bool AdminRequestHandler::handleHeapProfilerRequest(const std::string &cmd,
Transport *transport) {
string root = RuntimeOption::ProfilerOutputDir + "/" +
Process::HostName;
string file = root + "/hphp.prof";
if (cmd == "prof-heap-on") {
if (IsHeapProfilerRunning()) {
transport->sendString("HeapProfiler is already running.\n");
} else {
if (Util::mkdir(file)) {
// clean up leftovers
string cmd = "/bin/rm -f ";
cmd += file + ".*.heap";
Util::ssystem(cmd.c_str());
HeapProfilerStart(file.c_str());
HeapProfilerDump("start");
transport->sendString("OK\n");
} else {
transport->sendString("Unable to mkdir for profile data.\n");
}
}
return true;
}
if (cmd == "prof-heap-dump") {
if (!IsHeapProfilerRunning()) {
transport->sendString("HeapProfiler is not running.\n");
} else {
HeapProfilerDump("end");
transport->sendString("OK\n");
}
return true;
}
if (cmd == "prof-heap-off") {
if (!IsHeapProfilerRunning()) {
transport->sendString("HeapProfiler is not running.\n");
} else {
HeapProfilerDump("end");
HeapProfilerStop();
transport->sendString("OK\n");
const char *argv[] = {"", root.c_str(), "-name", "*.heap", NULL};
string files;
Process::Exec("find", argv, NULL, files);
vector<string> out;
Util::split('\n', files.c_str(), out, true);
if (out.size() > 1) {
string base = "--base=";
base += out[0];
pprof(out[out.size() - 1], base.c_str());
} else {
Logger::Error("Unable to find heap profiler output");
}
}
return true;
}
return false;
}
static void stop_cb (flux_t *h, flux_msg_handler_t *mh,
const flux_msg_t *msg, void *arg)
{
if (flux_request_decode (msg, NULL, NULL) < 0)
goto error;
#if WITH_TCMALLOC
if (!IsHeapProfilerRunning ()) {
errno = EINVAL;
goto error;
}
HeapProfilerStop();
#else
errno = ENOSYS;
goto error;
#endif /* WITH_TCMALLOC */
if (flux_respond (h, msg, 0, NULL) < 0)
FLUX_LOG_ERROR (h);
return;
error:
if (flux_respond (h, msg, errno, NULL) < 0)
FLUX_LOG_ERROR (h);
}
static void dump_cb (flux_t *h, flux_msg_handler_t *mh,
const flux_msg_t *msg, void *arg)
{
const char *reason;
if (flux_request_unpack (msg, NULL, "{s:s}", "reason", &reason) < 0)
goto error;
#if WITH_TCMALLOC
if (!IsHeapProfilerRunning ()) {
errno = EINVAL;
goto error;
}
HeapProfilerDump (reason);
#else
errno = ENOSYS;
goto error;
#endif
if (flux_respond (h, msg, 0, NULL) < 0)
FLUX_LOG_ERROR (h);
return;
error:
if (flux_respond (h, msg, errno, NULL) < 0)
FLUX_LOG_ERROR (h);
}
static void start_cb (flux_t *h, flux_msg_handler_t *mh,
const flux_msg_t *msg, void *arg)
{
const char *filename;
if (flux_request_unpack (msg, NULL, "{s:s}", "filename", &filename) < 0)
goto error;
#if WITH_TCMALLOC
if (IsHeapProfilerRunning ()) {
errno = EINVAL;
goto error;
}
HeapProfilerStart (filename);
#else
errno = ENOSYS;
goto error;
#endif
if (flux_respond (h, msg, 0, NULL) < 0)
FLUX_LOG_ERROR (h);
return;
error:
if (flux_respond (h, msg, errno, NULL) < 0)
FLUX_LOG_ERROR (h);
}
void read_mRNAs(FILE* f, GList<GSeqData>& seqdata, GList<GSeqData>* ref_data,
int check_for_dups, int qfidx, const char* fname, bool only_multiexon) {
//>>>>> read all transcripts/features from a GTF/GFF3 file
