Write restart command to savefile

src/io.c

@@ -1,5 +1,6 @@
 #include <stdbool.h>
 #include <stdlib.h>
+#include <string.h>
 #include "io.h"
 #include "navier-stokes.h"
 
@@ -113,3 +114,41 @@ int read_u(_Complex double* u, int K1, int K2, FILE* file){
 
   return 0;
 }
+
+// remove an entry from params string (inplace)
+int remove_entry(
+  char* param_str,
+  char* entry
+){
+  char* ptr;
+  char* rw_ptr;
+  char* bfr;
+  char* entry_ptr=entry;
+  int go=1;
+
+  for(ptr=param_str, rw_ptr=ptr; *ptr!='\0'; ptr++){
+    for(bfr=ptr,entry_ptr=entry; *bfr==*entry_ptr; bfr++, entry_ptr++){
+      // check if reached end of entry
+      if(*(bfr+1)=='=' && *(entry_ptr+1)=='\0'){
+	go=0;
+	break;
+      }
+    }
+    if(go==1){
+      *rw_ptr=*ptr;
+      rw_ptr++;
+    }
+    //reset
+    if(*ptr==';'){
+      go=1;
+    }
+  }
+  *rw_ptr='\0';
+
+  // remove trailing ';'
+  if (param_str[strlen(param_str)-1]==';'){
+    *(param_str+(strlen(param_str)-1))='\0';
+  }
+
+  return 0;
+}

src/io.h

@@ -9,4 +9,7 @@ int write_u(_Complex double* u, int K1, int K2, FILE* file);
 // read u from file
 int read_u(_Complex double* u, int K1, int K2, FILE* file);
 
+// remove an entry from params string (inplace)
+int remove_entry(char* param_str, char* entry);
+
 #endif

src/main.c

@@ -13,6 +13,8 @@
 #include "init.h"
 #include "int_tools.h"
 
+#include "io.h"
+
 // structure to store parameters, to make it easier to pass parameters to CLI functions
 typedef struct nstrophy_parameters {
   double init_en; // initial value for the energy for ins and enstrophy for rns
@@ -135,6 +137,11 @@ int main (
   print_params(parameters, initfile_str, stderr);
   print_params(parameters, initfile_str, stdout);
 
+  // free initfile_str
+  if(initfile_str!=NULL){
+    free(initfile_str);
+  }
+
   // run command
   if (command==COMMAND_UK){
     uk(parameters.K1, parameters.K2, parameters.N1, parameters.N2, parameters.nsteps, parameters.nu, parameters.delta, parameters.L, u0, g, parameters.irreversible, parameters.print_freq, parameters.starting_time, nthreads, savefile);
@@ -142,7 +149,7 @@ int main (
   else if(command==COMMAND_EEA){
     // register signal handler to handle aborts
     signal(SIGINT, sig_handler);
-    eea(parameters.K1, parameters.K2, parameters.N1, parameters.N2, parameters.nsteps, parameters.nu, parameters.delta, parameters.L, u0, g, parameters.irreversible, parameters.print_freq, parameters.avg_window, parameters.starting_time, nthreads, savefile);
+    eea(parameters.K1, parameters.K2, parameters.N1, parameters.N2, parameters.nsteps, parameters.nu, parameters.delta, parameters.L, u0, g, parameters.irreversible, parameters.print_freq, parameters.avg_window, parameters.starting_time, nthreads, savefile, (char*)argv[0], param_str, savefile_str);
   }
   else if(command==COMMAND_QUIET){
     quiet(parameters.K1, parameters.K2, parameters.N1, parameters.N2, parameters.nsteps, parameters.nu, parameters.delta, parameters.L, u0, g, parameters.irreversible, nthreads, savefile);
@@ -217,6 +224,7 @@ int print_params(
   return 0;
 }
 
+
 // read command line arguments
 #define CP_FLAG_PARAMS 1
 #define CP_FLAG_NTHREADS 2
@@ -570,7 +578,8 @@ int set_parameter(
     // matches any argument that starts with 'file:'
     else if (strncmp(rhs,"file:",5)==0){
       parameters->init=INIT_FILE;
-      *initfile_str=(char*)rhs+5;
+      *initfile_str=calloc(sizeof(char), strlen(rhs)-5);
+      strcpy(*initfile_str, rhs+5);
     }
     else{
       fprintf(stderr, "error: unrecognized initial condition '%s'\n",rhs);

src/navier-stokes.c

@@ -2,6 +2,7 @@
 #include "io.h"
 #include <math.h>
 #include <stdlib.h>
+#include <string.h>
 
