[alexxy/gromacs.git] / docs / user-guide / environment-variables.rst

.. 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 )

Environment Variables
=====================

|Gromacs| programs may be influenced by the use of
environment variables.  First of all, the variables set in
the ``GMXRC`` file are essential for running and
compiling |Gromacs|. Some other useful environment variables are
listed in the following sections. Most environment variables function
by being set in your shell to any non-NULL value. Specific
requirements are described below if other values need to be set. You
should consult the documentation for your shell for instructions on
how to set environment variables in the current shell, or in configuration
files for future shells. Note that requirements for exporting
environment variables to jobs run under batch control systems vary and
you should consult your local documentation for details.

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
        name, and this variable controls the maximum number of
        backups that will be made, default 99. If set to 0 it fails to
        run if any output file already exists. And if set to -1 it
        overwrites any output file without making a backup.

``GMX_NO_QUOTES``
        if this is explicitly set, no cool quotes
        will be printed at the end of a program.

``GMX_SUPPRESS_DUMP``
        prevent dumping of step files during
        (for example) blowing up during failure of constraint
        algorithms.

``GMX_TPI_DUMP``
        dump all configurations to a :ref:`pdb`
        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``,
        ``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
        as the |Gromacs| tool (which might not be what you want).
        Be careful not to use a command which blocks the terminal
        (e.g. ``vi``), since multiple instances might be run.

``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.
        This can be handy for debugging purposes, because it ensures
        that all files are always totally up-to-date.

``GMX_LOGO_COLOR``
        set display color for logo in :ref:`gmx view`.

``GMX_PRINT_LONGFORMAT``
        use long float format when printing
        decimal values.

``GMX_COMPELDUMP``
        Applies for computational electrophysiology setups
        only (see reference manual). The initial structure gets dumped to
        :ref:`pdb` file, which allows to check whether multimeric channels have
        the correct PBC representation.

``GMX_TRAJECTORY_IO_VERBOSITY``
        Defaults to 1, which prints frame count e.g. when reading trajectory
        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
        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).

``GMX_DISABLE_GPU_TIMING``
        Disables GPU timings in the log file for OpenCL.

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
        during domain decomposition, so it should typically be
        0 (never), 1 (every DD phase) or a multiple of :mdp:`nstlist`.

``GMX_DD_NST_DUMP_GRID``
        number of steps that elapse between dumping
        the current DD grid to a PDB file (default 0). This only takes effect
        during domain decomposition, so it should typically be
        0 (never), 1 (every DD phase) or a multiple of :mdp:`nstlist`.

``GMX_DD_DEBUG``
        general debugging trigger for every domain
        decomposition (default 0, meaning off). Currently only checks
        global-local atom index mapping for consistency.

``GMX_DD_NPULSE``
        over-ride the number of DD pulses used
        (default 0, meaning no over-ride). Normally 1 or 2.

``GMX_DISABLE_ALTERNATING_GPU_WAIT``
        disables the specialized polling wait path used to wait for the PME and nonbonded
        GPU tasks completion to overlap to do the reduction of the resulting forces that
        arrive first. Setting this variable switches to the generic path with fixed waiting
        order.

There are a number of extra environment variables like these
that are used in debugging - check the code!

Performance and Run Control
---------------------------
``GMX_DO_GALACTIC_DYNAMICS``
        planetary simulations are made possible (just for fun) by setting
        this environment variable, which allows setting :mdp:`epsilon-r` to -1 in the :ref:`mdp`
        file. Normally, :mdp:`epsilon-r` must be greater than zero to prevent a fatal error.
        See webpage_ for example input files for a planetary simulation.

``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_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_GPU_NB_ANA_EWALD``
        force the use of analytical Ewald kernels. Should be used only for benchmarking.

``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_CYCLE_ALL``
        times all code during runs.  Incompatible with threads.

``GMX_CYCLE_BARRIER``
        calls MPI_Barrier before each cycle start/stop call.

