also I tried to install it with difference versions of gcc: gcc/4.7.2 gcc/4.8.1 gcc/4.9.1 gcc/4.9.2
but segmentation error is still the same On Wed, Oct 21, 2015 at 10:20 AM, Ana Marija <sokovic.anamar...@gmail.com> wrote: > Hi, > > I installed gromacs 4.6.7 with plumed like this: > 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@login1:/lustre/beagle2/ams/lib2>ln -s > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a > ams@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 > CXX=CC > CXXFLAGS=-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_MOLFILE=1 > -D__PLUMED_INTERNAL_MOLFILE_PLUGINS=1 -D__PLUMED_MPI=1 > -D__PLUMED_HAS_CLOCK_GETTIME=1 -D__PLUMED_HAS_GETTIMEOFDAY=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/groplu/lib2 > LIBS=-ldl > SOEXT= > LD=CC > LDSO=CC -shared > GCCDEP=CC > prefix=/lustre/beagle2/ams/groplu/plumed-2.1.1 > ### > > make > make install > > export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH > > #1. Make a directory for modulefiles (e.g. > /lustre/beagle2/ams/new/modulefiles/) > #2. Copy file: cp > /lustre/beagle2/ams/new/gromacs/plumed-2.2.0/lib/plumed/modulefile > /lustre/beagle2/ams/new/modulefiles/plumed/2.2.0/ > #3. type "module use /lustre/beagle2/ams/new/modulefiles/" > #4. type "module load plumed/2.2.0" > > export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH > module use /lustre/beagle2/ams/new/modulefiles/ > module load plumed/2.2.0 > > ### 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@login1:/lustre/beagle2/ams/new/gromacs/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/new/gromacs/lib:$CMAKE_LIBRARY_PATH" > > #in /lustre/beagle2/ams/new/gromacs make directory lib > > ams@login1:/lustre/beagle2/ams/new/gromacs/lib>ln -s > /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a > ams@login1:/lustre/beagle2/ams/new/gromacs/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/new/gromacs/gromacs-4.6.7/build > -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/new/gromacs/lib/libblas.a > -DGMX_LAPACK_USER=/lustre/beagle2/ams/new/gromacs/lib/liblapack.a > -DCMAKE_SKIP_RPATH=ON > > > make > make install > > I am getting Segmentation error if I run it like this: > > #!/bin/bash > #PBS -N test > #PBS -j oe > #PBS -l walltime=01:00:00 > #PBS -l mppwidth=96 > > source /opt/modules/default/init/bash > > cd $PBS_O_WORKDIR > module swap PrgEnv-cray PrgEnv-gnu > export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH > module use /lustre/beagle2/ams/new/modulefiles/ > module load plumed/2.2.0 > export > LD_LIBRARY_PATH=/lustre/beagle2/ams/new/gromacs/gromacs-4.6.7/build/lib:$LD_LIBRARY_PATH > export LD_LIBRARY_PATH=/opt/fftw/3.3.4.0/abudhabi/lib/:$LD_LIBRARY_PATH > > aprun -n 1 -N 1 > /lustre/beagle2/gro/gromacs/gromacs-4.6.7/build/bin/grompp_mpi -f > /lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c > /lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p > /lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n > /lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr > > The same error happens if I install gromacs without plumed. > > Can somebody please advise me what to do here? > > Thanks > Ana > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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