Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2018-2023 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed is free software: you can redistribute it and/or modify
10 : it under the terms of the GNU Lesser General Public License as published by
11 : the Free Software Foundation, either version 3 of the License, or
12 : (at your option) any later version.
13 :
14 : plumed is distributed in the hope that it will be useful,
15 : but WITHOUT ANY WARRANTY; without even the implied warranty of
16 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 : GNU Lesser General Public License for more details.
18 :
19 : You should have received a copy of the GNU Lesser General Public License
20 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 : #include "core/ActionAtomistic.h"
23 : #include "core/ActionWithValue.h"
24 : #include "core/ActionPilot.h"
25 : #include "core/ActionRegister.h"
26 : #include "tools/Tools.h"
27 : #include "tools/PlumedHandle.h"
28 : #include "tools/Communicator.h"
29 : #include "core/PlumedMain.h"
30 : #include <cstring>
31 : #ifdef __PLUMED_HAS_DLOPEN
32 : #include <dlfcn.h>
33 : #endif
34 :
35 : #include <iostream>
36 :
37 : namespace PLMD {
38 : namespace generic {
39 :
40 : //+PLUMEDOC GENERIC PLUMED
41 : /*
42 : Embed a separate PLUMED instance.
43 :
44 : This command can be used to embed a separate PLUMED instance.
45 : Only required atoms will be passed to that instance, using an interface
46 : that is similar to the one used when calling PLUMED from the NAMD engine.
47 :
48 : Notice that the two instances are running in the same UNIX process, so that they cannot be perfectly isolated.
49 : However, most of the features are expected to work correctly.
50 :
51 : Notes:
52 : - The [LOAD](LOAD.md) action will not work correctly since registers will be shared among the two instances.
53 : In particular, the loaded actions will be visible to both guest and host irrespective of where they are loaded from.
54 : This can be fixed and will probably be fixed in a later version.
55 : - `CHDIR` is not thread safe.
56 : However, in most implementations there will be a single process running PLUMED, with perhaps multiple OpenMP threads
57 : spawn in order to parallelize the calculation of individual variables. So, this is likely not a problem.
58 : - MPI is working correctly. However, notice that the guest PLUMED will always run with a single process.
59 : Multiple replicas should be handled correctly.
60 :
61 : As an advanced feature, one can use the option `KERNEL` to select the version of the guest PLUMED instance.
62 : In particular, an empty `KERNEL` (default) implies that the guest PLUMED instance is the same as the host one
63 : (no library is loaded).
64 : On the other hand, `KERNEL=/path/to/libplumedKernel.so` will allow specifying a library to be loaded for the
65 : guest instance.
66 : In addition to those mentioned above, this feature has limitations mostly related to
67 : clashes in the symbols defined in the different instances of the PLUMED library.
68 : Clashes might be due by synonymous symbols from the PLUMED library or synonymous symbols
69 : from libraries linked to PLUMED, and would differ depending on the operating system you
70 : are using:
71 : - On OSX:
72 : - Symbols from the PLUMED library would clash. The only way to avoid is to load PLUMED dynamically:
73 : - If you are are using PLUMED with an MD code, it should be patched with `--runtime`.
74 : - If you are using PLUMED driver, you should launch the `plumed-runtime` executable (contained in the
75 : `prefix/lib/plumed/` directory) and export `PLUMED_KERNEL` equal to the path of the host kernel library
76 : (as usual in runtime loading). Notice that as of PLUMED 2.10 we load kernels with RTLD_LOCAL by default.
77 : - Symbols from dependent libraries should not clash since, as of version 2.5, we are using
78 : two-level namespace. Problems when loading previous versions should anyway be solved using runtime
79 : mode as explained above.
80 : - On Linux, any `KERNEL` should in principle work correctly. To achieve namespace separation we are loading
81 : the guest kernel with `RTLD_DEEPBIND`. However, this might create difficult to track problems in other linked libraries.
82 : - On Unix systems where `RTLD_DEEPBIND` is not available kernels will not load correctly.
83 : - In general, there might be unexpected crashes. Particularly difficult are situations where different
84 : kernels were compiled with different libraries.
