Changeset: be87d12afb98 for MonetDB
URL: https://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=be87d12afb98
Modified Files:
gdk/gdk_bat.c
gdk/gdk_tracer.h
monetdb5/scheduler/run_memo.c
sql/backends/monet5/vaults/bam/bam_db_interface.h
sql/backends/monet5/vaults/bam/bam_loader.c
sql/backends/monet5/vaults/bam/bam_wrapper.c
sql/backends/monet5/vaults/lidar/lidar.c
Branch: gdk_tracer
Log Message:
Compilation issues
diffs (truncated from 301 to 300 lines):
diff --git a/gdk/gdk_bat.c b/gdk/gdk_bat.c
--- a/gdk/gdk_bat.c
+++ b/gdk/gdk_bat.c
@@ -2114,7 +2114,7 @@ BATmode(BAT *b, bool transient)
#ifdef NDEBUG
/* assertions are disabled, turn failing tests into a message */
#undef assert
-#define assert(test) ((void) ((test) || WARNING(BAT_, "Assertion `%s'
failed\n", #test)))
+#define assert(test) ((void) ((test) || ERROR(BAT_, "Assertion `%s'
failed\n", #test)))
#endif
/* Assert that properties are set correctly.
diff --git a/gdk/gdk_tracer.h b/gdk/gdk_tracer.h
--- a/gdk/gdk_tracer.h
+++ b/gdk/gdk_tracer.h
@@ -89,11 +89,11 @@ typedef enum {
COMP( ACCEL ) \
COMP( TRACE ) \
COMP( CHECK_ ) \
- COMP( THRD ) \
+ COMP( THRD ) \
\
COMP( GEOM ) \
COMP( LIDAR ) \
- COMP( BAM ) \
+ COMP( BAM_ ) \
COMP( FITS ) \
COMP( SHP ) \
\
@@ -225,7 +225,10 @@ extern LOG_LEVEL LVL_PER_COMPONENT[COMPO
#define ERROR(COMP, MSG, ...) \
GDK_TRACER_LOG(M_ERROR, COMP, MSG, ## __VA_ARGS__) \
-#define WARNING(COMP, MSG, ...) \
+/* CHECK */
+// This was WARNING but this macro is defined in another file
+// also, included by GDK - Temp fix
+#define MDB_WARNING(COMP, MSG, ...) \
GDK_TRACER_LOG(M_WARNING, COMP, MSG, ## __VA_ARGS__) \
#define INFO(COMP, MSG, ...) \
diff --git a/monetdb5/scheduler/run_memo.c b/monetdb5/scheduler/run_memo.c
--- a/monetdb5/scheduler/run_memo.c
+++ b/monetdb5/scheduler/run_memo.c
@@ -177,7 +177,7 @@ RUNchoice(Client cntxt, MalBlkPtr mb, Ma
}
}
- DEBUG(MAL_MEMO, "Function target '%s' cost: %lld\n", getVarName(mb,
target), mincost);
+ DEBUG(MAL_MEMO, "Function target '%s' cost: %ld\n", getVarName(mb,
target), mincost);
(void) cntxt;
/* remove non-qualifying variables */
@@ -189,7 +189,7 @@ RUNchoice(Client cntxt, MalBlkPtr mb, Ma
propagateNonTarget(mb, pc + 1);
- DEBUG(MAL_MEMO, "Cost choice selected: %s %lld\n", getVarName(mb,
target), mincost);
+ DEBUG(MAL_MEMO, "Cost choice selected: %s %ld\n", getVarName(mb,
target), mincost);
debugFunction(MAL_MEMO, mb, stk, 1);
diff --git a/sql/backends/monet5/vaults/bam/bam_db_interface.h
b/sql/backends/monet5/vaults/bam/bam_db_interface.h
--- a/sql/backends/monet5/vaults/bam/bam_db_interface.h
+++ b/sql/backends/monet5/vaults/bam/bam_db_interface.h
@@ -38,7 +38,6 @@
}
#endif */
#define RUN_SQL(cntxt, sql, descr, msg) { \
- DEBUG(BAM, "%s\n", sql); \
msg = SQLstatementIntern(cntxt, sql, descr, TRUE, FALSE, NULL); \
}
diff --git a/sql/backends/monet5/vaults/bam/bam_loader.c
b/sql/backends/monet5/vaults/bam/bam_loader.c
