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Todo List
Member _gmx_sel_evaluate_subexpr (gmx_sel_evaluate_t *data, const gmx::SelectionTreeElementPointer &sel, gmx_ana_index_t *g)
The call to gmx_ana_index_difference() can take quite a lot of unnecessary time if the subexpression is evaluated either several times for the same group or for completely distinct groups. However, in the majority of cases, these situations occur when _gmx_sel_evaluate_subexpr_staticeval() can be used, so this should not be a major problem.
Member anonymous_namespace{minimize.cpp}::EnergyEvaluator::run (em_state_t *ems, rvec mu_tot, tensor vir, tensor pres, int64_t count, gmx_bool bFirst)
In practice, the same objects mu_tot, vir, and pres are always passed to this function, so we would rather have them as data members. However, their C-array types are unsuited for aggregate initialization. When the types improve, the call signature of this method can be reduced.
Member areAllGpuDevicesFromAmd (const gmx_gpu_info_t &gpuInfo)
An enumeration visible in the hardware module would make such checks more configurable, if we discover other needs in future.
File boxdeformation.cpp

The .mdp specification should have a boolean for this module.

grompp should set up fields in the tpr file that carry the information about the original box, then the deform module would can be build alongside the update module, rather than need to be set up before the checkpoint is read.

Member c_skipNeutralAtoms
Estimate performance differences.
Member c_usePadding
Estimate performance differences
Member CHECK_SEL (sel)
Get rid of this macro. It should now be possible to handle all errors using exceptions.
File clustsize.cpp
These will be superseded by tests of the new style analysis modules.
File compiler.cpp

Better error handling and memory management in error situations. At least, the main compilation function leaves the selection collection in a bad state if an error occurs.

The memory usage could still be optimized. Use of memory pooling could still be extended, and a lot of redundant gmin/gmax data could be eliminated for complex arithmetic expressions.

Page Custom selection methods
The modifier handling could be made more flexible and more generic; the current implementation does not allow many things which would be possible with slight changes in the internals of the library.
Member ddSendrecv (const gmx_domdec_t *dd, int ddDimensionIndex, int direction, T *sendBuffer, int numElementsToSend, T *receiveBuffer, int numElementsToReceive)
This function template is deprecated, new calls should be made to the version taking ArrayRef parameters and this function template removed when unused.
Member df_history_t
Split out into microstate and observables history.
Get rid of this (Redmine #950). It is not necessary for constructing paths on the systems that it currently supports, and is not reliable in parsing input paths either, since Windows needs to accept both instead of only DIR_SEPARATOR. At the very least, we should refactor the clients of this header so that they operate upon path objects rather than raw path strings.
File domdec_network.h
Wrap the raw dd_bcast in md.cpp into a higher-level function in the domdec module, then this file can be module-internal.
File evaluate.cpp
One of the major bottlenecks for selection performance is that all the evaluation is carried out for atoms. There are several cases when the evaluation could be done for residues or molecules instead, including keywords that select by residue and cases where residue centers are used as reference positions. Implementing this would require a mechanism for recognizing whether something can be evaluated by residue/molecule instead by atom, and converting selections by residue/molecule into selections by atom when necessary.
Member exist_output_file (const char *fnm_cp, int nfile, const t_filenm fnm[])
This could be implemented sanely with a for loop.
Member fit_acf (int ncorr, int fitfn, const gmx_output_env_t *oenv, gmx_bool bVerbose, real tbeginfit, real tendfit, real dt, real c1[], real *fit)
check parameters
Member ftype_is_bonded_potential (int ftype)
This function could go away when idef is not a big bucket of everything.
Class gmx::AbstractAnalysisArrayData
Add support for multiple data sets.
Class gmx::AbstractAnalysisData
Improve the exception-handling semantics. In most cases, it doesn't make much sense to continue data processing after one module fails, but having the alternative would not hurt.
Member gmx::AbstractAnalysisData::addColumnModule (int col, int span, AnalysisDataModulePointer module)

This method doesn't currently work in all cases with multipoint data or with multiple data sets. In particular, if the added module requests storage and uses getDataFrame(), it will behave unpredictably (most likely asserts).

Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

Member gmx::AbstractAnalysisData::applyModule (IAnalysisDataModule *module)
Currently, this method may not work correctly if module requests storage (addModule() has the same problem if called after data is started).
Member gmx::AbstractOptionStorage::processSet ()=0
Improve the call semantics.
Class gmx::AnalysisData
Parallel implementation is not complete.
Member gmx::AnalysisDataPlotSettings::plotFormat () const
Use a proper enum.
Class gmx::AnalysisDataStorage
Proper multi-threaded implementation.
Class gmx::AnalysisNeighborhood
Generalize the exclusion machinery to make it easier to use for other cases than atom-atom exclusions from the topology.
Class gmx::AnalysisNeighborhoodSearch

Make it such that reset() is not necessary to call in code that repeatedly assigns the result of AnalysisNeighborhood::initSearch() to the same variable (see sm_distance.cpp).

Consider removing minimumDistance(), as nearestPoint() already returns the distance.

Class gmx::ArrayRef< T >
This class is not complete. There are likely also methods missing (not required for current usage).
Class gmx::Awh
Update parameter reading and checkpointing, when general C++ framework is ready.
Member gmx::BiasParams::isCheckHistogramForAnomaliesStep (int64_t step) const
Currently this function just calls isCheckCoveringStep but the checks could be done less frequently.
Member gmx::BoxMatrix
Implement a full replacement for C-style real[DIM][DIM]
Member gmx::checkUserGpuIds (const gmx_gpu_info_t &gpu_info, const std::vector< int > &compatibleGpus, const std::vector< int > &gpuIds)
Note that the selected GPUs can be different on each rank, and the IDs of compatible GPUs can be different on each node, so this routine ought to do communication to determine whether all ranks are able to proceed. Currently this relies on the MPI runtime to kill the other processes because GROMACS lacks the appropriate infrastructure to do a good job of coordinating error messages and behaviour across MPMD ranks and multiple simulations.
Class gmx::compat::not_null< T >
Eliminate this when we require a version of C++ that supports std::not_null.
Member gmx::Constraints::setConstraints (const gmx_localtop_t &top, const t_mdatoms &md)
Make this a callback that is called automatically once a new domain has been made.
Member gmx::cshake (const int iatom[], int ncon, int *nnit, int maxnit, const real constraint_distance_squared[], real positions[], const real initial_displacements[], const real half_of_reduced_mass[], real omega, const real invmass[], const real distance_squared_tolerance[], real scaled_lagrange_multiplier[], int *nerror)
Make SHAKE use better data structures, in particular for iatom.
Member gmx::DataFileInfo::bFromDefaultDir
Consider replacing with an enum that identifies the source (current dir, GMXLIB, default).
Class gmx::detail::PaddingTraits< T >
Consider explicitly tying these types to the SimdTrait types. That would require depending on the SIMD module, or extracting the traits from it. This would also permit maxSimdWidthOfBaseType to be set more efficiently, e.g. as a metaprogramming max over the maximum width from different implementations.
Class gmx::ExceptionInitializer
With the exception of the reason string, information added with this class is not currently accessible through any public API, except for calling printFatalErrorMessage(), formatExceptionMessageToString() or formatExceptionMessageToFile(). This is not implemented as there is not yet need for it, and it is not clear what would be the best alternative for the access. It should be possible to refactor the internal implementation to suit the needs of such external access without requiring changes in code that throws these exceptions.
Member gmx::FileNameOption::libraryFile (bool bLibrary=true)
Currently, this flag only affects the help output. Callers must take care themselves to actually search the file in the library directories. It would be nicer to do this searching within the file name option implementation.
Class gmx::FileNameOptionManager
Most of the functionality in this class is specific to command line parsing, so it would be cleaner to replace this with an interface, and have the actual code in the commandline module.
Member gmx::getPageSize ()
Move this function into sysinfo.cpp where other OS-specific code/includes live
Member gmx::GromacsException::prependContext (const std::string &context)
The added information is currently not accessible through what(), nor through any other means except for calling printFatalErrorMessage(), formatExceptionMessageToString() or formatExceptionMessageToFile(). See ExceptionInitializer for more discussion.
Member gmx::HelpWriterContext::setReplacement (const std::string &search, const std::string &replace)
Improve semantics if the same search item is set multiple times.
Class gmx::HostAllocationPolicy
As a minor optimization, consider also having a stateless version of this policy, which might be slightly faster or more convenient to use in the cases where it is known at compile time that the allocation will be used to transfer to a GPU.
Member gmx::hwinfo_g
This should become a shared_ptr owned by e.g. Mdrunner::runner() that is shared across any threads as needed (e.g. for thread-MPI). That offers about the same run time performance as we get here, and avoids a lot of custom code.
Member gmx::initializeClfftLibrary ()

