Merge branch 'mpi_errors' into 'preview'

Mpi errors

Closes #163, #291, and #270

See merge request zih/hpcsupport/hpc-compendium!630

doc.zih.tu-dresden.de/docs/jobs_and_resources/mpi_issues.md

+# Known MPI-Usage Issues
+
+This pages holds known issues observed with MPI and concrete MPI implementations.
+
+## Mpirun on partition `alpha`and `ml`
+
+Using `mpirun` on partitions `alpha` and `ml` leads to wrong resource distribution when more than
+one node is involved. This yields a strange distribution like e.g. `SLURM_NTASKS_PER_NODE=15,1`
+even though `--tasks-per-node=8` was specified. Unless you really know what you're doing (e.g.
+use rank pinning via perl script), avoid using mpirun.
+
+Another issue arises when using the Intel toolchain: mpirun calls a different MPI and caused a
+8-9x slowdown in the PALM app in comparison to using srun or the GCC-compiled version of the app
+(which uses the correct MPI).
+
+## R Parallel Library on Multiple Nodes
+
+Using the R parallel library on MPI clusters has shown problems when using more than a few compute
+nodes. The error messages indicate that there are buggy interactions of R/Rmpi/OpenMPI and UCX.
+Disabling UCX has solved these problems in our experiments.
+
+We invoked the R script successfully with the following command:
+
+```console
+mpirun -mca btl_openib_allow_ib true --mca pml ^ucx --mca osc ^ucx -np 1 Rscript
+--vanilla the-script.R
+```
+
+where the arguments `-mca btl_openib_allow_ib true --mca pml ^ucx --mca osc ^ucx` disable usage of
+UCX.
+
+## MPI Function `MPI_Win_allocate`
+
+The function `MPI_Win_allocate` is a one-sided MPI call that allocates memory and returns a window
+object for RDMA operations (ref. [man page](https://www.open-mpi.org/doc/v3.0/man3/MPI_Win_allocate.3.php)).
+
+> Using MPI_Win_allocate rather than separate MPI_Alloc_mem + MPI_Win_create may allow the MPI
+> implementation to optimize the memory allocation. (Using advanced MPI)
+
+It was observed for at least for the `OpenMPI/4.0.5` module that using `MPI_Win_Allocate` instead of
+`MPI_Alloc_mem` in conjunction with `MPI_Win_create` leads to segmentation faults in the calling
+application . To be precise, the segfaults occurred at partition `romeo` when about 200 GB per node
+where allocated. In contrast, the segmentation faults vanished when the implementation was
+refactored to call the `MPI_Alloc_mem + MPI_Win_create` functions.

doc.zih.tu-dresden.de/mkdocs.yml

@@ -81,6 +81,7 @@ nav:
       - Compilers and Flags: software/compilers.md
       - GPU Programming: software/gpu_programming.md
       - Mathematics Libraries: software/math_libraries.md
+      - MPI Usage Issues: jobs_and_resources/mpi_issues.md
       - Debugging: software/debuggers.md
     - Performance Engineering Tools:
       - Overview: software/performance_engineering_overview.md