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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php