[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Ana Marija]

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.anamarija at 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 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
> 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 at 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 at 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 at 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
>