Input errors

  • not well-formed (invalid token): Seen if the input file does not have the correct xml syntax. Should be accompanied by a line number giving the point in the file where the syntax is incorrect.

  • mismatched tag: One of the closing tags does not have the same name as the corresponding opening tag. Could be caused either by a misspelling of one of the tags, or by having the closing tag in the wrong place. This last one is a standard part of the xml syntax, if the opening tag of one item is after the opening tag of a second, then its closing tag should be before the closing tag of the second. Should be accompanied by a line number giving the position of the closing tag.

  • Uninitialized value of type __ or Attribute/Field name __ is mandatory and was not found in the input for property __: The xml file is missing a mandatory tag, i.e. one without which the simulation cannot be initialized. Find which tag name is missing and add it.

  • Attribute/tag name __ is not a recognized property of __ objects: The first tag should not be found within the second set of tags. Check that the first tag is spelt correctly, and that it has been put in the right place.

  • __ is not a valid option (___): This attribute/tag only allows a certain range of inputs. Pick one of the items from the list given.

  • __ is an undefined unit for kind __ or __ is not a valid unit prefix or Unit __ is not structured with a prefix+base syntax: The unit input by the user is not correct. Make sure it corresponds to the correct dimensionality, and is spelt correctly.

  • Invalid literal for int() with base 10: __ or Invalid literal for float(): __ or __ does not represent a bool value: The data input by the user does not have the correct data type. See section Input file format and structure for what constitutes a valid integer/float/boolean value.

  • Error in list syntax: could not locate delimiters: The array input data did not have the required braces. For a normal array use [], for a dictionary use {}, and for a tuple use ().

  • The number of atom records does not match the header of xyz file: Self-explanatory.

  • list index out of range: This will normally occur if the configuration is initialized from an invalid input file. This will either cause the code to try to read part of the input file that does not exist, or to set the number of beads to zero which causes this error in a different place. Check that the input file has the correct syntax.

Initialization errors

  • Negative __ parameter specified.: Self-explanatory.

  • If you are initializing cell from cell side lengths you must pass the ’cell’ tag an array of 3 floats: If you are attempting to initialize a cell using the “abc” mode, the code expects three floats corresponding to the three side lengths.

  • If you are initializing cell from cell side lengths and angles you must pass the ’cell’ tag an array of 6 floats: If you are attempting to initialize a cell using the “abcABC” mode, the code expects six floats corresponding to the three side lengths, followed by the three angles in degrees.

  • Cell objects must contain a 3x3 matrix describing the cell vectors.: If you are attempting to initialize a cell using the “manual” mode, the code expects nine floats corresponding to the cell vector matrix side lengths. Note that the values of the lower-diagonal elements will be set to zero.

  • Array shape mismatch in q/p/m/names in beads input: The size of the array in question does not have the correct number of elements given the number of atoms and the number of beads used in the rest of the input. If the number of beads is nbeads and the number of atoms natoms, then q and p should have shape (nbeads, 3*natoms) and m and names should have shape (natoms,).

  • No thermostat/barostat tag provided for NVT/NPT simulation: Some ensembles can only be sampled if a thermostat and/or barostat have been defined, and so for simulations at constant temperature and/or pressure these tags are mandatory. If you wish to not use a thermostat/barostat, but still want to keep the ensemble the same, then use “dummy” mode thermostat/barostat, which simply does nothing.

  • Pressure/Temperature should be supplied for constant pressure/temperature simulation: Since in this case the ensemble is defined by these parameters, these must be input by the user. Add the appropriate tags to the input file.

  • Manual path mode requires (nbeads-1) frequencies, one for each internal mode of the path.: If the “mode” tag of “normal_modes” is set to “manual”, it will expect an array of frequencies, one for each of the internal normal modes of the ring polymers.

  • PA-CMD mode requires the target frequency of all the internal modes.: If the “mode” tag of “normal_modes” is set to “pa-cmd”, it will expect an array of one frequency, to which all the internal modes of the ring polymers will be set.

