Rupture Variation Generator v5.4.2 code changes

This page documents the code changes required to turn the stand-alone version, genslip-v5.4.2, into an API callable by the CyberShake post-processing.

In this document, $ROOT_DIR is taken to be the <CyberShake home>/software/RuptureCodes/RupGen-api-5.4.2 directory. GenRandV5.0 is the code as received from Rob Graves.

Installing files

Create src, include, lib, and bin directories inside $ROOT_DIR .
Inside src, create GenRandV5.0.
Copy rupgen_api.c from a previous API version into src.
Copy rupgen_defs.h from a previous API version into src.
Create a symlink to rupgen_defs.h in src/GenRand5.0.
Copy rupgen_api.h from a previous API version into src.
Create a symlink to rupgen_api.h in src/GenRand5.0.
Confusingly, there are two files named structure.h. One is in StandRupFormat and contains the structures needed for an SRF. The other is in GenRandV5.0 and contains the definition for complex, along with a few other supporting structures.
1. Copy the StandRupFormat/structure.h into src/srf_structure.h .
2. Copy the GenRandV5.0/structure.h into src/structure.h .
3. Create a symlink to both files in src/GenRandV5.0.
There are also two files named defs.h.
1. Copy GenRandV5.0/StandRupFormat/defs.h into src/GenRandV5.0/srf_defs.h .
2. Copy GenRandV5.0/defs.h into src/GenRandV5.0/defs.h .
From the code provided by Rob, copy the following files into src/GenRandV5.0. Some of them are only lightly used, but it's easier to copy in the entire file rather than only taking the needed functions:
- defs.h
- function.h
- include.h
- fourg.f
- genslip-v5.4.2.c
- gslip_srf_subs.c
- iofunc.c
- misc.c
- ruptime.c
- slip.c
- sliprate_subs.c
- srf_subs.c (from StandRupFormat)
- wafront2d-rwg.f
- makefile
Copy Makefile from a previous API version into src.

Editing files

In $ROOT_DIR/src

structure.h

At the top of the file, change '#include "StandRupFormat/structure.h"' to '#include srf_structure.h'
Above that line, add:
```
#ifndef STRUCT_H
#define STRUCT_H
```
At the end of the file, add:
```
#endif
```

srf_structure.h

At the top of the file, add:

#ifndef SRF_STRUCT_H
#define SRF_STRUCT_H

At the end of the file, add:
```
#endif
```

Makefile

Edit the GETPAR values to point to the getpar install.
Edit GENSLIP to have the same name as the GenRandV5.0 directory.
Edit the library creation line (under the librupgen.a target, starts with $(AR)) to point to the correct version of genslip.

In GenRandV5.0

defs.h

At the top of the file, add:

#ifndef DEFS_H
#define DEFS_H

#include "srf_defs.h"

Delete DEFAULT_SHAL_VRUP_FRAC, as it is not used anymore.
At the end of the file, add:
```
#endif
```

srf_defs.h

At the top of the file, add:
```
#ifndef SRF_DEFS_H
#define SRF_DEFS_H
```
Delete DEFAULT_SHAL_VRUP_FRAC, as it is not used anymore.
Delete the lines corresponding to RDONLY_FLAGS, RDWR_FLAGS, CROPTR_FLAGS, and the _FILE_OFFSET_BITS if statement, as this already exists in defs.h.
At the end of the file, add:
```
#endif
```

include.h

At the top of the file, add:

#ifndef RUPGEN_INCLUDE_H
#define RUPGEN_INCLUDE_H

At the end of the file, add:

#include <string.h>
#include "fftw3.h"

#include "rupgen_api.h"
#include "rupgen_defs.h"

#ifdef _USE_MEMCACHED
#include <libmemcached/memcached.h>
#endif

#endif

function.h

At the top of the file, add:

#ifndef RUPGEN_FUNC_H
#define RUPGEN_FUNC_H

#include "structure.h"

Change the entry for read_ruppars to _read_ruppars, like:

struct pointsource *_read_ruppars(char *,struct pointsource *,float *,int *,int *,float *,float *,float *,float *,float *,float *,float *);