Consider making a composite object that also handles on-demand compilation, managing lifetime of PME FFT kernel programs to avoid exhausting resources and/or recompiling kernels previously used. See Redmine #2535.

Consider implementing an appropriate flavor of the nifty counter idiom so that both static initialization and deinitialization can work in a fast, leak-free, and thread-safe way without imposing constraints on the calling code. See Redmine #2535.

Consider implementing an appropriate flavor of the nifty counter idiom so that both static initialization and deinitialization can work in a fast, leak-free, and thread-safe way without imposing constraints on the calling code. See Redmine #2535.

Consider implementing an appropriate flavor of the nifty counter idiom so that both static initialization and deinitialization can work in a fast, leak-free, and thread-safe way without imposing constraints on the calling code. See Redmine #2535.

Member gmx::internal::AnalysisDataStorageImpl::needStorage () const
This could be extended to non-multipoint data as well.
Member gmx::internal::AnalysisDataStorageImpl::pendingLimit_
Get rid of this alltogether, as it is no longer used much.
Class gmx::IOptionValueStore< T >
Try to make this more like a write-only interface, getting rid of the need to access the stored values through this interface. That would simplify things.
Class gmx::IRestraintPotential
Template headers can help to build compatible calculation methods with different input requirements. For reference, see
Member gmx::IRestraintPotential::bindSession (gmxapi::SessionResources *resources)
This should be more general than the RestraintPotential interface.
Member gmx::IRestraintPotential::evaluate (Vector r1, Vector r2, double t)=0
The virtual function call should be replaced by a (table of) function objects retrieved before the run.
Member gmx::IRestraintPotential::update (gmx::Vector v, gmx::Vector v0, double t)
: Provide gmxapi facility for plugin restraints to wrap themselves with a default implementation to let this class be pure virtual.
Class gmx::LegacyMdrunOptions

Modules in mdrun should acquire proper option handling so that all of these declarations and defaults are local to the modules.

Contextual aspects, such as working directory, MPI environment, and environment variable handling are more properly the role of SimulationContext, and should be moved there

Member gmx::LegacyMdrunOptions::oenv
Clarify initialization, ownership, and lifetime.
Member gmx::Lincs::ntask
This is mostly used to loop over task, which would be nicer to do with range-based for loops, but the thread index is used for constructing bit masks and organizing the virial output buffer, so other things need to change, first.
Class gmx::MDAtoms
Refactor this class and rename MDAtoms once the group scheme is removed.
Class gmx::Mdrunner

Most of the attributes should be declared by specific modules as command-line options. Accordingly, they do not conform to the naming scheme, because that would make for a lot of noise in the diff, only to have it change again when the options move to their modules.

Preparing logging and MPI contexts could probably be a higher-level responsibility, so that an Mdrunner would get made without needing to re-initialize these components (as currently happens always for the master rank, and differently for the spawned ranks with thread-MPI).

