xml2 cflags aren't propagated correctly about extrae HOT 8 OPEN

Gentle bump 🙂 @mofeing is still facing this issue in v4.1.7.

from extrae.

I'm not 100% sure this is the right solution, but something like

--- a/src/tracer/Makefile.am.orig
+++ b/src/tracer/Makefile.am
@@ -713,7 +713,7 @@
   libcudaompitracecf_la_CFLAGS = $(core_INCLUDES) $(core_CFLAGS) -DMPI_SUPPORT $(MPI_CFLAGS) $(PARALLEL_CFLAGS_MERGE_LIB) -DCUDA_SUPPORT $(WRAPPERS_CUDA_CFLAGS) -DOMP_SUPPORT
 endif
 
-libseqtrace_la_CFLAGS  = $(core_INCLUDES) $(core_CFLAGS) $(SEQUENTIAL_CFLAGS_MERGE_LIB)
+libseqtrace_la_CFLAGS  = $(core_INCLUDES) $(core_CFLAGS) $(SEQUENTIAL_CFLAGS_MERGE_LIB) $(XML2_CFLAGS)
 
 libmpitrace_la_CFLAGS  = $(core_INCLUDES) $(core_CFLAGS) -DMPI_SUPPORT $(MPI_CFLAGS) $(PARALLEL_CFLAGS_MERGE_LIB)
 libmpitracef_la_CFLAGS = $(core_INCLUDES) $(core_CFLAGS) -DMPI_SUPPORT $(MPI_CFLAGS) $(PARALLEL_CFLAGS_MERGE_LIB)
@@ -755,7 +755,7 @@
   libnanosmpitracecf_la_CFLAGS = $(core_INCLUDES) $(core_CFLAGS) -DNANOS_SUPPORT -DMPI_SUPPORT $(MPI_CFLAGS) $(PARALLEL_CFLAGS_MERGE_LIB)
 endif
 
-libpttrace_la_CFLAGS = $(core_INCLUDES) $(core_CFLAGS) -DPTHREAD_SUPPORT $(SEQUENTIAL_CFLAGS_MERGE_LIB) $(PTHREAD_CFLAGS)
+libpttrace_la_CFLAGS = $(core_INCLUDES) $(core_CFLAGS) -DPTHREAD_SUPPORT $(SEQUENTIAL_CFLAGS_MERGE_LIB) $(PTHREAD_CFLAGS) $(XML2_CFLAGS)
 
 libopenshmemtrace_la_CFLAGS = $(core_INCLUDES) $(core_CFLAGS) @OPENSHMEM_CFLAGS@ -DOPENSHMEM_SUPPORT $(SEQUENTIAL_CFLAGS_MERGE_LIB)
 

seems to fix the issue for me.

from extrae.

However after fixing the issue with the header files, I get a later error during linking:

[10:59:48] libtool: link: cc -std=gnu11 -I../../include -I../../src/common -I../../src/tracer -I../../src/tracer/wrappers/API -I../../src/tracer/clocks -I../../src/tracer/hwc -O -g -g -O2 -fno-optimize-sibling-calls -funwind-tables -Wall -W -o .libs/extrae-cmd extrae_cmd-extrae-cmd.o extrae_cmd-extrae-cmd-init.o extrae_cmd-extrae-cmd-emit.o extrae_cmd-extrae-cmd-fini.o  -L/workspace/destdir/lib64 ../../src/tracer/.libs/libseqtrace.so -L/workspace/destdir/lib/ -lpapi -lpfm -lunwind -ldl -lrt ../../src/merger/.libs/libmpi2prv.a -lm -lbfd -liberty -Wl,-rpath -Wl,/workspace/destdir/lib -Wl,-rpath -Wl,/workspace/destdir/lib64 -Wl,-rpath -Wl,/workspace/destdir/lib/
[10:59:48] ../../src/tracer/.libs/libseqtrace.so: undefined reference to `xmlFreeDoc'
[10:59:48] ../../src/tracer/.libs/libseqtrace.so: undefined reference to `xmlGetProp'
[10:59:48] ../../src/tracer/.libs/libseqtrace.so: undefined reference to `xmlCheckVersion'
[10:59:48] ../../src/tracer/.libs/libseqtrace.so: undefined reference to `xmlStrlen'
[10:59:48] ../../src/tracer/.libs/libseqtrace.so: undefined reference to `xmlCharStrdup'
[10:59:48] ../../src/tracer/.libs/libseqtrace.so: undefined reference to `xmlCleanupParser'
[10:59:48] ../../src/tracer/.libs/libseqtrace.so: undefined reference to `xmlStrcasecmp'
[10:59:48] ../../src/tracer/.libs/libseqtrace.so: undefined reference to `xmlStrsub'
[10:59:48] ../../src/tracer/.libs/libseqtrace.so: undefined reference to `xmlNodeListGetString'
[10:59:48] ../../src/tracer/.libs/libseqtrace.so: undefined reference to `xmlParseFile'
[10:59:48] ../../src/tracer/.libs/libseqtrace.so: undefined reference to `xmlFree'
[10:59:48] ../../src/tracer/.libs/libseqtrace.so: undefined reference to `xmlDocGetRootElement'
[10:59:48] collect2: error: ld returned 1 exit status
[10:59:48] make[3]: *** [Makefile:893: extrae-cmd] Error 1

The problem is that libseqtrace.so doesn't link to libxml2 at all:

sandbox:${WORKSPACE}/srcdir/extrae-4.1.2 # readelf -d ./src/tracer/.libs/libseqtrace.so

Dynamic section at offset 0x86a80 contains 29 entries:
  Tag        Type                         Name/Value
 0x0000000000000001 (NEEDED)             Shared library: [libpapi.so.7.0]
 0x0000000000000001 (NEEDED)             Shared library: [libpfm.so.4]
 0x0000000000000001 (NEEDED)             Shared library: [libunwind.so.8]
 0x0000000000000001 (NEEDED)             Shared library: [libdl.so.2]
 0x0000000000000001 (NEEDED)             Shared library: [librt.so.1]
 0x0000000000000001 (NEEDED)             Shared library: [libbfd-2.39.so]
 0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [ld-linux-x86-64.so.2]
 0x000000000000000e (SONAME)             Library soname: [libseqtrace-4.1.2.so]
 0x000000000000000f (RPATH)              Library rpath: [/workspace/destdir/lib64:/workspace/destdir/lib/]

Another patch like

--- a/src/tracer/Makefile.am.orig
+++ b/src/tracer/Makefile.am
@@ -834,7 +834,7 @@
 libnanosmpigaspitrace_la_LDFLAGS = $(COMMON_LINKER_FLAGS)
 libnanosgaspitrace_la_LDFLAGS = $(COMMON_LINKER_FLAGS)
 
-libseqtrace_la_LDFLAGS = $(COMMON_LINKER_FLAGS)
+libseqtrace_la_LDFLAGS = $(COMMON_LINKER_FLAGS) -lxml2
 
 libmpitrace_la_LDFLAGS = $(NEW_MPI_LIBS) $(COMMON_LINKER_FLAGS)
 libmpitracef_la_LDFLAGS = $(libmpitrace_la_LDFLAGS) # -static 

fixes the issue for me, but I'm sure there are better ways to do this.

from extrae.

XML2_CFLAGS are included in core_INCLUDES if HAVE_XML2 is defined during configure

Could you check your config.h and see if it is true in your compilation?

from extrae.

Please find attached the file config.log and src/tracer/Makefil of my build

• config.log
• src/tracer/Makefile

In the Makefile, XML2_CFLAGS is set correctly, but not used anywhere.

For reference, core_INCLUDES is

core_INCLUDES = -I$(TRACER_INC) -I$(HWC_INC) -I$(CLOCKS_INC) \
	-I$(INTERFACES_INC)/API -I$(INTERFACES_INC)/MPI \
	-I$(STATS_INC)/MPI -I$(WRAPPERS_INC)/API -I$(WRAPPERS_INC)/MPI \
	-I$(WRAPPERS_INC)/OMP -I$(WRAPPERS_INC)/pthread \
	-I$(WRAPPERS_INC)/CUDA -I$(WRAPPERS_INC)/OPENCL \
	-I$(WRAPPERS_INC)/fork -I$(WRAPPERS_INC)/MALLOC \
	-I$(WRAPPERS_INC)/IO -I$(WRAPPERS_INC)/SYSCALL \
	-I$(WRAPPERS_INC)/openshmem -I$(WRAPPERS_INC)/OPENACC \
	-I$(WRAPPERS_INC)/GASPI -I$(SAMPLING_DIR)/common \
	-I$(top_srcdir) -I$(top_srcdir)/include -I$(COMMON_INC) \
	$(UNWIND_CFLAGS) $(am__append_62) $(am__append_63) \
	-I$(SAMPLING_DIR)/timer $(am__append_64)

No mention to xml2.

from extrae.

I don't know if this is relevant, perhaps not because HAVE_XML2 is defined to 1 anyway, but in the config.log I shared above I see the lines

configure:38623: checking for libxml2 version >= 2.5.0
configure:38639: result: no (2.12.0)

which look questionable, to say the least.

from extrae.

Are you still facing this issue? At least in more recent versions, XML2_CFLAGS is used in src/tracer/Makefile.am:

if HAVE_XML2
core_INCLUDES += @XML2_CFLAGS@
endif

According to the config.log, HAVE_XML2 is set to 1, and XML2_CFLAGS has value:
XML2_CFLAGS='-I/workspace/destdir/include -I/workspace/destdir/include/libxml2'

Similarly, LDFLAGS are set through:
if HAVE_XML2
XML2_LINKER_FLAGS = @XML2_LDFLAGS@ @XML2_RPATH@ @XML2_LIBS@
endif

And later assigned to:
COMMON_LINKER_FLAGS =
...
$(XML2_LINKER_FLAGS)
...

Both core_INCLUDES and COMMON_LINKER_FLAGS seem to be used by all libraries. Have you tried with a more recent version of the tool, just in case this has been fixed in the meantime?

One thing that catches my eye in the config.log is that these variables are empty:
XML2_LIBS=''
XML2_LIB_xml2=''

Is it possible that the system only has a static version (libxml2.a) available? If so, can you try rebuilding libxml2 with the flag --enable-shared ?

from extrae.

Are you still facing this issue?

I can't test it right now, will let you know when I get a chance to try again.

Is it possible that the system only has a static version (libxml2.a) available?

No, we have the shared library.

from extrae.