Add an entry for get_rupt:

void get_rupt(struct velmodel* vm, float* h, float* srcd, float* recd, float* srcr, float* recr, double* p, double* rad, float* tt);

Add an entry for zapit:
```
void zapit(float* s,int n);
```

At the end of the file, add:

void write_srf1(struct standrupformat *srf,char *file,int bflag);
void write_srf2(struct standrupformat *srf,char *file,int bflag);

#ifdef _USE_MEMCACHED
int mc_genslip(int ac,char **av, rg_stats_t *stats, struct standrupformat* srf, int state, char* mc_server);
struct pointsource* _mc_read_ruppars(char *file,struct pointsource *psrc,float *mag,int *nx,int *ny,float *dx,float *dy,float *dtop,float *stk,float *dip,float *elon,float *elat, char* mc_server);
#else
int genslip(int ac,char **av, rg_stats_t *stats, struct standrupformat* srf, int state);
#endif

#endif

slip.c

In line 853, just before

arr = check_realloc(arr, n2*sizeof(fftwf_complex));

insert

fftwf_destroy_plan(plan);

In line 883, change the 'fftwf_free(arr)' to 'free(arr)'; since arr was allocated using check_malloc it should be freed with just free().

makefile

Edit the 2nd line that begins with OBJS so it contains

OBJS = iofunc.o misc.o slip.o ruptime.o srf_subs.o gslip_srf_subs.o geoproj_subs.o gslip_sliprate_subs.o wafront2d-rwg.o fourg.o

Delete the SRF_OBJS and FDRT_OBJS lines, 3-5.
Edit GETPARLIB and GETPARINC so it correctly points to the Getpar install in <CyberShake home>/software/Getpar .
Change CFLAGS to:
```
CFLAGS = ${UFLAGS} ${LF_FLAGS} 
```

Add:

# Uncomment for memcached support
MEMC = ../../../../../utils/libmemcached_1.0.18
CFLAGS := $(CFLAGS) -I${MEMC}/include -D_USE_MEMCACHED
LDLIBS := ${LDLIBS} -L${MEMC}/lib -lmemcached -L${OLCF_FFTW_ROOT}/lib

Delete all targets except genslip-v5.4.2, ${OBJS}, and clean.
Modify the genslip-v5.4.2 target. We need to remove unnecessary objects, and compile it to an object rather than an executable for inclusion in the genslip library. It should look like:

genslip-v5.4.2.o : genslip-v5.4.2.c ${OBJS}
        ${CC} ${CFLAGS} -c -o genslip-v5.4.2.o genslip-v5.4.2.c ${LDLIBS}

gslip_srf_subs.c

In line 175, add initialization for srf.np_seg, so we can free it without worry:

if (strcmp(srf[0].version, "2.0")==0) {
        srf[0].np_seg = NULL;
        srf[0].srf_hcmnt.cbuf = NULL;
}

Enclose lines 1166-1180 in an if statement:

if (strcmp(srf[0].version, "2.0")==0) {
        srf[0].srf_hcmnt.nline = 0;
        /*
        srf[0].nseg = 1;
        srf[0].np_seg = (int *)check_malloc((srf[0].nseg)*sizeof(int));
        srf[0].np_seg[0] = srf[0].srf_apnts.np;
        */

        /* 2018-04-02 updated for multiple segs */
        srf[0].nseg = srf[0].srf_prect.nseg;
        srf[0].np_seg = (int *)check_malloc((srf[0].nseg)*sizeof(int));

        for(iseg=0;iseg<nseg;iseg++)
           srf[0].np_seg[iseg] = prseg_ptr[iseg].nstk*prseg_ptr[0].ndip;

        /* end version 2.0 stuff, just in case */
}

iofunc.c

In line 179, change the function name read_ruppars to _read_ruppars:

struct pointsource *_read_ruppars(char *file,struct pointsource *psrc,float *mag,int *nx,int *ny,float *dx,float *dy,float *dtop,float *stk,float *dip,float *elon,float *elat)

Add the function _mc_add_file to the end of the file:

