4 |Gromacs| programs may be influenced by the use of
5 environment variables. First of all, the variables set in
6 the ``GMXRC`` file are essential for running and
7 compiling |Gromacs|. Some other useful environment variables are
8 listed in the following sections. Most environment variables function
9 by being set in your shell to any non-NULL value. Specific
10 requirements are described below if other values need to be set. You
11 should consult the documentation for your shell for instructions on
12 how to set environment variables in the current shell, or in configuration
13 files for future shells. Note that requirements for exporting
14 environment variables to jobs run under batch control systems vary and
15 you should consult your local documentation for details.
20 Print constraint virial and force virial energy terms.
23 |Gromacs| automatically backs up old
24 copies of files when trying to write a new file of the same
25 name, and this variable controls the maximum number of
26 backups that will be made, default 99. If set to 0 it fails to
27 run if any output file already exists. And if set to -1 it
28 overwrites any output file without making a backup.
31 if this is explicitly set, no cool quotes
32 will be printed at the end of a program.
35 prevent dumping of step files during
36 (for example) blowing up during failure of constraint
40 dump all configurations to a :ref:`pdb`
41 file that have an interaction energy less than the value set
42 in this environment variable.
45 ``GMX_VIEW_XVG``, ``GMX_VIEW_EPS`` and ``GMX_VIEW_PDB``, commands used to
46 automatically view :ref:`xvg`, :ref:`xpm`, :ref:`eps`
47 and :ref:`pdb` file types, respectively; they default to ``xv``, ``xmgrace``,
48 ``ghostview`` and ``rasmol``. Set to empty to disable
49 automatic viewing of a particular file type. The command will
50 be forked off and run in the background at the same priority
51 as the |Gromacs| tool (which might not be what you want).
52 Be careful not to use a command which blocks the terminal
53 (e.g. ``vi``), since multiple instances might be run.
55 ``GMX_VIRIAL_TEMPERATURE``
56 print virial temperature energy term
59 the size of the buffer for file I/O. When set
60 to 0, all file I/O will be unbuffered and therefore very slow.
61 This can be handy for debugging purposes, because it ensures
62 that all files are always totally up-to-date.
65 set display color for logo in :ref:`gmx view`.
67 ``GMX_PRINT_LONGFORMAT``
68 use long float format when printing
72 Applies for computational electrophysiology setups
73 only (see reference manual). The initial structure gets dumped to
74 :ref:`pdb` file, which allows to check whether multimeric channels have
75 the correct PBC representation.
79 ``GMX_PRINT_DEBUG_LINES``
80 when set, print debugging info on line numbers.
83 number of steps that elapse between dumping
84 the current DD to a PDB file (default 0). This only takes effect
85 during domain decomposition, so it should typically be
86 0 (never), 1 (every DD phase) or a multiple of :mdp:`nstlist`.
88 ``GMX_DD_NST_DUMP_GRID``
89 number of steps that elapse between dumping
90 the current DD grid to a PDB file (default 0). This only takes effect
91 during domain decomposition, so it should typically be
92 0 (never), 1 (every DD phase) or a multiple of :mdp:`nstlist`.
95 general debugging trigger for every domain
96 decomposition (default 0, meaning off). Currently only checks
97 global-local atom index mapping for consistency.
100 over-ride the number of DD pulses used
101 (default 0, meaning no over-ride). Normally 1 or 2.
103 There are a number of extra environment variables like these
104 that are used in debugging - check the code!
106 Performance and Run Control
107 ---------------------------
108 ``GMX_DO_GALACTIC_DYNAMICS``
109 planetary simulations are made possible (just for fun) by setting
110 this environment variable, which allows setting :mdp:`epsilon-r` to -1 in the :ref:`mdp`
111 file. Normally, :mdp:`epsilon-r` must be greater than zero to prevent a fatal error.
