[RFC] Work towards reusable CVCs #700

HanatoK · 2024-06-29T22:52:01Z

Well, I believe that no one would really like this PR. This PR uses a lot of hacks and workarounds in the backend to achieve reusable CVCs in SMP with limitations as less as possible (although I am not a big fan of distributing CVCs over threads), including:

Build a toy AST and determine the parallelization scheme by the depth of the node. At first glance, colvardeps looks like an AST but after playing with it I feel it is not a real one, and it really just checks the dependencies of features, and there is no true AST. It would be better if Colvars could be redesigned with a true AST and a dependency checker for it. The dependency checker should not own the AST;
Bypass the colvar class and take the cvc objects out to build the AST. I think that the colvar class should be completely removed;
I don't know why the smp_lock and smp_unlock in colvarproxy_namd are implemented as creating and destroying locks, so I have changed them;
Implement the chain rule in a dirty manner (see colvar::cvc::modify_children_cvcs_atom_gradients and propagate_colvar_force). When calling calc_gradients and apply_force of a CVC consisting of sub-CVCs, it now propagates the gradients and forces to all its sub-CVCs;
To avoid race condition in propagating the atom gradients when reusing CVCs, I have to use smp_lock. However, it is very coarse-grained so I expect an additional performance penalty. I thought there should be a lock tied to each atom group but found none.

In summary, I think that Colvars should be fundamentally changed to achieve better support of reusable components and parallelization.

This PR tries to solve #232, extends #644 and finishes:

Reusing the computation of the individual "nodes" in a pair of path CVs ("s" and "z").

HanatoK · 2024-06-30T23:16:05Z

After some thoughts I feel there is no way to make explicit gradients working correctly with reusable components, so I will disable it in this PR.

This does not work as Colvars was not designed with automatic differentiation in mind.

HanatoK · 2024-07-01T15:09:04Z

The problem of `calc_gradients()`

Colvars was not designed with automatic differentiation (AD) in mind. At first glance, it seems to perform the forward AD because for each CVC, the calc_gradients() is executed just after calc_value, but the colvar class, supposed to be a function of CVC, does not have explicit gradients with respect to the atoms. Conversely, colvar::communicate_forces just computes the gradients with respect to CVCs on-the-fly, which seems to be a backward AD implementation. Furthermore, the colvarvalue class has no gradient field, which is opposed to many other implementations like torch.tensor and PLMD::Value, and the CVC class does not store the gradients, either. All these factors make either forward AD or backward AD using calc_gradients() for CVCs of sub-CVCs difficult. The apply_force() code path is less broken as it looks consistent with backward AD and the backward propagation in PLUMED.

The problem of `colvardeps`

From the perspective of compiler or interpreter, when constructing the CVC object in colvar::cvc::cvc, Colvars is still in the stage of syntax analysis, parsing the syntax of the config file and trying to build a tree of colvardeps, but it ought to be noted that before running cvc::init the syntax analysis is not done. The weird design is that init_dependencies is called after the constructor of CVC and before cvc::init and checks the dependencies. In general, feature dependencies are a semantic thing, and that means that Colvars interleaves the syntax analysis with the semantic analysis, which, in my opinion, is a bad design.

AST Giacomo said that variables_active_smp is used for making the colvar object appearing in the loop multiple times for the original parallelization scheme. As I understand, this means that I can use variables_active directly to build the AST instead of the duplicated items in variables_active_smp.

jhenin · 2024-07-03T12:06:55Z

namd/src/colvarproxy_namd.C

+  if (it_find == cvc_info_map.end()) {
+    cvc_info_map.insert({parent, cvc_info{
+      // TODO: Here calc_cvc_values calls cvcs[i]->is_enabled() , which is is_enabled(int f = f_cv_active)
+      //       I know both f_cv_active and f_cvc_active are 0 but are they the same option??