  • WMAX-CMD mode requires [wmax, wtarget]. The normal modes will be scaled such that the first internal mode is at frequency wtarget and all the normal modes coincide at frequency wmax.: If the “mode” tag of “normal_modes” is set to “wmax-cmd”, it will expect an array of two frequencies, one two set the lowest frequency normal mode, and one for the other normal mode frequencies.

  • Number of beads __ doesn’t match GLE parameter nb= __: The matrices used to define the generalized Langevin equations of motion do not have the correct first dimension. If matrices have been downloaded from make sure that you have input the correct number of beads.

  • Initialization tries to match up structures with different atom numbers: If in the initialization any of the matrices has an array shape which do not correspond to the same number of atoms, then they cannot correspond to the same system. Check the size of the arrays specified if they have been input manually.

  • Cannot initialize single atom/bead as atom/bead index __ is larger than the number of atoms/beads: Self-explanatory. However, note that indices are counted from 0, so the first replica/atom is defined by an index 0, the second by an index 1, and so on.

  • Cannot initialize the momenta/masses/labels/single atoms before the size of the system is known.: In the code, a beads object is created to hold all the information related to the configuration of the system. However, until a position vector has been defined, this object is not created. Therefore, whichever arrays are being initialized individually, the position vector must always be initialized first.

  • Trying to resample velocities before having masses.: A Maxwell-Boltzmann distribution is partly defined by the atomic masses, and so the masses must be defined before the velocities can be resampled from this distribution.

  • Cannot thermalize a single bead: It does not make sense to initialize the momenta of only one of the beads, and so i-PI does not give this functionality.

  • Initializer could not initialize __: A property of the system that is mandatory to properly run the simulation has not been initialized in either the “initialize” section or the appropriate section in beads.

  • Ensemble does not have a thermostat to initialize or There is nothing to initialize in non-GLE thermostats or Checkpoint file does not contain usable thermostat data: These are raised if the user has tried to initialize the matrices for the GLE thermostats with a checkpoint file that either does not have a GLE thermostat or does not have a thermostat at all.

  • Size mismatch in thermostat initialization data: Called if the shape of the GLE matrices defined in the checkpoint file is different from those defined in the new simulation.

  • Replay can only read from PDB or XYZ files – or a single frame from a CHK file: If the user specifies a replay ensemble, the state of the system must be defined by either a configuration file or a checkpoint file, and cannot be specified manually.

Output errors

  • The stride length for the __ file output must be positive.: Self-explanatory

  • __ is not a recognized property/output trajectory: The string as defined in the “properties”/”trajectory” tag does not correspond to one of the available trajectories. Make sure that both the syntax is correct, and that the property has been spelt correctly.

  • Could not open file __ for output: Raised if there is a problem opening the file defined by the “filename” attribute.

  • Selected bead index __ does not exist for trajectory __: You have asked for the trajectory of a bead index greater than the number of the replicas of the system. Note that indices are counted from 0, so the first replica is defined by an index 0, the second by an index 1, and so on.

  • Incorrect format in unit specification __: Usually raised if one of the curly braces has been neglected.

  • Incorrect format in argument list __: This will be raised either if one of the brackets has been neglected, or if the delimiters between arguments, in this case “;”, are not correct. This is usually raised if, instead of separating the arguments using “;”, they are instead separated by “,”, since this causes the property array to be parsed incorrectly.

  • __ got an unexpected keyword argument __: This will occur if one of the argument lists of one of the properties specified by the user has a keyword argument that does not match any of those in the function to calculate it. Check the module to see which property this function is calculating, and what the correct keyword arguments are. Then check the “properties” tag, and find which of the arguments has been misspelt.

  • Must specify the index of atom_vec property: Any property which prints out a vector corresponding to one atom needs the index of that atom, as no default is specified.

  • Cannot output __ as atom/bead index __ is larger than the number of atoms/beads: Self-explanatory. However, note that indices are counted from 0, so the first replica/atom is defined by an index 0, the second by an index 1, and so on.

