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9. Errors

This section describes the various kinds of errors you can encounter when using SPPARKS.

9.1 Common problems
9.2 Reporting bugs
9.3 Error & warning messages

9.1 Common problems

A SPPARKS simulation typically has two stages, setup and run. Many SPPARKS errors are detected at setup time; others may not occur until the middle of a run.

SPPARKS tries to flag errors and print informative error messages so you can fix the problem. Of course SPPARKS cannot figure out your physics mistakes, like choosing too big a timestep or setting up an invalid lattice. If you find errors that SPPARKS doesn't catch that you think it should flag, please send an email to the developers.

If you get an error message about an invalid command in your input script, you can determine what command is causing the problem by looking in the log.spparks file or using the echo command to see it on the screen. For example you can run your script as

spk_linux -echo screen < in.script

For a given command, SPPARKS expects certain arguments in a specified order. If you mess this up, SPPARKS will often flag the error, but it may read a bogus argument and assign a value that is not what you wanted. E.g. if the input parser reads the string "abc" when expecting an integer value, it will assign the value of 0 to a variable.

Generally, SPPARKS will print a message to the screen and exit gracefully when it encounters a fatal error. Sometimes it will print a WARNING and continue on; you can decide if the WARNING is important or not. If SPPARKS crashes or hangs without spitting out an error message first then it could be a bug (see this section) or one of the following cases:

SPPARKS runs in the available memory each processor can allocate. All large memory allocations in the code are done via C-style malloc's which will generate an error message if you run out of memory. Smaller chunks of memory are allocated via C++ "new" statements. If you are unlucky you could run out of memory when one of these small requests is made, in which case the code will crash, since SPPARKS doesn't trap on those errors.

Illegal arithmetic can cause SPPARKS to run slow or crash. This is typically due to invalid physics and numerics that your simulation is computing. If you see wild energy values or NaN values in your SPPARKS output, something is wrong with your simulation.

In parallel, one way SPPARKS can hang is due to how different MPI implementations handle buffering of messages. If the code hangs without an error message, it may be that you need to specify an MPI setting or two (usually via an environment variable) to enable buffering or boost the sizes of messages that can be buffered.

9.2 Reporting bugs

If you are confident that you have found a bug in SPPARKS, please send an email to the developers.

First, check the "New features and bug fixes" section of the SPPARKS WWW site to see if the bug has already been reported or fixed.

If not, the most useful thing you can do for us is to isolate the problem. Run it on the smallest problem and fewest number of processors and with the simplest input script that reproduces the bug.

In your email, describe the problem and any ideas you have as to what is causing it or where in the code the problem might be. We'll request your input script and data files if necessary.

9.3 Error & warning messages

These are two alphabetic lists of the ERROR and WARNING messages SPPARKS prints out and the reason why. If the explanation here is not sufficient, the documentation for the offending command may help. Grepping the source files for the text of the error message and staring at the source code and comments is also not a bad idea! Note that sometimes the same message can be printed from multiple places in the code.

Errors:

