[mpich-discuss] moab linking error

Tue Jun 5 15:39:44 CDT 2012

hello, The issue I had yesterday seems to be resolved by configuring mpi 1.4.1 with "enable-lib-depend". For more info, please see below. Thanks, Iulian ----- Original Message -----
| Message: 4
| Date: Mon, 4 Jun 2012 23:18:35 -0500
| From: Dave Goodell <goodell at mcs.anl.gov>
| To: mpich <mpich-discuss at mcs.anl.gov>
| Subject: Re: [mpich-discuss] linking error in moab
| Message-ID: <BC2BCF6C-FEBB-4279-956A-50600DA51002 at mcs.anl.gov>
| Content-Type: text/plain; charset=us-ascii
| On Jun 4, 2012, at 7:49 PM CDT, Iulian Grindeanu wrote:
| > p3.cpp
| > iulian at T520-iuli:~/tmp$ more p3.cpp
| > #include <mpi.h>
| >
| > int main (int argc, char * argv[] )
| > {
| > MPI::Init(argc, argv);
| > MPI::Finalize();
| > return 0;
| > }
| > iulian at T520-iuli:~/tmp$
| That's a pretty simple test program in which I can't see anything
| obviously wrong.
| > If I am using my built version of mpich2, I get the same linking
| > error. Although, in MOAB, we are not using MPI:: style, only MPI_xxx
| > (c style)
| > mpicxx p3.cpp
| > /home/iulian/3rdparty/lib/mpich2/lib/libmpich.so: undefined
| > reference to `MPL_trfree'
| [snip]
| > `MPL_trDebugLevel'
| This Debian bug seems related:
| http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=653616
Yes, and I do have other issues with shared library (chained, or inter-library?) dependencies, on my laptop. I need to understand better these gold-linker issues. | > /home/iulian/3rdparty/lib/mpich2/lib/libmpich.so: undefined
| > reference to `MPL_trid'
| > collect2: ld returned 1 exit status
| > iulian at T520-iuli:~/tmp$ mpich2version
| > MPICH2 Version: 1.4.1p1
| > MPICH2 Release date: Thu Sep 1 13:53:02 CDT 2011
| > MPICH2 Device: ch3:nemesis
| > MPICH2 configure: --enable-sharedlibs=gcc --enable-shared
| > --with-pm=mpd:gforker --enable-totalview --enable-mpe --enable-fc
| > --enable-f77 --enable-cxx --prefix=/home/iulian/3rdparty/lib/mpich2
| > MPICH2 CC: gcc -O2
| > MPICH2 CXX: g++ -O2
| > MPICH2 F77: gfortran -O2
| > MPICH2 FC: f95 -O2
| I'd rather debug this build, since it has a much simpler configuration
| than the earlier one you posted. I don't see anything odd here.
| > iulian at T520-iuli:~/tmp$ mpicxx -show
| > g++ -I/home/iulian/3rdparty/lib/mpich2/include
| > -L/home/iulian/3rdparty/lib/mpich2/lib -Wl,-rpath
| > -Wl,/home/iulian/3rdparty/lib/mpich2/lib -lmpichcxx -lmpich -lopa
| > -lmpl -lrt -lpthread
| Same here, nothing obviously out of place. What output do you get from
| "ldd $HOME/3rdparty/lib/mpich2/lib/*.so"?
iulian at T520-iuli:~/tmp$ ldd $HOME/3rdparty/lib/mpich2/lib/*.so /home/iulian/3rdparty/lib/mpich2/lib/libfmpich.so: linux-vdso.so.1 => (0x00007fff831c9000) libmpich.so.3 => /home/iulian/3rdparty/lib/mpich2/lib/libmpich.so.3 (0x00007f313a908000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f313a52a000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f313a322000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f313a105000) /lib64/ld-linux-x86-64.so.2 (0x00007f313af10000) /home/iulian/3rdparty/lib/mpich2/lib/libmpichcxx.so: linux-vdso.so.1 => (0x00007fff2bdff000) libmpich.so.3 => /home/iulian/3rdparty/lib/mpich2/lib/libmpich.so.3 (0x00007f157dc66000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f157da2f000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f157d672000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f157d46a000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f157d24c000) /lib64/ld-linux-x86-64.so.2 (0x00007f157e26e000) /home/iulian/3rdparty/lib/mpich2/lib/libmpichf90.so: linux-vdso.so.1 => (0x00007fff00d40000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f3d1f4dd000) /lib64/ld-linux-x86-64.so.2 (0x00007f3d1fabf000) /home/iulian/3rdparty/lib/mpich2/lib/libmpich.so: linux-vdso.so.1 => (0x00007fff971ff000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f02e5f94000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f02e5d76000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f02e59b9000) /lib64/ld-linux-x86-64.so.2 (0x00007f02e65a3000) /home/iulian/3rdparty/lib/mpich2/lib/libmpl.so: linux-vdso.so.1 => (0x00007fff48cbb000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f20e4de6000) /lib64/ld-linux-x86-64.so.2 (0x00007f20e53cb000) /home/iulian/3rdparty/lib/mpich2/lib/libopa.so: linux-vdso.so.1 => (0x00007ffff35ff000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fa521790000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fa5213d2000) /lib64/ld-linux-x86-64.so.2 (0x00007fa521bd1000) iulian at T520-iuli:~/tmp$ | Does reconfiguring mpich2 with "--enable-lib-depend" fix the problem?
| I think this option was removed in 1.5a1 and later, but should still
| be present in 1.4.1p1.
YES!!!!!!!! thank you very much . | What output do you get from "mpicxx -Wl,--version"? I have no idea
| which distributions may have started using the gold linker by default,
| or possibly you've chosen to install it instead. A non-GNU-ld linker
| might be the reason that I can't reproduce this on my end.
| What does "env | grep '^LD'" give you?
So when I am testing my mpich2 build, I am setting also LD_LIBRARY_PATH ~/source/MOABpv$ env | grep '^LD' LD_LIBRARY_PATH=/home/iulian/3rdparty/lib/OCC652/lib:/home/iulian/lib/camal.5.1.0-Linux64/lib/Linux64:/home/iulian/3rdparty/hdf5-1.8.8-par-gcc:/home/iulian/lib/parallel/moab/lib:/home/iulian/lib/parallel/cgmcubit/lib:/home/iulian/lib/parallel/Lasso/lib:/home/iulian/3rdparty/Cubit-12.2/bin:/home/iulian/3rdparty/lib/mpich2/lib when I am using the mpich installed from deb file, the LD path is env | grep '^LD' LD_LIBRARY_PATH=/home/iulian/3rdparty/Cubit-12.2/bin:/home/iulian/lib/camal.5.1.0-Linux64/lib/Linux64:/home/iulian/3rdparty/hdf5-1.8.8-ser-gcc/lib:/usr/lib/x86_64-linux-gnu:/usr/lib Best Regards, Iulian | -Dave
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