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@login1:/lustre/beagle2/ams/lib2>ln -s /opt/cray/libsci/13.0.1/GNU/49/abudhabi/lib/libsci_gnu.a libblas.a ams@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@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@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@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-requ...@gromacs.org.