Adding site to bin it is not in: Internal SPPARKS error.
Adding site to illegal bin: Internal SPPARKS error.
All pair coeffs are not set: Self-explanatory.
All universe/uloop variables must have same # of values: Self-explanatory.
All variables in next command must be same style: Self-explanatory.
Another input script is already being processed: Cannot attempt to open a 2nd input script, when the original file is still being processed.
App cannot use both a KMC and rejection KMC solver: You cannot define both a solver and sweep option.
App did not set dt_sweep: Internal SPPARKS error.
App needs a KMC or rejection KMC solver: You must define either a solver or sweep option.
App relax requires a pair potential: Self-explanatory.
App style proc count is not valid for 1d simulation: There can only be 1 proc in y and z dimensions for 1d models.
App style proc count is not valid for 2d simulation: There can only be 1 proc in the z dimension for 2d models.
App_style command after simulation box is defined: Self-explanatory.
App_style specific command before app_style set: Self-explanatory.
Application cutoff is too big for processor sub-domain: There must be at least 2 bins per processor in each dimension where sectoring occurs.
Arccos of invalid value in variable formula: Argument of arccos() must be between -1 and 1.
Arcsin of invalid value in variable formula: Argument of arcsin() must be between -1 and 1.
Bad connectivity result: Internal SPPARKS error. Should not occur.
Box bounds are invalid: Lo bound >= hi bound.
Can only read neighbors for on-lattice applications: Self-explanatory.
Can only use ecoord command with app_style diffusion nonlinear: Self-explanatory.
Cannot color this combination of lattice and app: Coloring is not supported on this lattice for the neighbor dependencies of this application.
Cannot color wihtout a lattice definition of sites: Self-explanatory.
Cannot create box after simulation box is defined: Self-explanatory.
Cannot create box with this application style: This application does not support spatial domains.
Cannot create sites after sites already exist: Self-explanatory.
Cannot create sites with undefined lattice: Must use lattice commands first to define a lattice.
Cannot define Schwoebel barrier without Schwoebel model: Self-explanatory.
Cannot open diag style cluster dump file: Self-explanatory.
Cannot open diag_style cluster dump file: Self-explanatory.
Cannot open diag_style cluster output file: Self-explanatory.
Cannot open dump file: Self-explanatory.
Cannot open file %s: Self-explanatory.
Cannot open gzipped file: Self-explantory.
Cannot open input script %s: Self-explanatory.
Cannot open log.spparks: Self-explanatory.
Cannot open logfile %s: Self-explanatory.
Cannot open logfile: Self-explanatory.
Cannot open screen file: The screen file specified as a command-line argument cannot be opened. Check that the directory you are running in allows for files to be created.
Cannot open universe log file: For a multi-partition run, the master log file cannot be opened. Check that the directory you are running in allows for files to be created.
Cannot open universe screen file: For a multi-partition run, the master screen file cannot be opened. Check that the directory you are running in allows for files to be created.
Cannot read neighbors unless max neighbors is set: This is a setting in the header of the sites file.
Cannot read sites after sites already exist: Self-explanatory.
Cannot redefine variable as a different style: An equal-style variable can be re-defined but only if it was originally an equal-style variable.
Cannot run application until simulation box is defined: Self-explanatory.
Cannot use %s command until sites exist: This command requires sites exist before using it in an input script.
Cannot use KMC solver in parallel with no sectors: Self-explanatory.
Cannot use color/strict rejection KMC with sectors: Self-explanatory.
Cannot use create_sites basis with random lattice: Self-explanatory.
Cannot use diag_style cluster without a lattice defined: This diagnostic uses the lattice style to dump OpenDx files.
Cannot use dump_one for first snapshot in dump file: Self-explanatory.
Cannot use random rejection KMC in parallel with no sectors: Self-explanatory.
Cannot use raster rejection KMC in parallel with no sectors: Self-explanatory.
Cannot use region INF or EDGE when box does not exist: Can only define a region with these parameters after a simulation box has been defined.
Choice of sector stop led to no rKMC events: Self-explanatory.
Color stencil is incommensurate with lattice size: Since coloring induces a pattern of colors, this pattern must fit an integer number of times into a periodic lattice.
Could not find dump ID in dump_modify command: Self-explanatory.
Could not find dump ID in dump_one command: Self-explanatory.
Could not find dump ID in undump command: Self-explanatory.