The fact that f_cv_active and f_cvc_active have the same numerical value has no consequence, they should never be used in the same context, because they are respectively only meaningful in a colvar or cvc object. The colvardeps data of these two classes are non-overlapping. The relationship between them is a vertical (parent-child) dependency.

If we were to merge the two levels, then these two features would merge.

The issue is that in

colvars/src/colvar.cpp

Line 1437 in 0f2d682

if (!cvcs[i]->is_enabled()) continue;

, is_enabled() is called, and since there is no function parameter passed, so I think it would call

colvars/src/colvardeps.h

Line 167 in 0f2d682

inline bool is_enabled(int f = f_cv_active) const {

which checks f_cv_active instead of f_cvc_active. My code is to follow what the original calls in calc_cvc_values and I am not sure if I need to follow it the same way.

You're right, sorry. That is somewhat sloppy writing that I didn't remember well. It does rely on the "active" property being number 0.

colvars/src/colvardeps.h

Line 224 in 0f2d682

// NOTE that all feature enums should start with f_*_active

But a class inheriting from colvardeps could also override is_enabled() and change this convention.

How much effort do you think it would be to remove the default argument for this virtual function? Remember that this is one of the "issues" that clang-tidy was complaining about.

That would be very little effort. I'm happy to do that if that helps in any way.

jhenin · 2024-07-03T12:09:29Z

namd/src/colvarproxy_namd.C

+       it != cv->variables_active_smp()->end(); ++it) {
+    // TODO: Bad design! What will happen if CVC a is in a "colvar" block
+    // that does not support total_force_calc, but is then reused in
+    // another block that requires total_force_calc even if it supports Jacobian itself???


I don't see the problem here. Assuming a cvc can have several parents: the colvar that does require a total force can enable it in its children cvcs, even if other parents don't require (or support) it.

You are right. I just thought that if a colvar does not require the total force, then it would disable the corresponding feature of the children, but it seems the code do not check the dependency in that way.

It's the other way: disabled by default, and enabled on request - then disabled again if the refcount falls to zero.

HanatoK · 2024-07-03T19:35:46Z

namd/src/colvarproxy_namd.C

+                       lambda_fn, NULL, CKLOOP_NONE, NULL);
+  }
+  cvm::decrease_depth();
+  return cvm::get_error();


Parallelization and checking the error

When I wrote and test new code, I found that NAMD may not exit cleanly (some other threads were still running) if one thread was exited. I think the implementation of colvarproxy_namd::error or at least its use in the parallel region, needs to be revised to use a std::atomic<bool> to setup an error "bit" instead of calling NAMD_die directly. Then after all threads are finished and joined, we can use cvm::get_error() to check the error bit and exit if there is an error.

jhenin · 2024-07-04T15:05:22Z

The problem of colvardeps

From the perspective of compiler or interpreter, when constructing the CVC object in colvar::cvc::cvc, Colvars is still in the stage of syntax analysis, parsing the syntax of the config file and trying to build a tree of colvardeps, but it ought to be noted that before running cvc::init the syntax analysis is not done. The weird design is that init_dependencies is called after the constructor of CVC and before cvc::init and checks the dependencies. In general, feature dependencies are a semantic thing, and that means that Colvars interleaves the syntax analysis with the semantic analysis, which, in my opinion, is a bad design.

There seems to be a misunderstanding here. To clarify, the spirit of init_dependencies is not that it "checks dependencies" - rather, it initializes the static dependency tree between features. The proper dependency checking happens with calls to enable(), which happen either during the semantic analysis of the input, or throughout the run in case of dynamic dependencies.

HanatoK · 2024-07-04T15:44:46Z

The problem of colvardeps

From the perspective of compiler or interpreter, when constructing the CVC object in colvar::cvc::cvc, Colvars is still in the stage of syntax analysis, parsing the syntax of the config file and trying to build a tree of colvardeps, but it ought to be noted that before running cvc::init the syntax analysis is not done. The weird design is that init_dependencies is called after the constructor of CVC and before cvc::init and checks the dependencies. In general, feature dependencies are a semantic thing, and that means that Colvars interleaves the syntax analysis with the semantic analysis, which, in my opinion, is a bad design.

