[med-svn] [Git][med-team/t-coffee][master] Try to find the problem that causes coredump
Andreas Tille
gitlab at salsa.debian.org
Sun Sep 30 22:08:41 BST 2018
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 <tille at debian.org>
+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
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