[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Ana Marija sokovic.anamarija at gmail.com
Wed Oct 21 17:20:03 CEST 2015


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


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