There seems to be a misunderstanding here. To clarify, the spirit of init_dependencies is not that it "checks dependencies" - rather, it initializes the static dependency tree between features. The proper dependency checking happens with calls to enable(), which happen either during the semantic analysis of the input, or throughout the run in case of dynamic dependencies.

Thanks for the clarifications. You are right that init_dependencies only declares the dependencies. However, I think that the problem is still calling enable that tries to check the dependencies while still initializing the children CVCs, so for CVC of sub-CVCs, I cannot do the checking here:

colvars/src/colvarcomp_combination.cpp

Lines 58 to 60 in ff35f9c

    
           // TODO: I don't know why I cannot check this 
        
           // if (is_enabled(f_cvc_gradient)) 
        
               sub_cv->enable(f_cvc_gradient);

Also, I cannot use add_child in colvardeps to declare that a sub-CVC is a child of the other, as add_child also does dependency checking, so I think that it is a bad design to check dependencies while calling the initialization function. Calling the init means that Colvars is still parsing options, and the abstract syntax tree is not completely built, but the dependencies are semantic things that should be done after the AST is completely built.

In my opinion, the following structure should be separated from colvardeps,

colvars/src/colvardeps.h

Lines 155 to 162 in ff35f9c

    
           /// pointers to objects this object depends on 
        
           /// list should be maintained by any code that modifies the object 
        
           /// this could be secured by making lists of colvars / cvcs / atom groups private and modified through accessor functions 
        
           std::vector<colvardeps *> children; 
        
           /// pointers to objects that depend on this object 
        
           /// the size of this array is in effect a reference counter 
        
           std::vector<colvardeps *> parents;

to form the AST, and colvardeps should only be a feature-dependency checker, and not own the AST. Adding new children to the AST should not trigger the checker. In other words, it is better that colvardeps acts somewhat like an LLVM pass.

jhenin · 2024-07-10T09:50:33Z

Thanks @HanatoK , I now understand your point better and I fully agree!

To move the AST out of colvardeps and allow same-level dependencies, we need to deal with the fact that children objects of a CVC can be CVCs or atom groups, so those should be described by different parts of the feature tree.

jhenin · 2024-08-26T13:30:24Z

@HanatoK - this is a large and disruptive change set. I think there are items in there that we can agree on. Having an AST alongside the colvardeps class is one.

Your initial point 2 was: Bypass the colvar class and take the cvc objects out to build the AST. I think that the colvar class should be completely removed;
The colvar class is the main workhorse at the moment, but I suppose you mean merging the cvc and colvar classes into one. I generally agree with that idea, although that will give a large class, where only a small subset of features will be used by most instances.

giacomofiorin · 2024-09-16T14:16:27Z

@jhenin's comment is good. There are multiple small fixes here that are definitely worth integrating, but they are mixed with others that pertain to broader design issues.

I also agree that the AST could be the most immediate goal. We had discussed in the past the possibility of adding such functionality to colvardeps, but it also looked like that would amount to feature creep for that class.

If you are aware of suitable classes in the C++ standard library, can you suggest them?

HanatoK · 2024-09-25T15:31:29Z

@jhenin's comment is good. There are multiple small fixes here that are definitely worth integrating, but they are mixed with others that pertain to broader design issues.

I also agree that the AST could be the most immediate goal. We had discussed in the past the possibility of adding such functionality to colvardeps, but it also looked like that would amount to feature creep for that class.

If you are aware of suitable classes in the C++ standard library, can you suggest them?

