[gmx-users] gromacs 4.6.7 plumed -Segmentation fault
Szilárd Páll
pall.szilard at gmail.com
Thu Oct 22 16:31:28 CEST 2015
On Thu, Oct 22, 2015 at 4:27 PM, Ana Marija <sokovic.anamarija at gmail.com>
wrote:
> if I do that that I got: Illegal Instruction error
> which makes sense because I compiled gromacs with cross compiler for
> compute nodes
>
just use CC=gcc CXX=g++ or -DCMAKE_C_COMPILER=$(which gcc)
-DCMAKE_CXX_COMPILER=$(which g++) to get tools that you can run on the
login node.
>
> On Thu, Oct 22, 2015 at 9:23 AM, Barnett, James W <jbarnet4 at tulane.edu>
> wrote:
>
> > On Wed, 2015-10-21 at 10:20 -0500, Ana Marija 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/li
> > >
> >
> b64/libstdc++.a;/opt/cray/alps/default/lib64/libalpslli.a;/opt/cray/alps/defau
> > >
> >
> lt/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/de
> > >
> >
> fault/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.
> >
> > So it's not an issue with plumed.
> >
> > >
> > > Can somebody please advise me what to do here?
> >
> > Have you tried running grompp without using aprun (you would benefit
> doing
> > this
> > in an interactive session to see the output right away)?
> >
> > >
> > > Thanks
> > > Ana
> >
> >
> >
> > --
> > James "Wes" Barnett, Ph.D. Candidate
> > Louisiana Board of Regents Fellow
> >
> > Chemical and Biomolecular Engineering
> > Tulane University
> > 341-B Lindy Boggs Center for Energy and Biotechnology
> > 6823 St. Charles Ave
> > New Orleans, Louisiana 70118-5674
> > jbarnet4 at tulane.edu
> > --
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