85 :
86 :
87 : The following things need to be done to improve this action:
88 :
89 : - Add support for multiple time stepping (`STRIDE` different from 1).
90 : - Add the possibility to import CVs calculated in the host PLUMED instance into the guest PLUMED instance.
91 : Will be possible after \issue{83} will be closed.
92 : - Add the possibility to export CVs calculated in the guest PLUMED instance into the host PLUMED instance.
93 : Could be implemented using the `DataFetchingObject` class.
94 :
95 : ## Examples
96 :
97 : Here an example plumed file:
98 :
99 : ```plumed
100 : # plumed.dat
101 : p: PLUMED FILE=plumed2.dat
102 : PRINT ARG=p.bias FILE=COLVAR
103 : ```
104 :
105 : `plumed2.dat` can be an arbitrary plumed input file, for instance
106 :
107 : ```plumed
108 : #SETTINGS FILENAME=plumed2.dat
109 : # plumed2.dat
110 : d: DISTANCE ATOMS=1,10
111 : RESTRAINT ARG=d KAPPA=10 AT=2
112 : ```
113 :
114 : Now a more useful example.
115 : Imagine that you ran simulations using two different PLUMED input files.
116 : The files are long and complex and there are some clashes in the name of the variables (that is: same names
117 : are used in both files, same files are written, etc). In addition, files might have been written using different units (see [UNITS](UNITS.md)).
118 : If you want to run a single simulation with a bias potential
119 : that is the sum of the two bias potentials, you can:
120 : - Place the two input files, as well as all the files required by plumed, in separate directories `directory1` and `directory2`.
121 : - Run with the following input file in the parent directory:
122 :
123 : ```plumed
124 : # plumed.dat
125 : PLUMED FILE=plumed.dat CHDIR=directory1
126 : PLUMED FILE=plumed.dat CHDIR=directory2
127 : ```
128 :
129 : */
130 : //+ENDPLUMEDOC
131 :
132 : class Plumed:
133 : public ActionAtomistic,
134 : public ActionWithValue,
135 : public ActionPilot {
136 : /// True on root processor
137 : const bool root;
138 : /// Separate directory.
139 : const std::string directory;
140 : /// Interface to underlying plumed object.
141 : PlumedHandle p;
142 : /// API number.
143 : const int API;
144 : /// Self communicator
145 : Communicator comm_self;
146 : /// Intercommunicator
147 : Communicator intercomm;
148 : /// Detect first usage.
149 : bool first=true;
150 : /// Stop flag, used to stop e.g. in committor analysis
151 : int stop=0;
152 : /// Index of requested atoms.
153 : std::vector<int> index;
154 : /// Masses of requested atoms.
155 : std::vector<double> masses;
156 : /// Charges of requested atoms.
157 : std::vector<double> charges;
158 : /// Forces on requested atoms.
159 : std::vector<double> forces;
160 : /// Requested positions.
161 : std::vector<double> positions;
162 : /// Applied virial.
163 : Tensor virial;
164 : public:
165 : /// Constructor.
166 : explicit Plumed(const ActionOptions&);
167 : /// Documentation.