Member gmx::Mdrunner::addPotential (std::shared_ptr< IRestraintPotential > restraint, std::string name)
Mdrunner should fetch such resources from the SimulationContext rather than offering this public interface.
Member gmx::Mdrunner::cloneOnSpawnedThread () const
clarify (multiple) invariants during MD runner start-up. The runner state before and after launching threads is distinct enough that it should be codified in the invariants of different classes. That would mean that the object returned by this method would be of a different type than the object held by the client up to the point of call, and its name would be changed to "launchOnSpawnedThread" or something not including the word "clone".
Member gmx::MdrunnerBuilder::addBondedTaskAssignment (const char *bonded_opt)

Replace with modern strings or (better) enum classes.

Make optional and/or encapsulate into task assignment module.

Member gmx::MdrunnerBuilder::addDomainDecomposition (const DomdecOptions &options)
revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
Member gmx::MdrunnerBuilder::addElectrostatics (const char *pme_opt, const char *pme_fft_opt)

Replace with modern strings or (better) enum classes.

Make optional and/or encapsulate into electrostatics module.

Member gmx::MdrunnerBuilder::addFilenames (ArrayRef< const t_filenm > filenames)
Modules should manage their own filename options and defaults.
Member gmx::MdrunnerBuilder::addMultiSim (gmx_multisim_t *multisim)

Clarify semantics of specifying optional multisim work

Clarify ownership and management of multisim resources.

Member gmx::MdrunnerBuilder::addNonBonded (const char *nbpu_opt)

Replace with string or enum that we can have sensible defaults for.

Either the Builder or modular Director code should provide sensible defaults.

Member gmx::MdrunnerBuilder::addOutputEnvironment (gmx_output_env_t *outputEnvironment)
Allow client code to set up output environment and provide as a resource. This parameter is used to set up resources that are dependent on the execution environment and API context. Such resources should be retrieved by the simulator from a client-provided resource, but currently the resources are only fully initialized in Mdrunner.
Member gmx::MdrunnerBuilder::addReplicaExchange (const ReplicaExchangeParameters &params)
revisit whether we should be passing this parameter struct or a higher-level handle of some sort.
Member gmx::MdrunnerBuilder::addSimulationMethod (const MdrunOptions &options, real forceWarningThreshold)
Map these parameters to more appropriate encapsulating types. Find a better way to indicate "unspecified" than a magic value of the parameter type.
Member gmx::MdrunnerBuilder::MdrunnerBuilder (compat::not_null< SimulationContext * > context)
Find and implement appropriate abstraction layers for SimulationContext. At some point this parameter should become a constant reference or value instead of a pointer. Ref e.g.
Member gmx::OptionFlag
The flags related to default values are confusing, consider reorganizing them.
Member gmx::PaddedVector< T, Allocator >::PaddedVector (size_type count)
This should also be specialized by allocator, but std::vector for storage_ doesn't have such a constructor before C++14. Resolve.
Member gmx::PaddedVector< T, Allocator >::PaddedVector (size_type count, value_type const &v)
This should also be specialized by allocator, but std::vector for storage_ doesn't have such a constructor before C++14. Resolve.
Member gmx::Regex::Regex (const char *value)
Consider whether some other exception type would be better.
Member gmx::reportGpuUsage (const MDLogger &mdlog, bool userSetGpuIds, const GpuTaskAssignments &gpuTaskAssignmentOnRanksOfThisNode, size_t numGpuTasksOnThisNode, size_t numPpRanks, bool bPrintHostName, bool useGpuForBonded, PmeRunMode pmeRunMode)
It could be useful to report also whether any nodes differed, and in what way.
Class gmx::RestraintManager
This should be generalized as work description and factory functions in Context.
Member gmx::Selection::setEvaluateVelocities (bool bEnabled)
Implement it such that in the above case, hasVelocities() will return false for such frames.
Class gmx::SelectionOption

Support for specifying that an option accepts, e.g., two to four selections. Currently, only a fixed count or any number of selections is possible. In addition to allowing this in OptionTemplate, also SelectionOptionManager needs to be updated.

