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 config
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``.
136 times all code during runs. Incompatible with threads.
138 ``GMX_CYCLE_BARRIER``
139 calls MPI_Barrier before each cycle start/stop call.
142 build domain decomposition cells in the order
143 (z, y, x) rather than the default (x, y, z).
145 ``GMX_DD_USE_SENDRECV2``
146 during constraint and vsite communication, use a pair
147 of ``MPI_Sendrecv`` calls instead of two simultaneous non-blocking calls
148 (default 0, meaning off). Might be faster on some MPI implementations.
150 ``GMX_DLB_BASED_ON_FLOPS``
151 do domain-decomposition dynamic load balancing based on flop count rather than
152 measured time elapsed (default 0, meaning off).
153 This makes the load balancing reproducible, which can be useful for debugging purposes.
154 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.
156 ``GMX_DLB_MAX_BOX_SCALING``
157 maximum percentage box scaling permitted per domain-decomposition
158 load-balancing step (default 10)
160 ``GMX_DD_RECORD_LOAD``
161 record DD load statistics for reporting at end of the run (default 1, meaning on)
163 ``GMX_DD_NST_SORT_CHARGE_GROUPS``
164 number of steps that elapse between re-sorting of the charge
165 groups (default 1). This only takes effect during domain decomposition, so should typically
166 be 0 (never), 1 (to mean at every domain decomposition), or a multiple of :mdp:`nstlist`.
168 ``GMX_DETAILED_PERF_STATS``
169 when set, print slightly more detailed performance information
170 to the :ref:`log` file. The resulting output is the way performance summary is reported in versions
171 4.5.x and thus may be useful for anyone using scripts to parse :ref:`log` files or standard output.
173 ``GMX_DISABLE_SIMD_KERNELS``
174 disables architecture-specific SIMD-optimized (SSE2, SSE4.1, AVX, etc.)
175 non-bonded kernels thus forcing the use of plain C kernels.
177 ``GMX_DISABLE_CUDA_TIMING``
178 timing of asynchronously executed GPU operations can have a
179 non-negligible overhead with short step times. Disabling timing can improve performance in these cases.
181 ``GMX_DISABLE_GPU_DETECTION``
182 when set, disables GPU detection even if :ref:`gmx mdrun` was compiled
185 ``GMX_DISRE_ENSEMBLE_SIZE``
186 the number of systems for distance restraint ensemble
187 averaging. Takes an integer value.
190 emulate GPU runs by using algorithmically equivalent CPU reference code instead of
191 GPU-accelerated functions. As the CPU code is slow, it is intended to be used only for debugging purposes.
192 The behavior is automatically triggered if non-bonded calculations are turned off using ``GMX_NO_NONBONDED``
193 case in which the non-bonded calculations will not be called, but the CPU-GPU transfer will also be skipped.
196 disable exiting upon encountering a corrupted frame in an :ref:`edr`
197 file, allowing the use of all frames up until the corruption.
200 update forces when invoking ``mdrun -rerun``.
203 set in the same way as ``mdrun -gpu_id``, ``GMX_GPU_ID``
204 allows the user to specify different GPU id-s, which can be useful for selecting different
205 devices on different compute nodes in a cluster. Cannot be used in conjunction with ``mdrun -gpu_id``.
207 ``GMX_IGNORE_FSYNC_FAILURE_ENV``
208 allow :ref:`gmx mdrun` to continue even if
212 when set to a floating-point value, overrides the default tolerance of
213 1e-5 for force-field floating-point parameters.
215 ``GMX_MAXCONSTRWARN``
216 if set to -1, :ref:`gmx mdrun` will
217 not exit if it produces too many LINCS warnings.
220 use the generic C kernel. Should be set if using
221 the group-based cutoff scheme and also sets ``GMX_NO_SOLV_OPT`` to be true,
222 thus disabling solvent optimizations as well.
225 neighbor list balancing parameter used when running on GPU. Sets the
226 target minimum number pair-lists in order to improve multi-processor load-balance for better
227 performance with small simulation systems. Must be set to a positive integer, the default value
228 is optimized for NVIDIA Fermi and Kepler GPUs, therefore changing it is not necessary for
229 normal usage, but it can be useful on future architectures.
232 use neighbor list and kernels based on charge groups.
235 when set, print detailed neighbor search cycle counting.
237 ``GMX_NBNXN_EWALD_ANALYTICAL``
238 force the use of analytical Ewald non-bonded kernels,
239 mutually exclusive of ``GMX_NBNXN_EWALD_TABLE``.
241 ``GMX_NBNXN_EWALD_TABLE``
242 force the use of tabulated Ewald non-bonded kernels,
243 mutually exclusive of ``GMX_NBNXN_EWALD_ANALYTICAL``.