168 : static void registerKeywords( Keywords& keys );
169 : void prepare() override;
170 : void calculate() override;
171 : void apply() override;
172 : void update() override;
173 0 : unsigned getNumberOfDerivatives() override {
174 0 : return 0;
175 : }
176 92 : bool actionHasForces() override {
177 92 : return true;
178 : }
179 : };
180 :
181 : PLUMED_REGISTER_ACTION(Plumed,"PLUMED")
182 :
183 14 : void Plumed::registerKeywords( Keywords& keys ) {
184 14 : Action::registerKeywords( keys );
185 14 : ActionPilot::registerKeywords( keys );
186 14 : ActionAtomistic::registerKeywords( keys );
187 14 : keys.add("compulsory","STRIDE","1","stride different from 1 are not supported yet");
188 14 : keys.add("optional","FILE","input file for the guest PLUMED instance");
189 14 : keys.add("optional","KERNEL","kernel to be used for the guest PLUMED instance (USE WITH CAUTION!)");
190 14 : keys.add("optional","LOG","log file for the guest PLUMED instance. By default the host log is used");
191 14 : keys.add("optional","CHDIR","run guest in a separate directory");
192 14 : keys.addFlag("NOREPLICAS",false,"run multiple replicas as isolated ones, without letting them know that the host has multiple replicas");
193 28 : keys.addOutputComponent("bias","default","scalar","the instantaneous value of the bias potential");
194 14 : }
195 :
196 12 : Plumed::Plumed(const ActionOptions&ao):
197 : Action(ao),
198 : ActionAtomistic(ao),
199 : ActionWithValue(ao),
200 : ActionPilot(ao),
201 24 : root(comm.Get_rank()==0),
202 24 : directory([&]() {
203 : std::string directory;
204 24 : parse("CHDIR",directory);
205 12 : if(directory.length()>0) {
206 0 : log<<" running on separate directory "<<directory<<"\n";
207 : }
208 12 : return directory;
209 : }()),
210 24 : p([&]() {
211 : std::string kernel;
212 24 : parse("KERNEL",kernel);
213 12 : if(kernel.length()==0) {
214 11 : log<<" using the current kernel\n";
215 11 : return PlumedHandle();
216 : } else {
217 1 : log<<" using the kernel "<<kernel<<"\n";
218 1 : return PlumedHandle::dlopen(kernel.c_str());
219 : }
220 : }()),
221 24 : API([&]() {
222 12 : int api=0;
223 12 : p.cmd("getApiVersion",&api);
224 12 : log<<" reported API version is "<<api<<"\n";
225 : // note: this is required in order to have cmd performCalcNoUpdate and cmd update
226 : // as a matter of fact, any version <2.5 will not even load due to namespace pollution
227 12 : plumed_assert(api>3) << "API>3 is required for the PLUMED action to work correctly\n";
228 12 : return api;
229 24 : }()) {
230 12 : Tools::DirectoryChanger directoryChanger(directory.c_str());
231 :
232 : bool noreplicas;
233 12 : parseFlag("NOREPLICAS",noreplicas);
234 : int nreps;
235 12 : if(root) {
236 6 : nreps=multi_sim_comm.Get_size();
237 : }
238 12 : comm.Bcast(nreps,0);
239 12 : if(nreps>1) {
240 6 : if(noreplicas) {
241 0 : log<<" running replicas as independent (no suffix used)\n";
242 : } else {
243 6 : log<<" running replicas as standard multi replic (with suffix)\n";
244 6 : if(root) {
245 6 : intercomm.Set_comm(&multi_sim_comm.Get_comm());
246 6 : p.cmd("GREX setMPIIntercomm",&intercomm.Get_comm());
247 6 : p.cmd("GREX setMPIIntracomm",&comm_self.Get_comm());
248 3 : p.cmd("GREX init");
249 : }
250 : }
251 : } else {
252 6 : if(noreplicas) {
253 0 : log<<" WARNING: flag NOREPLICAS ignored since we are running without replicas\n";
254 : }
255 : }
256 :
257 12 : int natoms=getTotAtoms();
258 :
