From: Andrey Alekseenko Date: Thu, 4 Nov 2021 11:28:53 +0000 (+0000) Subject: Remove unused environment variables from docs X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?p=alexxy%2Fgromacs.git;a=commitdiff_plain;h=0da8ba6fea75b268a36e22ff9150e31133f88552 Remove unused environment variables from docs --- diff --git a/docs/user-guide/environment-variables.rst b/docs/user-guide/environment-variables.rst index 1f323174e1..5b0dc2a377 100644 --- a/docs/user-guide/environment-variables.rst +++ b/docs/user-guide/environment-variables.rst @@ -22,9 +22,6 @@ you should consult your local documentation for details. Output Control -------------- -``GMX_DUMP_NL`` - Neighbour list dump level; default 0. - ``GMX_MAXBACKUP`` |Gromacs| automatically backs up old copies of files when trying to write a new file of the same @@ -47,10 +44,10 @@ Output Control file that have an interaction energy less than the value set in this environment variable. -``GMX_VIEW_XPM`` - ``GMX_VIEW_XVG``, ``GMX_VIEW_EPS`` and ``GMX_VIEW_PDB``, commands used to - automatically view :ref:`xvg`, :ref:`xpm`, :ref:`eps` - and :ref:`pdb` file types, respectively; they default to ``xv``, ``xmgrace``, +``GMX_VIEW_XVG`` + ``GMX_VIEW_EPS`` and ``GMX_VIEW_PDB``, commands used to + automatically view :ref:`xvg`, :ref:`eps` + and :ref:`pdb` file types, respectively; they default to ``xmgrace``, ``ghostview`` and ``rasmol``. Set to empty to disable automatic viewing of a particular file type. The command will be forked off and run in the background at the same priority @@ -92,9 +89,6 @@ Output Control Debugging --------- -``GMX_PRINT_DEBUG_LINES`` - when set, print debugging info on line numbers. - ``GMX_DD_NST_DUMP`` number of steps that elapse between dumping the current DD to a PDB file (default 0). This only takes effect @@ -217,10 +211,6 @@ Performance and Run Control when set, disables GPU detection even if :ref:`gmx mdrun` was compiled with GPU support. -``GMX_GPU_APPLICATION_CLOCKS`` - setting this variable to a value of "0", "ON", or "DISABLE" (case insensitive) - allows disabling the CUDA GPU allication clock support. - ``GMX_DISRE_ENSEMBLE_SIZE`` the number of systems for distance restraint ensemble averaging. Takes an integer value. @@ -279,9 +269,6 @@ Performance and Run Control The default value is optimized for supported GPUs therefore changing it is not necessary for normal usage, but it can be useful on future architectures. -``GMX_NBLISTCG`` - use neighbor list and kernels based on charge groups. - ``GMX_NBNXN_CYCLE`` when set, print detailed neighbor search cycle counting. @@ -335,11 +322,6 @@ Performance and Run Control turns off update groups. May allow for a decomposition of more domains for small systems at the cost of communication during update. -``GMX_NSCELL_NCG`` - the ideal number of charge groups per neighbor searching grid cell is hard-coded - to a value of 10. Setting this environment variable to any other integer value overrides this hard-coded - value. - ``GMX_PME_NUM_THREADS`` set the number of OpenMP or PME threads; overrides the default set by :ref:`gmx mdrun`; can be used instead of the ``-npme`` command line option, @@ -360,17 +342,10 @@ Performance and Run Control ``GMX_REQUIRE_SHELL_INIT`` require that shell positions are initiated. -``GMX_REQUIRE_TABLES`` - require the use of tabulated Coulombic - and van der Waals interactions. - ``GMX_TPIC_MASSES`` should contain multiple masses used for test particle insertion into a cavity. The center of mass of the last atoms is used for insertion into the cavity. -``GMX_USE_GRAPH`` - use graph for bonded interactions. - ``GMX_VERLET_BUFFER_RES`` resolution of buffer size in Verlet cutoff scheme. The default value is 0.001, but can be overridden with this environment variable. @@ -406,12 +381,6 @@ Currently, several environment variables exist that help customize some aspects of the OpenCL_ version of |Gromacs|. They are mostly related to the runtime compilation of OpenCL kernels, but they are also used in device selection. -``GMX_OCL_NOGENCACHE`` - If set, disable caching for OpenCL kernel builds. Caching is - normally useful so that future runs can re-use the compiled - kernels from previous runs. Currently, caching is always - disabled, until we solve concurrency issues. - ``GMX_OCL_GENCACHE`` Enable OpenCL binary caching. Only intended to be used for development and (expert) testing as neither concurrency @@ -424,7 +393,7 @@ compilation of OpenCL kernels, but they are also used in device selection. ``GMX_OCL_DISABLE_FASTMATH`` Prevents the use of ``-cl-fast-relaxed-math`` compiler option. - Not: fast math is always disabled on Intel devices due to instability. + Note: fast math is always disabled on Intel devices due to instability. ``GMX_OCL_DUMP_LOG`` If defined, the OpenCL build log is always written to the @@ -440,8 +409,7 @@ compilation of OpenCL kernels, but they are also used in device selection. If defined, intermediate language code corresponding to the OpenCL build process is saved to file. Caching has to be - turned off in order for this option to take effect (see - ``GMX_OCL_NOGENCACHE``). + turned off in order for this option to take effect. - NVIDIA GPUs: PTX code is saved in the current directory with the name ``device_name.ptx`` @@ -508,16 +476,6 @@ Analysis and Core Functions the time unit used in output files, can be anything in fs, ps, ns, us, ms, s, m or h. -``MULTIPROT`` - name of the ``multiprot`` executable, used by the - contributed program ``do_multiprot``. - -``NCPUS`` - number of CPUs to be used for Gaussian QM calculation - -``GMX_TOTAL`` - name of the ``total`` executable used by the contributed - ``do_shift`` program. ``GMX_ENER_VERBOSE`` make :ref:`gmx energy` and :ref:`gmx eneconv`