 // compute solution as a function of time
 int uk(
@@ -93,7 +94,11 @@ int eea(
   unsigned int running_avg_window,
   unsigned int starting_time,
   unsigned int nthreads,
-  FILE* savefile
+  FILE* savefile,
+  // for interrupt recovery
+  char* cmd_string,
+  char* params_string,
+  char* savefile_string
 ){
   _Complex double* u;
   _Complex double* tmp1;
@@ -186,9 +191,9 @@ int eea(
 	avg_print_short_en+=enstrophy/short_len;
       }
 
-      if(t % print_freq ==0 && t>0){
+      if(t % print_freq ==0 && t>starting_time){
 	// compute averages
-	if (t > running_avg_window) {
+	if (t > running_avg_window + starting_time) {
 	  avg_e=save_print_short_e[nr_print_in_window]*((double)short_len/running_avg_window);
 	  avg_a=save_print_short_a[nr_print_in_window]*((double)short_len/running_avg_window);
 	  avg_en=save_print_short_en[nr_print_in_window]*((double)short_len/running_avg_window);
@@ -226,7 +231,7 @@ int eea(
       }
     }
 
-    if(t>running_avg_window && t%print_freq==0){
+    if(t>running_avg_window + starting_time && t%print_freq==0){
       fprintf(stderr,"%d % .8e % .8e % .8e % .8e % .8e % .8e % .8e\n",t,t*delta, avg_a, avg_e, avg_en, alpha, energy, enstrophy);
       printf("%8d % .15e % .15e % .15e % .15e % .15e % .15e % .15e\n",t,t*delta, avg_a, avg_e, avg_en, alpha, energy, enstrophy);
     }
@@ -237,6 +242,24 @@ int eea(
       if (savefile==NULL){
 	savefile=stderr;
       }
+      fprintf(savefile,"# Interrupted computation. Resume with\n");
+      // command to resume
+      fprintf(savefile,"#! ");
+
+      fprintf(savefile, cmd_string);
+
+      // params
+      // allocate buffer for params
+      char* params=calloc(sizeof(char), strlen(params_string));
+      strcpy(params, params_string);
+      remove_entry(params, "starting_time");
+      remove_entry(params, "init");
+      remove_entry(params, "nsteps");
+      fprintf(savefile," -p \"%s;starting_time=%u;nsteps=%u;init=file:%s\"", params, t+1, nsteps-t-1, savefile_string);
+      free(params);
+
+      fprintf(savefile," energy\n");
+
       break;
     }
   }

src/navier-stokes.h

@@ -20,7 +20,7 @@ typedef struct fft_vects {
 int uk( int K1, int K2, int N1, int N2, unsigned int nsteps, double nu, double delta, double L, _Complex double* u0, _Complex double* g, bool irreversible, unsigned int print_freq, unsigned int starting_time, unsigned int nthreadsl, FILE* savefile);
 
 // compute energy, enstrophy and alpha
-int eea( int K1, int K2, int N1, int N2, unsigned int nsteps, double nu, double delta, double L, _Complex double* u0, _Complex double* g, bool irreversible, unsigned int print_freq, unsigned int running_avg_window, unsigned int starting_time, unsigned int nthreads, FILE* savefile);
+int eea( int K1, int K2, int N1, int N2, unsigned int nsteps, double nu, double delta, double L, _Complex double* u0, _Complex double* g, bool irreversible, unsigned int print_freq, unsigned int running_avg_window, unsigned int starting_time, unsigned int nthreads, FILE* savefile, char* cmd_string, char* params_string, char* savefile_string);
 
 // compute solution as a function of time, but do not print anything (useful for debugging)
 int quiet( int K1, int K2, int N1, int N2, unsigned int nsteps, double nu, double delta, double L, _Complex double* u0, _Complex double* g, bool irreversible, unsigned int nthreads, FILE* savefile);