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 "core/PlumedMain.h"
29 : #include <cstring>
30 : #ifdef __PLUMED_HAS_DLOPEN
31 : #include <dlfcn.h>
32 : #endif
33 :
34 : #include <iostream>
35 :
36 : namespace PLMD {
37 : namespace generic {
38 :
39 : //+PLUMEDOC GENERIC PLUMED
40 : /*
41 : Embed a separate PLUMED instance.
42 :
43 : This command can be used to embed a separate PLUMED instance.
44 : Only required atoms will be passed to that instance, using an interface
45 : that is similar to the one used when calling PLUMED from the NAMD engine.
46 :
47 : Notice that the two instances are running in the same UNIX process, so that they cannot be perfectly isolated.
48 : However, most of the features are expected to work correctly.
49 :
50 : Notes:
51 : - The \ref LOAD action will not work correctly since registers will be shared among the two instances.
52 : In particular, the loaded actions will be visible to both guest and host irrespective of where they are loaded from.
53 : This can be fixed and will probably be fixed in a later version.
54 : - `CHDIR` is not thread safe.
55 : However, in most implementations there will be a single process running PLUMED, with perhaps multiple OpenMP threads
56 : spawn in order to parallelize the calculation of individual variables. So, this is likely not a problem.
57 : - MPI is working correctly. However, notice that the guest PLUMED will always run with a single process.
58 : Multiple replicas should be handled correctly.
59 :
60 : As an advanced feature, one can use the option `KERNEL` to select the version of the guest PLUMED instance.
61 : In particular, an empty `KERNEL` (default) implies that the guest PLUMED instance is the same as the host one
62 : (no library is loaded).
63 : On the other hand, `KERNEL=/path/to/libplumedKernel.so` will allow specifying a library to be loaded for the
64 : guest instance.
65 : In addition to those mentioned above, this feature has limitations mostly related to
66 : clashes in the symbols defined in the different instances of the PLUMED library:
67 : - On OSX, if you load a KERNEL with version >=2.5 there should be no problem thanks to the use
68 : of two-level namespaces.
69 : - On OSX, if you load a KERNEL with version <=2.4 there should be clashes in symbol resolution.
70 : The only possible workarounds are:
71 : - If you are are using PLUMED with an MD code, it should be patched with `--runtime` and you should
72 : `export PLUMED_LOAD_NAMESPACE=LOCAL` before starting the MD engine.
73 : - If you are using PLUMED driver, you should launch the `plumed-runtime` executable (contained in the
74 : `prefix/lib/plumed/` directory), export `PLUMED_KERNEL` equal to the path of the host kernel library
75 : (as usual in runtime loading) and `export PLUMED_LOAD_NAMESPACE=LOCAL` before launching `plumed-runtime driver`.
76 : - On Linux, any `KERNEL` should in principle work correctly. To achieve namespace separation we are loading
77 : the guest kernel with `RTLD_DEEPBIND`. However, this might create difficult to track problems in other linked libraries.
78 : - On Unix systems where `RTLD_DEEPBIND` is not available kernels will not load correctly.
79 : - In general, there might be unexpected crashes. Particularly difficult are situations where different
80 : kernels were compiled with different libraries.
81 :
82 : A possible solution for the symbol clashes (not tested) could be to recompile the alternative PLUMED
83 : versions using separate C++ namespaces (e.g. `./configure CPPFLAGS=-DPLMD=PLMD_2_3`).
84 :
85 : \todo
86 : - Add support for multiple time stepping (`STRIDE` different from 1).
87 : - Add the possibility to import CVs calculated in the host PLUMED instance into the guest PLUMED instance.
88 : Will be possible after \issue{83} will be closed.
89 : - Add the possibility to export CVs calculated in the guest PLUMED instance into the host PLUMED instance.
90 : Could be implemented using the `DataFetchingObject` class.
91 :
92 : \par Examples
93 :
94 : Here an example plumed file:
95 : \plumedfile
96 : # plumed.dat
97 : p: PLUMED FILE=plumed2.dat
98 : PRINT ARG=p.bias FILE=COLVAR
99 : \endplumedfile
100 : `plumed2.dat` can be an arbitrary plumed input file, for instance
101 : \plumedfile
102 : #SETTINGS FILENAME=plumed2.dat
103 : # plumed2.dat
104 : d: DISTANCE ATOMS=1,10
105 : RESTRAINT ARG=d KAPPA=10 AT=2
106 : \endplumedfile
107 :
108 : Now a more useful example.
109 : Imagine that you ran simulations using two different PLUMED input files.
