Hello, I freshly installed Gromacs 4.0, but when I run the test set 3.3.3, I get "segmentation fault error".
My installation script, no error during the compilation : $ pgcc -V pgcc 7.2-2 64-bit target on x86-64 Linux -tp k8-64 Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved. Copyright 2000-2008, STMicroelectronics, Inc. All Rights Reserved. ----------------------------------------- # tar -zxvf fftw-3.1.3.tar.gz # chown -R root.root fftw-3.1.3 # cd fftw-3.1.3 # ./configure --prefix=/usr/local/gromacs-4.0.0/fftw-3.1.3 --enable-float --enable-threads CC="pgcc" # make -j 9 2>&1 | tee fftw_single_make.txt # make install 2>&1 | tee fftw_single_install.txt # make distclean # ./configure --prefix=/usr/local/gromacs-4.0.0/fftw-3.1.3 --enable-threads CC="pgcc" # make -j 9 2>&1 | tee fftw_double_make.txt # make install 2>&1 | tee fftw_double_install.txt # make distclean # export CPPFLAGS='-I/usr/local/gromacs-4.0.0/fftw-3.1.3/include' # export LDFLAGS='-L/usr/local/gromacs-4.0.0/fftw-3.1.3/lib' # tar -zxvf gromacs-4.0.0.tar.gz # chown -R root.root gromacs-4.0.0 # cd gromacs-4.0.0 # ./configure --prefix=/usr/local/gromacs-4.0.0 --without-x CC="pgcc" 2>&1 | tee gromacs_single_configure.txt # make -j 9 2>&1 | tee gromacs_single_make.txt # make install 2>&1 | tee gromacs_single_install.txt # make distclean # ./configure --prefix=/usr/local/gromacs-4.0.0 --without-x --program-suffix=_d --enable-double CC="pgcc" 2>&1 | tee gromacs_double_configure.txt # make -j 9 2>&1 | tee gromacs_double_make.txt # make install 2>&1 | tee gromacs_double_install.txt # make distclean # ./configure --prefix=/usr/local/gromacs-par-4.0.0 --without-x --program-suffix=_mpi --enable-double --enable-mpi CC="mpicc" 2>&1 | tee gromacs_mpi_configure.txt # make -j 9 2>&1 | tee gromacs_mpi_make.txt # make install 2>&1 | tee gromacs_mpi_install.txt ------------------------------------------- First I run the test without mpi (/usr/local/gromacs-4.0.0) $ tar zxvf gmxtest-3.3.3.tgz $ cd gmxtest $ ./gmxtest.pl all All 16 simple tests PASSED All 14 complex tests PASSED sh: line 1: 28610 Erreur de segmentation (core dumped) mdrun >mdrun.out 2>&1 sh: line 1: 28658 Erreur de segmentation (core dumped) mdrun >mdrun.out 2>&1 ........ sh: line 1: 29980 Erreur de segmentation (core dumped) mdrun >mdrun.out 2>&1 All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 44 energies in the log file $ ./gmxtest.pl -double all sh: line 1: 32676 Instruction illégale (core dumped) mdrun_d
mdrun.out 2>&1
FAILED. Check files in imp1 sh: line 1: 32686 Instruction illégale (core dumped) mdrun_d
mdrun.out 2>&1
FAILED. Check files in imp36 sh: line 1: 32696 Instruction illégale (core dumped) mdrun_d
mdrun.out 2>&1
FAILED. Check files in morse 3 out of 16 simple tests FAILED sh: line 1: 32757 Erreur de segmentation (core dumped) mdrun_d
mdrun.out 2>&1
sh: line 1: 313 Instruction illégale (core dumped) mdrun_d
mdrun.out 2>&1
FAILED. Check files in aminoacids sh: line 1: 348 Erreur de segmentation (core dumped) mdrun_d
mdrun.out 2>&1
sh: line 1: 373 Instruction illégale (core dumped) mdrun_d
mdrun.out 2>&1
FAILED. Check files in dec+water sh: line 1: 383 Erreur de segmentation (core dumped) mdrun_d
mdrun.out 2>&1
sh: line 1: 407 Instruction illégale (core dumped) mdrun_d
mdrun.out 2>&1
FAILED. Check files in fe_test sh: line 1: 417 Erreur de segmentation (core dumped) mdrun_d
mdrun.out 2>&1
sh: line 1: 465 Erreur de segmentation (core dumped) mdrun_d
mdrun.out 2>&1
sh: line 1: 489 Erreur de segmentation (core dumped) mdrun_d
mdrun.out 2>&1
sh: line 1: 537 Instruction illégale (core dumped) mdrun_d
mdrun.out 2>&1
FAILED. Check files in urea sh: line 1: 547 Erreur de segmentation (core dumped) mdrun_d
mdrun.out 2>&1
4 out of 14 complex tests FAILED sh: line 1: 574 Instruction illégale (core dumped) mdrun_d
mdrun.out 2>&1
FAILED. Check files in kernel010 sh: line 1: 584 Instruction illégale (core dumped) mdrun_d
mdrun.out 2>&1
FAILED. Check files in kernel020 sh: line 1: 594 Instruction illégale (core dumped) mdrun_d
mdrun.out 2>&1
.................. ............ sh: line 1: 1186 Instruction illégale (core dumped) mdrun_d
mdrun.out 2>&1
FAILED. Check files in kernel333 sh: line 1: 1196 Instruction illégale (core dumped) mdrun_d
mdrun.out 2>&1
FAILED. Check files in kernel334 63 out of 63 kernel tests FAILED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Can you help me please? Antoine M _______________________________________________ gmx-users mailing list [email protected] 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