112 See webpage_ for example input files for a planetary simulation.
114 ``GMX_ALLOW_CPT_MISMATCH``
115 when set, runs will not exit if the
116 ensemble set in the :ref:`tpr` file does not match that of the
119 ``GMX_CUDA_NB_EWALD_TWINCUT``
120 force the use of twin-range cutoff kernel even if :mdp:`rvdw` equals
121 :mdp:`rcoulomb` after PP-PME load balancing. The switch to twin-range kernels is automated,
122 so this variable should be used only for benchmarking.
124 ``GMX_CUDA_NB_ANA_EWALD``
125 force the use of analytical Ewald kernels. Should be used only for benchmarking.
127 ``GMX_CUDA_NB_TAB_EWALD``
128 force the use of tabulated Ewald kernels. Should be used only for benchmarking.
130 ``GMX_CUDA_STREAMSYNC``
131 force the use of cudaStreamSynchronize on ECC-enabled GPUs, which leads
132 to performance loss due to a known CUDA driver bug present in API v5.0 NVIDIA drivers (pre-30x.xx).
133 Cannot be set simultaneously with ``GMX_NO_CUDA_STREAMSYNC``.
135 ``GMX_DISABLE_CUDALAUNCH``
136 disable the use of the lower-latency cudaLaunchKernel API even when supported (CUDA >=v7.0).
137 Should only be used for benchmarking purposes.
139 ``GMX_DISABLE_CUDA_TIMING``
140 Disables GPU timing of CUDA tasks; synonymous with ``GMX_DISABLE_GPU_TIMING``.
143 times all code during runs. Incompatible with threads.
145 ``GMX_CYCLE_BARRIER``
146 calls MPI_Barrier before each cycle start/stop call.
149 build domain decomposition cells in the order
150 (z, y, x) rather than the default (x, y, z).
152 ``GMX_DD_USE_SENDRECV2``
153 during constraint and vsite communication, use a pair
154 of ``MPI_Sendrecv`` calls instead of two simultaneous non-blocking calls
155 (default 0, meaning off). Might be faster on some MPI implementations.
157 ``GMX_DLB_BASED_ON_FLOPS``
158 do domain-decomposition dynamic load balancing based on flop count rather than
159 measured time elapsed (default 0, meaning off).
160 This makes the load balancing reproducible, which can be useful for debugging purposes.
161 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.
163 ``GMX_DLB_MAX_BOX_SCALING``
164 maximum percentage box scaling permitted per domain-decomposition
165 load-balancing step (default 10)
167 ``GMX_DD_RECORD_LOAD``
168 record DD load statistics for reporting at end of the run (default 1, meaning on)
170 ``GMX_DETAILED_PERF_STATS``
171 when set, print slightly more detailed performance information
172 to the :ref:`log` file. The resulting output is the way performance summary is reported in versions
173 4.5.x and thus may be useful for anyone using scripts to parse :ref:`log` files or standard output.
175 ``GMX_DISABLE_SIMD_KERNELS``
176 disables architecture-specific SIMD-optimized (SSE2, SSE4.1, AVX, etc.)
177 non-bonded kernels thus forcing the use of plain C kernels.
179 ``GMX_DISABLE_GPU_TIMING``
180 timing of asynchronously executed GPU operations can have a
181 non-negligible overhead with short step times. Disabling timing can improve performance in these cases.
183 ``GMX_DISABLE_GPU_DETECTION``
184 when set, disables GPU detection even if :ref:`gmx mdrun` was compiled
187 ``GMX_GPU_APPLICATION_CLOCKS``
188 setting this variable to a value of "0", "ON", or "DISABLE" (case insensitive)
189 allows disabling the CUDA GPU allication clock support.
191 ``GMX_DISRE_ENSEMBLE_SIZE``
192 the number of systems for distance restraint ensemble
193 averaging. Takes an integer value.
196 emulate GPU runs by using algorithmically equivalent CPU reference code instead of
197 GPU-accelerated functions. As the CPU code is slow, it is intended to be used only for debugging purposes.
198 The behavior is automatically triggered if non-bonded calculations are turned off using ``GMX_NO_NONBONDED``
199 case in which the non-bonded calculations will not be called, but the CPU-GPU transfer will also be skipped.