As far as I understand, the AST is just constructed as the same way as colvardeps that has pointers to children and parents nodes. colvardeps itself is actually an AST, but the issue is that it mixes up two goals, namely (i) determining the order of calculations of component and biases (the dependencies between colvardeps and its derived objects), and (ii) checking the feature-level compatibilities/dependencies. In other words, I think it is better to

Hold a root node of colvardeps in colvarmodule instead of separating std::vector<colvar *> and std::vector<colvarbias *> . The order of calculation can then be determined by traversing the colvardeps root node, calculating the children objects at first and then parent objects;
Make colvardeps focus on goal (i). colvardeps::add_child should just modify children and child->parents and not check the feature-level dependencies, and the same to remove_child. A tree of colvardeps* is constructed when reading the config file, but we skip checking the feature-level dependencies;
Make an independent feature-level dependency checker that takes the colvardeps* as a parameter. After a tree of colvardeps* is constructed or modified, this checker is expected to traverse the tree and check both the "static" and "dynamic" feature-level dependencies between children and parents;
For the feature-level dependencies, it might be better to avoid enable and disable, and derived classes of colvarcomp ought to use provide and require. The dynamic feature dependencies could be determined by the above dependency checker or another separate function that can traverse the tree of colvardeps*.

I mark the PR as draft as it seems too disruptive and might need further discussions.

jhenin · 2024-09-27T09:38:52Z

@HanatoK I've now looked at this in more detail. This has a lot of merit. What it would need to be merge-ready is at least:

Fewer TODOs and self-described hacks;
passing regression tests (now I see some failures in the NAMD-based library tests);
documentation of the user-facing changes.

One question: can this be done without implementing the AST design you described just above? If yes, I would rather separate these issues as much as possible and merge code that works to avoid letting this branch diverge too much.

Side note: I think you should be able to set your GH account so that the CI actions run in your fork, which would give us CI for this PR.

HanatoK · 2024-09-27T14:58:03Z

1. Fewer TODOs and self-described hacks;

Well, actually this PR was not intended to be merged into the master branch directly. Instead, I developed the code based on #644, generalized the idea of reusable CVCs and tried my best to solve the SMP issue.

2. passing regression tests (now I see some failures in the NAMD-based library tests);

This PR is based on #644 so I don't want it diverges from the reusable-cvcs branch. The NAMD tests fail because there is no devel branch from the NAMD's repository. reusable-cvcs should be rebased at first, and then I would rebase this PR.

3. documentation of the user-facing changes.

I tagged this PR with "request for comments" because I didn't think there would be a consensus about how to reuse CVCs, and I opened this PR mainly as a proof of concept to show that how to achieve reusable CVCs while retaining the idea of "distributing the CVCs over SMP threads". I will add the documentation if we have a consensus about reusability and parallelization.

One question: can this be done without implementing the AST design you described just above? If yes, I would rather separate these issues as much as possible and merge code that works to avoid letting this branch diverge too much.

I don't think so. It seems to me that @giacomofiorin likes the idea of moving some "special" CVCs out of the SMP loops and computing them serially. However, I think there will be more and more "special" CVCs relying on other CVCs and biases based on other biases in the future, so it is better to take a unified approach. As I have said in #709 (comment), there could be two approaches for parallelization, namely (i) distributing CVCs and biases over SMP threads, and (ii) using SMP threads to parallelize fine-grained loops like projecting hills, rotating atoms, calculating COMs and more. To achieve general reusability in (i), it has to use an AST or other similar things to determine the order of calculations of CVCs. Approach (ii) could be simpler as it only requires that the calculations of CVCs follow the order of their definitions appeared in the config file, which is what PLUMED does, although I suspect that building an AST could be more useful.

Side note: I think you should be able to set your GH account so that the CI actions run in your fork, which would give us CI for this PR.

It does run in my fork (see https://github.com/HanatoK/colvars/actions/runs/9766071847/job/26958200729).

giacomofiorin · 2024-09-27T15:57:16Z

I don't think so. It seems to me that @giacomofiorin likes the idea of moving some "special" CVCs out of the SMP loops and computing them serially. However, I think there will be more and more "special" CVCs relying on other CVCs and biases based on other biases in the future, so it is better to take a unified approach.