--- a/sql/backends/monet5/vaults/bam/bam_loader.c
+++ b/sql/backends/monet5/vaults/bam/bam_loader.c
@@ -119,14 +119,14 @@ run_process_bam_alignments(void *d)
bam_wrapper *bw;
for (;;) {
- DEBUG(BAM, "<Thread %d> Starting on next file\n",
data->thread_id);
+ DEBUG(BAM_, "<Thread %d> Starting on next file\n",
data->thread_id);
/* First, find out on which bam wrapper we have to work */
MT_lock_set(data->reader_lock);
if (*data->cur_file == data->nr_files - 1) {
/* The last file is already (being) processed, this
* thread is done */
MT_lock_unset(data->reader_lock);
- DEBUG(BAM,
+ DEBUG(BAM_,
"<Thread %d> No files left to work on; thread
done\n",
data->thread_id);
return;
@@ -134,13 +134,13 @@ run_process_bam_alignments(void *d)
(*data->cur_file) += 1;
bw = &data->bws[*data->cur_file];
MT_lock_unset(data->reader_lock);
- DEBUG(BAM,
+ DEBUG(BAM_,
"<Thread %d> Processing alignments of file '%s' (file
id " LLFMT ")\n",
data->thread_id, bw->file_location, bw->file_id);
if ((data->msg =
process_alignments(bw, data->failure)) != MAL_SUCCEED) {
- ERROR(BAM, "<Thread %d> Error while processing
alignments of file '%s' "
+ ERROR(BAM_, "<Thread %d> Error while processing
alignments of file '%s' "
"(file id " LLFMT ") (%s)\n",
data->thread_id,
bw->file_location, bw->file_id, data->msg);
REUSE_EXCEPTION(data->msg, MAL,
"run_process_bam_alignments",
@@ -152,11 +152,11 @@ run_process_bam_alignments(void *d)
if (*data->failure) {
/* process_bam_alignments returned because another
* thread failed and not because this thread failed */
- ERROR(BAM, "<Thread %d> Exit due to failure in other
thread\n", data->thread_id);
+ ERROR(BAM_, "<Thread %d> Exit due to failure in other
thread\n", data->thread_id);
return;
}
- DEBUG(BAM,
+ DEBUG(BAM_,
"<Thread %d> All alignments in file '%s' (file id "
LLFMT ") processed!\n",
data->thread_id, bw->file_location, bw->file_id);
}
@@ -190,7 +190,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
int i, errnr;
str msg = MAL_SUCCEED;
- DEBUG(BAM, "Loader started for %d BAM file%s\n", nr_files, (nr_files !=
1 ? "s" : ""));
+ DEBUG(BAM_, "Loader started for %d BAM file%s\n", nr_files, (nr_files
!= 1 ? "s" : ""));
/* Check sanity of input */
if (dbschema != 0 && dbschema != 1) {
@@ -225,7 +225,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
goto cleanup;
/* Get next file id from files table */
- DEBUG(BAM, "Retrieving next file id\n");
+ DEBUG(BAM_, "Retrieving next file id\n");
if ((msg = next_file_id(m, files_table, &cur_file_id)) != MAL_SUCCEED) {
goto cleanup;
}
@@ -243,7 +243,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
for (i = 0; i < nr_files; ++i) {
int fln = strlen(filenames[i]);
- DEBUG(BAM, "Initializing BAM wrapper for file '%s'\n",
filenames[i]);
+ DEBUG(BAM_, "Initializing BAM wrapper for file '%s'\n",
filenames[i]);
if ((msg =
init_bam_wrapper(bws + i, (IS_BAM(filenames[i], fln) ?