Class gmx::SimulationContext

This class should also handle aspects of simulation environment such as working directory and environment variables.

Impose sensible access restrictions. Either the SimulationContext should be passed to the Mdrunner as logically constant or a separate handle class can provide access to resources that have been allocated by (negotiated with) the client for the current simulation (or simulation segment). Non-const accessors to shared resources need to be associated with update signals that the simulation components (modules and runner) can subscribe to.

Member gmx::SimulationContext::communicationRecord_
Context should own communicator.
Member gmx::SurfaceAreaCalculator::calculate (const rvec *x, const t_pbc *pbc, int nat, int index[], int flags, real *area, real *volume, real **at_area, real **lidots, int *n_dots) const
Make the output options more C++-like, in particular for the array outputs.
Class gmx::test::AbstractTrajectoryAnalysisModuleTestFixture
Adding facilities to AnalysisData to check whether there are any output modules attached to the data object (directly or indirectly), marking the mocks as output modules, and using these checks in the tools instead of or in addition to the output file presence would be a superior. Also, the full file names should be deducible from the options.
Class gmx::test::AnalysisDataTestFixture
Support for arbitrary AnalysisDataValues (errors and missing values).
Class gmx::test::anonymous_namespace{pmetest.cpp}::PmeTest
Consider also using GpuTest class.
Member gmx::test::anonymous_namespace{simulationdatabase.cpp}::prepareDefaultMdpFieldValues (const char *simulationName)
ideally some of these default values should be the same as grompp uses, and sourced from the same place, but that code is a bit of a jungle until we transition to using IMdpOptions more.
Member gmx::test::checkEnergiesAgainstReferenceData (const std::string &energyFilename, const EnergyTolerances &energiesToMatch, TestReferenceChecker *checker)
This is quite similar to the functionality used in PmeTest, and we should consider reducing the duplication.
Member gmx::test::compareBox (const TrajectoryFrame &reference, const TrajectoryFrame &test, const TrajectoryFrameMatchSettings &matchSettings, const FloatingPointTolerance tolerance)
This could be streamlined when we have a proper 3D matrix class and view.
Class gmx::test::FloatingPointTolerance
The factory methods that take ULP difference could be better formulated as methods that take the acceptable number of incorrect bits and/or the number of accurate bits.
Member gmx::test::getKeys (const Map &m)
This returns a copy of the keys, which is convenient, but inefficient. Alternatively, this could return a view of the keys from a range rather than a container, but there's no implementation of that in C++11 at the moment.
Class gmx::test::SettleTest

This also tests that if the calling code requires velocities and virial updates, that those outputs do change, but does not test that those changes are correct.

Only no-PBC and cubic-PBC are tested here, but the correct function of the SIMD version of set_pbx_auic in all cases should be tested elsewhere.

Class gmx::test::TerminationHelper
This approach is not very elegant, but "stuff doesn't segfault or give a fatal error" is a useful result. We can improve it when we can mock out more do_md() functionality. Before that, we'd probably prefer not to run this test case in per-patchset verification, but this is the best we can do for now.
Member gmx::test::throwIfNonEmptyAndOnlyWhitespace (const std::string &s, const char *id)
Eliminate this limitation of TinyXML2. See e.g.
Member gmx::TextWriter::wrapperSettings ()
Wrapping is not currently implemented for code that writes partial lines with writeString().
Class gmx::TimeUnitManager

This class is independent of the options implementation. To ease reuse, it could be moved to the utility module, and only TimeUnitBehavior left here.

Member gmx::TopologyInformation::fillFromInputFile (const std::string &filename)
This should throw upon error but currently does not.
Class gmx::TrajectoryAnalysisSettings
Remove plain flags from the public interface.
Class gmx::TrajectoryFrame

Eventually t_trxframe should be replaced by a class such as this. Currently we need to introduce BoxMatrix so that we can have a normal C++ getter that returns the contents of a box matrix, since you cannot use a real[DIM][DIM] as a function return type.

