Hello, I compiled GROMACS version 4.0 on an AMD Opteron, running Red Hat Linux (RHEL4), with the Portland Group compilers, v. 7.2. The compilation appears to work fine, with the following procedure:
export CPPFLAGS=-I/usr/local/fftw-3.1.2/include export LDFLAGS=-L/usr/local/fftw-3.1.2/lib export CC=pgcc export F77=pgf77 export LIBS=-L/usr/X11R6/lib64 Configure with the options: --prefix=/usr/local/gromacs-4.0 --enable-double --enable-shared Then I edited 1 line in the libtool file generated by configure: replaced: hardcode_libdir_flag_spec="\${wl}--rpath \${wl}\$libdir" by: hardcode_libdir_flag_spec="-R\$libdir" The reason for this last step is that pgcc does not recognize the --rpath option. The equivalent option is -R. Then make make install worked fine. Then I did source /usr/local/gromacs-4.0/bin/GMXRC If I run any GROMACS binaries after this, by calling the name itself, e.g. grompp_d -h The program outputs a header line :-) G R O M A C S (-: and then I get a segmentation fault. And similarly for other commands, such as mdrun_d, pdb2gmx_d, etc. However, if I invoke the program with the full path, e.g. /usr/local/gromacs-4.0/bin/grompp_d -h then it is fine. I did an strace on both commands (without and with the full path) and it appears that the segmentation fault comes from the binary trying to open a file whose name is my environment PATH compounded many times until the filename is too long. Interestingly, when I compiled gromacs with gcc 3.4.6, both ways of invoking the binaries (with or without the full path) work fine. Compilation of v.3.3.3 using the PGI compilers resulted in the same problem (that is, invoking a binary without the full path generates a segmentation fault). I would really like to use gromacs compiled with the PGI compilers, and be able to invoke the binaries without the full path. I would appreciate any ideas how to get this problem resolved. Thank you very much, Shan-Ho _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php