[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

Szilárd Páll pall.szilard at gmail.com
Thu Oct 22 16:30:15 CEST 2015 

Hi Ana Marija,

This seems to have little or nothing to do with PLUMED. Given the
presentation it is quite unclear to me:
i) what exactly is the issue (grompp segfault?); what happens if you use
unmodified GROMACS source? What if you run on the login node (binaries
compiled for it). Do other tools, e.g. mdrun work?
ii) Where are these build steps from, they look strange (e.g. you shouldn't
have to set MPI_LIBRARY or symlink libsci_gnu).

BTW, you can generate your tpr input locally or anywhere else, you don't
need to do it on the machine where you're planning ot run int.

Cheers,
--
Szilárd

On Wed, Oct 21, 2015 at 5:20 PM, 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

More information about the gromacs.org_gmx-users mailing list