (32 threads on the test machine; the per-image loop's device memory scales with
`-N`, so `-N 8` lowers it on a smaller card): 6-9 GB for an ordinary 16M-pixel EIGER sweep with
a model, 12-15 GB for the 400 A virus capsid, 2-3 GB for the serial example. Host memory: 6-10 GB
a model, about 12 GB for the 400 A virus capsid, 2-3 GB for the serial example. Host memory: 6-10 GB
for the ordinary sweeps, 19-23 GB for the capsid, 12-15 GB for the walk-through on the CPU alone;
in general 0.6 GB + 0.3 GB per million reflection observations ([Installing Rugnux](docs/RUGNUX_INSTALL.md#memory)).
Disk: 0.1-1 GB of output per run (`<prefix>_unmerged.mtz` is the largest file; the optional
@@ -283,10 +283,8 @@ set was drawn by the run while the deposited model had been refined against thes
deposited model is placed by the rigid body; the benchmark in the paper starts it displaced so that
molecular replacement has to find all 45 chains ([Measuring Rugnux](docs/RUGNUX_BENCHMARKING.md#the-timing-benchmark)).
The capsid has the largest memory footprint and is dominated by the refinement, about 270 of its
390 s. On the 16 GB card of the test machine its device memory reached 12-15 GB over our runs, and
once the refinement ran out of device memory (`Refinement did not run: ... out of memory` in the
log; the run still finished with the merged data and the placed model). A laptop GPU or a CPU-only
machine takes several times longer.
390 s. On the 16 GB card of the test machine its device memory peaked at about 12 GB. A laptop
GPU or a CPU-only machine takes several times longer.
### Serial stills: lysozyme at SACLA
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@@ -292,7 +292,7 @@ Notes on the defaults:
nothing most often has a wrong header: the beam centre is measured on every run, but the distance
and the wavelength are indexed at the values stated — `--detector-distance` and `--wavelength` override them
(`--beam-x`/`--beam-y` the centre); serial stills that index poorly want the cell (`-C`). A run that ends
with `Killed` ran out of memory ([When host memory runs out](RUGNUX_INSTALL.md#out-of-host-memory)).
with `Killed` ran out of memory ([Out of host memory](RUGNUX_INSTALL.md#out-of-host-memory)).
With any question about a run, send `myrun_report.txt` and `myrun_log.txt`.
- Everything else is in [Running Rugnux](RUGNUX_TUTORIAL.md#running-rugnux) and the full
[Command-line options](RUGNUX_CLI.md).