Andreas Tille pushed to branch master at Debian Med / t-coffee
Commits: f9392d7a by Andreas Tille at 2018-09-30T21:08:16Z Try to find the problem that causes coredump - - - - - 2 changed files: - + debian/patches/debug.patch - debian/patches/series Changes: ===================================== debian/patches/debug.patch ===================================== @@ -0,0 +1,165 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Fri, 28 Sep 2018 14:24:07 +0200 +Bug-Debian: https://bugs.debian.org/909530 +Description: Try to find the problem that causes coredump + +--- a/t_coffee_source/util_lib/util_constraints_list.c ++++ b/t_coffee_source/util_lib/util_constraints_list.c +@@ -1335,6 +1335,7 @@ Constraint_list * undump_constraint_lis + int *entry, b, c, e, tot; + FILE *fp; + ++fprintf (stderr, "\nDEBUG %s(%i): file = %s", __FILE__, __LINE__, file); + if (!CL || !CL->residue_index)return CL; + entry=(int*)vcalloc ( CL->entry_len+1, sizeof (int)); + fp=vfopen (file, "r"); +@@ -2147,25 +2148,29 @@ Constraint_list* fork_read_n_constraint_ + int pid; + ns++; + pid=vvfork (NULL); ++fprintf (stderr, "\nDEBUG %s(%i): ns = %i, pid = %i, a = %i, n_list = %i", __FILE__, __LINE__, ns, pid, a, n_list); + if ( pid==0) + { + int in; + initiate_vtmpnam (NULL); + CL->local_stderr=vfopen("/dev/null", "w"); + in=CL->ne; ++fprintf (stderr, "\nDEBUG %s(%i): in = %i, fname[a] = %s, in_mode = %s, mem_mode = %s, weight_mode = %s", __FILE__, __LINE__, in, fname[a], in_mode, mem_mode, weight_mode); + CL=read_constraint_list (CL, fname[a], in_mode, mem_mode,weight_mode); + if (CL->ne>in)dump_constraint_list(CL,tmp_list[a], "w"); ++fprintf (stderr, "\nDEBUG %s(%i): before exit in = %i", __FILE__, __LINE__, in); + myexit (EXIT_SUCCESS); + } + else + { + //set_pid (pid); +- fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s", fname[a], ns); ++ fprintf ( local_stderr, "\n\t--- Process Method/Library/Aln %s (ns=%i)", fname[a], ns); + proclist[pid]=a; + if (ns>=nproc) + { + b=proclist[vwait(NULL)]; + fprintf (local_stderr, "\n\txxx Retrieved %s",fname[a]); ++fprintf (stderr, "\nDEBUG %s(%i): ns = %i, nproc = %i, tmp_list_b_%i_ = %s", __FILE__, __LINE__, ns, nproc, b, tmp_list[b]); + if (tmp_list[b] && check_file_exists (tmp_list[b])) + { + CL=undump_constraint_list(CL,tmp_list[b]); +@@ -2178,14 +2183,18 @@ Constraint_list* fork_read_n_constraint_ + while (ns) + { + int pid2; ++fprintf (stderr, "\nDEBUG %s(%i): before vwait(): pid2 = %i", __FILE__, __LINE__, pid2); + pid2=vwait(NULL); ++fprintf (stderr, "\nDEBUG %s(%i): after vwait()", __FILE__, __LINE__); + a=proclist[pid2]; + fprintf (local_stderr, "\n\txxx Retrieved %s",fname[a]); ++fprintf (stderr, "\nDEBUG %s(%i): n_list = %i, nproc = %i, tmp_list_a_%i_ = %s", __FILE__, __LINE__, ns, n_list, a, tmp_list[a]); + if (tmp_list[a] && check_file_exists (tmp_list[a])) + { + CL=undump_constraint_list (CL,tmp_list[a]); + } + ns--; ++fprintf (stderr, "\nDEBUG %s(%i): ns = %i", __FILE__, __LINE__, ns); + } + fprintf ( local_stderr, "\n\n\tAll Methods Retrieved\n"); + +@@ -2216,11 +2225,20 @@ Constraint_list* read_constraint_list(Co + Sequence *SL=NULL, *TS=NULL; + int a; + Constraint_list *SUBCL=NULL; +- static char *read_mode; ++ /*static char *read_mode;*/ ++ static char read_mode[STRING]; + char *fname; + ++fprintf (stderr, "\nDEBUG %s(%i): in_fname = %s, in_mode = %s, mem_mode = %s, weight_mode = %s", __FILE__, __LINE__, in_fname, in_mode, mem_mode, weight_mode); + fname=in_fname; +- if ( !read_mode)read_mode=(char*)vcalloc ( STRING, sizeof (char)); ++ /*if ( !read_mode)read_mode=(char*)vcalloc ( STRING, sizeof (char));*/ ++ ++if (read_mode) ++fprintf (stderr, "\nDEBUG %s(%i): read_mode = %s, STRING = %i", __FILE__, __LINE__, read_mode, STRING); ++else ++fprintf (stderr, "\nDEBUG %s(%i): STRING = %s, fname = %s", __FILE__, __LINE__, STRING, fname); ++sprintf ( read_mode, "structure"); ++fprintf (stderr, "\nDEBUG %s(%i): read_mode = %s, fname[0] = %c", __FILE__, __LINE__, STRING, fname[0]); + + if ( is_lib_list (in_fname))sprintf ( read_mode, "lib_list"); + else if ( in_mode)sprintf (read_mode, "%s", in_mode); +--- a/t_coffee_source/util_lib/util.c ++++ b/t_coffee_source/util_lib/util.c +@@ -4348,7 +4348,9 @@ pid_t vwait (pid_t *p) + + + p2=wait(&rv); ++fprintf (stderr, "\nDEBUG %s(%i): before check_process() p2 = %i", __FILE__, __LINE__, p2); + if (p2!=-1)rv=check_process("forked::T-Coffee", p2, rv,handle_failure); ++fprintf (stderr, "\nDEBUG %s(%i): after check_process() p2 = %i", __FILE__, __LINE__, p2); + if ( p) p[0]=rv; + + return p2; +@@ -4957,7 +4959,9 @@ int set_unique_dir_4_tcoffee (char *dir + void myexit (int signal) + { + ++fprintf (stderr, "\nDEBUG %s(%i): in myexit() signal = %i", __FILE__, __LINE__, signal); + if (clean_exit_started==1)return; //protects processes while they are doing a clean exit ++fprintf (stderr, "\nDEBUG %s(%i): in myexit() signal = %i", __FILE__, __LINE__, signal); + global_exit_signal=signal; + exit (global_exit_signal); //ONLY BARE EXIT!!!!!!!!!!!!!! + } +@@ -5589,6 +5593,7 @@ void dump_tcoffee(char *target, char *na + char *out_list; + + ++fprintf (stderr, "\nDEBUG %s(%i): dump_tcoffee() target = %s, nature = %s, pid = %i, ppid = %i", __FILE__, __LINE__, target, nature, getpid(), getppid()); + + if ((fp=fopen (target, "w"))) + { +@@ -5663,6 +5668,8 @@ void dump_error_file() + FILE *fp; + + ++fprintf (stderr, "\nDEBUG %s(%i): dump_error_file() pid = %i, ppid = %i", __FILE__, __LINE__, getpid(), getppid()); ++ + sprintf ( target, "%s",getenv("ERRORFILE_4_TCOFFEE")); + if (strstr (target, "NO")); + else +@@ -8962,6 +8969,9 @@ void clean_exit () + Tmpname *start; + int debug; + ++fprintf (stderr, "\nDEBUG %s(%i): clean_exit() pid = %i, ppid = %i", __FILE__, __LINE__, getpid(), getppid()); ++/* https://stackoverflow.com/questions/26256996/who-called-atexit */ ++/* abort(); */ + clean_exit_started=1;//prevent new locks + start=tmpname; + //1-start killing all the children +@@ -8979,6 +8989,7 @@ void clean_exit () + + if (is_rootpid()) + { ++fprintf (stderr, "\nDEBUG %s(%i): clean_exit() / is_rootpid()=true: pid = %i, ppid = %i", __FILE__, __LINE__, getpid(), getppid()); + + kill_child_pid(getpid()); + if (has_error_lock()) +@@ -8988,6 +8999,7 @@ void clean_exit () + warning_msg (stderr); + e=lock (getpid(), LERROR, LREAD, NULL); + ++fprintf (stderr, "\nDEBUG %s(%i): clean_exit() / has_error_lock()=true: e = '%s'\n", __FILE__, __LINE__, e); + + + //explicit the most common error messages +--- a/t_coffee_source/t_coffee_lib/t_coffee.c ++++ b/t_coffee_source/t_coffee_lib/t_coffee.c +@@ -4762,7 +4762,9 @@ get_cl_param(\ + } + else + { ++fprintf (stderr, "\nDEBUG %s(%i): before read_n_constraint_list(): infile = %s", __FILE__, __LINE__, infile); + CL=read_n_constraint_list (list_file,n_list,NULL, mem_mode,weight,type, le, CL, seq_source); ++fprintf (stderr, "\nDEBUG %s(%i): after read_n_constraint_list(): infile = %s", __FILE__, __LINE__, infile); + } + } + if ( CL->M)clean_aln=0; ===================================== debian/patches/series ===================================== @@ -7,3 +7,4 @@ mayhem.patch stable-linking-inputs.patch clustalw2.patch gcc-7.patch +# debug.patch View it on GitLab: https://salsa.debian.org/med-team/t-coffee/commit/f9392d7a431b804e92366cf0d18478a4bed275b1 -- View it on GitLab: https://salsa.debian.org/med-team/t-coffee/commit/f9392d7a431b804e92366cf0d18478a4bed275b1 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
