Merge pull request #18 from mhaseeb123/fix-hicops-sigabort

Fixes sigabort due to stack overflow in hicops when running with many threads

source/apps/gicops/gicops.cpp

@@ -326,14 +326,6 @@ status_t main(int_t argc, char_t* argv[])
         status = DSLIM_DeallocateSC();
     }
 
-    /* De-initialize the ion index */
-    if (status == SLM_SUCCESS)
-    {
-        /* De-initialize the ion index */
-        for (uint_t peplen = minlen; peplen <= maxlen; peplen++)
-            status = DSLIM_DeallocateIonIndex(slm_index + peplen - minlen);
-    }
-
 #if defined (USE_TIMEMORY)
     // stop instrumentation
     search_inst.stop();

source/apps/hicops/hicops.cpp

@@ -58,7 +58,7 @@ status_t main(int_t argc, char_t* argv[])
     auto env_tool = tim::get_env<std::string>("HICOPS_INST_COMPONENTS", "");
     auto env_enum = tim::enumerate_components(tim::delimit(env_tool));
     env_enum.erase(std::remove_if(env_enum.begin(), env_enum.end(),
-                                  [](int c) { return c == WALL_CLOCK || 
+                                  [](int c) { return c == WALL_CLOCK ||
                                                      c == CPU_UTIL; }),
                                   env_enum.end());
 
@@ -86,8 +86,8 @@ status_t main(int_t argc, char_t* argv[])
     // init MPI
     int provided = -1;
     status = MPI_Init_thread(&argc, &argv, MPI_THREAD_MULTIPLE, &provided);
-    
-    // Check if desired MPI level available 
+
+    // Check if desired MPI level available
     if (provided != MPI_THREAD_MULTIPLE)
     {
         std::cout << "************************ Warning: **************************\n";
@@ -333,7 +333,7 @@ status_t main(int_t argc, char_t* argv[])
     mem_tuple_t  search_mem_inst("search");
 #endif // USE_TIMEMORY
 
-    // Perform the distributed database search 
+    // Perform the distributed database search
     if (status == SLM_SUCCESS)
     {
         MARK_START(dslim_search);
@@ -355,14 +355,6 @@ status_t main(int_t argc, char_t* argv[])
         status = DSLIM_DeallocateSC();
     }
 
-    /* De-initialize the ion index */
-    if (status == SLM_SUCCESS)
-    {
-        /* De-initialize the ion index */
-        for (uint_t peplen = minlen; peplen <= maxlen; peplen++)
-            status = DSLIM_DeallocateIonIndex(slm_index + peplen - minlen);
-    }
-
 #if defined (USE_TIMEMORY)
     // stop instrumentation
     search_inst.stop();

source/core/cuda/superstep4/kernel.cu

@@ -42,7 +42,7 @@ extern gParams params;
 
 // -------------------------------------------------------------------------------------------- //
 
-namespace hcp 
+namespace hcp
 {
 
 namespace gpu
@@ -56,10 +56,10 @@ namespace s4
 
 struct compare_dhCell
 {
-    __host__ __device__ 
+    __host__ __device__
     bool operator()(dhCell lhs, dhCell rhs)
     {
-        return lhs.hyperscore < rhs.hyperscore; 
+        return lhs.hyperscore < rhs.hyperscore;
     }
 };
 
@@ -117,7 +117,7 @@ __host__ void freed_eValues()
     auto driver = hcp::gpu::cuda::driver::get_instance();
 
     auto &&d_evalues = getd_eValues();
-    
+
     if (d_evalues)
     {
         hcp::gpu::cuda::error_check(hcp::gpu::cuda::device_free_async(d_evalues, driver->stream[DATA_STREAM]));

source/core/dslim_fileout.cpp

@@ -65,10 +65,10 @@ status_t DFile_InitFiles()
                 string_t filename = common + "_" + std::to_string(f) + ".tsv";
                 tsvs[f].open(filename);
 
