"Fossies" - the Fresh Open Source Software Archive

Member "gromacs-2019.3/docs/user-guide/environment-variables.rst" (14 Jun 2019, 23649 Bytes) of package /linux/privat/gromacs-2019.3.tar.gz:


As a special service "Fossies" has tried to format the requested source page into HTML format (assuming markdown format). Alternatively you can here view or download the uninterpreted source code file. A member file download can also be achieved by clicking within a package contents listing on the according byte size field. See also the last Fossies "Diffs" side-by-side code changes report for "environment-variables.rst": 2018.4_vs_2019-rc1.

Environment Variables

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 . 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

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 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 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 . 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).

with the name device_name.ptx

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 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 to load the OpenCL kernels from a custom location. Use it only if you want to override 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.