202 disable exiting upon encountering a corrupted frame in an :ref:`edr`
203 file, allowing the use of all frames up until the corruption.
206 update forces when invoking ``mdrun -rerun``.
209 set in the same way as ``mdrun -gpu_id``, ``GMX_GPU_ID``
210 allows the user to specify different GPU id-s, which can be useful for selecting different
211 devices on different compute nodes in a cluster. Cannot be used in conjunction with ``mdrun -gpu_id``.
213 ``GMX_IGNORE_FSYNC_FAILURE_ENV``
214 allow :ref:`gmx mdrun` to continue even if
218 when set to a floating-point value, overrides the default tolerance of
219 1e-5 for force-field floating-point parameters.
221 ``GMX_MAXCONSTRWARN``
222 if set to -1, :ref:`gmx mdrun` will
223 not exit if it produces too many LINCS warnings.
226 use the generic C kernel. Should be set if using
227 the group-based cutoff scheme and also sets ``GMX_NO_SOLV_OPT`` to be true,
228 thus disabling solvent optimizations as well.
231 neighbor list balancing parameter used when running on GPU. Sets the
232 target minimum number pair-lists in order to improve multi-processor load-balance for better
233 performance with small simulation systems. Must be set to a non-negative integer,
234 the 0 value disables list splitting.
235 The default value is optimized for supported GPUs (NVIDIA Fermi to Maxwell),
236 therefore changing it is not necessary for normal usage, but it can be useful on future architectures.
239 use neighbor list and kernels based on charge groups.
242 when set, print detailed neighbor search cycle counting.
244 ``GMX_NBNXN_EWALD_ANALYTICAL``
245 force the use of analytical Ewald non-bonded kernels,
246 mutually exclusive of ``GMX_NBNXN_EWALD_TABLE``.
248 ``GMX_NBNXN_EWALD_TABLE``
249 force the use of tabulated Ewald non-bonded kernels,
250 mutually exclusive of ``GMX_NBNXN_EWALD_ANALYTICAL``.
252 ``GMX_NBNXN_SIMD_2XNN``
253 force the use of 2x(N+N) SIMD CPU non-bonded kernels,
254 mutually exclusive of ``GMX_NBNXN_SIMD_4XN``.
256 ``GMX_NBNXN_SIMD_4XN``
257 force the use of 4xN SIMD CPU non-bonded kernels,
258 mutually exclusive of ``GMX_NBNXN_SIMD_2XNN``.
261 disables optimized all-vs-all kernels.
263 ``GMX_NO_CART_REORDER``
264 used in initializing domain decomposition communicators. Rank reordering
265 is default, but can be switched off with this environment variable.
267 ``GMX_NO_LJ_COMB_RULE``
268 force the use of LJ paremeter lookup instead of using combination rules
269 in the non-bonded kernels.
271 ``GMX_NO_CUDA_STREAMSYNC``
272 the opposite of ``GMX_CUDA_STREAMSYNC``. Disables the use of the
273 standard cudaStreamSynchronize-based GPU waiting to improve performance when using CUDA driver API
274 ealier than v5.0 with ECC-enabled GPUs.
276 ``GMX_NO_INT``, ``GMX_NO_TERM``, ``GMX_NO_USR1``
277 disable signal handlers for SIGINT,
278 SIGTERM, and SIGUSR1, respectively.
281 do not use separate inter- and intra-node communicators.
284 skip non-bonded calculations; can be used to estimate the possible
285 performance gain from adding a GPU accelerator to the current hardware setup -- assuming that this is
286 fast enough to complete the non-bonded calculations while the CPU does bonded force and PME computation.
289 when set, do not add virial contribution to COM pull forces.
292 shell positions are not predicted.
295 turns off solvent optimizations; automatic if ``GMX_NB_GENERIC``
299 the ideal number of charge groups per neighbor searching grid cell is hard-coded
300 to a value of 10. Setting this environment variable to any other integer value overrides this hard-coded
304 set the number of OpenMP or PME threads (overrides the number guessed by
308 use P3M-optimized influence function instead of smooth PME B-spline interpolation.
310 ``GMX_PME_THREAD_DIVISION``
311 PME thread division in the format "x y z" for all three dimensions. The
312 sum of the threads in each dimension must equal the total number of PME threads (set in
316 if the number of domain decomposition cells is set to 1 for both x and y,
317 decompose PME in one dimension.
319 ``GMX_REQUIRE_SHELL_INIT``
320 require that shell positions are initiated.
322 ``GMX_REQUIRE_TABLES``
323 require the use of tabulated Coulombic
324 and van der Waals interactions.
327 the minimum value for soft-core sigma. **Note** that this value is set
328 using the :mdp:`sc-sigma` keyword in the :ref:`mdp` file, but this environment variable can be used
329 to reproduce pre-4.5 behavior with respect to this parameter.
332 should contain multiple masses used for test particle insertion into a cavity.
333 The center of mass of the last atoms is used for insertion into the cavity.
336 use graph for bonded interactions.
338 ``GMX_VERLET_BUFFER_RES``
339 resolution of buffer size in Verlet cutoff scheme. The default value is
340 0.001, but can be overridden with this environment variable.
343 Not strictly a |Gromacs| environment variable, but on large machines
344 the hwloc detection can take a few seconds if you have lots of MPI processes.
345 If you run the hwloc command `lstopo out.xml` and set this environment
346 variable to point to the location of this file, the hwloc library will use
347 the cached information instead, which can be faster.
350 the ``mpirun`` command used by :ref:`gmx tune_pme`.
353 the :ref:`gmx mdrun` command used by :ref:`gmx tune_pme`.
356 sets the default value for :mdp:`nstlist`, preventing it from being tuned during
357 :ref:`gmx mdrun` startup when using the Verlet cutoff scheme.
359 ``GMX_USE_TREEREDUCE``
360 use tree reduction for nbnxn force reduction. Potentially faster for large number of
361 OpenMP threads (if memory locality is important).
363 .. _opencl-management:
367 Currently, several environment variables exist that help customize some aspects
368 of the OpenCL_ version of |Gromacs|. They are mostly related to the runtime
369 compilation of OpenCL kernels, but they are also used in device selection.
371 ``GMX_OCL_NOGENCACHE``
372 If set, disable caching for OpenCL kernel builds. Caching is
373 normally useful so that future runs can re-use the compiled
374 kernels from previous runs. Currently, caching is always
375 disabled, until we solve concurrency issues.
378 Enable OpenCL binary caching. Only intended to be used for
379 development and (expert) testing as neither concurrency
380 nor cache invalidation is implemented safely!
382 ``GMX_OCL_NOFASTGEN``
383 If set, generate and compile all algorithm flavors, otherwise
384 only the flavor required for the simulation is generated and
387 ``GMX_OCL_DISABLE_FASTMATH``
388 Prevents the use of ``-cl-fast-relaxed-math`` compiler option.
391 If defined, the OpenCL build log is always written to the
392 mdrun log file. Otherwise, the build log is written to the
393 log file only when an error occurs.
396 If defined, it enables verbose mode for OpenCL kernel build.
397 Currently available only for NVIDIA GPUs. See ``GMX_OCL_DUMP_LOG``
398 for details about how to obtain the OpenCL build log.
400 ``GMX_OCL_DUMP_INTERM_FILES``
402 If defined, intermediate language code corresponding to the
403 OpenCL build process is saved to file. Caching has to be
404 turned off in order for this option to take effect (see
405 ``GMX_OCL_NOGENCACHE``).
407 - NVIDIA GPUs: PTX code is saved in the current directory
408 with the name ``device_name.ptx``
409 - AMD GPUs: ``.IL/.ISA`` files will be created for each OpenCL
410 kernel built. For details about where these files are
411 created check AMD documentation for ``-save-temps`` compiler
415 Use in conjunction with ``OCL_FORCE_CPU`` or with an AMD device.
416 It adds the debug flag to the compiler options (-g).
419 Disable optimisations. Adds the option ``cl-opt-disable`` to the
422 ``GMX_OCL_FORCE_CPU``
423 Force the selection of a CPU device instead of a GPU. This
424 exists only for debugging purposes. Do not expect |Gromacs| to
425 function properly with this option on, it is solely for the
426 simplicity of stepping in a kernel and see what is happening.
428 ``GMX_OCL_DISABLE_I_PREFETCH``
429 Disables i-atom data (type or LJ parameter) prefetch allowig
432 ``GMX_OCL_ENABLE_I_PREFETCH``
433 Enables i-atom data (type or LJ parameter) prefetch allowig
434 testing on platforms where this behavior is not default.
436 ``GMX_OCL_NB_ANA_EWALD``
437 Forces the use of analytical Ewald kernels. Equivalent of
438 CUDA environment variable ``GMX_CUDA_NB_ANA_EWALD``
440 ``GMX_OCL_NB_TAB_EWALD``
441 Forces the use of tabulated Ewald kernel. Equivalent
442 of CUDA environment variable ``GMX_OCL_NB_TAB_EWALD``
444 ``GMX_OCL_NB_EWALD_TWINCUT``
445 Forces the use of twin-range cutoff kernel. Equivalent of
446 CUDA environment variable ``GMX_CUDA_NB_EWALD_TWINCUT``
448 ``GMX_DISABLE_OCL_TIMING``
449 Disables timing for OpenCL operations
451 ``GMX_OCL_FILE_PATH``
452 Use this parameter to force |Gromacs| to load the OpenCL
453 kernels from a custom location. Use it only if you want to
454 override |Gromacs| default behavior, or if you want to test
457 Analysis and Core Functions
458 ---------------------------
460 accuracy in Gaussian L510 (MC-SCF) component program.
462 ``GMX_QM_ORCA_BASENAME``
463 prefix of :ref:`tpr` files, used in Orca calculations
464 for input and output file names.
467 when set to a nonzero value, Gaussian QM calculations will
468 iteratively solve the CP-MCSCF equations.
470 ``GMX_QM_MODIFIED_LINKS_DIR``
471 location of modified links in Gaussian.
474 used by :ref:`gmx do_dssp` to point to the ``dssp``
475 executable (not just its path).
478 directory where Gaussian is installed.
481 name of the Gaussian executable.
483 ``GMX_DIPOLE_SPACING``
484 spacing used by :ref:`gmx dipoles`.
487 sets the maximum number of residues to be renumbered by
488 :ref:`gmx grompp`. A value of -1 indicates all residues should be renumbered.
490 ``GMX_FFRTP_TER_RENAME``
491 Some force fields (like AMBER) use specific names for N- and C-
492 terminal residues (NXXX and CXXX) as :ref:`rtp` entries that are normally renamed. Setting
493 this environment variable disables this renaming.
496 ``gunzip`` executable, used by :ref:`gmx wham`.
499 name of X11 font used by :ref:`gmx view`.
502 the time unit used in output files, can be
503 anything in fs, ps, ns, us, ms, s, m or h.
505 ``GMX_QM_GAUSSIAN_MEMORY``
506 memory used for Gaussian QM calculation.
509 name of the ``multiprot`` executable, used by the
510 contributed program ``do_multiprot``.
513 number of CPUs to be used for Gaussian QM calculation
516 directory where Orca is installed.
519 simulated annealing step size for Gaussian QM calculation.
521 ``GMX_QM_GROUND_STATE``
522 defines state for Gaussian surface hopping calculation.
525 name of the ``total`` executable used by the contributed
526 ``do_shift`` program.
529 make :ref:`gmx energy` and :ref:`gmx eneconv`
533 where to find VMD plug-ins. Needed to be
534 able to read file formats recognized only by a VMD plug-in.
537 base path of VMD installation.
540 sets viewer to ``xmgr`` (deprecated) instead of ``xmgrace``.