//int imrna_counter=0;
#ifdef HEAPROFILE
if (IsHeapProfilerRunning())
HeapProfilerDump("00");
#endif
int loci_counter=0;
if (ref_data==NULL) ref_data=&seqdata;
bool isRefData=(&seqdata==ref_data);
//(f, transcripts_only)
GffReader* gffr=new GffReader(f, true); //load only transcript annotations
gffr->showWarnings(gtf_tracking_verbose);
// keepAttrs mergeCloseExons noExonAttrs
gffr->readAll(!isRefData, true, isRefData || gtf_tracking_largeScale);
//so it will read exon attributes only for low number of Cufflinks files
#ifdef HEAPROFILE
if (IsHeapProfilerRunning())
HeapProfilerDump("post_readAll");
#endif
int d=parse_mRNAs(gffr->gflst, seqdata, isRefData, check_for_dups, qfidx,only_multiexon);
#ifdef HEAPROFILE
if (IsHeapProfilerRunning())
HeapProfilerDump("post_parse_mRNAs");
#endif
if (gtf_tracking_verbose && d>0) {
if (isRefData) GMessage(" %d duplicate reference transcripts discarded.\n",d);
else GMessage(" %d redundant query transfrags discarded.\n",d);
}
//imrna_counter=gffr->mrnas.Count();
delete gffr; //free the extra memory and unused GffObjs
#ifdef HEAPROFILE
if (IsHeapProfilerRunning())
HeapProfilerDump("post_del_gffr");
#endif
//for each genomic sequence, cluster transcripts
int oriented_by_overlap=0;
int initial_unoriented=0;
int final_unoriented=0;
GStr bname(fname);
GStr s;
if (!bname.is_empty()) {
int di=bname.rindex('.');
if (di>0) bname.cut(di);
int p=bname.rindex('/');
if (p<0) p=bname.rindex('\\');
if (p>=0) bname.remove(0,p);
}
FILE* fdis=NULL;
FILE* frloci=NULL;
for (int g=0;g<seqdata.Count();g++) {
//find the corresponding refseqdata with the same gseq_id
int gseq_id=seqdata[g]->get_gseqid();
if (!isRefData) { //query data, find corresponding ref data
GSeqData* rdata=getRefData(gseq_id, *ref_data);
initial_unoriented+=seqdata[g]->umrnas.Count();
if (seqdata[g]->umrnas.Count()>0) {
oriented_by_overlap+=fix_umrnas(*seqdata[g], rdata, fdis);
final_unoriented+=seqdata[g]->umrnas.Count();
}
}
//>>>>> group mRNAs into locus-clusters (based on exon overlap)
cluster_mRNAs(seqdata[g]->mrnas_f, seqdata[g]->loci_f, qfidx);
cluster_mRNAs(seqdata[g]->mrnas_r, seqdata[g]->loci_r, qfidx);
if (!isRefData) {
cluster_mRNAs(seqdata[g]->umrnas, seqdata[g]->nloci_u, qfidx);
}
loci_counter+=seqdata[g]->loci_f.Count();
loci_counter+=seqdata[g]->loci_r.Count();
// if (refData) {
// if (frloci==NULL) {
// s=bname;
// s.append(".loci.lst");
// frloci=fopen(s.chars(), "w");
// }
// writeLoci(frloci, seqdata[g]->loci_f);
// writeLoci(frloci, seqdata[g]->loci_r);
// }//write ref loci
}//for each genomic sequence
if (fdis!=NULL) fclose(fdis);
if (frloci!=NULL) fclose(frloci);
if (initial_unoriented || final_unoriented) {
if (gtf_tracking_verbose) GMessage(" Found %d transfrags with undetermined strand (%d out of initial %d were fixed by overlaps)\n",
final_unoriented, oriented_by_overlap, initial_unoriented);
}
//if (fdis!=NULL) remove(s.chars()); remove 0-length file
#ifdef HEAPROFILE
if (IsHeapProfilerRunning())
HeapProfilerDump("post_cluster");
#endif
}
// static
bool LLAllocator::isProfiling()
{
return IsHeapProfilerRunning();
}