static int search_einp(int ninp, const t_inpfile *inp, const char *name)
{
int i;
if (inp==NULL)
return -1;
for(i=0; i<ninp; i++)
if (gmx_strcasecmp_min(name,inp[i].name) == 0)
return i;
return -1;
}
int get_eeenum(int *ninp, t_inpfile **inp, const char *name, const char **defs,
warninp_t wi)
{
int ii, i, j;
int n = 0;
char buf[STRLEN];
ii = get_einp(ninp, inp, name);
if (ii == -1)
{
(*inp)[(*ninp)-1].value = strdup(defs[0]);
return 0;
}
for (i = 0; (defs[i] != NULL); i++)
{
if (gmx_strcasecmp_min(defs[i], (*inp)[ii].value) == 0)
{
break;
}
}
if (defs[i] == NULL)
{
n += sprintf(buf, "Invalid enum '%s' for variable %s, using '%s'\n",
(*inp)[ii].value, name, defs[0]);
n += sprintf(buf+n, "Next time use one of:");
j = 0;
while (defs[j])
{
n += sprintf(buf+n, " '%s'", defs[j]);
j++;
}
if (wi != NULL)
{
warning_error(wi, buf);
}
else
{
fprintf(stderr, "%s\n", buf);
}
(*inp)[ii].value = strdup(defs[0]);
return 0;
}
return i;
}
int find_group(char s[], int ngrps, char **grpname)
{
int aa, i, n;
char string[STRLEN];
gmx_bool bMultiple;
bMultiple = FALSE;
n = strlen(s);
aa=NOTSET;
/* first look for whole name match */
if (aa==NOTSET)
for(i=0; i<ngrps; i++)
if (gmx_strcasecmp_min(s,grpname[i])==0) {
if(aa!=NOTSET)
bMultiple = TRUE;
aa=i;
}
/* second look for first string match */
if (aa==NOTSET)
for(i=0; i<ngrps; i++)
if (gmx_strncasecmp_min(s,grpname[i],n)==0) {
if(aa!=NOTSET)
bMultiple = TRUE;
aa=i;
}
/* last look for arbitrary substring match */
if (aa==NOTSET) {
upstring(s);
minstring(s);
for(i=0; i<ngrps; i++) {
strcpy(string, grpname[i]);
upstring(string);
minstring(string);
if (strstr(string,s)!=NULL) {
if(aa!=NOTSET)
bMultiple = TRUE;
aa=i;
}
}
}
if (bMultiple) {
printf("Error: Multiple groups '%s' selected\n", s);
aa=NOTSET;
}
return aa;
}
void replace_inp_entry(int ninp,t_inpfile *inp,const char *old_entry,const char *new_entry)
{
int i;
for(i=0; (i<ninp); i++) {
if (gmx_strcasecmp_min(old_entry,inp[i].name) == 0) {
if (new_entry) {
fprintf(stderr,"Replacing old mdp entry '%s' by '%s'\n",
inp[i].name,new_entry);
sfree(inp[i].name);
inp[i].name = strdup(new_entry);
} else {
fprintf(stderr,"Ignoring obsolete mdp entry '%s'\n",
inp[i].name);
inp[i].bObsolete = TRUE;
}
}
}
}
t_inpfile *read_inpfile(const char *fn, int *ninp,
char **cppopts,
warninp_t wi)
{
FILE *in;
char buf[STRLEN], lbuf[STRLEN], rbuf[STRLEN], warn_buf[STRLEN];
char *ptr, *cptr;
t_inpfile *inp = NULL;
int nin, lc, i, j, k;
/* setting cppopts from command-line options would be cooler */
gmx_bool allow_override = FALSE;
if (debug)
{
fprintf(debug, "Reading MDP file %s\n", fn);
}
in = ffopen(fn, "r");
nin = lc = 0;
do
{
ptr = fgets2(buf, STRLEN-1, in);
lc++;
set_warning_line(wi, fn, lc);
if (ptr)
{
/* Strip comment */
if ((cptr = strchr(buf, COMMENTSIGN)) != NULL)
{
*cptr = '\0';
}
/* Strip spaces */
trim(buf);
for (j = 0; (buf[j] != '=') && (buf[j] != '\0'); j++)
{
;
}
if (buf[j] == '\0')
{
if (j > 0)
{
if (debug)
{
fprintf(debug, "No = on line %d in file %s, ignored\n", lc, fn);
}
}
}
else
{
for (i = 0; (i < j); i++)
{
lbuf[i] = buf[i];
}
lbuf[i] = '\0';
trim(lbuf);
if (lbuf[0] == '\0')
{
if (debug)
{
fprintf(debug, "Empty left hand side on line %d in file %s, ignored\n", lc, fn);
}
}
else
{
for (i = j+1, k = 0; (buf[i] != '\0'); i++, k++)
{
rbuf[k] = buf[i];
}
rbuf[k] = '\0';
trim(rbuf);
if (rbuf[0] == '\0')
{
if (debug)
{
fprintf(debug, "Empty right hand side on line %d in file %s, ignored\n", lc, fn);
}
}
else
{
/* Now finally something sensible */
int found_index;
/* first check whether we hit the 'multiple_entries' option */
if (gmx_strcasecmp_min(eMultentOpt_names[eMultentOptName], lbuf) == 0)
{
/* we now check whether to allow overrides from here or not */
if (gmx_strcasecmp_min(eMultentOpt_names[eMultentOptNo], rbuf) == 0)
{
allow_override = FALSE;
}
