[gmx-users] segmentation fault during test set

[Antoine Migeon]

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