110 : The files are long and complex and there are some clashes in the name of the variables (that is: same names
111 : are used in both files, same files are written, etc). In addition, files might have been written using different units (see \ref UNITS`).
112 : If you want to run a single simulation with a bias potential
113 : that is the sum of the two bias potentials, you can:
114 : - Place the two input files, as well as all the files required by plumed, in separate directories `directory1` and `directory2`.
115 : - Run with the following input file in the parent directory:
116 : \plumedfile
117 : # plumed.dat
118 : PLUMED FILE=plumed.dat CHDIR=directory1
119 : PLUMED FILE=plumed.dat CHDIR=directory2
120 : \endplumedfile
121 :
122 : */
123 : //+ENDPLUMEDOC
124 :
125 : class Plumed:
126 : public ActionAtomistic,
127 : public ActionWithValue,
128 : public ActionPilot
129 : {
130 : /// True on root processor
131 : const bool root;
132 : /// Separate directory.
133 : const std::string directory;
134 : /// Interface to underlying plumed object.
135 : PlumedHandle p;
136 : /// API number.
137 : const int API;
138 : /// Self communicator
139 : Communicator comm_self;
140 : /// Intercommunicator
141 : Communicator intercomm;
142 : /// Detect first usage.
143 : bool first=true;
144 : /// Stop flag, used to stop e.g. in committor analysis
145 : int stop=0;
146 : /// Index of requested atoms.
147 : std::vector<int> index;
148 : /// Masses of requested atoms.
149 : std::vector<double> masses;
150 : /// Charges of requested atoms.
151 : std::vector<double> charges;
152 : /// Forces on requested atoms.
153 : std::vector<double> forces;
154 : /// Requested positions.
155 : std::vector<double> positions;
156 : /// Applied virial.
157 : Tensor virial;
158 : public:
159 : /// Constructor.
160 : explicit Plumed(const ActionOptions&);
161 : /// Documentation.
162 : static void registerKeywords( Keywords& keys );
163 : void prepare() override;
164 : void calculate() override;
165 : void apply() override;
166 : void update() override;
167 0 : unsigned getNumberOfDerivatives() override {
168 0 : return 0;
169 : }
170 : };
171 :
172 10443 : PLUMED_REGISTER_ACTION(Plumed,"PLUMED")
173 :
174 13 : void Plumed::registerKeywords( Keywords& keys ) {
175 13 : Action::registerKeywords( keys );
176 13 : ActionPilot::registerKeywords( keys );
177 13 : ActionAtomistic::registerKeywords( keys );
178 26 : keys.add("compulsory","STRIDE","1","stride different from 1 are not supported yet");
179 26 : keys.add("optional","FILE","input file for the guest PLUMED instance");
180 26 : keys.add("optional","KERNEL","kernel to be used for the guest PLUMED instance (USE WITH CAUTION!)");
181 26 : keys.add("optional","LOG","log file for the guest PLUMED instance. By default the host log is used");
182 26 : keys.add("optional","CHDIR","run guest in a separate directory");
183 26 : keys.addFlag("NOREPLICAS",false,"run multiple replicas as isolated ones, without letting them know that the host has multiple replicas");
184 26 : keys.addOutputComponent("bias","default","the instantaneous value of the bias potential");
185 13 : }
186 :
187 12 : Plumed::Plumed(const ActionOptions&ao):
188 : Action(ao),
189 : ActionAtomistic(ao),
190 : ActionWithValue(ao),
191 : ActionPilot(ao),
192 24 : root(comm.Get_rank()==0),
193 24 : directory([&]() {
194 : std::string directory;
195 24 : parse("CHDIR",directory);
196 12 : if(directory.length()>0) {
197 0 : log<<" running on separate directory "<<directory<<"\n";
198 : }
199 12 : return directory;
200 : }()),
201 24 : p([&]() {
202 : std::string kernel;
203 24 : parse("KERNEL",kernel);
204 12 : if(kernel.length()==0) {
205 11 : log<<" using the current kernel\n";
206 11 : return PlumedHandle();
207 : } else {
