Fix interruption of lyapunov

src/io.c

@@ -58,7 +58,7 @@ int write_vec2_bin(double* vec, int K1, int K2, FILE* file){
     return 0;
   }
 
-  fwrite(vec, sizeof(double), 2*K1*(2*K2+1)+K2, file);
+  fwrite(vec, sizeof(double), 2*(K1*(2*K2+1)+K2), file);
 
   return 0;
 }

src/lyapunov.c

@@ -52,6 +52,8 @@ int lyapunov(
   unsigned int nthreads,
   double* flow0,
   double* lyapunov_avg0,
+  double prevtime, // the previous time at which a QR decomposition was performed
+  double lyapunov_startingtime, // the time at which the lyapunov exponent computation was started (useful in interrupted computation)
   FILE* savefile,
   FILE* utfile,
   // for interrupt recovery
@@ -105,9 +107,6 @@ int lyapunov(
   double step=delta;
   double next_step=step;
 
-  // save times at which Lyapunov exponents are computed
-  double prevtime=starting_time;
-
   // iterate
   time=starting_time;
   while(final_time<0 || time<final_time){
@@ -155,8 +154,8 @@ int lyapunov(
       // average lyapunov
       for(i=0; i<MATSIZE; i++){
 	// exclude inf
-	if((! isinf(lyapunov[i])) && (time>starting_time)){
+	if((! isinf(lyapunov[i])) && (time>lyapunov_startingtime)){
-	  lyapunov_avg[i]=lyapunov_avg[i]*(prevtime-starting_time)/(time-starting_time)+lyapunov[i]*(time-prevtime)/(time-starting_time);
+	  lyapunov_avg[i]=lyapunov_avg[i]*(prevtime-lyapunov_startingtime)/(time-lyapunov_startingtime)+lyapunov[i]*(time-prevtime)/(time-lyapunov_startingtime);
 	}
       }
 
@@ -176,20 +175,20 @@ int lyapunov(
 
       // reset prevtime
       prevtime=time;
+    }
 
-      // catch abort signal
+    // catch abort signal
-      if (g_abort){
+    if (g_abort){
-	// print u to stderr if no savefile
+      // print u to stderr if no savefile
-	if (savefile==NULL){
+      if (savefile==NULL){
-	  savefile=stderr;
+	savefile=stderr;
-	}
-	break;
       }
+      break;
     }
   }
 
   if(savefile!=NULL){
-    lyapunov_save_state(flow, u, lyapunov_avg, savefile, K1, K2, cmd_string, params_string, savefile_string, utfile_string, utfile, COMMAND_LYAPUNOV, algorithm, step, time, nthreads);
+    lyapunov_save_state(flow, u, lyapunov_avg, prevtime, lyapunov_startingtime, savefile, K1, K2, cmd_string, params_string, savefile_string, utfile_string, utfile, COMMAND_LYAPUNOV, algorithm, step, time, nthreads);
   }
 
   // save final u to utfile in txt format
@@ -781,6 +780,8 @@ int lyapunov_save_state(
   double* flow,
   _Complex double* u,
   double* lyapunov_avg,
+  double prevtime,
+  double lyapunov_startingtime,
   FILE* savefile,
   int K1,
   int K2,
@@ -801,6 +802,10 @@ int lyapunov_save_state(
   if(savefile!=stderr && savefile!=stdout){
     // save tangent flow
     write_mat2_bin(flow,K1,K2,savefile);
+    // save time of QR decomposition
+    fwrite(&prevtime, sizeof(double), 1, savefile);
+    // save time at which the lyapunov computation started
+    fwrite(&lyapunov_startingtime, sizeof(double), 1, savefile);
     // save lyapunov averages
     write_vec2_bin(lyapunov_avg,K1,K2,savefile);
   }

src/lyapunov.h

@@ -20,7 +20,7 @@ limitations under the License.
 #include "navier-stokes.h"
 