-                tsvs[f] << "file\t" << "scan_num\t" << "prec_mass\t" << "charge\t" 
-                        << "retention_time\t" << "peptide\t" << "matched_ions\t" 
-                        << "total_ions\t" << "calc_pep_mass\t" << "mass_diff\t" 
-                        << "mod_info\t" << "hyperscore\t" << "expectscore\t" 
+                tsvs[f] << "file\t" << "scan_num\t" << "prec_mass\t" << "charge\t"
+                        << "retention_time\t" << "peptide\t" << "matched_ions\t"
+                        << "total_ions\t" << "calc_pep_mass\t" << "mass_diff\t"
+                        << "mod_info\t" << "hyperscore\t" << "expectscore\t"
                         << "num_hits" << std::endl;
             }
         }
@@ -115,28 +115,22 @@ status_t DFile_PrintScore(Index *index, uint_t specid, float_t pmass, hCell *psm
 
     Index * lclindex = index + psm->idxoffset;
     int_t peplen = lclindex->pepIndex.peplen;
+    if (peplen < params.min_len or peplen > params.max_len)
+    {
+        throw std::runtime_error("Invalid peptide length encountered. Aborting");
+    }
     int_t pepid = psm->psid;
 
-    /* The size is peplen + 1 to add the \0 character at the end */
-    char_t pepseq[peplen + 1];
-
-    /* Write the \0 character to the last position of pepseq buffer */
-    pepseq[peplen] = '\0';
-
-    /* Copy the rest of the string to the pepseq buffer */
-    strncpy((char_t *)&(pepseq[0]), lclindex->pepIndex.seqs +
-             (lclindex->pepEntries[psm->psid].seqID * peplen), peplen);
-
-    /* Make a string from the char [] */
-    string_t pep = pepseq;
+    auto *const pep_string = lclindex->pepIndex.seqs +
+             (lclindex->pepEntries[psm->psid].seqID * peplen);
 
     /* Print the PSM info to the file */
     tsvs[thno]         << queryfiles[psm->fileIndex];
     tsvs[thno] << '\t' << std::to_string(specid + 1);
     tsvs[thno] << '\t' << std::to_string(pmass);
     tsvs[thno] << '\t' << std::to_string(psm->pchg);
     tsvs[thno] << '\t' << std::to_string(psm->rtime);
-    tsvs[thno] << '\t' << pep;
+    tsvs[thno] << '\t' << std::string_view(pep_string, peplen);
     tsvs[thno] << '\t' << std::to_string(psm->sharedions);
     tsvs[thno] << '\t' << std::to_string(psm->totalions);
     tsvs[thno] << '\t' << std::to_string(lclindex->pepEntries[pepid].Mass);

source/core/dslim_query.cpp

@@ -310,7 +310,7 @@ status_t DSLIM_SearchManager(Index *index)
     // setup the comm and scheduling handles
     //
     if (status == SLM_SUCCESS)
-        status = DSLIM_Setup_Handles(); 
+        status = DSLIM_Setup_Handles();
 
     //
     // parallel database search
@@ -358,7 +358,7 @@ void GPU_DistributedSearch(Index *index)
             gBatchlock.unlock();
             break;
         }
-        
+
         // increase the gBatchID
         gBatchID++;
 
@@ -387,7 +387,7 @@ void GPU_DistributedSearch(Index *index)
         MARK_END(penal);
 
         auto penalty = ELAPSED_SECONDS(penal);
-        
+
         ptime += penalty;
 
 #ifndef DIAGNOSE
@@ -532,7 +532,7 @@ status_t DistributedSearch(Index *index)
             gBatchlock.unlock();
             break;
         }
-        
+
         // increase the gBatchID
         gBatchID++;
 
@@ -730,27 +730,12 @@ status_t DSLIM_Destroy_Handles(Index *index)
     }
 #endif /* USE_MPI */
 
-    //
-    // Deinitialize
-    //
-
-    /* Delete the scheduler object */
-    if (SchedHandle != nullptr)
-    {
-        /* Deallocate the scheduler module */
-        delete SchedHandle;
-        SchedHandle = nullptr;
-    }
-
     /* Deinitialize the IO module */
     status = DSLIM_Deinit_IO();
 
     if (status == SLM_SUCCESS && params.nodes == 1)
     {
         status = DFile_DeinitFiles();
-
-        delete[] ePtrs;
-        ePtrs = nullptr;
     }
 
     // deinitialize MS2 prep pointers
@@ -994,7 +979,7 @@ status_t DSLIM_QuerySpectrum(Queries<spectype_t> *ss, Index *index, uint_t idxch
                 if (resPtr->cpsms >= 1)
                 {
                     /* Extract the top PSM */
-                    hCell&& psm = resPtr->topK.getMax();
+                    hCell& psm = resPtr->topK.getMax();
 
                     /* Put it in the list */
                     CandidatePSMS[currSpecID + queries] = psm;
@@ -1370,7 +1355,7 @@ VOID DSLIM_IO_Threads_Entry()
 
         /* Extract a chunk and return the chunksize */
         status = Query->extractbatch<int>(QCHUNK, ioPtr, rem_spec);
-        
+
         // update remaining Query entries
         ioPtr->batchNum = Query->Curr_chunk();
         ioPtr->fileNum  = Query->getQfileIndex();

source/core/include/dslim_comm.h

@@ -41,7 +41,7 @@ class DSLIM_Comm
     friend status_t DSLIM_CarryForward(Index *index, DSLIM_Comm *CommHandle, expeRT *ePtr, hCell *CandidatePSMS, int_t cpsmSize);
     DSLIM_Comm();
     DSLIM_Comm(int_t);
-    virtual ~DSLIM_Comm();
+    ~DSLIM_Comm() = default;
     status_t AddBatch(int_t, int_t, int_t);
 };
 

source/core/include/dslim_fileout.h

@@ -26,7 +26,7 @@
 
 /* Function Definitions */
 status_t    DFile_PrintPartials(uint_t specid, Results *resPtr);
-status_t    DFile_PrintScore(Index *index, uint_t specid, 
+status_t    DFile_PrintScore(Index *index, uint_t specid,
                              float_t pmass, hCell *psm, double_t e_x, uint_t npsms);
 status_t    DFile_InitFiles();
 status_t    DFile_DeinitFiles();

source/core/include/expeRT.h

@@ -118,7 +118,7 @@ class expeRT
     expeRT();
 
     /* Destructor */
-    virtual ~expeRT();
+    ~expeRT();
 
     /* Function to reset the data */
     VOID ResetPartialVectors();

source/core/include/lwbuff.h

@@ -72,7 +72,7 @@ class lwbuff
         sem_init(&lockw, 0, 1);
     }
 
-    virtual ~lwbuff()
+    ~lwbuff()
     {
         cap = 0;
         thr_low = 0;

source/core/include/lwqueue.h

@@ -17,7 +17,7 @@
  *
  */
 
-#pragma once 
+#pragma once
 
 #include "common.hpp"
 #include <semaphore.h>
@@ -56,6 +56,10 @@ class lwqueue
     lwqueue(int_t dcap)
     {
         cap = dcap;
+        if (cap <= 0)
+        {
+            throw std::runtime_error("lwqueue initialized with zero capacity. Aborting");
+        }
         arr = new T[cap];
         filled = 0;
         head = 0;
@@ -86,6 +90,10 @@ class lwqueue
     lwqueue(int_t dcap, BOOL sem)
     {
         cap = dcap;
+        if (cap <= 0)
+        {
+            throw std::runtime_error("lwqueue initialized with zero capacity. Aborting");
+        }
         arr = new T[cap];
         filled = 0;
         head = 0;
@@ -120,7 +128,7 @@ class lwqueue
         }
     }
 
-    virtual ~lwqueue()
+    ~lwqueue()
     {
         delete[] arr;
         arr = NULL;

source/core/include/lwvector.h

@@ -57,6 +57,8 @@ class lwvector
     lwvector(int_t dsiz)
     {
         cap = dsiz;
+        if (cap <= 0)
+            throw std::runtime_error("lwvector created with zero capacity. Aborting");
         arr = new T [cap];
         head = 0;
         tail = 0;
@@ -78,6 +80,8 @@ class lwvector
     lwvector(T *p1, T *p2)
     {
         cap = 2 * std::distance(p1, p2);
+        if (cap <= 0)
+            throw std::runtime_error("lwvector created with zero capacity. Aborting");
         arr = new T[cap];
         head = 0;
         tail = 0;
@@ -93,6 +97,9 @@ class lwvector
 
     lwvector(int_t dsiz, T val)
     {
+        if (dsiz <= 0)
+            throw std::runtime_error("lwvector created with zero size. Aborting");
+
         arr = new T [dsiz];
         cap = dsiz;
         head = 0;
@@ -144,7 +151,7 @@ class lwvector
         }
     }
 
-    virtual ~lwvector()
+    ~lwvector()
     {
         head = tail = 0;
         sze = cap = 0;