Consider a std::optional work-alike type for expressing that a field may or may not have content.

Class gmx_hw_opt_t
During mdrunner(), if the user has left any of these values at their defaults (which tends to mean "choose automatically"), then those values are over-written with the result of such automation. This creates problems for the subsequent code in knowing what was done, why, and reporting correctly to the user. Find a way to improve this.
Member gmx_pme_init (const t_commrec *cr, const NumPmeDomains &numPmeDomains, const t_inputrec *ir, int homenr, gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj, gmx_bool bReproducible, real ewaldcoeff_q, real ewaldcoeff_lj, int nthread, PmeRunMode runMode, PmeGpu *pmeGpu, const gmx_device_info_t *gpuInfo, PmeGpuProgramHandle pmeGpuProgram, const gmx::MDLogger &mdlog)
We should evolve something like a GpuManager that holds gmx_device_info_t * and PmeGpuProgramHandle and perhaps other related things whose lifetime can/should exceed that of a task (or perhaps task manager). See Redmine #2522.
Member gmx_pme_init (const t_commrec *cr, const NumPmeDomains &numPmeDomains, const t_inputrec *ir, int homenr, gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj, gmx_bool bReproducible, real ewaldcoeff_q, real ewaldcoeff_lj, int nthread, PmeRunMode runMode, PmeGpu *pmeGpu, const gmx_device_info_t *gpuInfo, PmeGpuProgramHandle pmeGpuProgram, const gmx::MDLogger &mdlog)
We should evolve something like a GpuManager that holds gmx_device_info_t * and PmeGpuProgramHandle and perhaps other related things whose lifetime can/should exceed that of a task (or perhaps task manager). See Redmine #2522.
Member GMX_UNUSED_VALUE (value)
Deprecated - use gmx_unused
Class GpuParallel3dFft
Make this class actually parallel over multiple GPUs
File grid.h
: Replace this by a more generic grid class once that is available.
File grompp.cpp
Refactor SimulationRunner to split off SimulationPreparer, so that integration tests of grompp can stand apart from tests of mdrun.
File handlerestart.cpp
Clean up the error-prone logic here. Add doxygen.
File handlerestart.h
There may be other code in runner.cpp etc. that can usefully live here
Class history_t
Rename this with a more descriptive name.
File hostallocator.h
This should not be in the public API, but it needs to be for the moment because state.h is in that API.
File indexutil.cpp
Tests for other functions, at least the set operations.
File invertmatrix.cpp
Test error conditions when they throw exceptions
File legacyenergy.cpp
These will be superseded by tests of the energyanalysis modules.
File mempool.h
Document these functions.
Group module_domdec
Get domdec stuff out of mdtypes/commrec.h
File nbsearch.cpp
The grid implementation could still be optimized in several different ways:
  • A better heuristic for selecting the grid size or falling back to a simple all-pairs search.
  • A multi-level grid implementation could be used to be able to use small grids for short cutoffs with very inhomogeneous particle distributions without a memory cost.
File nbsearch.cpp
Increase coverage of these tests for different corner cases: other PBC cases than full 3D, large cutoffs (larger than half the box size), etc. At least some of these probably don't work correctly.
Member pbc_rvec_sub (const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
This kind of code appears in many places. Consolidate it
Member pmalloc (void **h_ptr, size_t nbytes)
This function should allocate page-locked memory to help reduce D2H and H2D transfer times, similar with pmalloc from
File pme-gpu-constants.h
The values are currently common to both CUDA and OpenCL implementations, but should be reconsidered when we tune the OpenCL implementation. See Redmine #2528.
File pme-gpu-types-host.h
Some renaming/refactoring, which does not impair the performance: – bringing the function names up to guidelines – PmeGpuSettings -> PmeGpuTasks – refining GPU notation application (#2053) – renaming coefficients to charges (?)
Member pme_gpu_reinit_computation (const gmx_pme_t *pme, gmx_wallcycle *wcycle)
Rename this function to clear – it clearly only does output resetting and we should be clear about what the function does..
Member pme_gpu_task_enabled (const gmx_pme_t *pme)
This is a rather static data that should be managed by the hardware assignment manager. For now, it is synonymous with the active PME codepath (in the absence of dynamic switching).
Member pme_run_mode (const gmx_pme_t *pme)
This is a rather static data that should be managed by the higher level task scheduler.
Member PmeGpu::kernelParams
Test whether this should be copied to the constant GPU memory once for each computation (or even less often with no box updates) instead of being an argument.
Class PmeGpuProgramImpl
In future if we would need to react to either user input or auto-tuning to compile different kernels, then we might wish to revisit the number of kernels we pre-compile, and/or the management of their lifetime.
Member PmeRunMode
: make this enum class with gmx_pme_t C++ refactoring
Member PmeShared::previousBox

