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 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 xvg, xpm, eps and 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 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 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 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 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 epsilon-r to -1 in the mdp file. Normally, 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_CUDA_NB_EWALD_TWINCUT
force the use of twin-range cutoff kernel even if rvdw equals 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
force the use of analytical Ewald kernels. Should be used only for benchmarking.
GMX_CUDA_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_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 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 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 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 edr file, allowing the use of all frames up until the corruption.
GMX_FORCE_UPDATE
update forces when invoking mdrun -rerun.
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 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, 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 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_ALLVSALL
disables optimized all-vs-all kernels.
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_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 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 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_SCSIGMA_MIN
the minimum value for soft-core sigma. Note that this value is set using the sc-sigma keyword in the 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 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 gmx tune_pme.
MDRUN
the gmx mdrun command used by gmx tune_pme.
GMX_DISABLE_DYNAMICPRUNING
disables dynamic pair-list pruning. Note that 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 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

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_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.

Analysis and Core Functions

GMX_QM_ACCURACY
accuracy in Gaussian L510 (MC-SCF) component program.
GMX_QM_ORCA_BASENAME
prefix of 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 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 gmx dipoles.
GMX_MAXRESRENUM
sets the maximum number of residues to be renumbered by 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 rtp entries that are normally renamed. Setting this environment variable disables this renaming.
GMX_PATH_GZIP
gunzip executable, used by gmx wham.
GMX_FONT
name of X11 font used by gmx view.
GMXTIMEUNIT
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 gmx energy and 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.