 // compute Lyapunov exponents
-int lyapunov( int K1, int K2, int N1, int N2, double final_time, double lyapunov_reset, unsigned int lyapunov_trigger, double nu, double delta, double L, double adaptive_tolerance, double adaptive_factor, double max_delta, unsigned int adaptive_cost, _Complex double* u0, _Complex double* g, bool irreversible, bool keep_en_cst, double target_en, unsigned int algorithm, unsigned int algorithm_lyapunov, double starting_time, unsigned int nthreads, double* flow0, double* lyapunov_avg0, FILE* savefile, FILE* utfile, const char* cmd_string, const char* params_string, const char* savefile_string, const char* utfile_string);
+int lyapunov( int K1, int K2, int N1, int N2, double final_time, double lyapunov_reset, unsigned int lyapunov_trigger, double nu, double delta, double L, double adaptive_tolerance, double adaptive_factor, double max_delta, unsigned int adaptive_cost, _Complex double* u0, _Complex double* g, bool irreversible, bool keep_en_cst, double target_en, unsigned int algorithm, unsigned int algorithm_lyapunov, double starting_time, unsigned int nthreads, double* flow0, double* lyapunov_avg0, double prevtime, double lyapunov_startingtime, FILE* savefile, FILE* utfile, const char* cmd_string, const char* params_string, const char* savefile_string, const char* utfile_string);
 
 // comparison function for qsort
 int compare_double(const void* x, const void* y);
@@ -57,7 +57,7 @@ int lyapunov_init_tmps( double ** lyapunov, double ** lyapunov_avg, double ** fl
 int lyapunov_free_tmps( double * lyapunov, double * lyapunov_avg, double * flow, _Complex double * u, double * tmp1, double * tmp2, double * tmp3, _Complex double * tmp4, _Complex double * tmp5, _Complex double * tmp6, _Complex double * tmp7, _Complex double * tmp8, _Complex double * tmp9, _Complex double * tmp10, double * tmp11, fft_vect fftu1, fft_vect fftu2, fft_vect fftu3, fft_vect fftu4, fft_vect fft1, fft_vect ifft, unsigned int algorithm, unsigned int algorithm_lyapunov);
 
 // save state of lyapunov computation
-int lyapunov_save_state( double* flow, _Complex double* u, double* lyapunov_avg, FILE* savefile, int K1, int K2, const char* cmd_string, const char* params_string, const char* savefile_string, const char* utfile_string, FILE* utfile, unsigned int command, unsigned int algorithm, double step, double time, unsigned int nthreads);
+int lyapunov_save_state( double* flow, _Complex double* u, double* lyapunov_avg, double prevtime, double lyapunov_startingtime, FILE* savefile, int K1, int K2, const char* cmd_string, const char* params_string, const char* savefile_string, const char* utfile_string, FILE* utfile, unsigned int command, unsigned int algorithm, double step, double time, unsigned int nthreads);
 
 #endif
 

src/main.c

@@ -85,7 +85,7 @@ _Complex double* set_driving(nstrophy_parameters parameters);
 // set initial condition
 _Complex double* set_init(nstrophy_parameters* parameters);
 // set initial tangent flow for lyapunov exponents
-int set_lyapunov_flow_init( double** lyapunov_flow0, double** lyapunov_avg0, nstrophy_parameters parameters);
+int set_lyapunov_flow_init( double** lyapunov_flow0, double** lyapunov_avg0, double* lyapunov_prevtime, double* lyapunov_startingtime, nstrophy_parameters parameters);
 
 // signal handler
 void sig_handler (int signo);
@@ -121,6 +121,8 @@ int main (
   _Complex double *g;
   double* lyapunov_flow0;
   double* lyapunov_avg0;
+  double lyapunov_prevtime;
+  double lyapunov_startingtime;
   dstring savefile_str;
   dstring utfile_str;
   dstring initfile_str;
@@ -232,7 +234,7 @@ int main (
   u0=set_init(&parameters);
   // set initial condition for the lyapunov flow
   if (command==COMMAND_LYAPUNOV){
-    set_lyapunov_flow_init(&lyapunov_flow0, &lyapunov_avg0, parameters);
+    set_lyapunov_flow_init(&lyapunov_flow0, &lyapunov_avg0, &lyapunov_prevtime, &lyapunov_startingtime, parameters);
   }
 