259 12 : plumed_assert(getStride()==1) << "currently only supports STRIDE=1";
260 :
261 12 : double dt=getTimeStep();
262 :
263 : std::string file;
264 24 : parse("FILE",file);
265 12 : if(file.length()>0) {
266 12 : log<<" with input file "<<file<<"\n";
267 : } else {
268 0 : plumed_error() << "you must provide an input file\n";
269 : }
270 :
271 : bool inherited_logfile=false;
272 : std::string logfile;
273 24 : parse("LOG",logfile);
274 12 : if(logfile.length()>0) {
275 0 : log<<" with log file "<<logfile<<"\n";
276 0 : if(root) {
277 0 : p.cmd("setLogFile",logfile.c_str());
278 : }
279 12 : } else if(log.getFILE()) {
280 12 : log<<" with inherited log file\n";
281 12 : if(root) {
282 6 : p.cmd("setLog",log.getFILE());
283 : }
284 : inherited_logfile=true;
285 : } else {
286 0 : log<<" with log on stdout\n";
287 0 : if(root) {
288 0 : p.cmd("setLog",stdout);
289 : }
290 : }
291 :
292 12 : checkRead();
293 :
294 12 : if(root) {
295 6 : p.cmd("setMDEngine","plumed");
296 : }
297 :
298 12 : double engunits=getUnits().getEnergy();
299 12 : if(root) {
300 6 : p.cmd("setMDEnergyUnits",&engunits);
301 : }
302 :
303 12 : double lenunits=getUnits().getLength();
304 12 : if(root) {
305 6 : p.cmd("setMDLengthUnits",&lenunits);
306 : }
307 :
308 12 : double timunits=getUnits().getTime();
309 12 : if(root) {
310 6 : p.cmd("setMDTimeUnits",&timunits);
311 : }
312 :
313 12 : double chaunits=getUnits().getCharge();
314 12 : if(root) {
315 6 : p.cmd("setMDChargeUnits",&chaunits);
316 : }
317 12 : double masunits=getUnits().getMass();
318 12 : if(root) {
319 6 : p.cmd("setMDMassUnits",&masunits);
320 : }
321 :
322 12 : double kbt=getkBT();
323 12 : if(root) {
324 6 : p.cmd("setKbT",&kbt);
325 : }
326 :
327 12 : int res=0;
328 12 : if(getRestart()) {
329 0 : res=1;
330 : }
331 12 : if(root) {
332 6 : p.cmd("setRestart",&res);
333 : }
334 :
335 12 : if(root) {
336 6 : p.cmd("setNatoms",&natoms);
337 : }
338 12 : if(root) {
339 6 : p.cmd("setTimestep",&dt);
340 : }
341 12 : if(root) {
342 6 : p.cmd("setPlumedDat",file.c_str());
343 : }
344 :
345 24 : addComponentWithDerivatives("bias");
346 12 : componentIsNotPeriodic("bias");
347 :
348 12 : if(inherited_logfile) {
349 12 : log<<"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n";
350 : }
351 12 : if(root) {
352 6 : p.cmd("init");
353 : }
354 12 : if(inherited_logfile) {
355 12 : log<<"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n";
356 : }
357 12 : }
358 :
359 164 : void Plumed::prepare() {
360 164 : Tools::DirectoryChanger directoryChanger(directory.c_str());
361 164 : int step=getStep();
362 164 : if(root) {
363 89 : p.cmd("setStep",&step);
364 : }
365 164 : if(root) {
366 89 : p.cmd("prepareDependencies");
367 : }
368 164 : int ene=0;
369 164 : if(root) {
370 89 : p.cmd("isEnergyNeeded",&ene);
371 : }
372 164 : if(ene) {
373 0 : plumed_error()<<"It is not currently possible to use ENERGY in a guest PLUMED";
374 : }
375 164 : int n=0;
376 164 : if(root) {
377 89 : p.cmd("createFullList",&n);
378 : }
379 164 : const int *pointer=nullptr;
380 164 : if(root) {
381 89 : p.cmd("getFullList",&pointer);
382 : }
383 164 : bool redo=(index.size()!=n);
384 164 : if(first) {
385 : redo=true;
386 : }
387 164 : first=false;
388 164 : if(root && !redo)
389 4245 : for(int i=0; i<n; i++)
390 4178 : if(index[i]!=pointer[i]) {
391 : redo=true;
392 : break;
393 : };
394 164 : if(root && redo) {
395 22 : index.resize(n);
396 22 : masses.resize(n);