BAM : SAM),
filenames[i], cur_file_id++,
dbschema)) != MAL_SUCCEED) {
@@ -253,7 +253,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
/* Parse all headers */
for (i = 0; i < nr_files; ++i) {
- DEBUG(BAM, "Parsing header for file '%s'\n",
+ DEBUG(BAM_, "Parsing header for file '%s'\n",
filenames[i]);
if ((msg = process_header(bws + i)) != MAL_SUCCEED) {
goto cleanup;
@@ -265,7 +265,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
* QNAME */
if (dbschema == 1) {
for (i = 0; i < nr_files; ++i) {
- DEBUG(BAM, "Checking sortedness for BAM file '%s'\n",
filenames[i]);
+ DEBUG(BAM_, "Checking sortedness for BAM file '%s'\n",
filenames[i]);
if (bws[i].ord != ORDERING_QUERYNAME) {
msg = createException(MAL, "bam_loader",
SQLSTATE(BA000) "Only
BAM files that are sorted on queryname can be inserted into the pairwise
storage schema; "
@@ -280,7 +280,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
/* Create alignment storage */
for (i = 0; i < nr_files; ++i) {
- DEBUG(BAM, "Creating alignment tables for file '%s'\n",
filenames[i]);
+ DEBUG(BAM_, "Creating alignment tables for file '%s'\n",
filenames[i]);
if ((dbschema == 0
&& (msg = create_alignment_storage_0(cntxt,
"bam.create_storage_0",
@@ -295,7 +295,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
/* Now create threads to read alignment data of different files */
- DEBUG(BAM, "Creating reader threads\n");
+ DEBUG(BAM_, "Creating reader threads\n");
if ((reader_threads =
(MT_Id *) GDKmalloc(nr_threads * sizeof(MT_Id))) == NULL) {
msg = createException(MAL, "bam_loader", SQLSTATE(HY001)
MAL_MALLOC_FAIL);
@@ -322,7 +322,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
}
}
- DEBUG(BAM, "Waiting for reader threads to finish\n");
+ DEBUG(BAM_, "Waiting for reader threads to finish\n");
/* Wait until all threads finish and collect their
* messages. Though it is not very likely, it could be the
* case that more than 1 thread generates an error message (not
@@ -368,7 +368,7 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
goto cleanup;
}
- DEBUG(BAM, "Copying data into DB\n");
+ DEBUG(BAM_, "Copying data into DB\n");
/* All threads finished succesfully, copy all data into DB */
for (i = 0; i < nr_files; ++i) {
if ((msg = copy_into_db(cntxt, bws + i)) != MAL_SUCCEED) {
@@ -390,10 +390,10 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
destroy_reader_thread_data(r_thread_data);
if (msg != MAL_SUCCEED) {
- ERROR(BAM, "Error on processing BAM files: %s\n", msg);
+ ERROR(BAM_, "Error on processing BAM files: %s\n", msg);
}
- DEBUG(BAM, "Loader finished processing %d BAM file%s\n", nr_files,
(nr_files != 1 ? "s" : ""));
+ DEBUG(BAM_, "Loader finished processing %d BAM file%s\n", nr_files,
(nr_files != 1 ? "s" : ""));
return msg;
}
diff --git a/sql/backends/monet5/vaults/bam/bam_wrapper.c
b/sql/backends/monet5/vaults/bam/bam_wrapper.c
--- a/sql/backends/monet5/vaults/bam/bam_wrapper.c
+++ b/sql/backends/monet5/vaults/bam/bam_wrapper.c
@@ -1327,11 +1327,11 @@ check_alignment_buffers(bam_wrapper *bw,
}
if (resized[0])
- DEBUG(BAM, "Increased size of qname buffer to: %d
characters\n", alig->qname_size);
+ DEBUG(BAM_, "Increased size of qname buffer to: %d
characters\n", alig->qname_size);
if (resized[1])
- DEBUG(BAM, "Increased size of cigar buffer to: %d
characters\n", alig->cigar_size);
+ DEBUG(BAM_, "Increased size of cigar buffer to: %d
characters\n", alig->cigar_size);
if (resized[2])
- DEBUG(BAM, "Increased size of seq and qual buffers to: %d
characters\n", alig->seq_size);
+ DEBUG(BAM_, "Increased size of seq and qual buffers to: %d
characters\n", alig->seq_size);
return (alig->cigar != NULL && alig->seq != NULL
&& alig->qual != NULL);
@@ -1356,7 +1356,7 @@ check_qname_buffer(alignment * alig, int
if (tmp == NULL)
return 0;
alig->qname = tmp;
- DEBUG(BAM, "Increased size of qname buffer to: %d
characters\n", alig->qname_size);
+ DEBUG(BAM_, "Increased size of qname buffer to: %d
characters\n", alig->qname_size);
}
return alig->qname != NULL;
}
@@ -1378,7 +1378,7 @@ check_rname_rnext_buffers(alignment * al
if (tmp == NULL)
return 0;
alig->rnext = tmp;
- DEBUG(BAM, "Increased size of cigar buffer to: %d
characters\n", alig->rname_size);
+ DEBUG(BAM_, "Increased size of cigar buffer to: %d
characters\n", alig->rname_size);
}
return alig->rname != NULL && alig->rnext != NULL;
}
@@ -1396,7 +1396,7 @@ check_cigar_buffer(alignment * alig, int
if (tmp == NULL)
return 0;
alig->cigar = tmp;
- DEBUG(BAM, "Increased size of cigar buffer to: %d
characters\n", alig->cigar_size);
+ DEBUG(BAM_, "Increased size of cigar buffer to: %d
characters\n", alig->cigar_size);
}
return alig->cigar != NULL;
}
@@ -1417,7 +1417,7 @@ check_seq_qual_buffers(alignment * alig,
if (tmp == NULL)
return 0;
alig->qual = tmp;
- DEBUG(BAM, "Increased size of seq and qual buffers to: %d
characters\n", alig->seq_size);
+ DEBUG(BAM_, "Increased size of seq and qual buffers to: %d
characters\n", alig->seq_size);
}
return alig->seq != NULL && alig->qual != NULL;
}
@@ -1434,7 +1434,7 @@ check_aux_buffer(alignment * alig, int c
if (tmp == NULL)
return 0;
alig->aux = tmp;
- DEBUG(BAM, "Increased size of aux buffer to: %d characters\n",
alig->aux_size);
+ DEBUG(BAM_, "Increased size of aux buffer to: %d characters\n",
alig->aux_size);
}
return alig->aux != NULL;
}
@@ -2317,7 +2317,7 @@ process_alignments(bam_wrapper * bw, bit
}
}
nr_aligs = new_nr_aligs;
- DEBUG(BAM, "<bam_loader> Increased size
of alignment buffer to: %d alignments\n", nr_aligs);
+ DEBUG(BAM_, "<bam_loader> Increased
size of alignment buffer to: %d alignments\n", nr_aligs);
}
}
}
diff --git a/sql/backends/monet5/vaults/lidar/lidar.c
b/sql/backends/monet5/vaults/lidar/lidar.c
--- a/sql/backends/monet5/vaults/lidar/lidar.c
+++ b/sql/backends/monet5/vaults/lidar/lidar.c
@@ -175,7 +175,7 @@ void print_lidar_header(LASHeaderH heade
DEBUG(LIDAR, " User : '%s'\n", pszVLRUser);
DEBUG(LIDAR, " Description : '%s'\n",
pszVLRDescription);
DEBUG(LIDAR, " ID : '%hu'\n",
nVLRRecordId);
- DEBUG(LIDAR, " Length : %hu\n", , nVLRLength);
+ DEBUG(LIDAR, " Length : %hu\n", nVLRLength);
MT_lock_set(&mt_lidar_lock);
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