   // if init_enstrophy is not set in the parameters, then compute it from the initial condition
@@ -315,7 +317,10 @@ int main (
     quiet(parameters.K1, parameters.K2, parameters.N1, parameters.N2, parameters.final_time, parameters.nu, parameters.delta, parameters.L, parameters.adaptive_tolerance, parameters.adaptive_factor, parameters.max_delta, parameters.adaptive_cost, parameters.starting_time, u0, g, parameters.irreversible, parameters.keep_en_cst, parameters.init_enstrophy, parameters.algorithm, nthreads, savefile);
   }
   else if(command==COMMAND_LYAPUNOV){
-    lyapunov(parameters.K1, parameters.K2, parameters.N1, parameters.N2, parameters.final_time, parameters.lyapunov_reset, parameters.lyapunov_trigger, parameters.nu, parameters.delta, parameters.L, parameters.adaptive_tolerance, parameters.adaptive_factor, parameters.max_delta, parameters.adaptive_cost, u0, g, parameters.irreversible, parameters.keep_en_cst, parameters.init_enstrophy, parameters.algorithm, parameters.algorithm_lyapunov, parameters.starting_time, nthreads, lyapunov_flow0, lyapunov_avg0, savefile, utfile, (char*)argv[0], dstring_to_str_noinit(&param_str), dstring_to_str_noinit(&savefile_str), dstring_to_str_noinit(&utfile_str));
+    // register signal handler to handle aborts
+    signal(SIGINT, sig_handler);
+    signal(SIGTERM, sig_handler);
+    lyapunov(parameters.K1, parameters.K2, parameters.N1, parameters.N2, parameters.final_time, parameters.lyapunov_reset, parameters.lyapunov_trigger, parameters.nu, parameters.delta, parameters.L, parameters.adaptive_tolerance, parameters.adaptive_factor, parameters.max_delta, parameters.adaptive_cost, u0, g, parameters.irreversible, parameters.keep_en_cst, parameters.init_enstrophy, parameters.algorithm, parameters.algorithm_lyapunov, parameters.starting_time, nthreads, lyapunov_flow0, lyapunov_avg0, lyapunov_prevtime, lyapunov_startingtime, savefile, utfile, (char*)argv[0], dstring_to_str_noinit(&param_str), dstring_to_str_noinit(&savefile_str), dstring_to_str_noinit(&utfile_str));
   }
   else if(command==0){
     fprintf(stderr, "error: no command specified\n");
@@ -1170,6 +1175,8 @@ _Complex double* set_init(
 int set_lyapunov_flow_init(
   double** lyapunov_flow0,
   double** lyapunov_avg0,
+  double* lyapunov_prevtime,
+  double* lyapunov_startingtime,
   nstrophy_parameters parameters
 ){
   *lyapunov_flow0=calloc(4*(parameters.K1*(2*parameters.K2+1)+parameters.K2)*(parameters.K1*(2*parameters.K2+1)+parameters.K2),sizeof(double));
@@ -1178,6 +1185,10 @@ int set_lyapunov_flow_init(
   if(parameters.init_flow_file){
     // read flow
     read_mat2_bin(*lyapunov_flow0, parameters.K1, parameters.K2, parameters.initfile);
+    // read time of last QR decomposition
+    fread(lyapunov_prevtime, sizeof(double), 1, parameters.initfile);
+    // read time at which lyapunov computation was started
+    fread(lyapunov_startingtime, sizeof(double), 1, parameters.initfile);
     // read averages
     read_vec2_bin(*lyapunov_avg0, parameters.K1, parameters.K2, parameters.initfile);
   } else {
@@ -1192,6 +1203,11 @@ int set_lyapunov_flow_init(
 	}
       }
     }
+    // init prevtime
+    *lyapunov_prevtime=parameters.starting_time;
+    // init starting_time
+    *lyapunov_startingtime=parameters.starting_time;
+    // init averages
     for(i=0;i<2*(parameters.K1*(2*parameters.K2+1)+parameters.K2);i++){
       (*lyapunov_avg0)[i]=0;
     }