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,
--
MC Pedro Alberto Valiente Flores
Centro de Estudios de Proteínas
Facultad de Biología
Universidad de La Habana
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