#ifdef _USE_MEMCACHED
void _mc_add_file(char* filename, char** file_buffer, memcached_st* mst) {
        memcached_return ret;
        uint32_t flags = 0;

        FILE* fpr = fopfile(filename, "rb");
        //Get file size so we know how big to make the file buffer
        fseek(fpr, 0, SEEK_END);
        long file_length = ftell(fpr);
        fseek(fpr, 0, SEEK_SET);
        *file_buffer = check_malloc(sizeof(char) * (file_length+1));
        memset(*file_buffer, '\0', file_length+1);
        int part_id = 0;
        long read = fread(*file_buffer, 1, file_length, fpr);
        if (read!=file_length) {
                fprintf(stderr, "READ ERROR - %ld attempted %ld read.\n", file_length, read);
                exit(1);
        }
        char* file_key = check_malloc(sizeof(char) * (strlen(filename) + 4));
        char buffer[1000*1000];
        //Memcached thinks this is 1 MB
        int ONE_MB = 1000*1000;
        int i=0;
        while (i*ONE_MB < file_length) {
                int to_copy = ONE_MB;
                if (file_length - i*ONE_MB < ONE_MB) {
                        to_copy = file_length - i*ONE_MB;
                }
                sprintf(file_key, "%s.%d", filename, i);
                memcpy(buffer, (*file_buffer)+i*ONE_MB, to_copy);

                ret = memcached_set(mst, file_key, strlen(file_key), buffer, strlen(buffer), 0, flags);
                if (ret!=MEMCACHED_SUCCESS) {
                        printf("Caching of %s failed.\n", file_key);
                        printf("%s\n", memcached_strerror(mst, ret));
                        printf("value length: %d bytes\n", strlen(buffer));
                }
                i++;
                memset(buffer, '\0', ONE_MB);
        }
        //Commit number of parts
        int num_parts = i;
        char* parts_key = check_malloc(sizeof(char) * (strlen(filename) + 1));
        strcpy(parts_key, filename);
        ret = memcached_set(mst, parts_key, strlen(parts_key), (char*)(&num_parts), sizeof(int), 0, flags);
        if (ret!=MEMCACHED_SUCCESS) {
                printf("Caching of %s failed.\n", parts_key);
                printf("%s\n", memcached_strerror(mst, ret));
        }
        free(file_key);
        free(parts_key);
        fclose(fpr);
}

Add the definition of _mc_read_ruppars:

struct pointsource* _mc_read_ruppars(char *file,struct pointsource *psrc,float *mag,int *nx,int *ny,float *dx,float *dy,float *dtop,float *stk,float *dip,float *elon,float *elat, char* mc_server)
{
       FILE *fpr, *fopfile();
       float area;
       int i, nn;
       char str[1024];

       double rperd = 0.017453293;
       int ONE_MB = 1000*1000; //This is what memcached thinks 1 MB is
       *dtop = 1.0e+15;
       *stk = 0.0;
       *dip = 0.0;
       *elon = 0.0;
       *elat = 0.0;

       char* buffer;
       char* file_data;
       int* num_parts;

        printf("Using %s as memcached server.\n", mc_server);

        memcached_return ret;
        memcached_st* mst;

        mst = memcached_create(NULL);
        memcached_server_st *server = memcached_server_list_append(NULL, mc_server, 11211, &ret);

        ret = memcached_server_push(mst, server);
        memcached_server_free(server);

        uint32_t flags = 0;

        //See if file parts is in cache
        //key is filename + "_" + part
        char* parts_key = check_malloc(sizeof(char) * (strlen(file) + 1));
        strcpy(parts_key, file);