Manage this on higher level.

Alternatively, when this structure is used by CPU PME code, make use of this field there as well.

File pmetest.cpp

Extend and generalize this for more multi-rank tests (-npme 0, -npme 2, etc).

Implement death tests (e.g. for PME GPU decomposition).

File pointers.h
Replace comments referring to c++14-constexpr with constexpr when we require C++14.
File poscalc.cpp

There is probably some room for optimization in the calculation of positions with bases. In particular, the current implementation may do a lot of unnecessary copying. The interface would need to be changed to make it possible to use the same output positions for several calculations.

The current algorithm for setting up base calculations could be improved in cases when there are calculations that cannot use a common base but still overlap partially (e.g., with three calculations A, B, and C such that A could use both B and C as a base, but B and C cannot use the same base). Setting up the bases in an optimal manner in every possible situation can be quite difficult unless several bases are allowed for one calculation, but better heuristics could probably be implemented. For best results, the setup should probably be postponed (at least partially) to gmx_ana_poscalc_init_eval().

Member read_checkpoint_data (const char *filename, int *simulation_part, t_commrec *cr, gmx_bool bTryToAppendFiles, int nfile, const t_filenm fnm[], const char *part_suffix, gmx_bool *bAddPart, bool *bDoAppendFiles)
Clean this up (next patch)
This flag overlaps with the function of v.nalloc field, and could probably be removed, making memory management simpler. Currently, the v.nalloc field is not kept up-to-date in all cases when this flag is changed and is used in places where this flag is not, so this would require a careful investigation of the selection code.
Page Selection compilation
Some combinations of method parameter flags are not yet properly treated by the compiler or the evaluation functions in evaluate.cpp. All the ones used by currently implemented methods should work, but new combinations might not.
Member set_over_alloc_dd (gmx_bool set)
This is mdrun-specific, so it might be better to put this and over_alloc_dd() much higher up.
Member set_zones_size (gmx_domdec_t *dd, matrix box, const gmx_ddbox_t *ddbox, int zone_start, int zone_end, int numMovedChargeGroupsInHomeZone)
When converting domdec to use proper classes, all these variables should be private and a method should return the correct count depending on an internal state.
File simulationsignal.cpp
Move this to mdrunutility module alongside gathering multi-simulation communication infrastructure there.
File simulationsignal.h
Move this to mdrunutility module alongside gathering multi-simulation communication infrastructure there.
File sm_insolidangle.cpp

The implementation could be optimized quite a bit.

Move the covered fraction stuff somewhere else and make it more generic (along the lines it is handled in selection.h and trajana.h in the old C API).

File snprintf.h
When all callers of snprintf compile as C++, perhaps use gmx::formatString() everywhere instead of snprintf.
Class t_state
Move pure observables history to ObservablesHistory.
File testasserts.h

The implementation is somewhat ugly, and accesses some Google Test internals. Could be nice to clean it up a bit.