  • Couldn’t find an atom that matched the argument of __: For certain properties, you can specify an atom index or label, so that the property is averaged only over the atoms that match it. If however no atom labels match the argument given, then the average will be undefined. Note that for properties which are cumulatively counted rather than averaged, this error is not raised, and if no atom matches the label given 0 will be returned.

Socket errors

  • Address already in use: This is called if the server socket is already being used by the host network. There are several possible reasons for getting this error. Firstly, it might simply be that two simulations are running concurrently using the same host and port number. In this case simply change the port number of one of the simulations. Secondly, you can get this error if you try to rerun a simulation that previously threw an exception, since it takes a minute or so before the host will disconnect the server socket if it is not shut down cleanly. In this case, simply wait for it to disconnect, and try again. Finally, you will get this error if you try to use a restricted port number (i.e. below 1024) while not root. You should always use a non-restricted port number for i-PI simulations.

  • Error opening unix socket. Check if a file /tmp/ipi___ exists, and remove it if unused.: Similar to the above error, but given if you are using a unix socket rather than an internet socket. Since this binds locally the socket can be removed by the user, which means that it is not necessary to wait for the computer to automatically disconnect an unused server socket.

  • Port number __ out of acceptable range: The port number must be between 1 and 65535, and should be greater than 1024. Change the port number accordingly.

  • Slot number __ out of acceptable range: The slot number must be between 1 and 5. Change the slot number accordingly.

  • ’NoneType’ object has no attribute ’Up’: This is called if an exception is raised during writing the data to output, and so the thread that deals with the socket is terminated uncleanly. Check the stack trace for the original exception, since this will be the actual source of the problem. Also note that, since the socket thread was not cleaned up correctly, the server socket may not have been disconnected properly and you may have to wait for a minute before you can restart a simulation using the same host and port number.

Mathematical errors

  • math domain error: If the cell parameters are defined using the side lengths and angles, with either a pdb file or using the “abcABC” initialization mode, then for some value of the angles it is impossible to construct a valid cell vector matrix. This will cause the code to attempt to take the square root of a negative number, which gives this exception.

  • overflow encountered in exp: Sometimes occurs in NPT runs when the simulation box “explodes”. Make sure you have properly equilibrated the system before starting and that the timestep is short enough to not introduce very large integration errors.

I-PI is slow!

i-PI is not designed to be highly efficient, but it should not be the bottleneck in your calculations. Most of the time, if you see a major slow-down, there is a problem with your setup. Here are some tricks you can try.

  • use a UNIX domain socket: if you run on a single node, it is much faster to use mode=”unix” in your <ffsocket> classes. This uses a shared-memory communication process, that avoids much of the network latency of a TCP/IP socket.

  • reduce latency: if you have a VERY fast forcefield (with force evaluation below ~1ms) it might help to set the <latency> parameter of <ffsocket> to a small value, 1e-4s or less

  • reduce I/O: outputting hundreds of beads configurations at each time step is going to be slow in any scenario, but particularly so when using text files and Python. Reduce the output frequency using a larger stride, and/or flush less often.

  • reduce the stride of internal checkpoints: to guarantee that soft exits leave the simulation in a state that can be restarted safely, i-PI stores the internal state of the simulation at each step. Particularly for complicated setups, the overhead can be substantial. You can reduce the frequency by which the internal state is stored using the safe_stride attribute in the <simulation> tag. Note that doing so increases the risk that the RESTART file saved upon soft exit will be inconsistent with the sate of the outputs, so that restarting a simulaiton will leave broken or discontinuous output files.

  • profile i-PI: if you still think i-PI is being unreasonably slow, you can contact the developers - your setup might have revealed some kind of bottleneck. It will help us if you can also generate a profiler output from your run (possibly with only a small number of steps). You can generate a profiler log by running i-PI with -p option, e.g. i-pi -p input.xml. You will need to install the yappi profiler.