[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Barnett, James W]

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