[gmx-users] Gromacs 4.6.7 plumed /segmentation error with imput files

[Ana Marija]

HI,

I installed Gromacs 4.6.7 with plumed 2.2.0, also I generated input files
using this gromacs.
But I am getting this error:
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
_pmiu_daemon(SIGCHLD): [NID 00029] [c0-0c0s1n3] [Thu Oct 15 15:25:51 2015]
PE RANK 0 exit signal Segmentation fault

But when I use imput files generated with gromacs 4.5.5  with gromacs 4.6.7
it works.
I don't understand this -- is gromacs-4.6.7 is a flaw version that can not
generate input files?
And it not what I am doing wrong in my installation?

I installed 4.6.7  via following process:

module swap PrgEnv-cray PrgEnv-gnu
module load fftw/3.3.4.0
module load cray-mpich/7.0.5
module load gsl/1.15
module load cmake
#in /lustre/beagle2/ams/new/gromacs make directory lib2

mkdir lib2

ams at login1:/lustre/beagle2/ams/lib2>ln -s
/opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
ams at login1:/lustre/beagle2/ams/lib2>ln -s
/opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a

tar zxvf plumed-2.2.0.tgz
cd plumed-2.2.0

./configure CC=cc CXX=CC F77=ftn
LDFLAGS="-L/lustre/beagle2/ams/new/gromacs/lib2"
--prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0 --enable-mpi
--disable-basic-warnings --disable-openmp

<strong>###Makefile.conf should look like this, if not please delete all
extra stuff before proceeding to make step</strong>
CC=cc
FC=gfortran
LDF90=gfortran
CFLAGS=-g -O2 -fPIC
CXX=CC
CXXFLAGS=-O -fPIC
CXXFLAGS_NOOPENMP=-O -fPIC
CPPFLAGS= -DPACKAGE_NAME=\"PLUMED\" -DPACKAGE_TARNAME=\"plumed\"
-DPACKAGE_VERSION=\"2\" -DPACKAGE_STRING=\"PLUMED\ 2\"
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DSTDC_HEADERS=1
-DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1
-DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -D__PLUMED_HAS_EXTERNAL_BLAS=1
-D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1
-D__PLUMED_HAS_MPI=1 -D__PLUMED_HAS_CLOCK_GETTIME=1
-D__PLUMED_HAS_GETTIMEOFDAY=1 -D__PLUMED_HAS_READDIR_R=1
-D__PLUMED_HAS_CREGEX=1 -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_HAS_EXECINFO=1
-D__PLUMED_HAS_ZLIB=1 -DNDEBUG=1 -D_REENTRANT=1
LDFLAGS=
DYNAMIC_LIBS=-lstdc++ -lz -ldl  -L/lustre/beagle2/ams/new/gromacs/lib2
LIBS=-ldl
SOEXT=
LD=CC
LDSO=CC -shared
GCCDEP=CC
prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0
program_transform_name=s,x,x,
program_can_run_mpi=yes
program_can_run=yes
LD_RO=ld -r -o
exec_prefix=${prefix}
bindir=${exec_prefix}/bin
libdir=${exec_prefix}/lib
includedir=${prefix}/include
datarootdir=${prefix}/share
datadir=${datarootdir}
docdir=${datarootdir}/doc/plumed
htmldir=${docdir}
program_name=plumed
###

make
make install

export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH

#1. Make a directory for modulefiles (e.g. /lustre/beagle2/ams/modulefiles/)
#2. Copy file
/lustre/beagle2/ams/groplu/plumed-2.1.1/lib/plumed/src/lib/modulefile into
/lustre/beagle2/ams/modulefiles/plumed/2.1.1/
#3. type "module use /lustre/beagle2/ams/modulefiles/"
#4. type "module load plumed/2.1.1"

export PATH=/lustre/beagle2/ams/groplu/plumed-2.1.1/bin:$PATH
module use /lustre/beagle2/ams/modulefiles/
module load plumed/2.1.1

### instal gromacs 4.6.7
wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz
tar zxvf gromacs-4.6.7.tar.gz
cd gromacs-4.6.7/
ams at login1:/lustre/beagle2/ams/groplu/gromacs-4.6.7>plumed-patch -p --static


PLUMED patching tool

1) amber14        3) gromacs-4.6.7    5) lammps-6Apr13    7) namd-2.9
2) gromacs-4.5.5    4) gromacs-5.0    6) namd-2.8        8) qespresso-5.0.2

Choose the best matching code/version:3

mkdir build
cd build


export BUILD_WITH_INSTALL_RPATH=TRUE
export INSTALL_RPATH=""
export SKIP_BUILD_RPATH=TRUE
export
CMAKE_LIBRARY_PATH="/lustre/beagle2/ams/groplu/lib:$CMAKE_LIBRARY_PATH"

#in /lustre/beagle2/ams/groplu make directory lib

ams at login1:/lustre/beagle2/ams/lib>ln -s
/opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
ams at login1:/lustre/beagle2/ams/lib>ln -s
/opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a liblapack.a


cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
-DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
-DMPI_LIBRARY="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpich.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libfmpich_gnu_49.a;/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/lib/libmpl.a;/opt/cray/pmi/default/lib64/libpmi.a;/opt/cray/rca/default/lib64/librca.a;/opt/gcc/4.9.1/snos/lib64/libgfortran.a;/opt/gcc/4.9.1/snos/lib64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/default/lib64/libalpsutil.a;/opt/gcc/4.9.1/snos/lib64/libgomp.a;/opt/gcc/4.9.1/snos/lib64/libquadmath.a;/opt/cray/ugni/default/lib64/libugni.a;/opt/cray/udreg/default/lib64/libudreg.a;/opt/cray/xpmem/default/lib64/libxpmem.a;/opt/cray/wlm_detect/default/lib64/libwlm_detect.a;/lib64/libdl.so.2"
-DMPI_INCLUDE_PATH="/opt/cray/mpt/7.0.5/gni/mpich2-gnu/49/include"
-DCMAKE_CXX_COMPILER=CC -DCMAKE_C_COMPILER=cc -DGMX_FORCE_CXX=ON
-DGMX_DOUBLE=OFF -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/groplu/gromacs-4.6.7/build
-DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/groplu/lib/libblas.a
-DGMX_LAPACK_USER=/lustre/beagle2/ams/groplu/lib/liblapack.a
-DCMAKE_SKIP_RPATH=ON


make
make install

Any help with this would be greatly appreciated,

Thanks
Ana