208 1 : log<<" using the kernel "<<kernel<<"\n";
209 1 : return PlumedHandle::dlopen(kernel.c_str());
210 : }
211 : }()),
212 24 : API([&]() {
213 12 : int api=0;
214 24 : p.cmd("getApiVersion",&api);
215 12 : log<<" reported API version is "<<api<<"\n";
216 : // note: this is required in order to have cmd performCalcNoUpdate and cmd update
217 : // as a matter of fact, any version <2.5 will not even load due to namespace pollution
218 12 : plumed_assert(api>3) << "API>3 is required for the PLUMED action to work correctly\n";
219 12 : return api;
220 24 : }())
221 : {
222 12 : Tools::DirectoryChanger directoryChanger(directory.c_str());
223 :
224 : bool noreplicas;
225 12 : parseFlag("NOREPLICAS",noreplicas);
226 : int nreps;
227 12 : if(root) nreps=multi_sim_comm.Get_size();
228 12 : comm.Bcast(nreps,0);
229 12 : if(nreps>1) {
230 6 : if(noreplicas) {
231 0 : log<<" running replicas as independent (no suffix used)\n";
232 : } else {
233 6 : log<<" running replicas as standard multi replic (with suffix)\n";
234 6 : if(root) {
235 6 : intercomm.Set_comm(&multi_sim_comm.Get_comm());
236 9 : p.cmd("GREX setMPIIntercomm",&intercomm.Get_comm());
237 9 : p.cmd("GREX setMPIIntracomm",&comm_self.Get_comm());
238 6 : p.cmd("GREX init");
239 : }
240 : }
241 : } else {
242 6 : if(noreplicas) {
243 0 : log<<" WARNING: flag NOREPLICAS ignored since we are running without replicas\n";
244 : }
245 : }
246 :
247 12 : int natoms=plumed.getAtoms().getNatoms();
248 :
249 12 : plumed_assert(getStride()==1) << "currently only supports STRIDE=1";
250 :
251 12 : double dt=getTimeStep();
252 :
253 : std::string file;
254 24 : parse("FILE",file);
255 12 : if(file.length()>0) {
256 12 : log<<" with input file "<<file<<"\n";
257 0 : } else plumed_error() << "you must provide an input file\n";
258 :
259 : bool inherited_logfile=false;
260 : std::string logfile;
261 24 : parse("LOG",logfile);
262 12 : if(logfile.length()>0) {
263 0 : log<<" with log file "<<logfile<<"\n";
264 0 : if(root) p.cmd("setLogFile",logfile.c_str());
265 12 : } else if(log.getFILE()) {
266 12 : log<<" with inherited log file\n";
267 18 : if(root) p.cmd("setLog",log.getFILE());
268 : inherited_logfile=true;
269 : } else {
270 0 : log<<" with log on stdout\n";
271 0 : if(root) p.cmd("setLog",stdout);
272 : }
273 :
274 12 : checkRead();
275 :
276 18 : if(root) p.cmd("setMDEngine","plumed");
277 :
278 12 : double engunits=plumed.getAtoms().getUnits().getEnergy();
279 18 : if(root) p.cmd("setMDEnergyUnits",&engunits);
280 :
281 12 : double lenunits=plumed.getAtoms().getUnits().getLength();
282 18 : if(root) p.cmd("setMDLengthUnits",&lenunits);
283 :
284 12 : double timunits=plumed.getAtoms().getUnits().getTime();
285 18 : if(root) p.cmd("setMDTimeUnits",&timunits);
286 :
287 12 : double chaunits=plumed.getAtoms().getUnits().getCharge();
288 18 : if(root) p.cmd("setMDChargeUnits",&chaunits);
289 12 : double masunits=plumed.getAtoms().getUnits().getMass();
290 18 : if(root) p.cmd("setMDMassUnits",&masunits);
291 :
292 12 : double kbt=plumed.getAtoms().getKbT();
293 18 : if(root) p.cmd("setKbT",&kbt);
294 :
295 12 : int res=0;
296 12 : if(getRestart()) res=1;
297 18 : if(root) p.cmd("setRestart",&res);
298 :
299 18 : if(root) p.cmd("setNatoms",&natoms);
300 18 : if(root) p.cmd("setTimestep",&dt);
301 18 : if(root) p.cmd("setPlumedDat",file.c_str());
302 :
303 12 : addComponentWithDerivatives("bias");
304 12 : componentIsNotPeriodic("bias");
305 :
306 12 : if(inherited_logfile) log<<"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n";
307 18 : if(root) p.cmd("init");
308 12 : if(inherited_logfile) log<<"++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n";
309 12 : }
310 :
311 164 : void Plumed::prepare() {
