.. 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
=====================
Output Control
--------------
-``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
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
files. Set to 0 for quiet operation.
``GMX_ENABLE_GPU_TIMING``
- Enables GPU timings in the log file for CUDA. Note that CUDA timings
- are incorrect with multiple streams, as happens with domain
+ Enables GPU timings in the log file for CUDA and SYCL. Note that CUDA
+ timings are incorrect with multiple streams, as happens with domain
decomposition or with both non-bondeds and PME on the GPU (this is
also the main reason why they are not turned on by default).
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
arrive first. Setting this variable switches to the generic path with fixed waiting
order.
+``GMX_TEST_REQUIRED_NUMBER_OF_DEVICES``
+ sets the number of GPUs required by the test suite. By default, the test suite would
+ fall-back to using CPU if GPUs could not be detected. Set it to a positive integer value
+ to ensure that at least this at least this number of usable GPUs are detected. Default:
+ 0 (not testing GPU availability).
+
There are a number of extra environment variables like these
that are used in debugging - check the code!
to localized bonded interaction distribution; optimal value dependent on
system and hardware, default value is 4.
-``GMX_CUDA_NB_EWALD_TWINCUT``
+``GMX_GPU_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,
so this variable should be used only for benchmarking.
-``GMX_CUDA_NB_ANA_EWALD``
+``GMX_GPU_NB_ANA_EWALD``
force the use of analytical Ewald kernels. Should be used only for benchmarking.
-``GMX_CUDA_NB_TAB_EWALD``
+``GMX_GPU_NB_TAB_EWALD``
force the use of tabulated Ewald kernels. Should be used only for benchmarking.
``GMX_DISABLE_CUDA_TIMING``
Deprecated. Use ``GMX_DISABLE_GPU_TIMING`` instead.
+``GMX_GPU_DD_COMMS``
+ perform domain decomposition halo exchange communication operations (on coordinate and force buffers)
+ directly on GPU memory spaces, without the staging of data through CPU memory, where possible.
+
+``GMX_GPU_PME_PP_COMMS``
+ when the simulation uses a separate PME rank, perform communication operations between PP and PME rank
+ (for coordinate and force buffers) directly on GPU memory spaces, without the staging of data through CPU
+ memory, where possible.
+
+``GMX_GPU_SYCL_NO_SYNCHRONIZE``
+ disable synchronizations between different GPU streams in SYCL build, instead relying on SYCL runtime to
+ do scheduling based on data dependencies. Experimental.
+
``GMX_CYCLE_ALL``
times all code during runs. Incompatible with threads.
``GMX_DISABLE_GPU_TIMING``
timing of asynchronously executed GPU operations can have a
non-negligible overhead with short step times. Disabling timing can improve performance in these cases.
+ Timings are disabled by default with CUDA and SYCL.
``GMX_DISABLE_GPU_DETECTION``
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.
``GMX_FORCE_UPDATE``
update forces when invoking ``mdrun -rerun``.
+``GMX_FORCE_UPDATE_DEFAULT_GPU``
+ Force update to run on the GPU by default, overriding the ``mdrun -update auto`` option. Works similar to setting
+ ``mdrun -update gpu``, but (1) falls back to the CPU code-path, if set with input that is not supported and
+ (2) can be used to run update on GPUs in multi-rank cases. The latter case should be
+ considered experimental since it lacks substantial testing. Also, GPU update is only supported with the GPU direct
+ communications and ``GMX_FORCE_UPDATE_DEFAULT_GPU`` variable should be set simultaneously with ``GMX_GPU_DD_COMMS``
+ and ``GMX_GPU_PME_PP_COMMS`` environment variables in multi-rank case. Does not override ``mdrun -update cpu``.
+
``GMX_GPU_ID``
set in the same way as ``mdrun -gpu_id``, ``GMX_GPU_ID``
allows the user to specify different GPU IDs for different ranks, which can be useful for selecting different
runtime permits this variable to be different for different ranks. Cannot be used
in conjunction with ``mdrun -gputasks``. Has all the same requirements as ``mdrun -gputasks``.
+``GMX_GPU_DISABLE_COMPATIBILITY_CHECK``
+ Disables the hardware compatibility check in OpenCL and SYCL. Useful for developers
+ and allows testing the OpenCL/SYCL kernels on non-supported platforms without source code modification.
+
``GMX_IGNORE_FSYNC_FAILURE_ENV``
allow :ref:`gmx mdrun` to continue even if
a file is missing.
if set to -1, :ref:`gmx mdrun` will
not exit if it produces too many LINCS warnings.
-``GMX_NB_GENERIC``
- use the generic C kernel. Should be set if using
- the group-based cutoff scheme and also sets ``GMX_NO_SOLV_OPT`` to be true,
- thus disabling solvent optimizations as well.
-
``GMX_NB_MIN_CI``
neighbor list balancing parameter used when running on GPU. Sets the
target minimum number pair-lists in order to improve multi-processor load-balance for better
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.
``GMX_NOPREDICT``
shell positions are not predicted.
-``GMX_NO_SOLV_OPT``
- turns off solvent optimizations; automatic if ``GMX_NB_GENERIC``
- is enabled.