else if (gmx_strcasecmp_min(eMultentOpt_names[eMultentOptLast], rbuf) == 0)
{
allow_override = TRUE;
}
else
{
sprintf(warn_buf,
"Parameter \"%s\" should either be %s or %s\n",
lbuf,
eMultentOpt_names[eMultentOptNo],
eMultentOpt_names[eMultentOptLast]);
warning_error(wi, warn_buf);
}
}
else
{
/* it is a regular option; check for duplicates */
found_index = search_einp(nin, inp, lbuf);
if (found_index == -1)
{
/* add a new item */
srenew(inp, ++nin);
inp[nin-1].inp_count = 1;
inp[nin-1].count = 0;
inp[nin-1].bObsolete = FALSE;
inp[nin-1].bSet = FALSE;
inp[nin-1].name = strdup(lbuf);
inp[nin-1].value = strdup(rbuf);
}
else
{
if (!allow_override)
{
sprintf(warn_buf,
"Parameter \"%s\" doubly defined (and multiple assignments not allowed)\n",
lbuf);
warning_error(wi, warn_buf);
}
else
{
/* override */
sfree(inp[found_index].value);
inp[found_index].value = strdup(rbuf);
sprintf(warn_buf,
"Overriding existing parameter \"%s\" with value \"%s\"\n",
lbuf, rbuf);
warning_note(wi, warn_buf);
}
}
}
}
}
}
}
}
while (ptr);
ffclose(in);
if (debug)
{
fprintf(debug, "Done reading MDP file, there were %d entries in there\n",
nin);
}
*ninp = nin;
return inp;
}
nb_kernel_t *
nb_kernel_list_findkernel(FILE gmx_unused * log,
const char * arch,
const char * electrostatics,
const char * electrostatics_modifier,
const char * vdw,
const char * vdw_modifier,
const char * geometry,
const char * other,
const char * vf)
{
int i;
unsigned int index;
nb_kernel_info_t * kernelinfo_ptr;
if (kernel_list_hash_size == 0)
{
return NULL;
}
index = nb_kernel_hash_func(arch,
electrostatics,
electrostatics_modifier,
vdw,
vdw_modifier,
geometry,
other,
vf) % kernel_list_hash_size;
kernelinfo_ptr = NULL;
while ( (i = kernel_list_hash[index]) != -1)
{
if (!gmx_strcasecmp_min(kernel_list[i].architecture, arch) &&
!gmx_strcasecmp_min(kernel_list[i].electrostatics, electrostatics) &&
!gmx_strcasecmp_min(kernel_list[i].electrostatics_modifier, electrostatics_modifier) &&
!gmx_strcasecmp_min(kernel_list[i].vdw, vdw) &&
!gmx_strcasecmp_min(kernel_list[i].vdw_modifier, vdw_modifier) &&
!gmx_strcasecmp_min(kernel_list[i].geometry, geometry) &&
!gmx_strcasecmp_min(kernel_list[i].other, other) &&
!gmx_strcasecmp_min(kernel_list[i].vf, vf))
{
kernelinfo_ptr = kernel_list+i;
break;
}
index = (index+1) % kernel_list_hash_size;
}
if (debug && kernelinfo_ptr != NULL)
{
fprintf(debug,
"NB kernel %s() with architecture '%s' used for neighborlist with\n"
" Elec: '%s', Modifier: '%s'\n"
" Vdw: '%s', Modifier: '%s'\n"
" Geom: '%s', Other: '%s', Calc: '%s'\n\n",
kernelinfo_ptr->kernelname, arch, electrostatics, electrostatics_modifier,
vdw, vdw_modifier, geometry, other, vf);
}
/* If we did not find any kernel the pointer will still be NULL */
return (kernelinfo_ptr != NULL) ? kernelinfo_ptr->kernelptr : NULL;
}
void
gmx_nonbonded_set_kernel_pointers(FILE *log, t_nblist *nl)
{
const char * elec;
const char * elec_mod;
const char * vdw;
const char * vdw_mod;
const char * geom;
const char * other;
const char * vf;
struct
{
const char * arch;
int simd_padding_width;
}
arch_and_padding[] =
{
/* Single precision */
#if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER) && !(defined GMX_DOUBLE)
{ "avx_256_single", 8 },
#endif
#if (defined GMX_SIMD_X86_AVX_128_FMA) && !(defined GMX_DOUBLE)
{ "avx_128_fma_single", 4 },
#endif
#if (defined GMX_SIMD_X86_SSE4_1) && !(defined GMX_DOUBLE)
{ "sse4_1_single", 4 },
#endif
#if (defined GMX_SIMD_X86_SSE2) && !(defined GMX_DOUBLE)
{ "sse2_single", 4 },
#endif
/* Double precision */
#if (defined GMX_SIMD_X86_AVX_256_OR_HIGHER && defined GMX_DOUBLE)
{ "avx_256_double", 4 },
#endif
#if (defined GMX_SIMD_X86_AVX_128_FMA && defined GMX_DOUBLE)
/* Sic. Double precision 2-way SIMD does not require neighbor list padding,
* since the kernels execute a loop unrolled a factor 2, followed by
* a possible single odd-element epilogue.
*/
{ "avx_128_fma_double", 1 },
#endif
#if (defined GMX_SIMD_X86_SSE2 && defined GMX_DOUBLE)
/* No padding - see comment above */
{ "sse2_double", 1 },
#endif
#if (defined GMX_SIMD_X86_SSE4_1 && defined GMX_DOUBLE)
/* No padding - see comment above */
{ "sse4_1_double", 1 },
#endif
#if (defined GMX_SIMD_SPARC64_HPC_ACE && defined GMX_DOUBLE)
/* No padding - see comment above */
{ "sparc64_hpc_ace_double", 1 },
#endif
{ "c", 1 },
};
int narch = asize(arch_and_padding);
int i;
if (nonbonded_setup_done == FALSE)
{
/* We typically call this setup routine before starting timers,
* but if that has not been done for whatever reason we do it now.
*/
gmx_nonbonded_setup(NULL, FALSE);
}
/* Not used yet */
other = "";
nl->kernelptr_vf = NULL;
nl->kernelptr_v = NULL;
nl->kernelptr_f = NULL;
elec = gmx_nbkernel_elec_names[nl->ielec];
elec_mod = eintmod_names[nl->ielecmod];
vdw = gmx_nbkernel_vdw_names[nl->ivdw];
vdw_mod = eintmod_names[nl->ivdwmod];
geom = gmx_nblist_geometry_names[nl->igeometry];
if (nl->type == GMX_NBLIST_INTERACTION_ADRESS)
{
nl->kernelptr_vf = (void *) gmx_nb_generic_adress_kernel;
nl->kernelptr_f = (void *) gmx_nb_generic_adress_kernel;
nl->simd_padding_width = 1;
return;
}
if (nl->type == GMX_NBLIST_INTERACTION_FREE_ENERGY)
{
nl->kernelptr_vf = (void *) gmx_nb_free_energy_kernel;
nl->kernelptr_f = (void *) gmx_nb_free_energy_kernel;
nl->simd_padding_width = 1;
}
else if (!gmx_strcasecmp_min(geom, "CG-CG"))
{
nl->kernelptr_vf = (void *) gmx_nb_generic_cg_kernel;
nl->kernelptr_f = (void *) gmx_nb_generic_cg_kernel;
nl->simd_padding_width = 1;
}
else
{
/* Try to find a specific kernel first */
for (i = 0; i < narch && nl->kernelptr_vf == NULL; i++)
{
nl->kernelptr_vf = (void *) nb_kernel_list_findkernel(log, arch_and_padding[i].arch, elec, elec_mod, vdw, vdw_mod, geom, other, "PotentialAndForce");
nl->simd_padding_width = arch_and_padding[i].simd_padding_width;
}
for (i = 0; i < narch && nl->kernelptr_f == NULL; i++)
{
nl->kernelptr_f = (void *) nb_kernel_list_findkernel(log, arch_and_padding[i].arch, elec, elec_mod, vdw, vdw_mod, geom, other, "Force");
nl->simd_padding_width = arch_and_padding[i].simd_padding_width;
/* If there is not force-only optimized kernel, is there a potential & force one? */
if (nl->kernelptr_f == NULL)
{
nl->kernelptr_f = (void *) nb_kernel_list_findkernel(NULL, arch_and_padding[i].arch, elec, elec_mod, vdw, vdw_mod, geom, other, "PotentialAndForce");
nl->simd_padding_width = arch_and_padding[i].simd_padding_width;
}
}
/* Give up. If this was a water kernel, leave the pointer as NULL, which
* will disable water optimization in NS. If it is a particle kernel, set
* the pointer to the generic NB kernel.
*/
if (nl->kernelptr_vf == NULL && !gmx_strcasecmp_min(geom, "Particle-Particle"))
{
nl->kernelptr_vf = (void *) gmx_nb_generic_kernel;
nl->kernelptr_f = (void *) gmx_nb_generic_kernel;
nl->simd_padding_width = 1;
if (debug)
{
fprintf(debug,
"WARNING - Slow generic NB kernel used for neighborlist with\n"
" Elec: '%s', Modifier: '%s'\n"
" Vdw: '%s', Modifier: '%s'\n"
" Geom: '%s', Other: '%s'\n\n",
elec, elec_mod, vdw, vdw_mod, geom, other);
}
}
}
return;
}