Create_box command before app_style set: Self-explanatory.
Create_box region ID does not exist: Self-explanatory.
Create_box region must be of type inside: Self-explanatory.
Create_sites command before app_style set: Self-explanatory.
Create_sites command before simulation box is defined: Self-explanatory.
Create_sites region ID does not exist: Self-explanatory.
Creating a quantity application does not support: The application defines what variables it supports. You cannot set a variable with the create_sites command for a variable that isn't supported.
Diag dump_style does not work if ncluster > 2^31: Self-explanatory.
Diag dump_style incompatible with lattice style: Not all lattice styles can be output as OpenDx files.
Diag propensity requires KMC solve be performed: Only KMC solvers compute a propensity for sites and the system.
Diag style cluster dump file name too long: Self-explanatory.
Diag style incompatible with app style: The lattice styles of the diagnostic and the on-lattice application must match.
Diag cluster dvalue in neighboring clusters do not match: Internal SPPARKS error.
Diag cluster ivalue in neighboring clusters do not match: Internal SPPARKS error.
Diag_style command before app_style set: Self-explanatory.
Diag_style diffusion requires app_style diffusion: Self-explanatory.
Did not assign all sites correctly: One or more sites in the read_sites file were not assigned to a processor correctly.
Did not create correct number of sites: One or more created sites were not assigned to a processor correctly.
Dimension command after lattice is defined: Self-explanatory.
Dimension command after simulation box is defined: Self-explanatory.
Divide by 0 in variable formula: Self-explanatory.
Dump ID already exists: Self-explanatory.
Dump command before app_style set: Self-explanatory.
Dump command can only be used for spatial applications: Self-explanatory.
Dump requires propensity but no KMC solve performed: Only KMC solvers compute propensity for sites.
Dump_modify command before app_style set: Self-explanatory.
Dump_one command before app_style set: Self-explanatory.
Dumping a quantity application does not support: The application defines what variables it supports. You cannot output a variable in a dump that isn't supported.
Failed to allocate %ld bytes for array %s: Your SPPARKS simulation has run out of memory. You need to run a smaller simulation or on more processors.
Failed to reallocate %ld bytes for array %s: Your SPPARKS simulation has run out of memory. You need to run a smaller simulation or on more processors.
Ghost connection was not found: Internal SPPARKS error. Should not occur.
Ghost site was not found: Internal SPPARKS error. Should not occur.
Illegal ... command: Self-explanatory. Check the input script syntax and compare to the documentation for the command. You can use -echo screen as a command-line option when running SPPARKS to see the offending line.
Incorrect args for pair coefficients: Self-explanatory.
Incorrect lattice neighbor count: Internal SPPARKS error.
Incorrect site format in data file: Self-explanatory.
Incorrect value format in data file: Self-explanatory.
Input line too long after variable substitution: This is a hard (very large) limit defined in the input.cpp file.
Input line too long: %s: This is a hard (very large) limit defined in the input.cpp file.
Invalid command-line argument: One or more command-line arguments is invalid. Check the syntax of the command you are using to launch SPPARKS.
Invalid dump_modify threshold operator: Self-explanatory.
Invalid event count for app_style test/group: Number of events must be > 0.
Invalid keyword in dump command: Self-explanatory.
Invalid math function in variable formula: The math function is not recognized.
Invalid number of sectors: Self-explanatory.
Invalid pair style: Self-explanatory.
Invalid probability bounds for app_style test/group: Self-explanatory.
Invalid probability bounds for solve_style group: Self-explanatory.
Invalid probability delta for app_style test/group: Self-explanatory.
Invalid region style: Self-explanatory.
Invalid site ID in Sites section of data file: Self-explanatory.
Invalid syntax in variable formula: Self-explanatory.
Invalid variable evaluation in variable formula: A variable used in a formula could not be evaluated.
Invalid variable in next command: Self-explanatory.
Invalid variable name in variable formula: Variable name is not recognized.
Invalid variable name: Variable name used in an input script line is invalid.
Invalid variable style with next command: Variable styles equal and world cannot be used in a next command.
Invalid volume setting: Volume must be set to value > 0.
KMC events are not implemented in app: Not every application supports KMC solvers.
Label wasn't found in input script: Self-explanatory.
Lattice command before app_style set: Self-explanatory.
Lattice style does not match dimension: Self-explanatory.