        size_t incoming_size;
        num_parts = (int*) memcached_get(mst, parts_key, strlen(parts_key), &incoming_size, &flags, &ret);
        if (num_parts==NULL) {
                printf("Key %s hasn't been cached, adding.\n", parts_key);
                _mc_add_file(file, &file_data, mst);
        } else {
                printf("Found key %s, num parts is %d.\n", parts_key, *num_parts);
                printf("Looking for parts.\n");
                //See if all the parts are actually around
                file_data = check_malloc(sizeof(char) * (ONE_MB * *num_parts + 1));
                memset(file_data, '\0', ONE_MB* *num_parts + 1);
                char* file_key = check_malloc(sizeof(char) * (strlen(file) + 4));
                size_t incoming;
                for (i=0; i<*num_parts; i++) {
                        sprintf(file_key, "%s.%d", file, i);
                        buffer = (char*) memcached_get(mst, file_key, strlen(file_key), &incoming, &flags, &ret);
                        if (buffer==NULL) {
                                printf("Piece %s was missing, adding file %s.\n", file_key, file);
                                //This piece is missing
                                //Easiest to add the whole file
                                free(file_data);
                                _mc_add_file(file, &file_data, mst);
                                break;
                        } else {
                                memcpy(file_data+i*ONE_MB, buffer, incoming);
                        }
                }
                free(file_key);
        }

        free(parts_key);
        memcached_free(mst);

        char* tok;
        tok = strtok(file_data, "\n"); /* Probability = <float> */

        tok = strtok(NULL, "\n"); /* Magnitude = <float> */
        sscanf(tok,"%*s %*s %f",mag);

        tok = strtok(NULL, "\n");   /* GridSpacing = <float> */
        sscanf(tok,"%*s %*s %f",dx);

        if(*dx == (float)(0.0))
           {
           fprintf(stderr,"***** input error\n");
           fprintf(stderr,"      GridSpacing = 0.0, exiting...\n");
           exit(-1);
           }

        *dy = *dx;

        tok = strtok(NULL, "\n");   /* NumRows = <int> */
        sscanf(tok,"%*s %*s %d",ny);

        tok = strtok(NULL, "\n");   /* NumCols = <int> */
        sscanf(tok,"%*s %*s %d",nx);

        tok = strtok(NULL, "\n");/* header comment */
        psrc = (struct pointsource *)check_realloc(psrc,(*nx)*(*ny)*sizeof(struct pointsource));

        area = (*dx)*(*dy)*1.0e+10;  /* km -> cm */

        for(i=0;i<(*nx)*(*ny);i++)
           {
           tok = strtok(NULL, "\n");   /* Lat , Lon , Depth , Rake , Dip , Strike */
           sscanf(tok,"%f %f %f %f %f %f",&psrc[i].lat,
                                          &psrc[i].lon,
                                          &psrc[i].dep,
                                          &psrc[i].rak,
                                          &psrc[i].dip,
                                          &psrc[i].stk);

           psrc[i].area = area;

           if(psrc[i].dep < *dtop)
              *dtop = psrc[i].dep;

           *stk = *stk + psrc[i].stk;
           *dip = *dip + psrc[i].dip;
           }
        *stk = *stk/((*nx)*(*ny));
        *dip = *dip/((*nx)*(*ny));

        nn = 0;
        for(i=0;i<(*nx)*(*ny);i++)
           {
           if(psrc[i].dep < (*dtop + 0.01))
              {
              *elon = *elon + psrc[i].lon;
              *elat = *elat + psrc[i].lat;
              nn++;
              }
           }

        /* adjust for half subfault width */
        *dtop = (*dtop) - 0.5*(*dx)*sin((*dip)*rperd);

        if(nn == 0)
           nn++;

        *elon = *elon/nn;
        *elat = *elat/nn;

        free(file_data);

        return(psrc);
}
#endif

misc.c

In line 68, modify zapit to use a for-loop and specify a return type. The function should become:
```
void zapit(float* s,int n)
{
int i;
for (i=0; i<n; i++) {
        s[i] = 0.0;
}
```

Add the free_srf_ptrs function to clean up everything:

void free_srf_ptrs(struct standrupformat* srf) {
        struct srf_planerectangle srf_prect = srf->srf_prect;
        struct srf_allpoints srf_apnts = srf->srf_apnts;

        free(srf_prect.prectseg);
        int i;
        for (i=0; i<srf_apnts.np; i++) {
                free(srf_apnts.apntvals[i].stf1);
                free(srf_apnts.apntvals[i].stf2);
                free(srf_apnts.apntvals[i].stf3);
        }
        free(srf_apnts.apntvals);
        if (strcmp(srf->version,"2.0")==0) {
                free(srf->np_seg);
                free(srf->srf_hcmnt.cbuf);
        }
}

genslip-v5.4.2.c

This is where the majority of changes are made to turn this into an API. I recommend having an original copy for reference.

Note that line numbers are approximate.

In line 352, change from

int main(int ac,char **av)

to

#ifdef _USE_MEMCACHED
int mc_genslip(int ac, char** av, rg_stats_t *stats, struct standrupformat* srf, int state, char* memcached_server)
#else
int genslip(int ac,char **av, rg_stats_t *stats, struct standrupformat* srf, int state)
#endif

In line 444, after

struct velmodel rvmod;

add initializations:

rvmod.vs = rvmod.invb2 = NULL;
rvmod.th = NULL;

In line 449, after float delh, hx, hg, gwid2, *gbnd, *gwid, shypo_mseg, *rvfac_seg;
add initializations:
```
rvfac_seg = gbnd = gwid = NULL;
```
Delete SRF definition in line 584:
```
struct standrupformat srf;
```

After line 601:

int outbin = 0;

Add

int doslip = -1;
int dohypo = -1;

In line 622, after

double dh, *fdrt, *rslw, *fspace;

add initializations:

fdrt = rslw = fspace = NULL;

In line 626, after

int ixs, iys, nsring, ntot, *ispace;

add initialization:

ispace = NULL;

Change 'srf.version' to 'srf->version' in line 631.
In line 636, change the default version to 2.0:
```
sprintf(srf->version,"2.0");
```

In line 699, after 'getpar("outbin","d",&outbin);', add:

getpar("doslip","d",&doslip);
getpar("dohypo","d",&dohypo);

In line 707-9, change all the 'srf.version' to 'srf->version'.

In line 959, change

 psrc_orig = read_ruppars(infile,psrc_orig,&mag,&nstk,&ndip,&dstk,&ddip,&dtop,&avgstk,&avgdip,&elon,&elat);

to

#ifdef _USE_MEMCACHED
   psrc_orig = _mc_read_ruppars(infile,psrc_orig,&mag,&nstk,&ndip,&dstk,&ddip,&dtop,&avgstk,&avgdip,&elon,&elat,memcached_server);
#else
   psrc_orig = _read_ruppars(infile,psrc_orig,&mag,&nstk,&ndip,&dstk,&ddip,&dtop,&avgstk,&avgdip,&elon,&elat);
#endif

In line 1012, change '&srf' to 'srf'.
In line 1016, change '&srf' to 'srf'.

In line 1315, after 'dhypo = dhypo_frac*fwid;', add:

stats->numslip = ns;
stats->numhypo = nh;

if (state==GET_STATS) {
   free(rvfac_seg);
   free(gbnd);
   free(gwid);
   free(psrc);
   free(psrc_orig);
   free(slip_c);
   free(rake_c);
   free(tsfac1_c);
   free(rtime1_c);
   free(rough_c);
   free(tsfac2_c);
   free(rtime2_c);
   free(slip_r);
   free(rake_r);
   free(tsfac1_r);
   free(rtime1_r);
   free(rough_r);
   free(tsfac2_r);
   free(rtime2_r);
   free(stk_r);
   free(dip_r);
   free(psrc_rake);
   return 0;
}

if (dohypo>=nh) {
        fprintf(stderr,"Error:  You requested hypocenter ID %d but from infile %s genslip calculates %d hypocenters.\n", dohypo, infile, nh);
        exit(1);
}

if (doslip>=ns) {
        fprintf(stderr,"Error:  You requested slip ID %d but from infile %s genslip calculates %d slips.\n", doslip, infile, ns);
        exit(2);
}

if (ns<-1 || nh<-1) {
        fprintf(stderr, "Error: hypocenter and slip ID need to be >= -1.");
        exit(3);
}

In line 1363, after:

for(js=0;js<ns;js++)    /* loop over slip/rupture realizations */
   {

add

   if (doslip!=-1 && js>doslip) {
        //We've already done the slip we need, break out of the loop
        break;
   }

   if (doslip!=-1 && js<doslip) {
        //Haven't gotten to the right slip yet, continue
        continue;
   }