245 ``GMX_NBNXN_SIMD_2XNN``
246 force the use of 2x(N+N) SIMD CPU non-bonded kernels,
247 mutually exclusive of ``GMX_NBNXN_SIMD_4XN``.
249 ``GMX_NBNXN_SIMD_4XN``
250 force the use of 4xN SIMD CPU non-bonded kernels,
251 mutually exclusive of ``GMX_NBNXN_SIMD_2XNN``.
254 disables optimized all-vs-all kernels.
256 ``GMX_NO_CART_REORDER``
257 used in initializing domain decomposition communicators. Rank reordering
258 is default, but can be switched off with this environment variable.
260 ``GMX_NO_CUDA_STREAMSYNC``
261 the opposite of ``GMX_CUDA_STREAMSYNC``. Disables the use of the
262 standard cudaStreamSynchronize-based GPU waiting to improve performance when using CUDA driver API
263 ealier than v5.0 with ECC-enabled GPUs.
265 ``GMX_NO_INT``, ``GMX_NO_TERM``, ``GMX_NO_USR1``
266 disable signal handlers for SIGINT,
267 SIGTERM, and SIGUSR1, respectively.
270 do not use separate inter- and intra-node communicators.
273 skip non-bonded calculations; can be used to estimate the possible
274 performance gain from adding a GPU accelerator to the current hardware setup -- assuming that this is
275 fast enough to complete the non-bonded calculations while the CPU does bonded force and PME computation.
278 when set, do not add virial contribution to COM pull forces.
280 ``GMX_NOCHARGEGROUPS``
281 disables multi-atom charge groups, i.e. each atom
282 in all non-solvent molecules is assigned its own charge group.
285 shell positions are not predicted.
288 turns off solvent optimizations; automatic if ``GMX_NB_GENERIC``
292 the ideal number of charge groups per neighbor searching grid cell is hard-coded
293 to a value of 10. Setting this environment variable to any other integer value overrides this hard-coded
297 set the number of OpenMP or PME threads (overrides the number guessed by
301 use P3M-optimized influence function instead of smooth PME B-spline interpolation.
303 ``GMX_PME_THREAD_DIVISION``
304 PME thread division in the format "x y z" for all three dimensions. The
305 sum of the threads in each dimension must equal the total number of PME threads (set in
309 if the number of domain decomposition cells is set to 1 for both x and y,
310 decompose PME in one dimension.
312 ``GMX_REQUIRE_SHELL_INIT``
313 require that shell positions are initiated.
315 ``GMX_REQUIRE_TABLES``
316 require the use of tabulated Coulombic
317 and van der Waals interactions.
320 the minimum value for soft-core sigma. **Note** that this value is set
321 using the :mdp:`sc-sigma` keyword in the :ref:`mdp` file, but this environment variable can be used
322 to reproduce pre-4.5 behavior with respect to this parameter.
325 should contain multiple masses used for test particle insertion into a cavity.
326 The center of mass of the last atoms is used for insertion into the cavity.
329 use graph for bonded interactions.
331 ``GMX_VERLET_BUFFER_RES``
332 resolution of buffer size in Verlet cutoff scheme. The default value is
333 0.001, but can be overridden with this environment variable.
336 the ``mpirun`` command used by :ref:`gmx tune_pme`.
339 the :ref:`gmx mdrun` command used by :ref:`gmx tune_pme`.
342 sets the default value for :mdp:`nstlist`, preventing it from being tuned during
343 :ref:`gmx mdrun` startup when using the Verlet cutoff scheme.
345 ``GMX_USE_TREEREDUCE``
346 use tree reduction for nbnxn force reduction. Potentially faster for large number of
347 OpenMP threads (if memory locality is important).
349 .. _opencl-management:
353 Currently, several environment variables exist that help customize some aspects
354 of the OpenCL_ version of |Gromacs|. They are mostly related to the runtime
355 compilation of OpenCL kernels, but they are also used in device selection.
357 ``GMX_OCL_NOGENCACHE``
358 If set, disable caching for OpenCL kernel builds. Caching is
359 normally useful so that future runs can re-use the compiled
360 kernels from previous runs. Currently, caching is always
361 disabled, until we solve concurrency issues.
363 ``GMX_OCL_NOFASTGEN``
364 If set, generate and compile all algorithm flavors, otherwise
365 only the flavor required for the simulation is generated and
369 Adds the option ``cl-fast-relaxed-math`` to the compiler
370 options (in the CUDA version this is enabled by default, it is likely that
371 the same will happen with the OpenCL version soon)
374 If defined, the OpenCL build log is always written to file.
375 The file is saved in the current directory with the name
376 ``OpenCL_kernel_file_name.build_status`` where
377 ``OpenCL_kernel_file_name`` is the name of the file containing the
378 OpenCL source code (usually ``nbnxn_ocl_kernels.cl``) and
379 build_status can be either SUCCEEDED or FAILED. If this
380 environment variable is not defined, the default behavior is
383 - Debug build: build log is always written to file
384 - Release build: build log is written to file only in case of errors.