Log of zero/negative in variable formula: Self-explanatory.
Mask logic not implemented in app: Not every application supports masking.
Mismatch in counting for dbufclust: Self-explanatory.
Must read Sites before Neighbors: Self-explanatory.
Must read Sites before Values: Self-explanatory.
Must use -in switch with multiple partitions: A multi-partition simulation cannot read the input script from stdin. The -in command-line option must be used to specify a file.
Must use create_sites box for on-lattice applications: Self-explanatory.
Must use value option before basis option in create_sites command: Self-explanatory.
No reactions defined for chemistry app: Use the add_reaction command to specify one or more reactions.
No solver class defined: Self-explanatory.
Number of sites does not match existing sites: File being read by read_sites command is not consistent with sites already defined.
One or more sites have invalid values: The application only allows sites to be initialized with specific values.
PBC remap of site failed: Internal SPPARKS error.
Pair_coeff command before app_style set: Self-explanatory.
Pair_coeff command before pair_style is defined: Self-explanatory.
Pair_style command before app_style set: Self-explanatory.
Power by 0 in variable formula: Self-explanatory.
Processor partitions are inconsistent: The total number of processors in all partitions must match the number of processors LAMMPS is running on.
Processors command after simulation box is defined: Self-explanatory.
Random lattice has no connectivity: The cutoff distance is likely too short.
Reaction ID %s already exists: Cannot re-define a reaction.
Reaction cannot have more than MAX_PRODUCT products: Self-explanatory.
Reaction has no numeric rate: Self-explanatory.
Reaction must have 0,1,2 reactants: Self-explanatory.
Read_sites command before app_style set: Self-explanatory.
Read_sites simluation box different that current box: Self-explanatory.
Region command before app_style set: Self-explanatory.
Region intersect region ID does not exist: Self-explanatory.
Region union region ID does not exist: Self-explanatory.
Rejection events are not implemented in app: Self-explanatory.
Reset_time command before app_style set: Self-explanatory.
Reuse of region ID: Self-explanatory.
Run command before app_style set: Self-explanatory.
Run upto value is before current time: Self-explanatory.
Seed command has not been used: The seed command must be used if another command requires random numbers.
Set command before sites exist: Self-explanatory.
Set command region ID does not exist: Self-explanatory.
Set if test on quantity application does not support: The application defines what variables it supports. You cannot do an if test with the set command on a variable that isn't supported.
Setting a quantity application does not support: The application defines what variables it supports. You cannot set a variable with the set command on a variable that isn't supported.
Simulation box is not multiple of current lattice settings: This likely occurred because the lattice was re-defined after the simulation box was created.
Site not in my bin domain: Internal SPPARKS error.
Site-site interaction was not found: Internal SPPARKS error.
Solve_style command before app_style set: Self-explanatory.
Species ID %s already exists: Self-explanatory.
Species ID %s does not exist: Self-explanatory.
Sqrt of negative in variable formula: Self-explanatory.
Stats command before app_style set: Self-explanatory.
Substitution for illegal variable: Self-explanatory.
Threshold for a quantity application does not support: The application defines what variables it supports. You cannot do a threshold test with the dump command on a variable that isn't supported.
Too many neighbors per site: Internal SPPARKS error.
Unbalanced quotes in input line: No matching end double quote was found following a leading double quote.
Undump command before app_style set: Self-explanatory.
Unexpected end of data file: Self-explanatory.
Universe/uloop variable count < # of partitions: A universe or uloop style variable must specify a number of values >= to the number of processor partitions.
Unknown command: %s: The command is not known to SPPARKS. Check the input script.
Unknown identifier in data file: %s: Self-explanatory.
Unknown species in reaction command: Self-explanatory.
Unrecognized command: The command is assumed to be application specific, but is not known to SPPARKS. Check the input script.
Use of region with undefined lattice: The lattice command must be used before defining a geometric region.
Variable name must be alphanumeric or underscore characters: Self-explanatory.
World variable count doesn't match # of partitions: A world-style variable must specify a number of values equal to the number of processor partitions.

9. Errors

9.1 Common problems

9.2 Reporting bugs

9.3 Error & warning messages

Errors:

Warnings: