[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Thu Oct 22 16:27:11 CEST 2015

if I do that that I got: Illegal Instruction error
which makes sense because I compiled gromacs with cross compiler for
compute nodes

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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