``GMX_DD_ORDER_ZYX``
        build domain decomposition cells in the order
        (z, y, x) rather than the default (x, y, z).

``GMX_DD_USE_SENDRECV2``
        during constraint and vsite communication, use a pair
        of ``MPI_Sendrecv`` calls instead of two simultaneous non-blocking calls
        (default 0, meaning off). Might be faster on some MPI implementations.

``GMX_DLB_BASED_ON_FLOPS``
        do domain-decomposition dynamic load balancing based on flop count rather than
        measured time elapsed (default 0, meaning off).
        This makes the load balancing reproducible, which can be useful for debugging purposes.
        A value of 1 uses the flops; a value > 1 adds (value - 1)*5% of noise to the flops to increase the imbalance and the scaling.

``GMX_DLB_MAX_BOX_SCALING``
        maximum percentage box scaling permitted per domain-decomposition
        load-balancing step (default 10)

``GMX_DD_RECORD_LOAD``
        record DD load statistics for reporting at end of the run (default 1, meaning on)

``GMX_DETAILED_PERF_STATS``
        when set, print slightly more detailed performance information
        to the :ref:`log` file. The resulting output is the way performance summary is reported in versions
        4.5.x and thus may be useful for anyone using scripts to parse :ref:`log` files or standard output.

``GMX_DISABLE_SIMD_KERNELS``
        disables architecture-specific SIMD-optimized (SSE2, SSE4.1, AVX, etc.)
        non-bonded kernels thus forcing the use of plain C kernels.

``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.

``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_EMULATE_GPU``
        emulate GPU runs by using algorithmically equivalent CPU reference code instead of
        GPU-accelerated functions. As the CPU code is slow, it is intended to be used only for debugging purposes.

``GMX_ENX_NO_FATAL``
        disable exiting upon encountering a corrupted frame in an :ref:`edr`
        file, allowing the use of all frames up until the corruption.

``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
        devices on different compute nodes in a cluster.  Cannot be used in conjunction with ``mdrun -gpu_id``.

``GMX_GPUTASKS``
        set in the same way as ``mdrun -gputasks``, ``GMX_GPUTASKS`` allows the mapping
        of GPU tasks to GPU device IDs to be different on different ranks, if e.g. the MPI
        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_IGNORE_FSYNC_FAILURE_ENV``
        allow :ref:`gmx mdrun` to continue even if
        a file is missing.

``GMX_LJCOMB_TOL``
        when set to a floating-point value, overrides the default tolerance of
        1e-5 for force-field floating-point parameters.

``GMX_MAXCONSTRWARN``
        if set to -1, :ref:`gmx mdrun` will
        not exit if it produces too many LINCS warnings.

``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
        performance with small simulation systems. Must be set to a non-negative integer,
        the 0 value disables list splitting.
        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_NBNXN_EWALD_ANALYTICAL``
        force the use of analytical Ewald non-bonded kernels,
        mutually exclusive of ``GMX_NBNXN_EWALD_TABLE``.

``GMX_NBNXN_EWALD_TABLE``
        force the use of tabulated Ewald non-bonded kernels,
        mutually exclusive of ``GMX_NBNXN_EWALD_ANALYTICAL``.

``GMX_NBNXN_SIMD_2XNN``
        force the use of 2x(N+N) SIMD CPU non-bonded kernels,
        mutually exclusive of ``GMX_NBNXN_SIMD_4XN``.

``GMX_NBNXN_SIMD_4XN``
        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_CART_REORDER``
        used in initializing domain decomposition communicators. Rank reordering
        is default, but can be switched off with this environment variable.

``GMX_NO_LJ_COMB_RULE``
        force the use of LJ paremeter lookup instead of using combination rules
        in the non-bonded kernels.

``GMX_NO_INT``, ``GMX_NO_TERM``, ``GMX_NO_USR1``
        disable signal handlers for SIGINT,
        SIGTERM, and SIGUSR1, respectively.

