Clarify the GMX_BUILD_MDRUN_ONLY full testing instructions.

For full testing of an MDRUN_ONLY installation, the documentation
suggests installing over a non MDRUN_ONLY installation. This change
attempts to clarify the use case and normalize the important aspects
of the CMake command lines.

Fixes #3723

diff --git a/docs/install-guide/index.rst b/docs/install-guide/index.rst
index 438802188eb78613ac41e85463fb4d712cd0bb6c..c40015459307c910ba2beb340287468ebecffd2b 100644 (file)
--- a/docs/install-guide/index.rst
+++ b/docs/install-guide/index.rst
@@ -1054,11 +1054,15 @@ are individual failed tests it could be a sign of a compiler bug, or
 that a tolerance is just a tiny bit too tight. Check the output files
 the script directs you too, and try a different or newer compiler if
 the errors appear to be real. If you cannot get it to pass the
-regression tests, you might try dropping a line to the gmx-users
-mailing list, but then you should include a detailed description of
+regression tests, you might try dropping a line to the
+`|Gromacs| users forum <https://gromacs.bioexcel.eu/c/gromacs-user-forum>`__,
+but then you should include a detailed description of
 your hardware, and the output of ``gmx mdrun -version`` (which contains
 valuable diagnostic information in the header).
 
+Testing for MDRUN_ONLY executables
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
 A build with ``-DGMX_BUILD_MDRUN_ONLY`` cannot be tested with
 ``make check`` from the build tree, because most of the tests
 require a full build to run things like ``grompp``. To test such an
@@ -1072,19 +1076,24 @@ directory:
 
     mkdir build-normal
     cd build-normal
-    cmake .. -DCMAKE_INSTALL_PREFIX=/your/installation/prefix/here
+    # First, build and install normally to allow full testing of the standalone simulator.
+    cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/your/installation/prefix/here
     make -j 4
     make install
     cd ..
     mkdir build-mdrun-only
     cd build-mdrun-only
-    cmake .. -DGMX_MPI=ON -DGMX_GPU=CUDA -DGMX_BUILD_MDRUN_ONLY=ON -DCMAKE_INSTALL_PREFIX=/your/installation/prefix/here
+    # Next, build and install the GMX_BUILD_MDRUN_ONLY version (optional).
+    cmake .. -DGMX_MPI=ON -DGMX_BUILD_MDRUN_ONLY=ON -DCMAKE_INSTALL_PREFIX=/your/installation/prefix/here
     make -j 4
     make install
     cd /to/your/unpacked/regressiontests
     source /your/installation/prefix/here/bin/GMXRC
     ./gmxtest.pl all -np 2
 
+Non-standard suffix
+~~~~~~~~~~~~~~~~~~~
+
 If your mdrun program has been suffixed in a non-standard way, then
 the ``./gmxtest.pl -mdrun`` option will let you specify that name to the
 test machinery. You can use ``./gmxtest.pl -double`` to test the
@@ -1093,6 +1102,9 @@ to stop the test harness attempting to check that the programs can
 be run. You can use ``./gmxtest.pl -mpirun srun`` if your command to
 run an MPI program is called ``srun``.
 
+Running MPI-enabled tests
+~~~~~~~~~~~~~~~~~~~~~~~~~
+
 The ``make check`` target also runs integration-style tests that may run
 with MPI if ``GMX_MPI=ON`` was set. To make these work with various possible
 MPI libraries, you may need to