-
``GMX_NO_UPDATEGROUPS``
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,
+ :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``
``GMX_PME_THREAD_DIVISION``
PME thread division in the format "x y z" for all three dimensions. The
sum of the threads in each dimension must equal the total number of PME threads (set in
- `GMX_PME_NTHREADS`).
+ :envvar:`GMX_PME_NTHREADS`).
``GMX_PMEONEDD``
if the number of domain decomposition cells is set to 1 for both x and y,
``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_SCSIGMA_MIN``
- the minimum value for soft-core sigma. **Note** that this value is set
- using the :mdp:`sc-sigma` keyword in the :ref:`mdp` file, but this environment variable can be used
- to reproduce pre-4.5 behavior with respect to this parameter.
-
``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.
``HWLOC_XMLFILE``
Not strictly a |Gromacs| environment variable, but on large machines
the hwloc detection can take a few seconds if you have lots of MPI processes.
- If you run the hwloc command `lstopo out.xml` and set this environment
+ If you run the hwloc command :command:`lstopo out.xml` and set this environment
variable to point to the location of this file, the hwloc library will use
the cached information instead, which can be faster.
by mdrun. Values should be between the pruning frequency value
(1 for CPU and 2 for GPU) and :mdp:`nstlist` ``- 1``.
-``GMX_USE_TREEREDUCE``
- use tree reduction for nbnxn force reduction. Potentially faster for large number of
- OpenMP threads (if memory locality is important).
-
.. _opencl-management:
OpenCL management
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
``GMX_OCL_DISABLE_FASTMATH``
Prevents the use of ``-cl-fast-relaxed-math`` compiler option.
+ 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
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``
- - AMD GPUs: ``.IL/.ISA`` files will be created for each OpenCL
+ with the name ``device_name.ptx``
+ - AMD GPUs: ``.IL/.ISA`` files will be created for each OpenCL
kernel built. For details about where these files are
created check AMD documentation for ``-save-temps`` compiler
option.
Enables i-atom data (type or LJ parameter) prefetch allowing
testing on platforms where this behavior is not default.
-``GMX_OCL_NB_ANA_EWALD``
- Forces the use of analytical Ewald kernels. Equivalent of
- CUDA environment variable ``GMX_CUDA_NB_ANA_EWALD``
-
-``GMX_OCL_NB_TAB_EWALD``
- Forces the use of tabulated Ewald kernel. Equivalent
- of CUDA environment variable ``GMX_OCL_NB_TAB_EWALD``
-
-``GMX_OCL_NB_EWALD_TWINCUT``
- Forces the use of twin-range cutoff kernel. Equivalent of
- CUDA environment variable ``GMX_CUDA_NB_EWALD_TWINCUT``
-
``GMX_OCL_FILE_PATH``
Use this parameter to force |Gromacs| to load the OpenCL
kernels from a custom location. Use it only if you want to
override |Gromacs| default behavior, or if you want to test
your own kernels.
-``GMX_OCL_DISABLE_COMPATIBILITY_CHECK``
- Disables the hardware compatibility check. Useful for developers
- and allows testing the OpenCL kernels on non-supported platforms
- (like Intel iGPUs) without source code modification.
-
``GMX_OCL_SHOW_DIAGNOSTICS``
Use Intel OpenCL extension to show additional runtime performance
diagnostics.
Analysis and Core Functions
---------------------------
-``GMX_QM_ACCURACY``
- accuracy in Gaussian L510 (MC-SCF) component program.
-
-``GMX_QM_ORCA_BASENAME``
- prefix of :ref:`tpr` files, used in Orca calculations
- for input and output file names.
-
-``GMX_QM_CPMCSCF``
- when set to a nonzero value, Gaussian QM calculations will
- iteratively solve the CP-MCSCF equations.
-
-``GMX_QM_MODIFIED_LINKS_DIR``
- location of modified links in Gaussian.
``DSSP``
used by :ref:`gmx do_dssp` to point to the ``dssp``
executable (not just its path).
-``GMX_QM_GAUSS_DIR``
- directory where Gaussian is installed.
-
-``GMX_QM_GAUSS_EXE``
- name of the Gaussian executable.
-
``GMX_DIPOLE_SPACING``
spacing used by :ref:`gmx dipoles`.
terminal residues (NXXX and CXXX) as :ref:`rtp` entries that are normally renamed. Setting
this environment variable disables this renaming.
-``GMX_PATH_GZIP``
- ``gunzip`` executable, used by :ref:`gmx wham`.
-
``GMX_FONT``
name of X11 font used by :ref:`gmx view`.
the time unit used in output files, can be
anything in fs, ps, ns, us, ms, s, m or h.
-``GMX_QM_GAUSSIAN_MEMORY``
- memory used for Gaussian QM calculation.
-
-``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_ORCA_PATH``
- directory where Orca is installed.
-
-``GMX_QM_SA_STEP``
- simulated annealing step size for Gaussian QM calculation.
-
-``GMX_QM_GROUND_STATE``
- defines state for Gaussian surface hopping 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`
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff