static int cpustr_to_cpulist_scatter(bstring bcpustr, int* cpulist, int length)
{
topology_init();
CpuTopology_t cpuid_topology = get_cpuTopology();
affinity_init();
AffinityDomains_t affinity = get_affinityDomains();
char* cpustring = bstr2cstr(bcpustr, '\0');
if (bstrchrp(bcpustr, ':', 0) != BSTR_ERR)
{
int insert = 0;
int suitidx = 0;
int* suitable = (int*)malloc(affinity->numberOfAffinityDomains*sizeof(int));
if (!suitable)
{
bcstrfree(cpustring);
return -ENOMEM;
}
for (int i=0; i<affinity->numberOfAffinityDomains; i++)
{
if (bstrchrp(affinity->domains[i].tag, cpustring[0], 0) != BSTR_ERR)
{
suitable[suitidx] = i;
suitidx++;
}
}
int* sortedList = (int*) malloc(affinity->domains[suitable[0]].numberOfProcessors * sizeof(int));
if (!sortedList)
{
free(suitable);
bcstrfree(cpustring);
return -ENOMEM;
}
for (int off=0;off<affinity->domains[suitable[0]].numberOfProcessors;off++)
{
for(int i=0;i < suitidx; i++)
{
cpulist_sort(affinity->domains[suitable[i]].processorList, sortedList, affinity->domains[suitable[i]].numberOfProcessors);
cpulist[insert] = sortedList[off];
insert++;
if (insert == length)
goto scatter_done;
}
}
scatter_done:
bcstrfree(cpustring);
free(sortedList);
free(suitable);
return insert;
}
bcstrfree(cpustring);
return 0;
}
void hash_file(hash *hashtable[], char *file, unsigned int tablesize)
{
FILE *fp;
bstring buffer;
bstring value;
int poseq;
fp = fopen(file, "r");
if (fp == NULL)
{
fp = fopen(file, "w+"); /* create the file */
if (fp == NULL)
fprintf(stderr, "Could not create file (%s)\n", file);
return;
}
while ((buffer = bgets((bNgetc) fgetc, fp, '\n')) != NULL)
{
/* seriously, wtf is a \10 doing in my buffer you
c********r? let's get rid of it: */
poseq = bstrchrp(buffer, '=', 0);
value = bmidstr(buffer, poseq+1, blength(buffer) - poseq - 2);
btrunc(buffer, poseq);
/*printf("%s=%s\n", bdata(buffer), bdata(value));*/
hash_add(hashtable, buffer, value, tablesize);
}
fclose(fp);
bdestroy(buffer);
bdestroy(value);
}
/**
* Argument:
* fn - a file name
* Return:
* a bstring with a line if successful, NULL otherwise.
*/
bstring alder_file_firstline(const char *fn)
{
char buf[BUFLEN];
bstring bline = NULL;
int len = 0;
int status = 0;
int s = alder_file_exist(fn);
if (s == 0) {
return 0;
}
s = alder_file_isgzip(fn);
if (s == 1) {
// open it with zlib.
gzFile gz = gzopen(fn, "rb");
if (gz == NULL) return NULL;
len = gzread(gz, buf, sizeof(buf));
if (len <= 0) {
gzclose(gz);
return NULL;
}
if (len <= 0) {
status = -1;
}
gzclose(gz);
} else {
// open it with a regular fopen or open.
FILE *fp = fopen(fn, "rb");
if (fp == NULL) return NULL;
len = (int)fread(buf, sizeof(char), BUFLEN, fp);
if (len <= 0) {
status = -1;
}
fclose(fp);
}
if (status == 0) {
bstring bbuffer = blk2bstr (buf, len);
int pos = bstrchrp (bbuffer, '\n', 0);
if (pos == BSTR_ERR) {
bline = bstrcpy(bbuffer);
} else {
bline = bHead(bbuffer, pos);
}
bdestroy(bbuffer);
}
return bline;
}
void Parse_print_error(const char *message, bstring content, int at, int line_number)
{
int prev_nl = bstrrchrp(content, '\n', at);
int next_nl = bstrchrp(content, '\n', at);
if(prev_nl < 0) {
log_err("%s AT '%c' on line %d:\n%.*s\n%*s", message,
bchar(content, at), line_number-1,
next_nl, bdata(content),
at, "^");
} else {
log_err("%s AT '%c' on line %d:%.*s\n%*s", message,
bchar(content, at), line_number,
next_nl - prev_nl, bdataofs(content, prev_nl),
at - prev_nl, "^");
}
}
static void normalize_space(bstring str) {
int i=0;
while(i<blength(str)) {
int spaceStart = bstrchrp(str,' ',i);
if (spaceStart == BSTR_ERR)
break;
//we found it, now look for the end of this space sequence
int spaceLen = 1; //exclusive
while(str->data[spaceStart+spaceLen] == ' ')
spaceLen++;
if (spaceLen > 1) {
//multiple spaces
bdelete(str,spaceStart+1,spaceLen-1);
}
i = spaceStart+1;
}
}
/**
* Argument:
* fn - file names
* Return:
* An ordered file names.
*/
alder_seqid_file_t * alder_seqid_file_init(struct bstrList *fn)
{
// Test if all of the files exist.
// Determine the file type (text or gzip).
// Use the first line to determine file formats (FASTA or FASTQ).
// Read the first sequence name of each file.
// Pair files using sequence names.
alder_seqid_file_t *v = malloc(sizeof(alder_seqid_file_t));
int numberOfFile = fn->qty;
v->filename = bstrVectorCreate(numberOfFile);
v->type = malloc(numberOfFile * sizeof(int));
v->format = malloc(numberOfFile * sizeof(int));
v->pair = malloc(numberOfFile * sizeof(int));
for (int i = 0; i < fn->qty; i++) {
int s = alder_file_exist(bdata(fn->entry[i]));
if (s == 0) {
alder_seqid_file_free(v);
return NULL;
}
}
for (int i = 0; i < fn->qty; i++) {
int s = alder_file_isgzip(bdata(fn->entry[i]));
if (s == 1) {
v->type[i] = 2;
} else {
v->type[i] = 1;
}
}
for (int i = 0; i < fn->qty; i++) {
int s = alder_file_whatformat(bdata(fn->entry[i]));
if (s == 1) {
v->format[i] = 1;
} else if (s == 2) {
v->format[i] = 2;
} else {
alder_seqid_file_free(v);
return NULL;
}
}
struct bstrList *bnames = bstrVectorCreate(fn->qty);
for (int i = 0; i < fn->qty; i++) {
bstring s = alder_file_firstline(bdata(fn->entry[i]));
int posFirstSpace = bstrchrp(s, ' ', 0);
bstring bword = NULL;
if (posFirstSpace != BSTR_ERR) {
bword = bHead(s, posFirstSpace);
} else {
bword = bstrcpy(s);
}
bdestroy(s);
bstring bname = bTail(bword, bword->slen - 1);
bdestroy(bword);
bstrVectorAdd(bnames, bdata(bname));
bdestroy(bname);
}
for (int i = 0; i < fn->qty; i++) {
v->pair[i] = -1;
for (int j = 0; j < fn->qty; j++) {
if (i == j) continue;
if (!bstrcmp(bnames->entry[i], bnames->entry[j])) {
v->pair[i] = j;
}
}
}
int *pairCount = malloc(numberOfFile * sizeof(int));
memset(pairCount, 0, numberOfFile*sizeof(int));
for (int i = 0; i < fn->qty; i++) {
int j = v->pair[i];
pairCount[j]++;
}
for (int i = 0; i < fn->qty; i++) {
if (pairCount[i] > 1) {
free(pairCount);
alder_seqid_file_free(v);
return NULL;
}
}
free(pairCount);
///////////////////////////////////////////////////////////////////////////
// Order pairs.
int pairI = 0;
alder_vector_pair_t * pair = alder_vector_pair_t_alloc(fn->qty);
for (int i = 0; i < fn->qty; i++) {
if (v->pair[i] >= 0) {
int alreadPaired = 0;
for (int j = 0; j < pairI; j++) {
if (pair->data[j].first == i ||
pair->data[j].second== i) {
alreadPaired = 1;
break;
}
}
if (alreadPaired == 0) {
if (i < v->pair[i]) {
pair->data[pairI].first = i;
pair->data[pairI].second= v->pair[i];
} else {
pair->data[pairI].first = v->pair[i];
pair->data[pairI].second= i;
}
pairI++;
}
}
}
for (int i = 0; i < fn->qty; i++) {
if (v->pair[i] < 0) {
pair->data[pairI].first = i;
pair->data[pairI].second= -1;
pairI++;
}
}
alder_seqid_file_t *v2 = malloc(sizeof(alder_seqid_file_t));
v2->filename = bstrVectorCreate(numberOfFile);
v2->type = malloc(numberOfFile * sizeof(int));
v2->format = malloc(numberOfFile * sizeof(int));
v2->pair = malloc(numberOfFile * sizeof(int));
int seqidIndex = 0;
for (int i = 0; i < pairI; i++) {
int first = pair->data[i].first;
int second = pair->data[i].second;
assert(first >= 0);
bstrVectorAdd(v2->filename, bdata(fn->entry[first]));
v2->type[seqidIndex] = v->type[first];
v2->format[seqidIndex] = v->format[first];
if (second >= 0) {
v2->pair[seqidIndex] = seqidIndex + 1;
} else {
v2->pair[seqidIndex] = -1;
}
seqidIndex++;
if (second >= 0) {
bstrVectorAdd(v2->filename, bdata(fn->entry[second]));
v2->type[seqidIndex] = v->type[second];
v2->format[seqidIndex] = v->format[second];
v2->pair[seqidIndex] = seqidIndex - 1;
seqidIndex++;
}
}
assert(seqidIndex == numberOfFile);
#if 0
for (int i = 0; i < fn->qty; i++) {
int j = v->pair[i];
if (j < 0) {
fprintf(stdout, "%2d %10s: %10s (%d) - no pair (%d)\n", i,
bdata(fn->entry[i]),
bdata(bnames->entry[i]), pairCount[i], j);
} else {
fprintf(stdout, "%2d %10s: %10s (%d) - pair %10s (%d)\n", i,
bdata(fn->entry[i]),
bdata(bnames->entry[i]), pairCount[i], bdata(fn->entry[j]), j);
}
}
fprintf(stdout, "\n");
for (int i = 0; i < fn->qty; i++) {
fprintf(stdout, "%2d %10s: format (%d), type (%d), pair (%d)\n", i,
bdata(v2->filename->entry[i]),
v2->format[i], v2->type[i], v2->pair[i]);
}
#endif
alder_seqid_file_free(v);
alder_vector_pair_t_free(pair);
bstrVectorDelete(bnames);
return v2;
}
int cpustr_to_cpulist(char* cpustring, int* cpulist, int length)
{
int insert = 0;
int len = 0;
int ret = 0;
bstring bcpustr = bfromcstr(cpustring);
struct bstrList* strlist = bstrListCreate();
bstring scattercheck = bformat("scatter");
topology_init();
CpuTopology_t cpuid_topology = get_cpuTopology();
strlist = bsplit(bcpustr, '@');
int* tmpList = (int*)malloc(length * sizeof(int));
if (tmpList == NULL)
{
bstrListDestroy(strlist);
bdestroy(scattercheck);
bdestroy(bcpustr);
return -ENOMEM;
}
for (int i=0; i< strlist->qty; i++)
{
if (binstr(strlist->entry[i], 0, scattercheck) != BSTR_ERR)
{
ret = cpustr_to_cpulist_scatter(strlist->entry[i], tmpList, length);
insert += cpulist_concat(cpulist, insert, tmpList, ret);
}
else if (bstrchrp(strlist->entry[i], 'E', 0) == 0)
{
ret = cpustr_to_cpulist_expression(strlist->entry[i], tmpList, length);
insert += cpulist_concat(cpulist, insert, tmpList, ret);
}
else if (bstrchrp(strlist->entry[i], 'L', 0) == 0)
{
ret = cpustr_to_cpulist_logical(strlist->entry[i], tmpList, length);
insert += cpulist_concat(cpulist, insert, tmpList, ret);
}
else if (cpuid_topology->activeHWThreads < cpuid_topology->numHWThreads)
{
fprintf(stdout, "INFO: You are running LIKWID in a cpuset with %d CPUs, only logical numbering allowed\n", cpuid_topology->activeHWThreads);
if (((bstrchrp(strlist->entry[i], 'N', 0) == 0) ||
(bstrchrp(strlist->entry[i], 'S', 0) == 0) ||
(bstrchrp(strlist->entry[i], 'C', 0) == 0) ||
(bstrchrp(strlist->entry[i], 'M', 0) == 0)) &&
(bstrchrp(strlist->entry[i], ':', 0) != BSTR_ERR))
{
bstring newstr = bformat("L:");
bconcat(newstr, strlist->entry[i]);
ret = cpustr_to_cpulist_logical(newstr, tmpList, length);
insert += cpulist_concat(cpulist, insert, tmpList, ret);
bdestroy(newstr);
}
else
{
bstring newstr = bformat("L:N:");
bconcat(newstr, strlist->entry[i]);
ret = cpustr_to_cpulist_logical(newstr, tmpList, length);
insert += cpulist_concat(cpulist, insert, tmpList, ret);
bdestroy(newstr);
}
}
else if (((bstrchrp(strlist->entry[i], 'N', 0) == 0) ||
(bstrchrp(strlist->entry[i], 'S', 0) == 0) ||
(bstrchrp(strlist->entry[i], 'C', 0) == 0) ||
(bstrchrp(strlist->entry[i], 'M', 0) == 0)) &&
(bstrchrp(strlist->entry[i], ':', 0) != BSTR_ERR))
{
bstring newstr = bformat("L:");
bconcat(newstr, strlist->entry[i]);
ret = cpustr_to_cpulist_logical(newstr, tmpList, length);
insert += cpulist_concat(cpulist, insert, tmpList, ret);
bdestroy(newstr);
}
else
{
ret = cpustr_to_cpulist_physical(strlist->entry[i], tmpList, length);
insert += cpulist_concat(cpulist, insert, tmpList, ret);
}
}
free(tmpList);
bstrListDestroy(strlist);
return insert;
}
static int cpustr_to_cpulist_physical(bstring bcpustr, int* cpulist, int length)
{
topology_init();
CpuTopology_t cpuid_topology = get_cpuTopology();
affinity_init();
AffinityDomains_t affinity = get_affinityDomains();
bstring bdomain;
bstring blist;
int domainidx = -1;
if (bstrchrp(bcpustr, ':', 0) != BSTR_ERR)
{
struct bstrList* strlist = bstrListCreate();
strlist = bsplit(bcpustr, ':');
bdomain = bstrcpy(strlist->entry[0]);
blist = bstrcpy(strlist->entry[1]);
bstrListDestroy(strlist);
}
else
{
bdomain = bformat("N");
blist = bstrcpy(bcpustr);
}
for (int i=0; i<affinity->numberOfAffinityDomains; i++)
{
if (bstrcmp(bdomain, affinity->domains[i].tag) == 0)
{
domainidx = i;
break;
}
}
if (domainidx < 0)
{
fprintf(stderr, "Cannot find domain %s\n", bdata(bdomain));
bdestroy(bdomain);
bdestroy(blist);
return 0;
}
struct bstrList* strlist = bstrListCreate();
strlist = bsplit(blist, ',');
int insert = 0;
for (int i=0;i< strlist->qty; i++)
{
if (bstrchrp(strlist->entry[i], '-', 0) != BSTR_ERR)
{
struct bstrList* indexlist = bstrListCreate();
indexlist = bsplit(strlist->entry[i], '-');
if (atoi(bdata(indexlist->entry[0])) <= atoi(bdata(indexlist->entry[1])))
{
for (int j=atoi(bdata(indexlist->entry[0])); j<=atoi(bdata(indexlist->entry[1]));j++)
{
if (cpu_in_domain(domainidx, j))
{
cpulist[insert] = j;
insert++;
if (insert == length)
{
bstrListDestroy(indexlist);
goto physical_done;
}
}
else
{
fprintf(stderr, "CPU %d not in domain %s\n", j, bdata(affinity->domains[domainidx].tag));
}
}
}
else
{
for (int j=atoi(bdata(indexlist->entry[0])); j>=atoi(bdata(indexlist->entry[1]));j--)
{
if (cpu_in_domain(domainidx, j))
{
cpulist[insert] = j;
insert++;
if (insert == length)
{
bstrListDestroy(indexlist);
goto physical_done;
}
}
else
{
fprintf(stderr, "CPU %d not in domain %s\n", j, bdata(affinity->domains[domainidx].tag));
}
}
}
bstrListDestroy(indexlist);
}
else
{
int cpu = atoi(bdata(strlist->entry[i]));
if (cpu_in_domain(domainidx, cpu))
{
cpulist[insert] = cpu;
insert++;
if (insert == length)
{
goto physical_done;
}
}
else
{
fprintf(stderr, "CPU %d not in domain %s\n", cpu, bdata(affinity->domains[domainidx].tag));
}
}
}
physical_done:
bstrListDestroy(strlist);
bdestroy(bdomain);
bdestroy(blist);
return insert;
}
static int cpustr_to_cpulist_logical(bstring bcpustr, int* cpulist, int length)
{
topology_init();
CpuTopology_t cpuid_topology = get_cpuTopology();
affinity_init();
AffinityDomains_t affinity = get_affinityDomains();
int domainidx = -1;
bstring bdomain;
bstring blist;
if (bstrchrp(bcpustr, 'L', 0) != 0)
{
fprintf(stderr, "Not a valid CPU expression\n");
return 0;
}
struct bstrList* strlist = bstrListCreate();
strlist = bsplit(bcpustr, ':');
if (strlist->qty != 3)
{
fprintf(stderr, "ERROR: Invalid expression, should look like L:<domain>:<indexlist> or be in a cpuset\n");
bstrListDestroy(strlist);
return 0;
}
bdomain = bstrcpy(strlist->entry[1]);
blist = bstrcpy(strlist->entry[2]);
bstrListDestroy(strlist);
for (int i=0; i<affinity->numberOfAffinityDomains; i++)
{
if (bstrcmp(bdomain, affinity->domains[i].tag) == 0)
{
domainidx = i;
break;
}
}
if (domainidx < 0)
{
fprintf(stderr, "Cannot find domain %s\n", bdata(bdomain));
return 0;
}
int *inlist = malloc(affinity->domains[domainidx].numberOfProcessors * sizeof(int));
if (inlist == NULL)
{
return -ENOMEM;
}
int ret = cpulist_sort(affinity->domains[domainidx].processorList, inlist, affinity->domains[domainidx].numberOfProcessors);
strlist = bstrListCreate();
strlist = bsplit(blist, ',');
int insert = 0;
for (int i=0; i< strlist->qty; i++)
{
if (bstrchrp(strlist->entry[i], '-', 0) != BSTR_ERR)
{
struct bstrList* indexlist = bstrListCreate();
indexlist = bsplit(strlist->entry[i], '-');
if (atoi(bdata(indexlist->entry[0])) <= atoi(bdata(indexlist->entry[1])))
{
for (int j=atoi(bdata(indexlist->entry[0])); j<=atoi(bdata(indexlist->entry[1]));j++)
{
cpulist[insert] = inlist[j];
insert++;
if (insert == length)
{
bstrListDestroy(indexlist);
goto logical_done;
}
}
}
else
{
for (int j=atoi(bdata(indexlist->entry[0])); j>=atoi(bdata(indexlist->entry[1]));j--)
{
cpulist[insert] = inlist[j];
insert++;
if (insert == length)
{
bstrListDestroy(indexlist);
goto logical_done;
}
}
}
bstrListDestroy(indexlist);
}
else
{
cpulist[insert] = inlist[atoi(bdata(strlist->entry[i]))];
insert++;
if (insert == length)
{
goto logical_done;
}
}
}
logical_done:
free(inlist);
bstrListDestroy(strlist);
return insert;
}
static int cpustr_to_cpulist_expression(bstring bcpustr, int* cpulist, int length)
{
topology_init();
CpuTopology_t cpuid_topology = get_cpuTopology();
affinity_init();
AffinityDomains_t affinity = get_affinityDomains();
bstring bdomain;
int domainidx = -1;
int count = 0;
int stride = 0;
int chunk = 0;
if (bstrchrp(bcpustr, 'E', 0) != 0)
{
fprintf(stderr, "Not a valid CPU expression\n");
return 0;
}
struct bstrList* strlist = bstrListCreate();
strlist = bsplit(bcpustr, ':');
if (strlist->qty == 3)
{
bdomain = bstrcpy(strlist->entry[1]);
count = atoi(bdata(strlist->entry[2]));
stride = 1;
chunk = 1;
}
else if (strlist->qty == 5)
{
bdomain = bstrcpy(strlist->entry[1]);
count = atoi(bdata(strlist->entry[2]));
chunk = atoi(bdata(strlist->entry[3]));
stride = atoi(bdata(strlist->entry[4]));
}
for (int i=0; i<affinity->numberOfAffinityDomains; i++)
{
if (bstrcmp(bdomain, affinity->domains[i].tag) == 0)
{
domainidx = i;
break;
}
}
if (domainidx < 0)
{
fprintf(stderr, "Cannot find domain %s\n", bdata(bdomain));
bstrListDestroy(strlist);
return 0;
}
int offset = 0;
int insert = 0;
for (int i=0;i<count;i++)
{
for (int j=0;j<chunk && offset+j<affinity->domains[domainidx].numberOfProcessors;j++)
{
cpulist[insert] = affinity->domains[domainidx].processorList[offset + j];
insert++;
if (insert == length)
goto expression_done;
}
offset += stride;
if (offset >= affinity->domains[domainidx].numberOfProcessors)
{
offset = 0;
}
if (insert >= count)
goto expression_done;
}
bstrListDestroy(strlist);
return 0;
expression_done:
bstrListDestroy(strlist);
return insert;
}
static int
parse_server_xport_option(allium_ptcfg *cfg, const bstring arg_str)
{
struct allium_ptcfg_method_s *m;
struct allium_ptcfg_xport_opt_s *opt;
bstring transport;
bstring key;
bstring value;
int i, j;
assert(cfg);
assert(arg_str);
if (0 == blength(arg_str))
return (-1);
/*
* Figure out what transport this argument is for. We don't need to
* unescape method names as they conform to "[a-zA-Z_][a-zA-Z0-9_]*"
*/
i = bstrchr(arg_str, ':');
if (BSTR_ERR == i)
return (-1);
transport = bmidstr(arg_str, 0, i);
if (NULL == transport)
return (-1);
m = get_method(cfg, bdata(transport));
bdestroy(transport); /* Done with the transport at this point */
if (NULL == m)
return (-1);
/*
* Figure out what key the transport is expecting the value for.
*
* XXX: If people want to use the escaped characters in their keys they
* get what they deserve (Note this as a gotcha and fix it when people
* cry about it).
*/
j = bstrchrp(arg_str, '=', i);
if (BSTR_ERR == j)
return (-1);
key = bmidstr(arg_str, i + 1, j - i - 1);
if (NULL == key)
return (-1);
opt = get_xport_opt(m, key);
if ((NULL != opt) || (0 == blength(key))) {
/* We don't support redefining existing key/value pairs */
bdestroy(key);
return (-1);
}
/* Parse the value, unescaping as needed */
value = bmidstr(arg_str, j + 1, blength(arg_str) - j - 1);
if (NULL == value) {
bdestroy(key);
return (-1);
}
unescape_opt_value(value);
/* Stash it away so people can get to it */
opt = calloc(1, sizeof(*opt));
if (NULL == opt) {
bdestroy(key);
bdestroy_safe(value);
return (-1);
}
opt->key = key;
opt->value = value;
opt->next = m->xport_opts;
m->xport_opts = opt;
return (0);
}