387 If defined, it enables verbose mode for OpenCL kernel build.
388 Currently available only for NVIDIA GPUs. See ``GMX_OCL_DUMP_LOG``
389 for details about how to obtain the OpenCL build log.
391 ``GMX_OCL_DUMP_INTERM_FILES``
393 If defined, intermediate language code corresponding to the
394 OpenCL build process is saved to file. Caching has to be
395 turned off in order for this option to take effect (see
396 ``GMX_OCL_NOGENCACHE``).
398 - NVIDIA GPUs: PTX code is saved in the current directory
399 with the name ``device_name.ptx``
400 - AMD GPUs: ``.IL/.ISA`` files will be created for each OpenCL
401 kernel built. For details about where these files are
402 created check AMD documentation for ``-save-temps`` compiler
406 Use in conjunction with ``OCL_FORCE_CPU`` or with an AMD device.
407 It adds the debug flag to the compiler options (-g).
410 Disable optimisations. Adds the option ``cl-opt-disable`` to the
413 ``GMX_OCL_FORCE_CPU``
414 Force the selection of a CPU device instead of a GPU. This
415 exists only for debugging purposes. Do not expect |Gromacs| to
416 function properly with this option on, it is solely for the
417 simplicity of stepping in a kernel and see what is happening.
419 ``GMX_OCL_NB_ANA_EWALD``
420 Forces the use of analytical Ewald kernels. Equivalent of
421 CUDA environment variable ``GMX_CUDA_NB_ANA_EWALD``
423 ``GMX_OCL_NB_TAB_EWALD``
424 Forces the use of tabulated Ewald kernel. Equivalent
425 of CUDA environment variable ``GMX_OCL_NB_TAB_EWALD``
427 ``GMX_OCL_NB_EWALD_TWINCUT``
428 Forces the use of twin-range cutoff kernel. Equivalent of
429 CUDA environment variable ``GMX_CUDA_NB_EWALD_TWINCUT``
431 ``GMX_DISABLE_OCL_TIMING``
432 Disables timing for OpenCL operations
434 ``GMX_OCL_FILE_PATH``
435 Use this parameter to force |Gromacs| to load the OpenCL
436 kernels from a custom location. Use it only if you want to
437 override |Gromacs| default behavior, or if you want to test
440 Analysis and Core Functions
441 ---------------------------
443 accuracy in Gaussian L510 (MC-SCF) component program.
445 ``GMX_QM_ORCA_BASENAME``
446 prefix of :ref:`tpr` files, used in Orca calculations
447 for input and output file names.
450 when set to a nonzero value, Gaussian QM calculations will
451 iteratively solve the CP-MCSCF equations.
453 ``GMX_QM_MODIFIED_LINKS_DIR``
454 location of modified links in Gaussian.
457 used by :ref:`gmx do_dssp` to point to the ``dssp``
458 executable (not just its path).
461 directory where Gaussian is installed.
464 name of the Gaussian executable.
466 ``GMX_DIPOLE_SPACING``
467 spacing used by :ref:`gmx dipoles`.
470 sets the maximum number of residues to be renumbered by
471 :ref:`gmx grompp`. A value of -1 indicates all residues should be renumbered.
473 ``GMX_FFRTP_TER_RENAME``
474 Some force fields (like AMBER) use specific names for N- and C-
475 terminal residues (NXXX and CXXX) as :ref:`rtp` entries that are normally renamed. Setting
476 this environment variable disables this renaming.
479 ``gunzip`` executable, used by :ref:`gmx wham`.
482 name of X11 font used by :ref:`gmx view`.
485 the time unit used in output files, can be
486 anything in fs, ps, ns, us, ms, s, m or h.
488 ``GMX_QM_GAUSSIAN_MEMORY``
489 memory used for Gaussian QM calculation.
492 name of the ``multiprot`` executable, used by the
493 contributed program ``do_multiprot``.
496 number of CPUs to be used for Gaussian QM calculation
499 directory where Orca is installed.
502 simulated annealing step size for Gaussian QM calculation.
504 ``GMX_QM_GROUND_STATE``
505 defines state for Gaussian surface hopping calculation.
508 name of the ``total`` executable used by the contributed
509 ``do_shift`` program.
512 make :ref:`gmx energy` and :ref:`gmx eneconv`
516 where to find VMD plug-ins. Needed to be
517 able to read file formats recognized only by a VMD plug-in.
520 base path of VMD installation.
523 sets viewer to ``xmgr`` (deprecated) instead of ``xmgrace``.