``GMX_NO_NODECOMM``
        do not use separate inter- and intra-node communicators.

``GMX_NO_NONBONDED``
        skip non-bonded calculations; can be used to estimate the possible
        performance gain from adding a GPU accelerator to the current hardware setup -- assuming that this is
        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_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.

``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,
        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.

``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
        :envvar:`GMX_PME_NTHREADS`).

``GMX_PMEONEDD``
        if the number of domain decomposition cells is set to 1 for both x and y,
        decompose PME in one dimension.

``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.

``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 :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.

``MPIRUN``
        the ``mpirun`` command used by :ref:`gmx tune_pme`.

``MDRUN``
        the :ref:`gmx mdrun` command used by :ref:`gmx tune_pme`.

``GMX_DISABLE_DYNAMICPRUNING``
        disables dynamic pair-list pruning. Note that :ref:`gmx mdrun` will
        still tune nstlist to the optimal value picked assuming dynamic pruning. Thus
        for good performance the -nstlist option should be used.

``GMX_NSTLIST_DYNAMICPRUNING``
        overrides the dynamic pair-list pruning interval chosen heuristically
        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
-----------------
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
        nor cache invalidation is implemented safely!

``GMX_OCL_NOFASTGEN``
        If set, generate and compile all algorithm flavors, otherwise
        only the flavor required for the simulation is generated and
        compiled.

``GMX_OCL_DISABLE_FASTMATH``
        Prevents the use of ``-cl-fast-relaxed-math`` compiler option.

``GMX_OCL_DUMP_LOG``
        If defined, the OpenCL build log is always written to the
        mdrun log file. Otherwise, the build log is written to the
        log file only when an error occurs.

``GMX_OCL_VERBOSE``
        If defined, it enables verbose mode for OpenCL kernel build.
        Currently available only for NVIDIA GPUs. See ``GMX_OCL_DUMP_LOG``
        for details about how to obtain the OpenCL build log.

``GMX_OCL_DUMP_INTERM_FILES``

        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``).

            - 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
              kernel built.  For details about where these files are
              created check AMD documentation for ``-save-temps`` compiler
              option.

``GMX_OCL_DEBUG``
        Use in conjunction with ``OCL_FORCE_CPU`` or with an AMD device.
        It adds the debug flag to the compiler options (-g).

``GMX_OCL_NOOPT``
        Disable optimisations. Adds the option ``cl-opt-disable`` to the
        compiler options.

``GMX_OCL_FORCE_CPU``
        Force the selection of a CPU device instead of a GPU.  This
        exists only for debugging purposes. Do not expect |Gromacs| to
        function properly with this option on, it is solely for the
        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 allowing
        testing.

``GMX_OCL_ENABLE_I_PREFETCH``
        Enables i-atom data (type or LJ parameter) prefetch allowing
        testing on platforms where this behavior is not default.

``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
---------------------------

``DSSP``
        used by :ref:`gmx do_dssp` to point to the ``dssp``
        executable (not just its path).

``GMX_DIPOLE_SPACING``
        spacing used by :ref:`gmx dipoles`.

``GMX_MAXRESRENUM``
        sets the maximum number of residues to be renumbered by
        :ref:`gmx grompp`. A value of -1 indicates all residues should be renumbered.

``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.

``GMX_PATH_GZIP``
        ``gunzip`` executable, used by :ref:`gmx wham`.

``GMX_FONT``
        name of X11 font used by :ref:`gmx view`.

``GMXTIMEUNIT``
        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`
        loud and noisy.

``VMD_PLUGIN_PATH``
        where to find VMD plug-ins. Needed to be
        able to read file formats recognized only by a VMD plug-in.

``VMDDIR``
        base path of VMD installation.

``GMX_USE_XMGR``
        sets viewer to ``xmgr`` (deprecated) instead of ``xmgrace``.