I totally agree with having a unified approach, which would be a win-win for users and developers alike. But that would take significant effort, during which we would need to keep master release-ready.

Although GROMACS and LAMMPS have somewhat predictable release schedules, they are also not in sync: one in the Winter, one in Summer. I guess this may be related to the times of the year when people prefer to be inside working in Stockholm vs. Albuquerque :-D And NAMD and VMD do not follow a regular schedule.

I do not see the two approaches as antithetical, either: (i) was just easier to implement than (ii), and there was also less pressure to implement (ii) in NAMD, which already provided at least centers of mass computed using domain decomposition.

HanatoK · 2024-09-27T16:37:45Z

I do not see the two approaches as antithetical, either: (i) was just easier to implement than (ii), and there was also less pressure to implement (ii) in NAMD, which already provided at least centers of mass computed using domain decomposition.

My impression is that parallelizing both the calculations of CVs and their inner loops (COM, COG, and rotating positions) could make the code much more complicated. Approach (i) only works well with CPUs, while approach (ii) could be easily ported to GPUs or similar accelerators. Calculating two CVs simultaneously on two "GPU threads" of the same GPU device could kill the performance.

HanatoK · 2024-10-24T01:40:11Z

It just reminds me that if we want to compute CVCs in parallel, we may need to lock the get_group_force_object() in

colvars/src/colvaratoms.cpp

Lines 1487 to 1489 in 2c6c712

    
           cvm::atom_group::group_force_object cvm::atom_group::get_group_force_object() { 
        
             return cvm::atom_group::group_force_object(this); 
        
           }

Because CVCs A and B may rely on C, and in C the atom group has a fitting group. In such case, it would be better to implement a lock attached to the atom group, the first one (either A or B) accessing the apply_force() of C should obtain the lock, while the second one should wait for the lock.

jhenin · 2024-12-11T14:13:50Z

How do we move forward on this?
We can either:

merge this into the reusable-cvcs branch and continue work on Allow reusing computation and data between CVC objects #644
merge Allow reusing computation and data between CVC objects #644 and rebase this on master

Either way, this remains a somewhat unwieldy branch but I think parts of it can be extracted and merged separately to make this one easier to follow.

HanatoK added 3 commits June 29, 2024 16:47

Many band-aid fixes to Colvars underlying design issues

ac82aa9

Fix the old code path

db99497

Add reusable component test for nn

f4d4e54

HanatoK requested review from giacomofiorin and jhenin June 29, 2024 22:52

Kill the explicit gradient support in CV of CVs

fa82bbf

This does not work as Colvars was not designed with automatic differentiation in mind.

HanatoK changed the title ~~More band-aid fixes to Colvars~~ [RFC] More band-aid fixes to Colvars Jul 1, 2024

HanatoK marked this pull request as ready for review July 1, 2024 19:25

jhenin reviewed Jul 3, 2024

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HanatoK commented Jul 3, 2024

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HanatoK marked this pull request as draft September 25, 2024 15:31

giacomofiorin mentioned this pull request Oct 18, 2024

Bias-exchange metadynamics implementation #734

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jhenin changed the title ~~[RFC] More band-aid fixes to Colvars~~ [RFC] Work towards reusable CVCs Oct 24, 2024

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The problem of `colvardeps`

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The problem of `colvardeps`

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[RFC] Work towards reusable CVCs #700

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[RFC] Work towards reusable CVCs #700

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The problem of calc_gradients()

The problem of colvardeps

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Parallelization and checking the error

jhenin commented Jul 4, 2024

The problem of colvardeps

HanatoK commented Jul 4, 2024

The problem of colvardeps

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The problem of `calc_gradients()`

The problem of `colvardeps`

The problem of `colvardeps`

The problem of `colvardeps`

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