[gmx-users] problems compiling gromacs 4.0.5 in Ubuntu 9.0.4
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Nov 20 23:21:22 CET 2009
pedro alberto valiente flores wrote:
> Hi:
> I ' am trying to compile gromacs 4.0.5 in Ubuntu 9.0.4 I use the
> following command line in the configure script
> ./configure --enable-mpi --program-suffix=_405_mpi --prefix=
> $HOME/software/gmx405 MPICC=$HOME/software/openmpi-1.2.8/bin/mpicc
> CPPFLAGS="-I$HOME/software/openmpi-1.2.8/include/
> -I$HOME/software/fftw-3.2/include/"
> LDFLAGS="-L$HOME/software/openmpi-1.2.8/lib/
> -L$HOME/software/fftw-3.2/lib/"
> LD_LIBRARY_FLAGS=$HOME/software/openmpi-1.2.8/lib/
> --enable-shared
I would start by getting a non-shared-library version to work - there
are fewer constraints there. I'm surprised that you didn't find a
--with-fft=fftw3 configure option necessary.
Shared libraries are most useful for the GROMACS tools, which do not
benefit from linking with MPI. So, if you really want shared libraries,
use ./configure --enable-shared && make install for the tools and
./configure --enable-mpi && make install-mdrun for the MPI-useful bit.
Above all follow this page:
http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions
> previuosly I compile openmpi in $HOME/software/openmpi-1.2.8 and
> fftw-3.2 in $HOME/software/fftw-3.2
> I export the programs in my .bashrc using
> export PATH=$PATH:"$SOFTWARE/openmpi-1.2.8/bin/":"$SOFTWARE/gmx405/bin/"
> export LD_LIBRARY_PATH="$SOFTWARE/openmpi-1.2.8/lib/"
It's usually superior to follow the advice here
http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions#Getting_access_to_GROMACS_after_installation
but I suspect your problem transcends that.
> but when I tried to execute any command as example:
>
> *** buffer overflow detected ***: mdrun_405_mpi terminated
> ======= Backtrace: =========
> /lib/libc.so.6(__fortify_fail+0x37)[0x7fc8609ee2c7]
> /lib/libc.so.6[0x7fc8609ec170]
> /lib/libc.so.6[0x7fc8609eaf7d]
> /home/valiente/software/gmx405/lib/libgmx_mpi.so.5(get_libdir
> +0x23f)[0x7fc8626a7dff]
> /home/valiente/software/gmx405/lib/libgmx_mpi.so.5(low_libfn
> +0x1b4)[0x7fc8626a8024]
> /home/valiente/software/gmx405/lib/libgmx_mpi.so.5(low_libopen
> +0x15)[0x7fc8626a80c5]
> /home/valiente/software/gmx405/lib/libgmx_mpi.so.5[0x7fc862695819]
> /home/valiente/software/gmx405/lib/libgmx_mpi.so.5(bromacs
> +0x21)[0x7fc862695bb1]
> /home/valiente/software/gmx405/lib/libgmx_mpi.so.5(CopyRight
> +0xe8)[0x7fc862695fc8]
> mdrun_405_mpi[0x4248cc]
> /lib/libc.so.6(__libc_start_main
> +0xe6)[0x7fc86090d5a6]
> mdrun_405_mpi[0x404db9]
> ======= Memory map:
> ========
> 00400000-00431000 r-xp 00000000 08:18
> 3303014 /home/valiente/software/gmx405/bin/mdrun_405_mpi
> 00630000-00631000 r--p 00030000 08:18
> 3303014 /home/valiente/software/gmx405/bin/mdrun_405_mpi
> 00631000-00633000 rw-p 00031000 08:18
> 3303014 /home/valiente/software/gmx405/bin/mdrun_405_mpi
> 00633000-00634000 rw-p 00633000 00:00
> 0
> 01dc9000-01df0000 rw-p 01dc9000 00:00 0
> [heap]
> 7fc85f88d000-7fc85f8a3000 r-xp 00000000 08:19
> 196741 /lib/libgcc_s.so.1
> 7fc85f8a3000-7fc85faa3000 ---p 00016000 08:19
> 196741 /lib/libgcc_s.so.1
> 7fc85faa3000-7fc85faa4000 r--p 00016000 08:19
> 196741 /lib/libgcc_s.so.1
> 7fc85faa4000-7fc85faa5000 rw-p 00017000 08:19
> 196741 /lib/libgcc_s.so.1
> 7fc85faa5000-7fc85fab1000 r-xp 00000000 08:19
> 199944 /lib/libnss_files-2.9.so
> 7fc85fab1000-7fc85fcb0000 ---p 0000c000 08:19
> 199944 /lib/libnss_files-2.9.so
> 7fc85fcb0000-7fc85fcb1000 r--p 0000b000 08:19
> 199944 /lib/libnss_files-2.9.so
> 7fc85fcb1000-7fc85fcb2000 rw-p 0000c000 08:19
> 199944 /lib/libnss_files-2.9.so
> 7fc85fcb2000-7fc85fcbc000 r-xp 00000000 08:19
> 199946 /lib/libnss_nis-2.9.so
> 7fc85fcbc000-7fc85febb000 ---p 0000a000 08:19
> 199946 /lib/libnss_nis-2.9.so
> 7fc85febb000-7fc85febc000 r--p 00009000 08:19
> 199946 /lib/libnss_nis-2.9.so
> 7fc85febc000-7fc85febd000 rw-p 0000a000 08:19
> 199946 /lib/libnss_nis-2.9.so
> 7fc85febd000-7fc85fec5000 r-xp 00000000 08:19
> 199942 /lib/libnss_compat-2.9.so
> 7fc85fec5000-7fc8600c4000 ---p 00008000 08:19
> 199942 /lib/libnss_compat-2.9.so
> 7fc8600c4000-7fc8600c5000 r--p 00007000 08:19
> 199942 /lib/libnss_compat-2.9.so
> 7fc8600c5000-7fc8600c6000 rw-p 00008000 08:19
> 199942 /lib/libnss_compat-2.9.so
> 7fc8600c6000-7fc8600cb000 r-xp 00000000 08:19
> 615150 /usr/lib/libXdmcp.so.6.0.0
> 7fc8600cb000-7fc8602ca000 ---p 00005000 08:19
> 615150 /usr/lib/libXdmcp.so.6.0.0
> 7fc8602ca000-7fc8602cb000 rw-p 00004000 08:19
> 615150 /usr/lib/libXdmcp.so.6.0.0
> 7fc8602cb000-7fc8602cd000 r-xp 00000000 08:19
> 409812 /usr/lib/libXau.so.6.0.0
> 7fc8602cd000-7fc8604cc000 ---p 00002000 08:19
> 409812 /usr/lib/libXau.so.6.0.0
> 7fc8604cc000-7fc8604cd000 r--p 00001000 08:19
> 409812 /usr/lib/libXau.so.6.0.0
> 7fc8604cd000-7fc8604ce000 rw-p 00002000 08:19
> 409812 /usr/lib/libXau.so.6.0.0
> 7fc8604ce000-7fc8604e9000 r-xp 00000000 08:19
> 409821 /usr/lib/libxcb.so.1.1.0
> 7fc8604e9000-7fc8606e8000 ---p 0001b000 08:19
> 409821 /usr/lib/libxcb.so.1.1.0
> 7fc8606e8000-7fc8606e9000 r--p 0001a000 08:19
> 409821 /usr/lib/libxcb.so.1.1.0
> 7fc8606e9000-7fc8606ea000 rw-p 0001b000 08:19
> 409821 /usr/lib/libxcb.so.1.1.0
> 7fc8606ea000-7fc8606ed000Aborted
>
>
> However, If I execute cd $HOME/software/gmx405/bin
> ./mdrun_405_mpi the program works fine
That suggests your LD_RUN_PATH isn't set right.
> In addition if I execute the commands as root they work fine too.
That might suggest you installed one or other library as root. Since
you're installing to user space, you should never have been root. It's
hard to imagine root's default LD_RUN_PATH works for some reason.
Mark
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