397 22 : forces.resize(3*n);
398 22 : positions.resize(3*n);
399 22 : charges.resize(n);
400 1043 : for(int i=0; i<n; i++) {
401 1021 : index[i]=pointer[i];
402 : };
403 22 : p.cmd("setAtomsNlocal",&n);
404 22 : p.cmd("setAtomsGatindex",index.data(), {index.size()});
405 : }
406 164 : if(root) {
407 89 : p.cmd("clearFullList");
408 : }
409 164 : int tmp=0;
410 164 : if(root && redo) {
411 22 : tmp=1;
412 : }
413 164 : comm.Bcast(tmp,0);
414 164 : if(tmp) {
415 34 : int s=index.size();
416 34 : comm.Bcast(s,0);
417 34 : if(!root) {
418 12 : index.resize(s);
419 : }
420 34 : comm.Bcast(index,0);
421 : std::vector<AtomNumber> numbers;
422 34 : numbers.reserve(index.size());
423 2138 : for(auto i : index) {
424 2104 : numbers.emplace_back(AtomNumber::index(i));
425 : }
426 34 : requestAtoms(numbers);
427 : }
428 164 : }
429 :
430 134 : void Plumed::calculate() {
431 134 : Tools::DirectoryChanger directoryChanger(directory.c_str());
432 134 : if(root) {
433 74 : p.cmd("setStopFlag",&stop);
434 : }
435 134 : Tensor box=getPbc().getBox();
436 134 : if(root)
437 74 : p.cmd("setBox",&box[0][0], {3,3});
438 :
439 134 : virial.zero();
440 24875 : for(int i=0; i<forces.size(); i++) {
441 24741 : forces[i]=0.0;
442 : }
443 4238 : for(int i=0; i<masses.size(); i++) {
444 4104 : masses[i]=getMass(i);
445 : }
446 4238 : for(int i=0; i<charges.size(); i++) {
447 4104 : charges[i]=getCharge(i);
448 : }
449 :
450 134 : if(root)
451 74 : p.cmd("setMasses",masses.data(), {masses.size()});
452 134 : if(root)
453 74 : p.cmd("setCharges",charges.data(), {charges.size()});
454 134 : if(root)
455 74 : p.cmd("setPositions",positions.data(), {masses.size(),3});
456 134 : if(root) {
457 74 : p.cmd("setForces",forces.data(),forces.size());
458 : }
459 134 : if(root)
460 74 : p.cmd("setVirial",&virial[0][0], {3,3});
461 :
462 :
463 134 : if(root)
464 4178 : for(unsigned i=0; i<getNumberOfAtoms(); i++) {
465 4104 : positions[3*i+0]=getPosition(i)[0];
466 4104 : positions[3*i+1]=getPosition(i)[1];
467 4104 : positions[3*i+2]=getPosition(i)[2];
468 : }
469 :
470 134 : if(root) {
471 74 : p.cmd("shareData");
472 : }
473 134 : if(root) {
474 74 : p.cmd("performCalcNoUpdate");
475 : }
476 :
477 134 : int s=forces.size();
478 134 : comm.Bcast(s,0);
479 134 : if(!root) {
480 60 : forces.resize(s);
481 : }
482 134 : comm.Bcast(forces,0);
483 134 : comm.Bcast(virial,0);
484 :
485 134 : double bias=0.0;
486 134 : if(root) {
487 74 : p.cmd("getBias",&bias);
488 : }
489 134 : comm.Bcast(bias,0);
490 134 : getPntrToComponent("bias")->set(bias);
491 134 : }
492 :
493 104 : void Plumed::apply() {
494 104 : Tools::DirectoryChanger directoryChanger(directory.c_str());
495 104 : std::vector<double> fforces( forces.size() + 9, 0 );
496 19580 : for(unsigned i=0; i<forces.size(); i++) {
497 19476 : fforces[i] += forces[i];
498 : }
499 416 : for(unsigned i=0; i<3; ++i)
500 1248 : for(unsigned j=0; j<3; ++j) {
501 936 : fforces[forces.size()+3*i+j] = virial[i][j];
502 : }
503 104 : unsigned ind=0;
504 104 : setForcesOnAtoms( fforces, ind );
505 104 : }
506 :
507 104 : void Plumed::update() {
508 104 : Tools::DirectoryChanger directoryChanger(directory.c_str());
509 104 : if(root) {
510 59 : p.cmd("update");
511 : }
512 104 : comm.Bcast(stop,0);
513 104 : if(stop) {
514 0 : log<<" Action " << getLabel()<<" asked to stop\n";
515 0 : plumed.stop();
516 : }
517 104 : }
518 :
519 : }
520 : }
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