[gmx-users] Gromacs 4.6.7 plumed /segmentation error with imput files

[Mark Abraham]

Hi,

4.6.7 is fine, but you are probably having trouble with the fact that your
login node is a different kind of machine from your compute node, and
you'll need to consult your local docs for how to set up the cross
compilation environment to work correctly (and then how to tell PLUMED
about it). There's generally no reason to want to run grompp on the compute
nodes, nor mdrun on the login nodes, but if I'm right then the way they've
designed your infrastructure requires you to know what you'll plan to do
later. 4.5.5 doesn't complain because that version is too old for the
GROMACS build system to know the difference between your nodes, so it can
do nothing wrong (but also nothing good).

Mark

On Fri, Oct 16, 2015 at 5:21 PM Ana Marija <sokovic.anamarija at gmail.com>
wrote:

> HI,
>
> I installed Gromacs 4.6.7 with plumed 2.2.0, also I generated input files
> using this gromacs.
> But I am getting this error:
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> _pmiu_daemon(SIGCHLD): [NID 00029] [c0-0c0s1n3] [Thu Oct 15 15:25:51 2015]
> PE RANK 0 exit signal Segmentation fault
>
> But when I use imput files generated with gromacs 4.5.5  with gromacs 4.6.7
> it works.
> I don't understand this -- is gromacs-4.6.7 is a flaw version that can not
> generate input files?
> And it not what I am doing wrong in my installation?
>
> I installed 4.6.7  via following process:
>
> 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 -fPIC
> CXX=CC
> CXXFLAGS=-O -fPIC
> CXXFLAGS_NOOPENMP=-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_EXTERNAL_BLAS=1
> -D__PLUMED_HAS_EXTERNAL_LAPACK=1 -D__PLUMED_HAS_MOLFILE_PLUGINS=1
> -D__PLUMED_HAS_MPI=1 -D__PLUMED_HAS_CLOCK_GETTIME=1
> -D__PLUMED_HAS_GETTIMEOFDAY=1 -D__PLUMED_HAS_READDIR_R=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/new/gromacs/lib2
> LIBS=-ldl
> SOEXT=
> LD=CC
> LDSO=CC -shared
> GCCDEP=CC
> prefix=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0
> program_transform_name=s,x,x,
> program_can_run_mpi=yes
> program_can_run=yes
> LD_RO=ld -r -o
> exec_prefix=${prefix}
> bindir=${exec_prefix}/bin
> libdir=${exec_prefix}/lib
> includedir=${prefix}/include
> datarootdir=${prefix}/share
> datadir=${datarootdir}
> docdir=${datarootdir}/doc/plumed
> htmldir=${docdir}
> program_name=plumed
> ###
>
> make
> make install
>
> export PATH=/lustre/beagle2/ams/new/gromacs/plumed-2.2.0/bin:$PATH
>
> #1. Make a directory for modulefiles (e.g.
> /lustre/beagle2/ams/modulefiles/)
> #2. Copy file
> /lustre/beagle2/ams/groplu/plumed-2.1.1/lib/plumed/src/lib/modulefile into
> /lustre/beagle2/ams/modulefiles/plumed/2.1.1/
> #3. type "module use /lustre/beagle2/ams/modulefiles/"
> #4. type "module load plumed/2.1.1"
>
> export PATH=/lustre/beagle2/ams/groplu/plumed-2.1.1/bin:$PATH
> module use /lustre/beagle2/ams/modulefiles/
> module load plumed/2.1.1
>
> ### 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/groplu/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/groplu/lib:$CMAKE_LIBRARY_PATH"
>
> #in /lustre/beagle2/ams/groplu make directory lib
>
> ams at login1:/lustre/beagle2/ams/lib>ln -s
> /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a
> ams at login1:/lustre/beagle2/ams/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/groplu/gromacs-4.6.7/build
> -DGMX_X11=OFF -DGMX_BLAS_USER=/lustre/beagle2/ams/groplu/lib/libblas.a
> -DGMX_LAPACK_USER=/lustre/beagle2/ams/groplu/lib/liblapack.a
> -DCMAKE_SKIP_RPATH=ON
>
>
> make
> make install
>
> Any help with this would be greatly appreciated,
>
> Thanks
> Ana
> --
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