Hi Evgenii, I can confirm that adding
LIBS=“-lutil” to the configure command for OpenMPI resolved the reported issue. Thanks again for your help! Michael > On 23 Nov 2015, at 20:05 , Evgenii Stepanov <eugeni.stepa...@gmail.com> wrote: > > I think so. What probably happens here is MSan confuses the configure > script into thinking that openpty is available without -lutil, but > what's actually available is just a stub that tries calling the real > openpty and fails, unless libutil is linked. > > On Mon, Nov 23, 2015 at 10:41 AM, Schlottke-Lakemper, Michael > <m.schlottke-lakem...@aia.rwth-aachen.de> wrote: >> Hi Evgenii, >> >> Just to clarify: you mean I should re-compile OpenMPI and add “-lutil” to >> LDFLAGS at configure time? >> >> Yours >> >> Michael >> >>> On 23 Nov 2015, at 18:07 , Evgenii Stepanov <eugeni.stepa...@gmail.com> >>> wrote: >>> >>> This is caused by missing -lutil. >>> FTR, http://llvm.org/viewvc/llvm-project?rev=245619&view=rev >>> >>> On Mon, Nov 23, 2015 at 7:33 AM, Schlottke-Lakemper, Michael via >>> cfe-users <cfe-users@lists.llvm.org> wrote: >>>> Hi folks, >>>> >>>> When running “mpirun” of an msan-instrumented installation of OpenMPI, I >>>> get the following error: >>>> >>>> $> mpirun -n 1 hostname >>>> [aia308:48324] *** Process received signal *** >>>> [aia308:48324] Signal: Segmentation fault (11) >>>> [aia308:48324] Signal code: Address not mapped (1) >>>> [aia308:48324] Failing at address: (nil) >>>> [aia308:48324] [ 0] >>>> /pds/opt/openmpi-1.8.7-clang-msan/lib64/libopen-pal.so.6(+0x123ca1)[0x7f9e21c90ca1] >>>> [aia308:48324] [ 1] mpirun[0x42b602] >>>> [aia308:48324] [ 2] /lib64/libpthread.so.0(+0xf890)[0x7f9e21250890] >>>> [aia308:48324] *** End of error message *** >>>> Segmentation fault >>>> >>>> Running it through gdb and printing the stacktrace, I get the following >>>> additional information: >>>> $> gdb -ex r --args mpirun -n 1 hostname >>>> #0 0x0000000000000000 in ?? () >>>> #1 0x000000000042bd5b in __interceptor_openpty () at >>>> /pds/opt/install/llvm/llvm-20151121-r253770-src/projects/compiler-rt/lib/msan/msan_interceptors.cc:1355 >>>> #2 0x00007ffff7705a7c in opal_openpty (amaster=0x7fffffffacf8, >>>> aslave=0x7fffffffacfc, name=0x0, termp=0x0, winp=0x0) at >>>> ../../../openmpi-1.8.7/opal/util/opal_pty.c:116 >>>> #3 0x00007ffff7b31e9a in orte_iof_base_setup_prefork >>>> (opts=0x7ffffffface8) at >>>> ../../../../openmpi-1.8.7/orte/mca/iof/base/iof_base_setup.c:89 >>>> #4 0x00007fffefea465a in odls_default_fork_local_proc >>>> (context=0x72400000bb80, child=0x72400000b880, >>>> environ_copy=0x73400001ec00, jobdat=0x722000009d80) at >>>> ../../../../../openmpi-1.8.7/orte/mca/odls/default/odls_default_module.c:860 >>>> #5 0x00007ffff7b3cfb8 in orte_odls_base_default_launch_local (fd=-1, >>>> sd=4, cbdata=0x70600002da80) at >>>> ../../../../openmpi-1.8.7/orte/mca/odls/base/odls_base_default_fns.c:1544 >>>> #6 0x00007ffff77459d7 in event_process_active_single_queue >>>> (base=0x72a00000fc80, activeq=0x71000000bdc0) at >>>> ../../../../../../openmpi-1.8.7/opal/mca/event/libevent2021/libevent/event.c:1367 >>>> #7 0x00007ffff773bb92 in event_process_active (base=0x72a00000fc80) at >>>> ../../../../../../openmpi-1.8.7/opal/mca/event/libevent2021/libevent/event.c:1437 >>>> #8 0x00007ffff7738fd7 in opal_libevent2021_event_base_loop >>>> (base=0x72a00000fc80, flags=1) at >>>> ../../../../../../openmpi-1.8.7/opal/mca/event/libevent2021/libevent/event.c:1647 >>>> #9 0x000000000048f651 in orterun (argc=4, argv=0x7fffffffcea8) at >>>> ../../../../openmpi-1.8.7/orte/tools/orterun/orterun.c:1133 >>>> #10 0x000000000048b20c in main (argc=4, argv=0x7fffffffcea8) at >>>> ../../../../openmpi-1.8.7/orte/tools/orterun/main.c:13 >>>> >>>> I suspect that has something to do with using some non-msan-instrumented >>>> system libraries, but how can I find out which library is the problem and >>>> what to do to fix it? Any ideas? >>>> >>>> Regards, >>>> >>>> Michael >>>> >>>> P.S.: I compiled OpenMPI with the following configure command (the >>>> wildcard blacklist was necessary because OpenMPI just has too many issues >>>> with msan…): >>>> >>>> printf "fun:*\n" > blacklist.txt && \ >>>> CC=clang CXX=clang++ \ >>>> CFLAGS="-g -fsanitize=memory -fno-omit-frame-pointer >>>> -fsanitize-memory-track-origins -fsanitize-blacklist=`pwd`/blacklist.txt" \ >>>> CXXFLAGS="-g -fsanitize=memory -fno-omit-frame-pointer >>>> -fsanitize-memory-track-origins -fsanitize-blacklist=`pwd`/blacklist.txt" \ >>>> ../openmpi-1.8.7/configure --prefix=/pds/opt/openmpi-1.8.7-clang-msan >>>> --disable-mpi-fortran >>>> _______________________________________________ >>>> cfe-users mailing list >>>> cfe-users@lists.llvm.org >>>> http://lists.llvm.org/cgi-bin/mailman/listinfo/cfe-users >> _______________________________________________ cfe-users mailing list cfe-users@lists.llvm.org http://lists.llvm.org/cgi-bin/mailman/listinfo/cfe-users
