Hi Tariq, Yes this has come up previously.. First if you are cross-compiling, you need to set RUNSERIAL and RUNPARALLEL to whatever you use to launch mpi programs on your systems. Below is the reply from a user who reported this problem and investigated with a Linux expert to try and figure out what is going on. In short, setting the RTLD_DEEPBIND environment variable to 0 resolved his segfault with mvapich.
Thanks, Mohamad > If you set the environment variable RTLD_DEEPBIND to 0 then the > segfault disappears. I'm trying to better understand this, but works > by altering the behaviour of glibc when loading NSS modules. The > symbol resolution order seems to change with it set (for the better in > this case). > I think I've figured out who is in the "wrong here". This is a result > of a patch SuSE applied to glibc to dlopen NSS libraries with the > RTLD_DEEPBIND flag which puts the symbols inside the library ahead of > the global scope. This results in the behaviour we saw earlier where > the > free() called by the dlopen'd libnss_sss was resolved to the glibc lib > required by libnss_sss instead of the global scope which resolved and > bound free() to mvapich2's libmpi. > > The environment variable I found works by disabling this behaviour and > making it the glibc default, where symbols in dlopen()'d libraries > aren't put ahead of the global scope. > > SuSE has a legitimate reason for their patch, but the solution to this > issue is to set the RTLD_DEEPBIND environment variable to "0" to > resolve the segfaults. From: Hdf-forum [mailto:[email protected]] On Behalf Of Baig, Tariq Sent: Friday, June 12, 2015 8:52 AM To: [email protected] Subject: [Hdf-forum] secfault when building with mvapich2-1.9a2 Dear all, when compiling parallel hdf5 I get the the following strange error: make[2]: Entering directory `/usr/bmp/chaste_libs_mvapich/hdf5-1.8.11/src' LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \ sed -e 's/-L/:/g' -e 's/ //g'`" \ ./H5make_libsettings > H5lib_settings.c || \ (test $HDF5_Make_Ignore && echo "*** Error ignored") || \ (rm -f H5lib_settings.c ; exit 1) /bin/sh: line 4: 78738 Segmentation fault LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | sed -e 's/-L/:/g' -e 's/ //g'`" ./H5make_libsettings > H5lib_settings.c There is one previous post on this list mentioning this problem, did a solution come up in the meantime ? Thanks in advance, tariq
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