312 164 : Tools::DirectoryChanger directoryChanger(directory.c_str());
313 164 : int step=getStep();
314 253 : if(root) p.cmd("setStep",&step);
315 253 : if(root) p.cmd("prepareDependencies");
316 164 : int ene=0;
317 253 : if(root) p.cmd("isEnergyNeeded",&ene);
318 164 : if(ene) plumed_error()<<"It is not currently possible to use ENERGY in a guest PLUMED";
319 164 : int n=0;
320 253 : if(root) p.cmd("createFullList",&n);
321 164 : const int *pointer=nullptr;
322 253 : if(root) p.cmd("getFullList",&pointer);
323 164 : bool redo=(index.size()!=n);
324 164 : if(first) redo=true;
325 164 : first=false;
326 4409 : if(root && !redo) for(int i=0; i<n; i++) if(index[i]!=pointer[i]) { redo=true; break;};
327 164 : if(root && redo) {
328 22 : index.resize(n);
329 22 : masses.resize(n);
330 22 : forces.resize(3*n);
331 22 : positions.resize(3*n);
332 22 : charges.resize(n);
333 1043 : for(int i=0; i<n; i++) {
334 1021 : index[i]=pointer[i];
335 : };
336 44 : p.cmd("setAtomsNlocal",&n);
337 44 : p.cmd("setAtomsGatindex",index.data(),index.size());
338 : }
339 253 : if(root) p.cmd("clearFullList");
340 164 : int tmp=0;
341 164 : if(root && redo) {
342 22 : tmp=1;
343 : }
344 164 : comm.Bcast(tmp,0);
345 164 : if(tmp) {
346 34 : int s=index.size();
347 34 : comm.Bcast(s,0);
348 34 : if(!root) index.resize(s);
349 34 : comm.Bcast(index,0);
350 : std::vector<AtomNumber> numbers;
351 34 : numbers.reserve(index.size());
352 2138 : for(auto i : index) numbers.emplace_back(AtomNumber::index(i));
353 34 : requestAtoms(numbers);
354 : }
355 164 : }
356 :
357 134 : void Plumed::calculate() {
358 134 : Tools::DirectoryChanger directoryChanger(directory.c_str());
359 208 : if(root) p.cmd("setStopFlag",&stop);
360 134 : Tensor box=getPbc().getBox();
361 208 : if(root) p.cmd("setBox",&box[0][0],9);
362 :
363 134 : virial.zero();
364 24875 : for(int i=0; i<forces.size(); i++) forces[i]=0.0;
365 4238 : for(int i=0; i<masses.size(); i++) masses[i]=getMass(i);
366 4238 : for(int i=0; i<charges.size(); i++) charges[i]=getCharge(i);
367 :
368 208 : if(root) p.cmd("setMasses",masses.data(),masses.size());
369 208 : if(root) p.cmd("setCharges",charges.data(),charges.size());
370 208 : if(root) p.cmd("setPositions",positions.data(),positions.size());
371 208 : if(root) p.cmd("setForces",forces.data(),forces.size());
372 208 : if(root) p.cmd("setVirial",&virial[0][0],9);
373 :
374 :
375 4238 : if(root) for(unsigned i=0; i<getNumberOfAtoms(); i++) {
376 4104 : positions[3*i+0]=getPosition(i)[0];
377 4104 : positions[3*i+1]=getPosition(i)[1];
378 4104 : positions[3*i+2]=getPosition(i)[2];
379 : }
380 :
381 208 : if(root) p.cmd("shareData");
382 208 : if(root) p.cmd("performCalcNoUpdate");
383 :
384 134 : int s=forces.size();
385 134 : comm.Bcast(s,0);
386 134 : if(!root) forces.resize(s);
387 134 : comm.Bcast(forces,0);
388 134 : comm.Bcast(virial,0);
389 :
390 134 : double bias=0.0;
391 208 : if(root) p.cmd("getBias",&bias);
392 134 : comm.Bcast(bias,0);
393 134 : getPntrToComponent("bias")->set(bias);
394 134 : }
395 :
396 104 : void Plumed::apply() {
397 104 : Tools::DirectoryChanger directoryChanger(directory.c_str());
398 : auto & f(modifyForces());
399 6596 : for(unsigned i=0; i<getNumberOfAtoms(); i++) {
400 6492 : f[i][0]+=forces[3*i+0];
401 6492 : f[i][1]+=forces[3*i+1];
402 6492 : f[i][2]+=forces[3*i+2];
403 : }
404 : auto & v(modifyVirial());
405 104 : v+=virial;
406 104 : }
407 :
408 104 : void Plumed::update() {
409 104 : Tools::DirectoryChanger directoryChanger(directory.c_str());
410 163 : if(root) p.cmd("update");
411 104 : comm.Bcast(stop,0);
412 104 : if(stop) {
413 0 : log<<" Action " << getLabel()<<" asked to stop\n";
414 0 : plumed.stop();
415 : }
416 104 : }
417 :
418 : }
419 : }
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