In lines 1394-1403, change iterative calculation of shypo and dhypo to explicit. Delete

if(ih_scnt == nhypo_s)
         {
         ih_scnt = 0;
         ih_dcnt++;
         }

      shypo = hypo_s0 + ih_scnt*hypo_ds;
      dhypo = hypo_d0 + ih_dcnt*hypo_dd;

      ih_scnt++;

and replace with

      shypo = hypo_s0 + (js%nhypo_s)*hypo_ds;
      dhypo = hypo_d0 + (js/nhypo_s)*hypo_dd;

In line 2394, change '&srf' to 'srf'.

In the for loop starting in line 2452, we replace some of these calculations with refactored ones to pull out constants and take advantage of FMA. Specifically, make the following changes:

Before the for loop, define the following variables:

float half_ddip = 0.5*ddip;
float half_dstk_minus_half_flen = 0.5*dstk - 0.5*flen;
float half_flen_plus_shypo = 0.5*flen + shypo;
y0 = (deep_vrdep1-dtop)/sin(avgdip*rperd);
float deep_alpha = 1.0 + (deep_vrdep1-deep_rup*deep_vrdep1)/(deep_vrdep2-deep_vrdep1);
float deep_const = (deep_rup - 1.0)/(deep_vrdep2-deep_vrdep1);

Replace

yy = (j + 0.5)*ddip;

with

yy = j*ddip + half_ddip;

Replace

xx = (i+0.5)*dstk - 0.5*flen;

with

xx = i*dstk + half_dstk_minus_half_flen;

Replace

hg = (gbnd[ig]-0.5*flen)-shypo;

with

hg = gbnd[ig] - half_flen_plus_shypo;

Replace

vrfac = 1.0 + (deep_vrup - 1.0)*((psrc[ip].dep)-deep_vrdep1)/(deep_vrdep2-deep_vrdep1);

with

vrfac = deep_alpha + deep_const*psrc[ip].dep;

In line 2573, after 'psrc[j].rupt = psrc[j].rupt - tsmin + rupture_delay;', add:
```
if (dohypo!=ih || doslip!=js) {
    continue;
}
```
In line 2601, change '&srf' to 'srf'.
In line 2611, remove
```
free_srf_stf(&srf);
```
In line 2618, change '&srf' to 'srf'.
In line 2631, remove:
```
 write2srf(srf,str,outbin);
```
Writing out SRFs is done by calling write_srf() on the srf object.

At the very end of the function, we want to free everything not needed by the SRF object. Add:

free(rvfac_seg);
free(gbnd);
free(gwid);
free(psrc);
free(psrc_orig);
free(slip_c);
free(rake_c);
free(tsfac1_c);
free(rtime1_c);
free(rough_c);
free(tsfac2_c);
free(rtime2_c);
free(slip_r);
free(rake_r);
free(tsfac1_r);
free(rtime1_r);
free(rough_r);
free(tsfac2_r);
free(rtime2_r);
free(stk_r);
free(dip_r);
free(psrc_rake);
free(rspd);
free(vmod.vp);
free(vmod.vs);
free(vmod.den);
free(vmod.th);
free(vmod.dep);
free(vmod.mu);
free(vmod.invb2);
free(rvmod.vs);
free(rvmod.th);
free(rvmod.invb2);

return 0;

Once verification is complete, you may wish to comment out some of the print statements.

Compiling

Go back into the src directory and try to compile it with 'make'.

With v5.4.2, we are not including the -fno-expensive-optimizations flag, since backwards compatibility with Blue Waters and Titan isn't an issue.

Rupture Variation Generator v5.4.2 code changes

Contents

Installing files

Editing files

In $ROOT_DIR/src

structure.h

srf_structure.h

Makefile

In GenRandV5.0

defs.h

srf_defs.h

include.h

function.h

slip.c

makefile

gslip_srf_subs.c

iofunc.c

misc.c

genslip-v5.4.2.c

Compiling

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