+.. NOTE: Below is a useful bash one-liner to verify whether there are variables in this file
+.. no longer present in the code.
+.. ( export INPUT_FILE='docs/user-guide/environment-variables.rst' GIT_PAGER="cat "; for s in $(grep '^`' $INPUT_FILE | sed 's/`//g' | sed 's/,/ /g'); do count=$(git grep $s | grep -v $INPUT_FILE | wc -l); [ $count -eq 0 ] && printf "%-30s%s\n" $s $count; done ; )
+.. Another useful one-liner to find undocumentedvariables:
+.. ( export INPUT_FILE=docs/user-guide/environment-variables.rst; GIT_PAGER="cat "; for ss in `for s in $(git grep getenv | sed 's/.*getenv("\(.*\)".*/\1/' | sort -u | grep '^[A-Z]'); do [ $(grep $s $INPUT_FILE -c) -eq 0 ] && echo $s; done `; do git grep $ss ; done )
+
+.. TODO: still undocumented GMX_QM_GAUSSIAN_NCPUS
+
Environment Variables
=====================
``GMX_CONSTRAINTVIR``
Print constraint virial and force virial energy terms.
+``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
Be careful not to use a command which blocks the terminal
(e.g. ``vi``), since multiple instances might be run.
-``GMX_VIRIAL_TEMPERATURE``
- print virial temperature energy term
-
``GMX_LOG_BUFFER``
the size of the buffer for file I/O. When set
to 0, all file I/O will be unbuffered and therefore very slow.
ensemble set in the :ref:`tpr` file does not match that of the
:ref:`cpt` file.
+``GMX_BONDED_NTHREAD_UNIFORM``
+ Value of the number of threads per rank from which to switch from uniform
+ to localized bonded interaction distribution; optimal value dependent on
+ system and hardware, default value is 4.
+
``GMX_CUDA_NB_EWALD_TWINCUT``
force the use of twin-range cutoff kernel even if :mdp:`rvdw` equals
:mdp:`rcoulomb` after PP-PME load balancing. The switch to twin-range kernels is automated,
``GMX_CUDA_NB_TAB_EWALD``
force the use of tabulated Ewald kernels. Should be used only for benchmarking.
-``GMX_CUDA_STREAMSYNC``
- force the use of cudaStreamSynchronize on ECC-enabled GPUs, which leads
- to performance loss due to a known CUDA driver bug present in API v5.0 NVIDIA drivers (pre-30x.xx).
- Cannot be set simultaneously with ``GMX_NO_CUDA_STREAMSYNC``.
-
``GMX_DISABLE_CUDALAUNCH``
disable the use of the lower-latency cudaLaunchKernel API even when supported (CUDA >=v7.0).
Should only be used for benchmarking purposes.
``GMX_DISABLE_CUDA_TIMING``
- Disables GPU timing of CUDA tasks; synonymous with ``GMX_DISABLE_GPU_TIMING``.
+ Deprecated. Use ``GMX_DISABLE_GPU_TIMING`` instead.
``GMX_CYCLE_ALL``
times all code during runs. Incompatible with threads.
force the use of 4xN SIMD CPU non-bonded kernels,
mutually exclusive of ``GMX_NBNXN_SIMD_2XNN``.
+``GMX_NOOPTIMIZEDKERNELS``
+ deprecated, use ``GMX_DISABLE_SIMD_KERNELS`` instead.
+
``GMX_NO_ALLVSALL``
disables optimized all-vs-all kernels.
force the use of LJ paremeter lookup instead of using combination rules
in the non-bonded kernels.
-``GMX_NO_CUDA_STREAMSYNC``
- the opposite of ``GMX_CUDA_STREAMSYNC``. Disables the use of the
- standard cudaStreamSynchronize-based GPU waiting to improve performance when using CUDA driver API
- ealier than v5.0 with ECC-enabled GPUs.
-
``GMX_NO_INT``, ``GMX_NO_TERM``, ``GMX_NO_USR1``
disable signal handlers for SIGINT,
SIGTERM, and SIGUSR1, respectively.
fast enough to complete the non-bonded calculations while the CPU does bonded force and PME computation.
Freezing the particles will be required to stop the system blowing up.
-``GMX_NO_PULLVIR``
- when set, do not add virial contribution to COM pull forces.
+``GMX_PULL_PARTICIPATE_ALL``
+ disable the default heuristic for when to use a separate pull MPI communicator (at >=32 ranks).
``GMX_NOPREDICT``
shell positions are not predicted.
to a value of 10. Setting this environment variable to any other integer value overrides this hard-coded
value.
-``GMX_PME_NTHREADS``
- set the number of OpenMP or PME threads (overrides the number guessed by
- :ref:`gmx mdrun`.
+``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,
+ also useful to set heterogeneous per-process/-node thread count.
``GMX_PME_P3M``
use P3M-optimized influence function instead of smooth PME B-spline interpolation.
simplicity of stepping in a kernel and see what is happening.
``GMX_OCL_DISABLE_I_PREFETCH``
- Disables i-atom data (type or LJ parameter) prefetch allowig
+ Disables i-atom data (type or LJ parameter) prefetch allowing
testing.
``GMX_OCL_ENABLE_I_PREFETCH``
- Enables i-atom data (type or LJ parameter) prefetch allowig
+ Enables i-atom data (type or LJ parameter) prefetch allowing
testing on platforms where this behavior is not default.
``GMX_OCL_NB_ANA_EWALD``
sets the maximum number of residues to be renumbered by
:ref:`gmx grompp`. A value of -1 indicates all residues should be renumbered.
-``GMX_FFRTP_TER_RENAME``
+``GMX_NO_FFRTP_TER_RENAME``
Some force fields (like AMBER) use specific names for N- and C-
terminal residues (NXXX and CXXX) as :ref:`rtp` entries that are normally renamed. Setting
this environment variable disables this renaming.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017,2018, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \brief A boolean which tells whether the complex and real grids for cuFFT are different or same. Currenty true. */
bool performOutOfPlaceFFT;
/*! \brief A boolean which tells if the CUDA timing events are enabled.
- * True by default, disabled by setting the environment variable GMX_DISABLE_CUDA_TIMING.
- * FIXME: this should also be disabled if any other GPU task is running concurrently on the same device,
+ * False by default, can be enabled by setting the environment variable GMX_ENABLE_GPU_TIMING.
+ * Note: will not be reliable when multiple GPU tasks are running concurrently on the same device context,
* as CUDA events on multiple streams are untrustworthy.
*/
bool useTiming;
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff