[gmx-users] problems compiling gromacs 4.0.5 in Ubuntu 9.0.4
Yasuyuki Araki
yasu.araki at gmail.com
Tue Nov 24 03:52:04 CET 2009
Dear pedro alberto valiente flores and gmx-users
Your situation seems quite similar to my old report on Tue Sep 8,
[gmx-users] Using gromacs 4.0.5 built with FORTIFY_SOURCE feature.
After that, I had a chance to report and solve this problem by a
kind help of gentoo linux bugzilla.
Please see
http://bugs.gentoo.org/show_bug.cgi?id=284431.
Im my case, the reason for the overflow of get_libdir() funciton
is too long "PATH" environmental variable.
Please check your PATH env. variable length, just
echo $PATH | wc -m
If this command returns over 512, your situation is almost the same
to me.
If so, try this following patch,
http://repo.or.cz/w/gromacs.git/commit/53a07a791c1b7e4ed832ed4842928ad5139c1f41
Regards,
Y. Araki
> 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
>
> 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/"
>
> 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
> In addition if I execute the commands as root they work fine too.
> How can I fix this problems?
> sincerely best regards,
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